@book {Jiahua2023, year = {Submitted}, publisher = {Springer}, organization = {Springer}, url = {https://link.springer.com/book/10.1007/978-981-99-6141-2}, author = {Chen, Jiahua title=Statistical inference under mixture models{\textquoteright}} } @article {Campbell17, title = {Automated scalable Bayesian inference via Hilbert coresets}, journal = {arXiv:1710.05053}, year = {Submitted}, author = {Trevor Campbell and Tamara Broderick} } @article {11317, title = {Detecting and adjusting for preferential monitoring site location: A case study of air pollution with novel R packages}, journal = {Evironmetrics}, year = {Submitted}, abstract = {

The paper concerns preferential siting, i.e. the sampling of sites in networks of monitors designed to measure the levels of atmospheric air pollution over a specified geographical region. More precisely, a case study demonstrates the use of an R software package that detects such preferentiality in the Southern California Air Quality Basin, i.e. SOCAB, in the siting of monitors very fine particulate matter, i.e. PM10 monitors. It then demonstrates newly published R software that simultaneously maps, over time and space, both the P M10 field and the binary selection process. It thus calculates the impact of such preferential sampling on estimates of the annual level of PM10. Furthermore, that new software enables the spatial prediction of those levels at unmonitored locations

in California. P M10 was chosen for the case study because of its harmful impact on human health and because it has been monitored over a substantial period. The SOCAB was selected, because of its historical importance in the develop- ment of the US Air Quality Standards (AQS). The paper thus demonstrates the value of the two software packages while showing the impact of preferential sampling on estimates of PM10 over an important geographical domain.

} } @unpublished {10010, title = {A fast Monte Carlo test for preferential sampling}, year = {Submitted}, abstract = {

The preferential sampling of locations chosen to observe a spatio-temporal process has been identified as a major problem across multiple fields. Predictions of the process can be severely biased when standard statistical methodologies are applied to preferentially sampled data without adjustment. Currently, methods that can adjust for preferential sampling are rarely implemented in the software packages most popular with researchers. Furthermore, they are technically demanding to design and fit. This paper presents a fast and intuitive Monte Carlo test for detecting preferential sampling. The test can be applied across a wide range of data types. Importantly, the method can also help with the discovery of a set of informative covariates that can sufficiently control for the preferential sampling. The discovery of these covariates can justify continued use of standard methodologies. A thorough simulation study is presented to demonstrate both the power and validity of the test in various data settings. The test is shown to attain high power for non-Gaussian data with sample sizes as low as 50. Finally, two previously-published case studies are revisited and new insights into the nature of the informative sampling are gained. The test can be implemented with the R package PStestR

}, author = {Joe Watson} } @unpublished {10009, title = {A general framework for estimating the spatio-temporal distribution of a species using multiple data types}, year = {Submitted}, abstract = {

Species distribution models (SDMs) are useful tools to help ecologists quantify species-environment relationships, and they are increasingly used to help determine the impacts of climate and habitat changes on species. In practice, data are often collections of presence-only sightings from citizen scientists, whose search effort may be highly heterogeneous throughout the study region. Many standard modelling approaches ignore search effort, which can severely bias SDMs. We present a novel marked spatio-temporal point process framework for combining data of differing type and quality. We apply this to combine multiple datasets collected on the endangered Southern Resident Killer Whales, to estimate their monthly effort-corrected space-use.

}, author = {Joe Watson and Ruth Joy and Dominic Tollit and Sheila J Thornton and Marie Auger-M{\'e}th{\'e}} } @article {11439, title = {Highly Multivariate Large-scale Spatial Stochastic Processes {\textendash} A Doubly Conditional Independence Approach.}, journal = {J Royal Statistical Society, Ser B}, year = {Submitted}, author = {Xiaoqing Chen}, editor = {Gavin Shaddick} } @article {10845, title = {Nondimensionalizing physical and statistical models: a unified approach}, journal = {Statistical Science}, year = {Submitted}, pages = {Submitted}, type = {Research paper}, abstract = {

This paper presents a version of the statistical invariance principle that incorporates constraints imposed by dimensional analysis. It does so by adapting Buckingham{\textquoteright}s Pi-theorem for deterministic models of physical processes based on vectors of attribute variables, to one for data models for stochastic processes based on random matrices of those attributes. Buckingham{\textquoteright}s method is meant for a priori modeling to reduce the number of attributes, thus simplifying experimental design, and reducing experimental costs.\  In contrast, this paper{\textquoteright}s proposal allows for more flexibility in modeling, including a stochasatic component that brings with it a measure of that model{\textquoteright}s uncertainty. The theory is extended to incorporate both a priori and a posteriori Bayesian modeling. A simple example of that extension to regression modelling is given.

}, author = {Tae Yoon Lee and James V Zidek and Nancy Heckman} } @unpublished {PENSE, title = {Proteomic biomarker study using novel robust penalized elastic net estimators}, journal = {Annals of Applied Statistics}, year = {Submitted}, note = {Submitted to the Annals of Applied Statistics}, author = {Cohen Freue, Gabriela V. and Kepplinger, David and Salibian-Barrera, Mat{\'\i}as and Smucler, Ezequiel} } @article {Huggins18, title = {Scalable Gaussian process inference with finite-data mean and variance guarantees}, journal = {arXiv:1806.10234}, year = {Submitted}, author = {Jonathan Huggins and Trevor Campbell and Mikolaj Kasprzak and Tamara Broderick} } @article {9753, title = {Adjusting for differential misclassification in matched case-control studies utilizing health administrative data}, journal = {Statistics in Medicine}, year = {In Press}, author = {H{\"o}gg, Tanja and Zhao, Yinshan and Gustafson, Paul and Petkau, John and Fisk, John and Marrie, Ruth Ann and Tremlett, Helen} } @article {Campbell18_TPAMI, title = {Dynamic clustering algorithms via small-variance analysis of Markov chain mixture models}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, year = {In Press}, author = {Trevor Campbell and Brian Kulis and Jonathan How} } @article {9410, title = {Optimizing marine spatial plans with animal tracking data}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, year = {In Press}, author = {Lennox, Robert J. and Engler-Palma, Cecilia and Kowarski, Katie and Filous, Alexander and Whitlock, Rebecca and Cooke, Steven J. and Auger-M{\'e}th{\'e}, Marie} } @article {Campbell18_B, title = {Truncated random measures}, journal = {Bernoulli}, year = {In Press}, author = {Trevor Campbell and Jonathan Huggins and Jonathan How and Tamara Broderick} } @article {whitematter, title = {Associative white matter tracts selectively predict sensorimotor learning}, journal = {Communications Biology}, volume = {7}, year = {2024}, pages = {762}, url = {https://doi.org/10.1038/s42003-024-06420-1}, author = {Vinci-Booher, S. and McDonald, D.J. and Berquist, E. and Pestilli, F} } @article {flusight2023, title = {Evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations}, journal = {Nature Communications}, volume = {15}, year = {2024}, pages = {6289}, url = {https://doi.org/10.1038/s41467-024-50601-9}, author = {Mathis, Sarabeth M. and Webber, Alexander E. and Le{\'o}n, Tom{\'a}s M. and Murray, Erin L. and Sun, Monica and White, Lauren A. and Brooks, Logan C. and Green, Alden and Hu, Addison J. and McDonald, Daniel J. and Rosenfeld, Roni and Shemetov, Dmitry and Tibshirani, Ryan J. and Kandula, Sasikiran and Pei, Sen and Shaman, Jeffrey and Yaari, Rami and Yamana, Teresa K. and Agarwal, Pulak and Balusu, Srikar and Gururajan, Gautham and Kamarthi, Harshavardhan and Prakash, B. Aditya and Raman, Rishi and Rodr{\'\i}guez, Alexander and Zhao, Zhiyuan and Meiyappan, Akilan and Omar, Shalina and Baccam, Prasith and Gurung, Heidi L. and Stage, Steve A. and Suchoski, Brad T. and Ajelli, Marco and Kummer, Allisandra G. and Litvinova, Maria and Ventura, Paulo C. and Wadsworth, Spencer and Niemi, Jarad and Carcelen, Erica and Hill, Alison L and Jung, Sung-mok and Lemaitre, Joseph C. and Lessler, Justin and Loo, Sara L and McKee, Clifton D. and Sato, Koji and Smith, Claire and Truelove, Shaun and McAndrew, Thomas and Ye, Wenxuan and Bosse, Nikos and Hlavacek, William S. and Lin, Yen Ting and Mallela, Abhishek and Chen, Ye and Lamm, Shelby M. and Lee, Jaechoul and Posner, Richard G. and Perofsky, Amanda C. and Viboud, C{\'e}cile and Clemente, Leonardo and Lu, Fred and Meyer, Austin G and Santillana, Mauricio and Chinazzi, Matteo and Davis, Jessica T. and Mu, Kunpeng and y Piontti, Ana Pastore and Vespignani, Alessandro and Xiong, Xinyue and Ben-Nun, Michal and Riley, Pete and Turtle, James and Hulme-Lowe, Chis and Jessa, Shakeel and Nagraj, V.P. and Turner, Stephen D. and Williams, Desiree and Basu, Avranil and Drake, John M. and Fox, Spencer J. and Gibson, Graham C. and Suez, Ehsan and Thommes, Edward W. and Cojocaru, Monica G. and Cramer, Estee Y. and Gerding, Aaron and Stark, Ariane and Ray, Evan L. and Reich, Nicholas G. and Shandross, Li and Wattanachit, Nutcha and Wang, Yijin and Zorn, Martha W. and Aawar, Majd Al and Srivastava, Ajitesh and Meyers, Lauren A. and Adiga, Aniruddha and Hurt, Benjamin and Kaur, Gursharn and Lewis, Bryan L. and Marathe, Madhav and Venkatramanan, Srinivasan and Butler, Patrick and Farabow, Andrew and Muralidhar, Nikhil and Ramakrishnan, Naren and Reed, Carrie and Biggerstaff, Matthew and Borchering, Rebecca K.} } @article {McDonaldSharpnack2019, title = {Exponential family trend filtering on lattices}, journal = {Electronic Journal of Statistics}, volume = {18}, year = {2024}, pages = {1749{\textendash}1814}, url = {https://doi.org/10.1214/24-EJS2241}, author = {Sadhanala, V. and Bassett, Robert and Sharpnack, James and McDonald, Daniel J.} } @article {rtestim, title = {rtestim: Time-varying reproduction number estimation with trend filtering}, journal = {PLOS Computational Biology}, volume = {20}, year = {2024}, pages = {e1012324}, url = {https://doi.org/10.1371/journal.pcbi.1012324}, author = {Liu, J. and Cai, Z. and Gustafson, P. and McDonald, D.J.} } @article {Subedi2024-es, title = {A scalable approach to topic modelling in single-cell data by approximate pseudobulk projection}, journal = {Life science alliance}, volume = {7}, number = {10}, year = {2024}, publisher = {Life Sci Alliance}, abstract = {Probabilistic topic modelling has become essential in many types of single-cell data analysis. Based on probabilistic topic assignments in each cell, we identify the latent representation of cellular states. A dictionary matrix, consisting of topic-specific gene frequency vectors, provides interpret {\textellipsis}}, author = {Subedi, S and Sumida, T S and Park, Y P} } @article {TuzhlinaHastie2023, title = {Smooth multi-period forecasting with application to prediction of COVID-19 cases}, journal = {Journal of Computational and Graphical Statistics}, volume = {33}, year = {2024}, pages = {955-967}, url = {https://doi.org/10.1080/10618600.2023.2285337}, author = {Tuzhilina, Elena and Hastie, Trevor J. and McDonald, Daniel J. and Tay, J. Kenneth and Tibshirani, Robert} } @article {sparsegl, title = {sparsegl: An R Package for Estimating Sparse Group Lasso}, journal = {Journal of Statistical Software}, volume = {110}, year = {2024}, pages = {1{\textendash}23}, url = {https://doi.org/10.18637/jss.v110.i06}, author = {Liang, Xiaoxuan and Cohen, Aaron and Heinsfeld, Anibal S{\'o}lon and Pestilli, Franco and McDonald, Daniel J.} } @article {11040, title = {Tree-based boosting with functional data}, journal = {Computational Statistics}, volume = {39}, year = {2024}, pages = {1587 - 1620}, doi = {https://doi.org/10.1007/s00180-023-01364-2}, author = {Xiaomeng Ju and Matias Salibian-Barrera} } @article {Xiong2023-ud, title = {Epigenomic dissection of Alzheimer{\textquoteright}s disease pinpoints causal variants and reveals epigenome erosion}, journal = {Cell}, volume = {186}, number = {20}, year = {2023}, month = {sep}, pages = {4422{\textendash}4437.e21}, abstract = {Summary Recent work has identified dozens of non-coding loci for Alzheimer{\textquoteright}s disease (AD) risk, but their mechanisms and AD transcriptional regulatory circuitry are poorly understood. Here, we profile epigenomic and transcriptomic landscapes of 850,000 nuclei from prefrontal cortexes of 92 individuals with and without AD to build a map of the brain regulome, including epigenomic profiles, transcriptional regulators, co-accessibility modules, and peak-to-gene links in a cell-type-specific manner. We develop methods for multimodal integration and detecting regulatory modules using peak-to-gene linking. We show AD risk loci are enriched in microglial enhancers and for specific TFs including SPI1, ELF2, and RUNX1. We detect 9,628 cell-type-specific ATAC-QTL loci, which we integrate alongside peak-to-gene links to prioritize AD variant regulatory circuits. We report differential accessibility of regulatory modules in late AD in glia and in early AD in neurons. Strikingly, late-stage AD brains show global epigenome dysregulation indicative of epigenome erosion and cell identity loss.}, keywords = {Alzheimer{\textquoteright}s disease, ATAC-QTL, epigenome, epigenome erosion, fine-mapping, GWAS, multimodal integration, peak-to-gene linking}, author = {Xiong, Xushen and James, Benjamin T and Boix, Carles A and Park, Yongjin P and Galani, Kyriaki and Victor, Matheus B and Sun, Na and Hou, Lei and Ho, Li-Lun and Mantero, Julio and Scannail, Aine Ni and Dileep, Vishnu and Dong, Weixiu and Mathys, Hansruedi and Bennett, David A and Tsai, Li-Huei and Kellis, Manolis} } @article {11282, title = {Gaussian mixture reduction with composite transportation divergence}, journal = {IEEE Transactions on Information Theory}, year = {2023}, doi = {doi.org/10.1109/TIT.2023.3323346}, author = {Zhang, Qiong and Zhang, Archer Gong and Chen, Jiahua} } @article {Sun2023-ti, title = {Human microglial state dynamics in Alzheimer{\textquoteright}s disease progression}, journal = {Cell}, volume = {186}, number = {20}, year = {2023}, pages = {4386{\textendash}4403.e29}, abstract = {Summary Altered microglial states affect neuroinflammation, neurodegeneration, and disease but remain poorly understood. Here, we report 194,000 single-nucleus microglial transcriptomes and epigenomes across 443 human subjects and diverse Alzheimer{\textquoteright}s disease (AD) pathological phenotypes. We annotate 12 microglial transcriptional states, including AD-dysregulated homeostatic, inflammatory, and lipid-processing states. We identify 1,542 AD-differentially-expressed genes, including both microglia-state-specific and disease-stage-specific alterations. By integrating epigenomic, transcriptomic, and motif information, we infer upstream regulators of microglial cell states, gene-regulatory networks, enhancer-gene links, and transcription-factor-driven microglial state transitions. We demonstrate that ectopic expression of our predicted homeostatic-state activators induces homeostatic features in human iPSC-derived microglia-like cells, while inhibiting activators of inflammation can block inflammatory progression. Lastly, we pinpoint the expression of AD-risk genes in microglial states and differential expression of AD-risk genes and their regulators during AD progression. Overall, we provide insights underlying microglial states, including state-specific and AD-stage-specific microglial alterations at unprecedented resolution.}, keywords = {Alzheimer{\textquoteright}s, cell states, disease-stage response, inflammation, iPSCs, microglia, single-cell, transcription factors}, author = {Sun, Na and Victor, Matheus B and Park, Yongjin P and Xiong, Xushen and Scannail, Aine Ni and Leary, Noelle and Prosper, Shaniah and Viswanathan, Soujanya and Luna, Xochitl and Boix, Carles A and James, Benjamin T and Tanigawa, Yosuke and Galani, Kyriaki and Mathys, Hansruedi and Jiang, Xueqiao and Ng, Ayesha P and Bennett, David A and Tsai, Li-Huei and Kellis, Manolis} } @article {10772, title = {Knots and their effect on the tensile strength of lumber}, journal = {Journal of Quality Technology}, year = {2023}, pages = {1-13}, type = {Research paper}, author = {Shuxian Fan and Samuel W;K. Wong and James V Zidek} } @article {PhamDing2020, title = {Less is more: Balancing noise reduction and data retention in fMRI with projection scrubbing}, journal = {Neuroimage}, volume = {270}, year = {2023}, pages = {119972}, url = {{https://doi.org/10.1016/j.neuroimage.2023.119972}, author = {Pham, Damon and Ding, Lei and McDonald, Daniel J. and Nebel, Mary Beth and Mejia, Amanda} } @article {Hou2023-kp, title = {Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease}, journal = {Nat. Genet.}, volume = {55}, number = {10}, year = {2023}, pages = {1665{\textendash}1676}, publisher = {nature.com}, abstract = {Genetic variants associated with complex traits are primarily noncoding, and their effects on gene-regulatory activity remain largely uncharacterized. To address this, we profile epigenomic variation of histone mark H3K27ac across 387 brain, heart, muscle and lung samples from Genotype-Tissue Expression (GTEx). We annotate 282 k active regulatory elements (AREs) with tissue-specific activity patterns. We identify 2,436 sex-biased AREs and 5,397 genetically influenced AREs associated with 130 k genetic variants (haQTLs) across tissues. We integrate genetic and epigenomic variation to provide mechanistic insights for disease-associated loci from 55 genome-wide association studies (GWAS), by revealing candidate tissues of action, driver SNPs and impacted AREs. Lastly, we build ARE-gene linking scores based on genetics (gLink scores) and demonstrate their unique ability to prioritize SNP-ARE-gene circuits. Overall, our epigenomic datasets, computational integration and mechanistic predictions provide valuable resources and important insights for understanding the molecular basis of human diseases/traits such as schizophrenia.}, author = {Hou, Lei and Xiong, Xushen and Park, Yongjin and Boix, Carles and James, Benjamin and Sun, Na and He, Liang and Patel, Aman and Zhang, Zhizhuo and Molinie, Benoit and Van Wittenberghe, Nicholas and Steelman, Scott and Nusbaum, Chad and Aguet, Fran{\c c}ois and Ardlie, Kristin G and Kellis, Manolis} } @article {11041, title = {Robust nonparametric regression: review and practical considerations}, journal = {Econometrics and Statistics}, year = {2023}, doi = {10.1016/j.ecosta.2023.04.004}, author = {Matias Salibian-Barrera} } @article {Subedi2023-fl, title = {Single-cell pair-wise relationships untangled by composite embedding model}, journal = {iScience}, volume = {26}, number = {2}, year = {2023}, month = {feb}, pages = {106025}, abstract = {In multicellular organisms, cell identity and functions are primed and refined through interactions with other surrounding cells. Here, we propose a scalable machine learning method, termed SPRUCE, which is designed to systematically ascertain common cell-cell communication patterns embedded in single-cell RNA-seq data. We applied our approach to investigate tumor microenvironments consolidating multiple breast cancer datasets and found seven frequently observed interaction signatures and underlying gene-gene interaction networks. Our results implicate that a part of tumor heterogeneity, especially within the same subtype, is better understood by differential interaction patterns rather than the static expression of known marker genes.}, keywords = {Cancer systems biology, machine learning, Transcriptomics}, author = {Subedi, Sishir and Park, Yongjin P} } @article {Sun2023-hn, title = {Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer{\textquoteright}s disease}, journal = {Nat. Neurosci.}, volume = {26}, number = {6}, year = {2023}, pages = {970{\textendash}982}, abstract = {Cerebrovascular dysregulation is a hallmark of Alzheimer{\textquoteright}s disease (AD), but the changes that occur in specific cell types have not been fully characterized. Here, we profile single-nucleus transcriptomes in the human cerebrovasculature in six brain regions from 220 individuals with AD and 208 age-matched controls. We annotate 22,514 cerebrovascular cells, including 11 subtypes of endothelial, pericyte, smooth muscle, perivascular fibroblast and ependymal cells. We identify 2,676 differentially expressed genes in AD, including downregulation of PDGFRB in pericytes, and of ABCB1 and ATP10A in endothelial cells, and validate the downregulation of SLC6A1 and upregulation of APOD, INSR and COL4A1 in postmortem AD brain tissues. We detect vasculature, glial and neuronal coexpressed gene modules, suggesting coordinated neurovascular unit dysregulation in AD. Integration with AD genetics reveals 125 AD differentially expressed genes directly linked to AD-associated genetic variants. Lastly, we show that APOE4 genotype-associated differences are significantly enriched among AD-associated genes in capillary and venule endothelial cells, as well as subsets of pericytes and fibroblasts.}, author = {Sun, Na and Akay, Leyla Anne and Murdock, Mitchell H and Park, Yongjin and Galiana-Melendez, Fabiola and Bubnys, Adele and Galani, Kyriaki and Mathys, Hansruedi and Jiang, Xueqiao and Ng, Ayesha P and Bennett, David A and Tsai, Li-Huei and Kellis, Manolis} } @book {11180, title = {Spatio{\textendash}Temporal Methods in Environmental Epidemiology with R}, year = {2023}, publisher = {CRC Press}, organization = {CRC Press}, author = {Shaddick, Gavin and Zidek, James V and Schmidt, Alexandra M} } @book {11281, title = {Statistical inference under mixture models}, series = {Springer-ICSA}, year = {2023}, author = {Jiahua Chen} } @unpublished {Ye2023-qz, title = {Tree-structured topic modelling of single-cell gene expression data uncovers hierarchical relationships between immune cell types}, journal = {bioRxiv}, year = {2023}, pages = {2023.11.06.565879}, abstract = {Immune cells undergo a series of differentiation steps following a lineage-tree structure stemming from hematopoietic stem cells. During differentiation of immune cells in both homeostasis and pathological processes, many gene regulatory mechanisms are shared by fully differentiated immune cell sub-types. In order to characterize these features quantitatively, we propose LaRCH, a tree-structured embedded topic model. In this model, single-cell gene expression profiles are represented by a mixture of topics consisting of latent features that follow an underlying tree structure, mirroring that of cellular differentiation{\textendash}nested cluster structures. We present findings of our model trained on simulated single-cell RNA sequencing (scRNA-seq) based on cell-sorted bulk RNA-seq data as well as on a scRNA-seq dataset of over 1.2 million cells from healthy individuals and individuals diagnosed with systemic lupus erythematosus (SLE). The cellular topic profiles estimated by our model markedly improve clustering accuracy over traditional latent variable models and illustrate transcriptomic differences between SLE phenotypes, revealing a pivotal role of multiple immune cell types in disease progression and relapse. Ultimately, LaRCH captures the hierarchical context between cellular subtypes by simultaneously identifying shared and distinct latent features amongst subsets of heterogeneous samples of cells. \#\#\# Competing Interest Statement The authors have declared no competing interest.}, author = {Ye, Patricia E and Zhang, Yichen and Klein Geltink, Ramon I and Park, Yongjin P} } @article {Zhang2023-qg, title = {Unraveling dynamically encoded latent transcriptomic patterns in pancreatic cancer cells by topic modeling}, journal = {Cell Genomics}, volume = {3}, number = {9}, year = {2023}, pages = {100388}, abstract = {Summary Building a comprehensive topic model has become an important research tool in single-cell genomics. With a topic model, we can decompose and ascertain distinctive cell topics shared across multiple cells, and the gene programs implicated by each topic can later serve as a predictive model in translational studies. Here, we present a Bayesian topic model that can uncover short-term RNA velocity patterns from a plethora of spliced and unspliced single-cell RNA-sequencing (RNA-seq) counts. We showed that modeling both types of RNA counts can improve robustness in statistical estimation and can reveal new aspects of dynamic changes that can be missed in static analysis. We showcase that our modeling framework can be used to identify statistically significant dynamic gene programs in pancreatic cancer data. Our results discovered that seven dynamic gene programs (topics) are highly correlated with cancer prognosis and generally enrich immune cell types and pathways.}, keywords = {machine learning, pancreatic cancer, pancreatic ductal adenocarcinoma, RNA velocity, single-cell RNA-seq, topic model, variational autoencoder}, author = {Zhang, Yichen and Khalilitousi, Mohammadali (sam) and Park, Yongjin P} } @article {10841, title = {Adaptive Design and Analysis Via Partitioning Trees for Emulation of a Complex Computer Code}, journal = {Journal of Computational and Graphical Statistics}, year = {2022}, pages = {1-12}, doi = {10.1080/10618600.2022.2039160}, url = {https://doi.org/10.1080/10618600.2022.2039160}, author = {Sonja Isberg and William J. Welch} } @article {11005, title = {Canadian contributions to environmetrics}, journal = {Canadian Journal of Statistics}, volume = {n/a}, year = {2022}, month = {11/2022}, type = {Review}, abstract = {

Abstract This article focuses on the importance of collaboration in statistics by Canadian researchers and highlights the contributions that Canadian statisticians have made to many research areas in environmetrics. We provide a discussion about different vehicles that have been developed for collaboration by Canadians in the environmetrics context as well as specific scientific areas that are focused on environmetrics research in Canada including climate science, forestry, and fisheries, which are areas of importance for natural resources in Canada.

}, keywords = {Canadian contributions, climate, environmetrics, fire science, fisheries, monitoring networks}, doi = {https://doi.org/10.1002/cjs.11743}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cjs.11743}, author = {Dean, Charmaine B. and El-Shaarawi, Abdel H. and Esterby, Sylvia R. and Mills Flemming, Joanna and Routledge, Richard D. and Taylor, Stephen W. and Woolford, Douglas G. and Zidek, James V. and Zwiers, Francis W.} } @article {10931, title = {Consistency of the MLE under a two-parameter gamma mixture model with a structural shape parameter}, journal = {Metrika}, volume = {??}, year = {2022}, url = {https://doi.org/10.1007/s00184-021-00856-9}, author = {He, Mingxin and Chen, Jiahua} } @article {10932, title = {Consistency of the MLE under two-parameter mixture models with a structural scale parameter}, journal = {Advances in Data Analysis and Classification}, volume = {16}, year = {2022}, pages = {125-154}, url = {http://doi.org/10.1007/s11634-021-00472-5}, author = {He, Mingxin and Chen, Jiahua} } @article {10929, title = {Density ratio model with data-adaptive basis function}, journal = {Journal of Multivariate Analysis}, volume = {191}, year = {2022}, author = {Zhang, Archer Gong and and Chen, Jiahua} } @article {10930, title = {Distributed learning of finite Gaussian mixtures}, journal = {Journal of Machine Learning Research}, volume = {23}, year = {2022}, pages = {1-40}, url = {\urlhttp://jmlr.org/papers/v23/21-0093.html}, author = {Zhang, Qiong and Chen, Jiahua} } @article {Cramer2021, title = {Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States}, journal = {Proceedings of the National Academy of Sciences}, volume = {119}, number = {15}, year = {2022}, pages = {e2113561119}, url = {https://www.pnas.org/doi/abs/10.1073/pnas.2113561119}, author = {Estee Y. Cramer and Evan L. Ray and Velma K. Lopez and Johannes Bracher and Andrea Brennen and Alvaro J. Castro Rivadeneira and Aaron Gerding and Tilmann Gneiting and Katie H. House and Yuxin Huang and Dasuni Jayawardena and Abdul H. Kanji and Ayush Khandelwal and Khoa Le and Anja M{\"u}hlemann and Jarad Niemi and Apurv Shah and Ariane Stark and Yijin Wang and Nutcha Wattanachit and Martha W. Zorn and Youyang Gu and Sansiddh Jain and Nayana Bannur and Ayush Deva and Mihir Kulkarni and Srujana Merugu and Alpan Raval and Siddhant Shingi and Avtansh Tiwari and Jerome White and Neil F. Abernethy and Spencer Woody and Maytal Dahan and Spencer Fox and Kelly Gaither and Michael Lachmann and Lauren Ancel Meyers and James G. Scott and Mauricio Tec and Ajitesh Srivastava and Glover E. George and Jeffrey C. Cegan and Ian D. Dettwiller and William P. England and Matthew W. Farthing and Robert H. Hunter and Brandon Lafferty and Igor Linkov and Michael L. Mayo and Matthew D. Parno and Michael A. Rowland and Benjamin D. Trump and Yanli Zhang-James and Samuel Chen and Stephen V. Faraone and Jonathan Hess and Christopher P. Morley and Asif Salekin and Dongliang Wang and Sabrina M. Corsetti and Thomas M. Baer and Marisa C. Eisenberg and Karl Falb and Yitao Huang and Emily T. Martin and Ella McCauley and Robert L. Myers and Tom Schwarz and Daniel Sheldon and Graham Casey Gibson and Rose Yu and Liyao Gao and Yian Ma and Dongxia Wu and Xifeng Yan and Xiaoyong Jin and Yu-Xiang Wang and YangQuan Chen and Lihong Guo and Yanting Zhao and Quanquan Gu and Jinghui Chen and Lingxiao Wang and Pan Xu and Weitong Zhang and Difan Zou and Hannah Biegel and Joceline Lega and Steve McConnell and V. P. Nagraj and Stephanie L. Guertin and Christopher Hulme-Lowe and Stephen D. Turner and Yunfeng Shi and Xuegang Ban and Robert Walraven and Qi-Jun Hong and Stanley Kong and Axel van de Walle and James A. Turtle and Michal Ben-Nun and Steven Riley and Pete Riley and Ugur Koyluoglu and David DesRoches and Pedro Forli and Bruce Hamory and Christina Kyriakides and Helen Leis and John Milliken and Michael Moloney and James Morgan and Ninad Nirgudkar and Gokce Ozcan and Noah Piwonka and Matt Ravi and Chris Schrader and Elizabeth Shakhnovich and Daniel Siegel and Ryan Spatz and Chris Stiefeling and Barrie Wilkinson and Alexander Wong and Sean Cavany and Guido Espa{\~n}a and Sean Moore and Rachel Oidtman and Alex Perkins and David Kraus and Andrea Kraus and Zhifeng Gao and Jiang Bian and Wei Cao and Juan Lavista Ferres and Chaozhuo Li and Tie-Yan Liu and Xing Xie and Shun Zhang and Shun Zheng and Alessandro Vespignani and Matteo Chinazzi and Jessica T. Davis and Kunpeng Mu and Ana Pastore y Piontti and Xinyue Xiong and Andrew Zheng and Jackie Baek and Vivek Farias and Andreea Georgescu and Retsef Levi and Deeksha Sinha and Joshua Wilde and Georgia Perakis and Mohammed Amine Bennouna and David Nze-Ndong and Divya Singhvi and Ioannis Spantidakis and Leann Thayaparan and Asterios Tsiourvas and Arnab Sarker and Ali Jadbabaie and Devavrat Shah and Nicolas Della Penna and Leo A. Celi and Saketh Sundar and Russ Wolfinger and Dave Osthus and Lauren Castro and Geoffrey Fairchild and Isaac Michaud and Dean Karlen and Matt Kinsey and Luke C. Mullany and Kaitlin Rainwater-Lovett and Lauren Shin and Katharine Tallaksen and Shelby Wilson and Elizabeth C. Lee and Juan Dent and Kyra H. Grantz and Alison L. Hill and Joshua Kaminsky and Kathryn Kaminsky and Lindsay T. Keegan and Stephen A. Lauer and Joseph C. Lemaitre and Justin Lessler and Hannah R. Meredith and Javier Perez-Saez and Sam Shah and Claire P. Smith and Shaun A. Truelove and Josh Wills and Maximilian Marshall and Lauren Gardner and Kristen Nixon and John C. Burant and Lily Wang and Lei Gao and Zhiling Gu and Myungjin Kim and Xinyi Li and Guannan Wang and Yueying Wang and Shan Yu and Robert C. Reiner and Ryan Barber and Emmanuela Gakidou and Simon I. Hay and Steve Lim and Chris Murray and David Pigott and Heidi L. Gurung and Prasith Baccam and Steven A. Stage and Bradley T. Suchoski and B. Aditya Prakash and Bijaya Adhikari and Jiaming Cui and Alexander Rodr{\'\i}guez and Anika Tabassum and Jiajia Xie and Pinar Keskinocak and John Asplund and Arden Baxter and Buse Eylul Oruc and Nicoleta Serban and Sercan O. Arik and Mike Dusenberry and Arkady Epshteyn and Elli Kanal and Long T. Le and Chun-Liang Li and Tomas Pfister and Dario Sava and Rajarishi Sinha and Thomas Tsai and Nate Yoder and Jinsung Yoon and Leyou Zhang and Sam Abbott and Nikos I. Bosse and Sebastian Funk and Joel Hellewell and Sophie R. Meakin and Katharine Sherratt and Mingyuan Zhou and Rahi Kalantari and Teresa K. Yamana and Sen Pei and Jeffrey Shaman and Michael L. Li and Dimitris Bertsimas and Omar Skali Lami and Saksham Soni and Hamza Tazi Bouardi and Turgay Ayer and Madeline Adee and Jagpreet Chhatwal and Ozden O. Dalgic and Mary A. Ladd and Benjamin P. Linas and Peter Mueller and Jade Xiao and Yuanjia Wang and Qinxia Wang and Shanghong Xie and Donglin Zeng and Alden Green and Jacob Bien and Logan Brooks and Addison J. Hu and Maria Jahja and Daniel McDonald and Balasubramanian Narasimhan and Collin Politsch and Samyak Rajanala and Aaron Rumack and Noah Simon and Ryan J. Tibshirani and Rob Tibshirani and Valerie Ventura and Larry Wasserman and Eamon B. O{\textquoteright}Dea and John M. Drake and Robert Pagano and Quoc T. Tran and Lam Si Tung Ho and Huong Huynh and Jo W. Walker and Rachel B. Slayton and Michael A. Johansson and Matthew Biggerstaff and Nicholas G. Reich} } @article {10927, title = {Permutation tests under a rotating sampling plan with clustered data}, journal = {Ann. Appl. Statist.}, volume = {16}, year = {2022}, pages = {936-958}, issn = {1932-6157}, doi = {10.1214/21-AOAS1526}, author = {Jiahua Chen and Yukun Liu and Carilyn G. Taylor and James V. Zidek} } @article {11183, title = {Permutation tests under a rotating sampling plan with clustered data}, journal = {The Annals of Applied Statistics}, volume = {16}, year = {2022}, pages = {936{\textendash}958}, author = {Chen, Jiahua and Liu, Yukun and Taylor, Carilyn G and Zidek, James V} } @article {DingMcDonald2019, title = {Sufficient principal component regression for genomics}, journal = {Bioinformatics Advances}, volume = {2}, year = {2022}, pages = {vbac033}, url = {https://doi.org/10.1093/bioadv/vbac033}, author = {Ding, Lei and Zentner, Gabriel E. and McDonald, Daniel J.} } @article {Zhao2021Analysis, title = {Analysis of high-dimensional Continuous Time Markov Chains using the Local Bouncy Particle Sampler}, journal = {Journal of Machine Learning Research}, volume = {22}, year = {2021}, pages = {1{\textendash}41}, author = {Tingting Zhao and Alexandre Bouchard-C{\^o}t{\'e}} } @article {9318, title = {Approximately Optimal Subset Selection for Statistical Design and Modelling}, journal = {Journal of Statistical Computation and Simulation}, year = {2021}, month = {03/2021}, pages = {1-13}, chapter = {Accepted Mar 2, 2021}, author = {Yu Wang and Nhu D Le and James V Zidek} } @article {Bouchard2021Blang, title = {Blang: Probabilitistic Programming for Combinatorial Spaces}, journal = {Journal of Statistical Software}, volume = {(Accepted)}, year = {2021}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Kevin Chern and Davor Cubranic and Sahand Hosseini and Justin Hume and Matteo Lepur and Zihui Ouyang and Giorgio Sgarbi} } @article {McDonaldBien2021, title = {Can Auxiliary Indicators Improve COVID-19 Forecasting and Hotspot Prediction?}, journal = {Proceedings of the National Academy of Sciences}, volume = {118}, year = {2021}, pages = {e2111453118}, url = {https://doi.org/10.1073/pnas.2111453118}, author = {McDonald, Daniel J and Bien, Jacob and Green, Alden and Hu, Addison J and DeFries, Nat and Hyun, Sangwon and Oliveira, Natalia L and Sharpnack, James and Tang, Jingjing and Tibshirani, Robert and Ventura, Val{\'e}rie and Wasserman, Larry and Tibshirani, Ryan J} } @article {Salehi2021Clonal, title = {Clonal fitness inferred from time-series modelling of single-cell cancer genomes}, journal = {Nature}, volume = {(Accepted)}, year = {2021}, author = {Sohrab Salehi and others} } @article {Park2021-rd, title = {CoCoA-diff: counterfactual inference for single-cell gene expression analysis}, journal = {Genome Biol.}, volume = {22}, number = {1}, year = {2021}, pages = {1{\textendash}23}, publisher = {BioMed Central}, abstract = {Finding a causal gene is a fundamental problem in genomic medicine. We present a causal inference framework, CoCoA-diff, that prioritizes disease genes by adjusting confounders without prior knowledge of control variables in single-cell RNA-seq data. We demonstrate that our method substantially improves statistical power in simulations and real-world data analysis of 70k brain cells collected for dissecting Alzheimer{\textquoteright}s disease. We identify 215 differentially regulated causal genes in various cell types, including highly relevant genes with a proper cell type context. Genes found in different types enrich distinctive pathways, implicating the importance of cell types in understanding multifaceted disease mechanisms.}, author = {Park, Yongjin P and Kellis, Manolis} } @article {10449, title = {Composite empirical likelihood for multisample clustered data}, journal = {J Nonparametric Statistics}, year = {2021}, pages = {Accepted Apr 2021}, author = {Jiahua Chen and Pengfei Li and Yukun Liu and James V Zidek} } @article {chen2021composite, title = {Composite empirical likelihood for multisample clustered data}, journal = {Journal of Nonparametric Statistics}, volume = {33}, number = {1}, year = {2021}, pages = {60{\textendash}81}, publisher = {Taylor \& Francis}, author = {Chen, Jiahua and Li, Pengfei and Liu, Yukun and Zidek, James V} } @article {Park2021-zp, title = {Counterfactual inference for single-cell gene expression analysis}, journal = {medRxiv}, year = {2021}, publisher = {Cold Spring Harbor Laboratory Press}, keywords = {My Papers}, author = {Park, Yongjin and Kellis, Manolis} } @proceedings {10382, title = {Ellipse detection and localization with applications to knots in sawn lumber images.}, journal = {2021 IEEE Winter Conference on Applications of Computer Vision (WACV)}, volume = {16(2)}, year = {2021}, pages = {3892-3901}, author = {Pan, Shenyi and Fan, Shuxian and Wong, Samuel and Zidek, James V and Rhodin, H} } @article {10933, title = {Empirical likelihood ratio test on quantiles under a density ratio model}, journal = {Electronic Journal of Statistics}, volume = {15}, year = {2021}, pages = {6191-6227}, url = {https://doi.org/10.1214/21-EJS1943}, author = {Zhang, Archer Gong and Chen, Jiahua} } @article {He2021-cc, title = {Exome-wide age-of-onset analysis reveals exonic variants in ERN1 and SPPL2C associated with Alzheimer{\textquoteright}s disease}, journal = {Transl. Psychiatry}, volume = {11}, number = {1}, year = {2021}, month = {feb}, pages = {146}, publisher = {Springer Science and Business Media LLC}, abstract = {Despite recent discoveries in genome-wide association studies (GWAS) of genomic variants associated with Alzheimer{\textquoteright}s disease (AD), its underlying biological mechanisms are still elusive. The discovery of novel AD-associated genetic variants, particularly in coding regions and from APOE ε4 non-carriers, is critical for understanding the pathology of AD. In this study, we carried out an exome-wide association analysis of age-of-onset of AD with 20,000 subjects and placed more emphasis on APOE ε4 non-carriers. Using Cox mixed-effects models, we find that age-of-onset shows a stronger genetic signal than AD case-control status, capturing many known variants with stronger significance, and also revealing new variants. We identified two novel variants, rs56201815, a rare synonymous variant in ERN1, and rs12373123, a common missense variant in SPPL2C in the MAPT region in APOE ε4 non-carriers. Besides, a rare missense variant rs144292455 in TACR3 showed the consistent direction of effect sizes across all studies with a suggestive significant level. In an attempt to unravel their regulatory and biological functions, we found that the minor allele of rs56201815 was associated with lower average FDG uptake across five brain regions in ADNI. Our eQTL analyses based on 6198 gene expression samples from ROSMAP and GTEx revealed that the minor allele of rs56201815 was potentially associated with elevated expression of ERN1, a key gene triggering unfolded protein response (UPR), in multiple brain regions, including the posterior cingulate cortex and nucleus accumbens. Our cell-type-specific eQTL analysis using 80,000 single nuclei in the prefrontal cortex revealed that the protective minor allele of rs12373123 significantly increased the expression of GRN in microglia, and was associated with MAPT expression in astrocytes. These findings provide novel evidence supporting the hypothesis of the potential involvement of the UPR to ER stress in the pathological pathway of AD, and also give more insights into underlying regulatory mechanisms behind the pleiotropic effects of rs12373123 in multiple degenerative diseases including AD and Parkinson{\textquoteright}s disease.}, keywords = {My Papers}, author = {He, Liang and Loika, Yury and Park, Yongjin and Genotype Tissue Expression (GTEx) consortium and Bennett, David A and Kellis, Manolis and Kulminski, Alexander M and Alzheimer{\textquoteright}s Disease Neuroimaging Initiative} } @article {PolicastroMcDonald2020, title = {Flexible analysis of TSS mapping data and detection of TSS shifts with TSRexploreR}, journal = {NAR Genomics and Bioinformatics}, volume = {3}, number = {2}, year = {2021}, pages = {1{\textendash}10}, url = {https://doi.org/10.1093/nargab/lqab051}, author = {Policastro, Robert A. and McDonald, Daniel J. and Brendel, Volker P. and Zentner, Gabriel E.} } @article {Xiong2021-uv, title = {Genetic drivers of m6A methylation in human brain, lung, heart and muscle}, journal = {Nat. Genet.}, year = {2021}, abstract = {The most prevalent post-transcriptional mRNA modification, N6-methyladenosine (m6A), plays diverse RNA-regulatory roles, but its genetic control in human tissues remains uncharted. Here we report 129 transcriptome-wide m6A profiles, covering 91 individuals and 4 tissues (brain, lung, muscle and heart) from GTEx/eGTEx. We integrate these with interindividual genetic and expression variation, revealing 8,843 tissue-specific and 469 tissue-shared m6A quantitative trait loci (QTLs), which are modestly enriched in, but mostly orthogonal to, expression QTLs. We integrate m6A QTLs with disease genetics, identifying 184 GWAS-colocalized m6A QTL, including brain m6A QTLs underlying neuroticism, depression, schizophrenia and anxiety; lung m6A QTLs underlying expiratory flow and asthma; and muscle/heart m6A QTLs underlying coronary artery disease. Last, we predict novel m6A regulators that show preferential binding in m6A QTLs, protein interactions with known m6A regulators and expression correlation with the m6A levels of their targets. Our results provide important insights and resources for understanding both cis and trans regulation of epitranscriptomic modifications, their interindividual variation and their roles in human disease.}, keywords = {My Papers}, author = {Xiong, Xushen and Hou, Lei and Park, Yongjin P and Molinie, Benoit and GTEx Consortium and Gregory, Richard I and Kellis, Manolis} } @article {McDonald2016, title = {Markov-switching State Space Models for Uncovering Musical Interpretation}, journal = {Annals of Applied Statistics}, volume = {15}, year = {2021}, pages = {1147{\textendash}1170}, url = {https://doi.org/10.1214/21-AOAS1457}, author = {McDonald, Daniel J. and McBride, Michael and Gu, Yupeng and Raphael, Christopher} } @article {zhang2021minimum, title = {Minimum Wasserstein Distance Estimator under Finite Location-scale Mixtures}, journal = {arXiv preprint arXiv:2107.01323}, year = {2021}, author = {Zhang, Qiong and Chen, Jiahua} } @article {10824, title = {Modelling multi-scale, state-switching functional data with hidden Markov models}, journal = {Canadian Journal of Statistics}, volume = {50}, year = {2021}, chapter = {327}, author = {Evan Sidrow and Nancy Heckman and Sarah M. E. Fortune and Andrew Trites and Ian Murphy and Marie Auger-M{\'e}th{\'e}} } @article {10928, title = {Monitoring test under nonparametric random effects model}, journal = {Journal of Nonparametric Statistics}, volume = {33}, year = {2021}, pages = {60-81}, url = {https://doi.org/10.1080/10485252.2021.1914337}, author = {Chen, Jiahua and Li, Pengfei and Liu Yukun and Zidek, James} } @article {Syed2021NonReversible, title = {Non-Reversible Parallel Tempering: a Scalable Highly Parallel MCMC Scheme}, journal = {Journal of Royal Statistical Society, Series B}, volume = {(Accepted)}, year = {2021}, author = {Saifuddin Syed and Alexandre Bouchard-C{\^o}t{\'e} and George Deligiannidis and Arnaud Doucet} } @article {Reinhart2021, title = {An Open Repository of Real-Time COVID-19 Indicators}, journal = {Proceedings of the National Academy of Sciences}, volume = {118}, year = {2021}, pages = {e2111452118}, url = {https://doi.org/10.1073/pnas.2111452118}, author = {Reinhart, Alex and Brooks, Logan and Jahja, Maria and Rumack, Aaron and Tang, Jingjing and Saeed, Wael Al and Arnold, Taylor and Basu, Amartya and Bien, Jacob and Cabrera, {\'A}ngel A. and Chin, Andrew and Chua, Eu Jing and Clark, Brian and DeFries, Nat and Forlizzi, Jodi and Gratzl, Samuel and Green, Alden and Haff, George and Han, Robin and Hu, Addison J. and Hyun, Sangwon and Joshi, Ananya and Kim, Jimi and Kuznetsov, Andrew and Motte-Kerr, Wichada La and Lee, Yeon Jin and Lee, Kenneth and Lipton, Zachary C. and Liu, Michael X. and Mackey, Lester and Mazaitis, Kathryn and McDonald, Daniel J. and Narasimhan, Balasubramanian and Oliveira, Natalia L. and Patil, Pratik and Perer, Adam and Politsch, Collin A. and Rajanala, Samyak and Rucker, Dawn and Shah, Nigam H. and Shankar, Vishnu and Sharpnack, James and Shemetov, Dmitry and Simon, Noah and Srivastava, Vishakha and Tan, Shuyi and Tibshirani, Robert and Tuzhilina, Elena and Van Nortwick, Ana Karina and Ventura, Val{\'e}rie and Wasserman, Larry and Weiss, Jeremy C. and Williams, Kristin and Rosenfeld, Roni and Tibshirani, Ryan J.} } @conference {Syed2021Parallel, title = {Parallel Tempering on Optimized Paths}, booktitle = {International Conference on Machine Learning (ICML)}, volume = {(Accepted)}, year = {2021}, author = {Saifuddin Syed and Vittorio Romaniello and Trevor Campbell and Alexandre Bouchard-C{\^o}t{\'e}} } @article {10621, title = {Permutation tests under a rotating sampling plan with clustered data}, journal = {Journal of nonparametric statistics}, volume = {33}, year = {2021}, month = {05/2021}, pages = {60-81}, type = {Journal article}, author = {Chen, Jiahua and Li,Pengfei and Liu, Yukun and Zidek, James V} } @article {10452, title = {RBF: An R package to compute a robust backfitting estimator for additive models}, journal = {The Journal of Open Source Software}, volume = {6}, year = {2021}, month = {04/2021}, doi = {10.21105/joss.02992}, author = {Alejandra Mart{\'\i}nez and Salibian-Barrera, M.} } @article {Boix2021-br, title = {Regulatory genomic circuitry of human disease loci by integrative epigenomics}, journal = {Nature}, volume = {590}, number = {7845}, year = {2021}, pages = {300{\textendash}307}, abstract = {Annotating the molecular basis of human disease remains an unsolved challenge, as 93\% of disease loci are non-coding and gene-regulatory annotations are highly incomplete1-3. Here we present EpiMap, a compendium comprising 10,000 epigenomic maps across 800 samples, which we used to define chromatin states, high-resolution enhancers, enhancer modules, upstream regulators and downstream target genes. We used this resource to annotate 30,000 genetic loci that were associated with 540 traits4, predicting trait-relevant tissues, putative causal nucleotide variants in enriched tissue enhancers and candidate tissue-specific target genes for each. We partitioned multifactorial traits into tissue-specific contributing factors with distinct functional enrichments and disease comorbidity patterns, and revealed both single-factor monotropic and multifactor pleiotropic loci. Top-scoring loci frequently had multiple predicted driver variants, converging through multiple enhancers with a common target gene, multiple genes in common tissues, or multiple genes and multiple tissues, indicating extensive pleiotropy. Our results demonstrate the importance of dense, rich, high-resolution epigenomic annotations for the investigation of complex traits.}, keywords = {My Papers}, author = {Boix, Carles A and James, Benjamin T and Park, Yongjin P and Meuleman, Wouter and Kellis, Manolis} } @article {10187, title = {Robust Boosting for Regression Problems}, journal = {Computational Statistics and Data Science}, volume = {153}, year = {2021}, doi = {10.1016/j.csda.2020.107065}, url = {https://arxiv.org/abs/2002.02054}, author = {Xiaomeng Ju and Matias Salibian-Barrera} } @article {10379, title = {Robust functional principal components for sparse longitudinal data}, journal = {Metron}, year = {2021}, doi = {10.1007/s40300-020-00193-3}, author = {Boente, Graciela and Salibian-Barrera, M.} } @unpublished {Park2021-mw, title = {Single-cell deconvolution of 3,000 post-mortem brain samples for eQTL and GWAS dissection in mental disorders}, journal = {Cold Spring Harbor Laboratory}, year = {2021}, pages = {2021.01.21.426000}, abstract = {Thousands of genetic variants acting in multiple cell types underlie complex disorders, yet most gene expression studies profile only bulk tissues, making it hard to resolve where genetic and non-genetic contributors act. This is particularly important for psychiatric and neurodegenerative disorders that impact multiple brain cell types with highly-distinct gene expression patterns and proportions. To address this challenge, we develop a new framework, SPLITR, that integrates single-nucleus and bulk RNA-seq data, enabling phenotype-aware deconvolution and correcting for systematic discrepancies between bulk and single-cell data. We deconvolved 3,387 post-mortem brain samples across 1,127 individuals and in multiple brain regions. We find that cell proportion varies across brain regions, individuals, disease status, and genotype, including genetic variants in TMEM106B that impact inhibitory neuron fraction and 4,757 cell-type-specific eQTLs. Our results demonstrate the power of jointly analyzing bulk and single-cell RNA-seq to provide insights into cell-type-specific mechanisms for complex brain disorders. \#\#\# Competing Interest Statement The authors have declared no competing interest.}, keywords = {1 CRS 2021, My Papers}, author = {Park, Yongjin and He, Liang and Davila-Velderrain, Jose and Hou, Lei and Mohammadi, Shahin and Mathys, Hansruedi and Peng, Zhuyu and Bennett, David and Tsai, Li-Huei and Kellis, Manolis} } @article {chen2021test, title = {Test for homogeneity with unordered paired observations}, journal = {Electronic Journal of Statistics}, volume = {15}, number = {1}, year = {2021}, pages = {1661{\textendash}1694}, publisher = {Institute of Mathematical Statistics and Bernoulli Society}, author = {Chen, Jiahua and Li, Pengfei and Qin, Jing and Yu, Tao} } @article {9962, title = {Approximately Optimal Spatial Design: How Good is it?}, journal = {Spatial Statistics}, volume = {37}, year = {2020}, pages = {100409}, author = {Yu Wang and Nhu D Le and James V Zidek} } @article {McDonald2020, title = {Book Review: Sufficient Dimension Reduction: Methods and Applications with R}, journal = {Journal of the American Statistical Association}, volume = {115}, year = {2020}, url = {https://doi.org/10.1080/01621459.2020.1759990}, author = {McDonald, Daniel J.} } @article {HomrighausenMcDonald2017, title = {Compressed and penalized linear regression}, journal = {Journal of Computational and Graphical Statistics}, volume = {29}, number = {2}, year = {2020}, pages = {309{\textendash}322}, url = {https://doi.org/10.1080/10618600.2019.1660179}, author = {Homrighausen, Darren and McDonald, Daniel J.} } @article {Chang.Joe2020, title = {Copula diagnostics for asymmetries and conditional dependence}, journal = {Journal of Applied Statistics}, volume = {47}, number = {9}, year = {2020}, month = {JUL 3}, pages = {1587-1615}, issn = {0266-4763}, doi = {10.1080/02664763.2019.1685080, Early Access Date = NOV 2019}, author = {Chang, Bo and Joe, Harry} } @article {9720, title = {CV}, year = {2020}, abstract = {

Current CV

}, author = {Joe Watson} } @article {10367, title = {Dealing with treatment-confounder feedback and sparse follow-up in longitudinal studies - application of a marginal structural model in a multiple sclerosis cohort. }, journal = {American Journal of Epidemiology}, volume = {189}, year = {2020}, pages = {To appear}, author = {Karim, ME and Tremlett, H and Zhu, F and Petkau, J and Kingwell, E} } @article {10376, title = {Dimensional Analysis in Statistical Modelling}, journal = {Statistical Science}, year = {2020}, pages = {Submitted}, author = {Lee, Tae Yoon and Zidek, James V and Heckman, N} } @article {10375, title = {Ellipse Detection and Localization with Applications to Knots in Sawn Lumber Images}, year = {2020}, author = {Pan, Shenyi and Fan, Shuxian and Wong, Samuel WK and Zidek, James V and Rhodin, Helge} } @article {Krupskii.Joe2020, title = {Flexible copula models with dynamic dependence and application to financial data}, journal = {Econometrics and Statistics}, volume = {16}, year = {2020}, month = {OCT}, pages = {148-167}, issn = {2468-0389}, doi = {10.1016/j.ecosta.2020.01.005}, author = {Krupskii, Pavel and Joe, Harry} } @article {chen2020homogeneity, title = {Homogeneity testing under finite location-scale mixtures}, journal = {Canadian Journal of Statistics}, volume = {48}, number = {4}, year = {2020}, pages = {670{\textendash}684}, publisher = {John Wiley \& Sons, Inc. Hoboken, USA}, author = {Chen, Jiahua and Li, Pengfei and Liu, Guanfu} } @article {Deligiannidis2020Randomized, title = {Randomized Hamiltonian Monte Carlo as Scaling Limit of the Bouncy Particle Sampler and Dimension-Free Convergence Rates}, journal = {Annals of Applied Probability}, volume = {(Accepted)}, year = {2020}, author = {George Deligiannidis and Daniel Paulin and Alexandre Bouchard-C{\^o}t{\'e} and Arnaud Doucet} } @article {10180, title = {Robust estimation for semi-functional linear regression models}, journal = {Computational Statistics and Data Analysis}, volume = {152}, year = {2020}, doi = {10.1016/j.csda.2020.107041}, url = {https://arxiv.org/abs/2006.16156}, author = {Boente, Graciela and Salibian-Barrera, M. and Vena, P.} } @article {10377, title = {Scientific versus statistical modelling: a unifying approach}, year = {2020}, author = {Lee, Tae Yoon and Zidek, James V} } @article {10368, title = {Should the number of acute exacerbations in the previous year be used to guide treatments in COPD? }, journal = {European Journal of Epidemiology}, volume = {35}, year = {2020}, pages = {To appear}, author = {Sadatsafavi, M and McCormack, J and Lee, TY and Petkau, J and Lynd, L and Sin, D} } @conference {Zhu2020Slice, title = {Slice Sampling for General Completely Random Measures}, booktitle = {Proceedings of the 36th Conference on Uncertainty in Artificial Intelligence (UAI)}, volume = {36}, year = {2020}, pages = {699{\textendash}708}, author = {Peiyuan Zhu and Alexandre Bouchard-C{\^o}t{\'e} and Trevor Campbell} } @article {yang2020small, title = {Small area mean estimation after effect clustering}, journal = {Journal of Applied Statistics}, volume = {47}, number = {4}, year = {2020}, pages = {602{\textendash}623}, publisher = {Taylor \& Francis}, author = {Yang, Zhihuang and Chen, Jiahua} } @article {10184, title = {Spatio-temporal downscaling for continental scale estimation of air pollution concentrations}, journal = {Journal of the Royal Statistical Society: Series C}, year = {2020}, pages = {Submitted}, author = {Thomas, M.L. and Shaddick, G. and Simpson, D. and de Hoogh, K. and Zidek, J.V.} } @article {yu2020three, title = {A three-parameter logistic regression model}, journal = {Statistical Theory and Related Fields}, year = {2020}, pages = {1{\textendash}10}, publisher = {Taylor \& Francis}, author = {Yu, Xiaoli and Li, Shaoting and Chen, Jiahua} } @article {Cooke.Joe.ea2020, title = {Vine copula regression for observational studies}, journal = {ASTA-Advances in Statistical Analysis}, volume = {104}, number = {2}, year = {2020}, month = {JUN}, pages = {141-167}, issn = {1863-8171}, doi = {10.1007/s10182-019-00353-5}, author = {Cooke, Roger M. and Joe, Harry and Chang, Bo} } @article {10366, title = {Adjusting for differential misclassification in matched case-control studies utilizing health administrative data.}, journal = {Statistics in Medicine}, volume = {38}, year = {2019}, pages = {3669-3681}, author = {H{\"o}gg, T and Zhao, Y and Gustafson, P and Petkau, J and Fisk, J and Marrie, RA and Tremlett, H} } @conference {KhodadadiMcDonald2018, title = {Algorithms for Estimating Trends in Global Temperature Volatility}, booktitle = {Proceedings of the 33rd AAAI Conference on Artificial Intelligence (AAAI-19)}, year = {2019}, publisher = {Association for the Advancement of Artificial Intelligence}, organization = {Association for the Advancement of Artificial Intelligence}, url = {https://doi.org/10.1609/aaai.v33i01.3301614}, author = {Khodadadi, A. and McDonald, D. J.}, editor = {Hentenryck, P. V. and Zhou, Z.-H.} } @article {Wang2019Annealed, title = {An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics}, journal = {Systematic Biology}, volume = {69}, year = {2019}, pages = {155{\textendash}183}, author = {Liangliang Wang and Shijia Wang and Alexandre Bouchard-C{\^o}t{\'e}} } @article {Wang2019Annealed, title = {An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics}, journal = {Systematic Biology}, volume = {(Accepted)}, year = {2019}, author = {Liangliang Wang and ~Shijia Wang and ~Alexandre Bouchard-C{\^o}t{\'e}} } @conference {chang2019antisymmetric, title = {AntisymmetricRNN: A Dynamical System View on Recurrent Neural Networks}, booktitle = {International Conference on Learning Representations}, year = {2019}, url = {https://openreview.net/forum?id=ryxepo0cFX}, author = {Chang, Bo and Chen, Minmin and Haber, Eldad and Chi, Ed H} } @article {9223, title = {Bayesian analysis of accumulated damage models in lumber reliability}, journal = {Technometrics}, volume = {61}, year = {2019}, pages = {1-14}, author = {Yang, Chun-Hao and Zidek, James V and Wong, Samuel W.K.} } @article {Park2019-hy, title = {Causal Mediation Analysis Leveraging Multiple Types of Summary Statistics Data}, year = {2019}, month = {jan}, abstract = {Summary statistics of genome-wide association studies (GWAS) teach causal relationship between millions of genetic markers and tens and thousands of phenotypes. However, underlying biological mechanisms are yet to be elucidated. We can achieve necessary interpretation of GWAS in a causal mediation framework, looking to establish a sparse set of mediators between genetic and downstream variables, but there are several challenges. Unlike existing methods rely on strong and unrealistic assumptions, we tackle practical challenges within a principled summary-based causal inference framework. We analyzed the proposed methods in extensive simulations generated from real-world genetic data. We demonstrated only our approach can accurately redeem causal genes, even without knowing actual individual-level data, despite the presence of competing non-causal trails.}, keywords = {1 CRS 2021, My Papers}, author = {Park, Yongjin and Sarkar, Abhishek and Nguyen, Khoi and Kellis, Manolis} } @article {R2019clonealign, title = {clonealign: statistical integration of independent single-cell RNA \& DNA-seq from human cancers}, journal = {Genome Biology}, volume = {(Accepted)}, year = {2019}, author = {Kieran R Campbell~et al.~} } @article {Campbell2019clonealign, title = {clonealign: statistical integration of independent single-cell RNA and DNA-seq from human cancers}, journal = {Genome Biology}, volume = {20}, year = {2019}, pages = {1{\textendash}12}, author = {Kieran Campbell and et al.} } @article {10370, title = {Comparison of statistical approaches dealing with time-dependent confounding in drug effectiveness studies}, journal = {Statistical Methods in Medical Research}, volume = {28}, year = {2019}, pages = {323-324 }, author = {Karim, ME and Petkau, J and Gustafson, P and Platt, RW} } @booklet {chen2019contemporary, title = {Contemporary Theory and Practice of Survey Sampling: A Celebration of Research Contributions of JNK Rao}, year = {2019}, author = {Chen, Jiahua and Wu, Changbao and Cai, Song and Torabi, Mahmoud} } @article {11182, title = {Data integration for high-resolution, continental-scale estimation of air pollution concentrations}, journal = {arXiv preprint arXiv:1907.00093}, year = {2019}, author = {Thomas, Matthew L and Shaddick, Gavin and Simpson, Daniel and de Hoogh, Kees and Zidek, James V} } @article {11181, title = {Data integration for high-resolution, continental-scale estimation of air pollution concentrations}, journal = {arXiv preprint arXiv:1907.00093}, year = {2019}, author = {Thomas, Matthew L and Shaddick, Gavin and Simpson, Daniel and de Hoogh, Kees and Zidek, James V} } @article {9951, title = {A discussion of {\textquoteleft}prior-based Bayesian information criterion{\textquoteright}}, journal = {Statistical Theory and Related Fields}, year = {2019}, pages = {1{\textendash}3}, author = {Chen, Jiahua and Feng, Zeny} } @article {9282, title = {The duration of load effect in lumber as stochastic degradation}, journal = {IEEE Transactions on Reliability}, year = {2019}, pages = {410-419}, author = {Wong, Samuel W.K. and Zidek, James V.} } @conference {Zolaktaf2019Efficient, title = {Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains}, booktitle = {The 25th International Conference on DNA Computing and Molecular Programming}, volume = {25}, year = {2019}, pages = {80{\textendash}99}, author = {Sedigheh Zolaktaf and Frits Dannenberg and Erik Winfree and Alexandre Bouchard-C{\^o}t{\'e} and Mark Schmidt and Anne Condon} } @article {10392, title = {EFHC1, implicated in juvenile myoclonic epilepsy, functions at the cilium and synapse to modulate dopamine signaling}, journal = {Elife}, volume = {8}, year = {2019}, pages = {e37271}, author = {Loucks, Catrina M and Park, Kwangjin and Walker, Denise S and McEwan, Andrea H and Timbers, Tiffany A and Ardiel, Evan L and Grundy, Laura J and Li, Chunmei and Johnson, Jacque-Lynne and Kennedy, Julie and others} } @article {Deligiannidis2019Exponential, title = {Exponential Ergodicity of the Bouncy Particle Sampler}, journal = {Annals of Statistics}, volume = {47}, year = {2019}, pages = {1268{\textendash}1287}, author = {George Deligiannidis and Alexandre Bouchard-C{\^o}t{\'e} and Arnaud Doucet} } @article {9961, title = {A General Theory for Preferential Sampling in Environmental Networks}, journal = {Annals of Applied Statistics}, year = {2019}, pages = {Accepted}, author = {Joe Watson and James V Zidek and Gavin Shaddick} } @article {9719, title = {A general theory for preferential sampling in environmental networks}, journal = {Annals of Applied Statistics}, number = {Volume 13, Number 4 (2019)}, year = {2019}, pages = {2662-2700}, abstract = {

This paper presents a general model framework for detecting the preferential sampling of environmental monitors recording an environmental process across space and/or time. This is achieved by considering the joint distribution of an environmental process with a site-selection process that considers where and when sites are placed to measure the process. The environmental process may be spatial, temporal or spatio-temporal in nature. By sharing random effects between the two processes, the joint model is able to establish whether site placement was stochastically dependent of the environmental process under study. Furthermore, if stochastic dependence is identified between the two processes, then inferences about the probability distribution of the spatio-temporal process will change, as will predictions made of the process across space and time. The embedding into a spatio-temporal framework also allows for the modelling of the dynamic site-selection process itself. Real-world factors affecting both the size and location of the network can be easily modelled and quantified. The general framework developed in this paper is designed to be easily and quickly fit using the R-INLA package. We apply this framework to a case study involving particulate air pollution over the UK where a major reduction in the size of a monitoring network through time occurred. It is demonstrated that a significant response-biased reduction in the air quality monitoring network occurred. We also show that the network was consistently unrepresentative of the levels of particulate matter seen across much of Great Britain throughout the operating life of the network. This may have led to a severe over-reporting of the levels across much of Great Britain.

}, author = {Watson, Joe and Zidek, V. James and Shaddick, Gavin} } @article {Joe2019, title = {Likelihood Inference for Generalized Integer Autoregressive Time Series Models}, journal = {EconometricS}, volume = {7}, number = {4}, year = {2019}, month = {DEC}, pages = {43}, doi = {10.3390/econometrics7040043}, author = {Joe, Harry} } @article {9380, title = {Methods for preferential sampling in geostatistics}, journal = {Journal of the Royal Statistical Society Series C}, volume = {68}, year = {2019}, month = {01/2019}, pages = {198}, chapter = {181}, doi = {10.1111/rssc.12286}, url = {https://dx.doi.org/10.1111/rssc.12286 }, author = {Dinsdale, Dinsdale.R. and Salibian-Barrera, Mat{\'\i}as} } @article {9350, title = {Model-based curve registration via stochastic approximation EM algorithm}, journal = {Computational Statistics and Data Analysis}, volume = {131}, year = {2019}, chapter = {159}, abstract = {

Functional data often exhibit both amplitude and phase variation around a common base shape, with phase variation represented by a so called warping function. The process of removing phase variation by curve alignment and inference of the warping functions is referred to as curve registration. When functional data are observed with substantial noise, model-based methods can be employed for simultaneous smoothing and curve registration. However, the nonlinearity of the model often renders the inference computationally challenging. An alternative method for model-based curve registration is proposed which is computationally more stable and efficient than existing approaches in the literature. The proposed method is applied to the analysis of elephant seal dive profiles. The result shows that more intuitive groupings can be obtained by clustering on phase variations via the predicted warping functions.

Original version:\ \  \ arXiv:1712.07265 [stat.ME]\  2017

}, url = {https://arxiv.org/abs/1712.07265}, author = {Eric Fu and Nancy Heckman} } @article {9673, title = {Modelling ocean temperatures from bio-probes under preferential sampling}, journal = {Annals of Applied Statistics}, volume = {13}, year = {2019}, pages = {713-745}, chapter = {713}, doi = {10.1214/18-AOAS1217}, url = {https://arxiv.org/abs/1901.02630}, author = {Dinsdale, Daniel R. and Salibian-Barrera, Mat{\'\i}as} } @article {9482, title = {Multi-parameter One-Sided Monitoring Tests}, journal = {Technometrics}, volume = {60}, year = {2019}, month = {2019}, chapter = {398}, url = {10.1093/biomet/asy068}, author = {Zhu, Guangyu and Chen, Jiahua} } @article {10365, title = {Multiple sclerosis: Effect of beta-interferon treatment on survival.}, journal = {Brain}, volume = {142}, year = {2019}, pages = {1324-1333}, author = {Kingwell, E and Leray, E and Zhu, F and Petkau, J and Edan, G and Oger, J and Tremlett, H} } @article {Luo2019perspective, title = {A new perspective on the benefits of the gene-environment independence in case-control studies}, journal = {The Canadian Journal of Statistics}, volume = {47}, year = {2019}, pages = {473{\textendash}486}, author = {Hao Luo and Gabriela V. Cohen Freue and Xin Zhao and Alexandre Bouchard-C{\^o}t{\'e} and Igor Burstyn and Paul Gustafson} } @article {Krupskii.Joe2019, title = {Nonparametric estimation of multivariate tail probabilities and tail dependence coefficients}, journal = {Journal of Multivariate Analysis}, volume = {172}, number = {SI}, year = {2019}, note = {Workshop on Dependence Modeling Tools for Risk Management, Ctr Recherches Mathematiques, Montreal, CANADA, OCT 02-05, 2017}, month = {JUL}, pages = {147-161}, publisher = {Canadian Stat Sci Inst}, issn = {0047-259X}, doi = {10.1016/j.jmva.2019.02.013}, author = {Krupskii, Pavel and Joe, Harry} } @article {Chang.Joe2019, title = {Prediction based on conditional distributions of vine copulas}, journal = {Computational Statistics \& Data Analysis}, volume = {139}, year = {2019}, month = {NOV}, pages = {45-63}, issn = {0167-9473}, doi = {10.1016/j.csda.2019.04.015}, author = {Chang, Bo and Joe, Harry} } @article {9781, title = {Prediction based on conditional distributions of vine copulas}, journal = {Computational Statistics \& Data Analysis}, volume = {139}, year = {2019}, pages = {45{\textendash}63}, author = {Chang, Bo and Joe, Harry} } @article {9778, title = {Robust elastic net estimators for variable selection and identification of proteomic biomarkers}, journal = {Annals of Applied Statistics}, volume = {13}, year = {2019}, month = {2019}, pages = {2065-2090}, chapter = {2065}, doi = {10.1214/19-AOAS1269}, url = {http://dx.doi.org/10.1214/19-AOAS1269}, author = {Cohen-Freue, Gabriela V. and Kepplinger, David and Salibian-Barrera, M. and Smucler, Ezequiel} } @conference {Cornish2019Scalable, title = {Scalable Metropolis-Hastings for Exact Bayesian Inference with Large Datasets}, booktitle = {International Conference on Machine Learning (ICML)}, volume = {97}, year = {2019}, pages = {1351{\textendash}1360}, author = {Robert Cornish and Paul Vanetti and Alexandre Bouchard-C{\^o}t{\'e} and George Deligiannidis and Arnaud Doucet} } @article {Hadley.Joe.ea2019, title = {On the selection of loss severity distributions to model operational risk}, journal = {Journal of Operational Risk}, volume = {14}, number = {3}, year = {2019}, pages = {73-94}, issn = {1744-6740}, doi = {10.21314/JOP.2019.229}, author = {Hadley, Daniel and Joe, Harry and Nolde, Natalia} } @article {zhuang2019semiparametric, title = {Semiparametric inference for the dominance index under the density ratio model}, journal = {Biometrika}, volume = {106}, number = {1}, year = {2019}, pages = {229{\textendash}241}, author = {Zhuang, W. W. and Hu, B. and Chen, J.} } @article {9283, title = {Sequential decision model for inference and prediction on non-uniform hypergraphs with application to knot matching from computational forestry}, journal = {Annals of Applied Statistics}, volume = {13}, year = {2019}, pages = {1678-1707 }, author = {Jun, Seong-Hwan and Wong, Samuel W.K. and Zidek, James V. and Bourchard-Cote, A.} } @article {Jun2019Sequential, title = {Sequential decision model for inference and prediction on non-uniform hypergraphs with application to knot matching from computational forestry}, journal = {Annals of Applied Statistics}, volume = {13}, year = {2019}, pages = {1678{\textendash}1707}, author = {Seong-Hwan Jun and Samuel W.K. Wong and James V. Zidek and Alexandre Bouchard-C{\^o}t{\'e}} } @article {9950, title = {Small area quantile estimation}, journal = {International Statistical Review}, volume = {87}, year = {2019}, pages = {S219{\textendash}S238}, author = {Chen, Jiahua and Liu, Yukun} } @article {chen2019small, title = {Small area quantile estimation via spline regression and empirical likelihood}, journal = {Survey Methodology 45-1}, volume = {45}, number = {1}, year = {2019}, pages = {81{\textendash}99}, author = {Chen, Zhanshou and Chen, Jiahua and Zhang, Qiong} } @article {Joe.Li2019, title = {Tail densities of skew-elliptical distributions}, journal = {Journal of Multivariate Analysis}, volume = {171}, year = {2019}, month = {MAY}, pages = {421-435}, issn = {0047-259X}, doi = {10.1016/j.jmva.2019.01.009}, author = {Joe, Harry and Li, Haijun} } @article {Fernandez.Cabana.ea2019, title = {Untangling serially dependent underreported count data for gender-based violence}, journal = {Statistics in Medicine}, volume = {38}, number = {22}, year = {2019}, month = {SEP 30}, pages = {4404-4422}, issn = {0277-6715}, doi = {10.1002/sim.8306, Early Access Date = JUL 2019}, author = {Fernandez-Fontelo, Amanda and Cabana, Alejandra and Joe, Harry and Puig, Pedro and Morina, David} } @conference {Chang.Pan.ea2019, title = {Vine copula structure learning via Monte Carlo tree search}, booktitle = {22ND International Conference on Artificial Intelligence and Statistics, Vol 89}, series = {Proceedings of Machine Learning Research}, volume = {89}, year = {2019}, note = {22nd International Conference on Artificial Intelligence and Statistics (AISTATS), Naha, JAPAN, APR 16-18, 2019}, pages = {353-361}, issn = {2640-3498}, author = {Chang, Bo and Pan, Shenyi and Joe, Harry}, editor = {Chaudhuri, K and Sugiyama, M} } @conference {chang2019vine, title = {Vine Copula Structure Learning via Monte Carlo Tree Search}, booktitle = {International Conference on Artificial Intelligence and Statistics}, year = {2019}, author = {Chang, Bo and Pan, Shenyi and Joe, Harry} } @conference {Campbell18_ICML, title = {Bayesian coreset construction via greedy iterative geodesic ascent}, booktitle = {International Conference on Machine Learning}, year = {2018}, author = {Trevor Campbell and Tamara Broderick} } @article {xia2018bayesian, title = {Bayesian inference for unidirectional misclassification of a binary response trait}, journal = {Statistics in medicine}, volume = {37}, number = {6}, year = {2018}, pages = {933{\textendash}947}, publisher = {Wiley Online Library}, author = {Xia, Michelle and Gustafson, Paul} } @conference {9661, title = {Bayesian Optimization Using Monotonicity Information and Its Application in Machine Learning Hyperparameter Tuning}, booktitle = {Proceedings of AutoML 2018 @ ICML/IJCAI-ECAI}, year = {2018}, url = {https://sites.google.com/site/automl2018icml/accepted-papers/59.pdf}, author = {Wang, W. and Welch, W. J.} } @article {8955, title = {Bayesian subset selection procedures with an application to lumber strength properties}, journal = {Sankhya Ser A}, year = {2018}, pages = {Accepted Aug 08, 2018}, author = {Kondo, Yumi and Zidek, James V and Taylor, Carolyn G and van Eeden, Constance} } @article {Bouchard2018Bouncy, title = {The Bouncy Particle Sampler: A non-reversible rejection-free Markov chain Monte Carlo method}, journal = {Journal of the American Statistical Association}, volume = {113}, year = {2018}, pages = {855{\textendash}867}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Sebastian J. Vollmer and Arnaud Doucet} } @article {karim2018comparison, title = {Comparison of statistical approaches dealing with time-dependent confounding in drug effectiveness studies}, journal = {Statistical methods in medical research}, volume = {27}, number = {6}, year = {2018}, pages = {1709{\textendash}1722}, publisher = {SAGE Publications Sage UK: London, England}, author = {Karim, Mohammad Ehsanul and Petkau, John and Gustafson, Paul and Platt, Robert W and Tremlett, Helen and BeAMS Study Group} } @article {9512, title = {Comparison of statistical approaches dealing with time-dependent confounding in drug effectiveness studies}, journal = {Statistical Methods in Medical Research}, volume = {27 }, year = {2018}, pages = {1709-1722}, doi = {10.1177/0962280216668554}, url = {http://journals.sagepub.com/doi/abs/10.1177/0962280216668554}, author = {Karim, M.E. and Petkau, J. and Gustafson, P. and Platt, R.W. and Tremlett, H. and BeAMS Study Group} } @article {campbell2018conditional, title = {Conditional equivalence testing: An alternative remedy for publication bias}, journal = {PloS one}, volume = {13}, number = {4}, year = {2018}, pages = {e0195145}, publisher = {Public Library of Science}, author = {Campbell, Harlan and Gustafson, Paul} } @article {9486, title = {Conditional extremes in asymmetric financial markets}, journal = {Journal of Business \& Economic Statistics}, year = {2018}, abstract = {

The global financial crisis of 2007{\textendash}2009 revealed the great extent to which systemic risk can jeopardize the stability of the entire financial system. An effective methodology to quantify systemic risk is at the heart of the process of identifying the so-called systemically important financial institutions for regulatory purposes as well as to investigate key drivers of systemic contagion. The article proposes a method for dynamic forecasting of CoVaR, a popular measure of systemic risk. As a first step, we develop a semi-parametric framework using asymptotic results in the spirit of extreme value theory (EVT) to model the conditional probability distribution of a bivariate random vector given that one of the components takes on a large value, taking into account important features of financial data such as asymmetry and heavy tails. In the second step, we embed the proposed EVT method into a dynamic framework via a bivariate GARCH process. An empirical analysis is conducted to demonstrate and compare the performance of the proposed methodology relative to a very flexible fully parametric alternative.

}, author = {Nolde, N. and Zhang, J.} } @article {8961, title = {Data Integration Model for Air Quality: A HierarchicalApproach to the Global Estimation of Exposures to Ambient Air Pollution.}, journal = {Applied Statistics}, volume = {67}, year = {2018}, month = {2018}, pages = {231-253}, author = {Shaddick, G and Thomas, M and Jobling, A and Brauer, M and van Donkelaar, A and Burnett, R and Chang, H and Cohen, A and Van Dingennen, R and Dora, C and Gumy, S and Liu, Y and Martin, R and Waller, L and West, J and Zidek, JV and Pruss-Usten, A} } @article {Joe2018, title = {Dependence properties of conditional distributions of some copula models}, journal = {Methodology and Computing in Applied Probability}, volume = {20}, number = {3, SI}, year = {2018}, pages = {975-1001}, doi = {10.1007/s11009-017-9544-9 ISSN = 1387-5841}, author = {Joe, H} } @article {9213, title = {Design of Monitoring Networks using k-Determinantal Point Processes}, journal = {Environmetrics}, volume = {29}, year = {2018}, month = {02/2018}, pages = {Accepted Oct 14, 2017}, author = {Resende-Casquilho, Camila and Le, Nhu D and Zidek, James V} } @article {8958, title = {Dimensional and statistical foundations for accumulated damage models.}, journal = {Wood Science and Technology}, volume = {52}, year = {2018}, month = {01/2018}, pages = {45-65}, author = {Wong, Samuel and Zidek, James V} } @article {Lee.Joe2018b, title = {Efficient computation of multivariate empirical distribution functions at the observed values}, journal = {Computational Statistics}, volume = {33}, year = {2018}, month = {SEP}, pages = {1413-1428}, doi = {10.1007/s00180-017-0771-x ISSN = 0943-4062}, author = {Lee, D and Joe, H} } @article {9481, title = {Empirical likelihood inference for multiple censored samples}, journal = { The Canadian Journal of Statistics}, volume = {46}, year = {2018}, pages = {232}, chapter = {212}, author = {Cai, Song and Chen, Jiahua} } @article {cai2018empirical, title = {Empirical likelihood inference for multiple censored samples}, journal = {Canadian Journal of Statistics}, volume = {46}, number = {2}, year = {2018}, pages = {212{\textendash}232}, author = {Cai, Song and Chen, Jiahua} } @article {Campbell18_EJS, title = {Exchangeable trait allocations}, journal = {Electronic Journal of Statistics}, volume = {12}, number = {2}, year = {2018}, pages = {2290{\textendash}2322}, author = {Trevor Campbell and Diana Cai and Tamara Broderick} } @article {9324, title = {Extreme value limit of the convolution of exponential and multivariate normal distributions: Link to the Husler- Reiss distribution}, journal = {Journal of Multivariate Analysis}, volume = {163}, year = {2018}, month = {2018}, pages = {80-95}, author = {Krupskii, P. and Joe, H. and Lee, D. and Genton, M.} } @article {Krupskii.Joe.ea2018, title = {Extreme-value limit of the convolution of exponential and multivariate normal distributions: Link to the Huesler-Reiss distribution}, journal = {Journal of Multivariate Analysis}, volume = {163}, year = {2018}, pages = {80-95}, doi = {10.1016/j.jmva.2017.10.006}, author = {Krupskii, P and Joe, H and Lee, D and Genton, M} } @article {Krupskii.Huser.ea2016, title = {Factor copula models for replicated spatial data}, journal = {Journal of the American Statistical Association,}, volume = {to appear.}, year = {2018}, month = {2018}, author = {Krupskii, P. and Huser, R. and Genton, M.} } @conference {chang2018generating, title = {Generating Handwritten Chinese Characters Using CycleGAN}, booktitle = {IEEE Winter Conference on Applications of Computer Vision}, year = {2018}, author = {Chang, Bo and Zhang, Qiong and Pan, Shenyi and Meng, Lili} } @article {shupler2018global, title = {Global estimation of exposure to fine particulate matter (PM2. 5) from household air pollution}, journal = {Environment international}, volume = {120}, year = {2018}, pages = {354{\textendash}363}, publisher = {Elsevier}, author = {Shupler, Matthew and Godwin, William and Frostad, Joseph and Gustafson, Paul and Arku, Raphael E and Brauer, Michael} } @conference {9441, title = {Improved Robust Estimation of the Residual Scale in High-Dimensional Problems with the Adaptive Elastic Net S-Estimator for Efficient Robust Penalized Linear Regression Methods}, booktitle = {JSM 2018}, year = {2018}, month = {08/2018}, address = {Vancouver, Canada}, author = {Kepplinger, David and Smucler, Ezequiel and Cohen Freue, Gabriela V.} } @conference {9442, title = {Improving the Robust Estimation of the Residual Scale in High Dimensional Regression Problems with Refitted Cross-Validation using an Elastic Net S-Estimator}, booktitle = {46th Annual Meeting of the Statistical Society of Canada}, year = {2018}, month = {06/2018}, address = {Montreal, Canada}, author = {Kepplinger, David and Cohen Freue, Gabriela V.} } @article {10391, title = {Insights into the roles of CMK-1 and OGT-1 in interstimulus interval-dependent habituation in Caenorhabditis elegans}, journal = {Proceedings of the Royal Society B}, volume = {285}, year = {2018}, pages = {20182084}, author = {Ardiel, Evan L and McDiarmid, Troy A and Timbers, Tiffany A and Lee, Kirsten CY and Safaei, Javad and Pelech, Steven L and Rankin, Catharine H} } @article {Zhang2018Interfaces, title = {Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer}, journal = {Cell}, volume = {(Accepted)}, year = {2018}, author = {Allen Zhang and others} } @article {Zhang2018Interfaces, title = {Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer}, journal = {Cell}, volume = {173}, year = {2018}, pages = {1755{\textendash}1769}, author = {Allen Zhang and others} } @article {9522, title = { A joint model for mixed and censored longitudinal data and survival data, with application to HIV vaccine studies}, journal = {Biostatistics}, volume = {19}, year = {2018}, chapter = {374}, author = {Yu, T and Wu, L and Gilbert, P} } @article {9367, title = {Linear Factor Copula Models and Their Properties}, journal = {Scandinavian Journal of Statistics}, volume = {to appear}, year = {2018}, author = {Krupskii, P. and Genton, M.} } @article {9520, title = {A Mechanistic Nonlinear Model for Truncated and Mis-Measured Time-varying Covariates in Survival Models, with Applications in HIV/AIDS}, journal = {Journal of the Royal Statistical Society, C}, year = {2018}, author = {Zhang, H and Wu, L} } @article {9384, title = {Methods for preferential sampling in geostatistics}, journal = {Journal of the Royal Statistical Society Series C}, year = {2018}, abstract = {

Preferential sampling in geostatistics occurs when the locations at which observations are made may depend on the spatial process that underlines the correlation structure of the measurements.We show that previously proposed Monte Carlo estimates for the likelihood function may not be approximating the desired function. Furthermore, we argue that, for preferential sampling of moderate complexity, alternative and widely available numerical methods to approximate the likelihood function produce better results than Monte Carlo methods. We illustrate our findings on the Galicia data set analysed previously in the literature.

}, keywords = {Geostatistics, Laplace approximation, Point processes, Preferential sampling, Template model builder}, doi = {https://doi.org/10.1111/rssc.12286}, author = {Dinsdale, Daniel R. and Salibian-Barrera, Mat{\'\i}as} } @article {9445, title = {Mining healthcare data for markers of the multiple sclerosis prodrome}, journal = {Multiple Sclerosis and Related Disorders}, year = {2018}, author = {Tanja H{\"o}gg and Jose Wijnands and Elaine Kingwell and Feng Zhu and Xinya Lu and Charity Evans and John Fisk and Ruth Ann Marrie and Yinshan Zhao and Helen Tremlett} } @article {9404, title = {Model-based curve registration via stochastic approximation EM algorithm}, journal = {Computational Statistics and Data Analysis}, volume = {to appear}, year = {2018}, abstract = {

Functional data often exhibit both amplitude and phase variation around a common base shape, with phase variation represented by a so called warping function. The process of removing phase variation by curve alignment and inference of the warping functions is referred to as curve registration. When functional data are observed with substantial noise, model-based methods can be employed for simultaneous smoothing and curve registration. However, the nonlinearity of the model often renders the inference computationally challenging. An alternative method for model-based curve registration is proposed which is computationally more stable and efficient than existing approaches in the literature. The proposed method is applied to the analysis of elephant seal dive profiles. The result shows that more intuitive groupings can be obtained by clustering on phase variations via the predicted warping functions.

Original version:\ \  \ arXiv:1712.07265 [stat.ME]\  2017
}, url = {https://arxiv.org/abs/1712.07265}, author = {Eric Fu and Nancy Heckman} } @article {9521, title = {Modeling semi-continuous longitudinal data with order constraints}, journal = {Statistics in Medicine}, year = {2018}, author = {Zhou, G and Wu, L} } @conference {zhao2018modular, title = {Modular Generative Adversarial Networks}, booktitle = {European Conference on Computer Vision}, year = {2018}, author = {Zhao, Bo and Chang, Bo and Jie, Zequn and Sigal, Leonid} } @article {Dorri2018MuClone, title = {MuClone: somatic mutation detection and classification through probabilistic integration of clonal population information}, journal = {Communications Biology}, volume = {2}, year = {2018}, pages = {1{\textendash}10}, author = {Fatemeh Dorri and Sean Jewell and Alexandre Bouchard-C{\^o}t{\'e} and Sohrab Shah} } @article {Dorri2018MuClone, title = {MuClone: somatic mutation detection and classification through probabilistic integration of clonal population information}, journal = {Communications Biology~}, volume = {2}, year = {2018}, author = {Fatemeh Dorri and Sean Jewell and Alexandre Bouchard-C{\^o}t{\'e} and Sohrab Shah} } @conference {chang2018multilevel, title = {Multi-level Residual Networks from Dynamical Systems View}, booktitle = {International Conference on Learning Representations}, year = {2018}, url = {https://openreview.net/forum?id=SyJS-OgR-}, author = {Chang, Bo and Meng, Lili and Haber, Eldad and Tung, Frederick and Begert, David} } @article {9952, title = {Multi-Parameter One-Sided Monitoring Tests}, journal = {Technometrics}, volume = {60}, year = {2018}, pages = {398{\textendash}407}, author = {Zhu, Guangyu and Chen, Jiahua} } @article {Lee.Joe2018, title = {Multivariate extreme value copulas with factor and tree dependence structures}, journal = {Extremes}, volume = {21}, year = {2018}, month = {MAR}, pages = {147-176}, doi = {10.1007/s10687-017-0298-0 ISSN = 1386-1999}, author = {Lee, D and Joe, H} } @article { ISI:000454597800001, title = {Parsimonious graphical dependence models constructed from vines}, journal = {Canadian Journal of Statistics}, volume = {46}, number = {4}, year = {2018}, month = {DEC}, pages = {532-555}, issn = {0319-5724}, doi = {10.1002/cjs.11481}, author = {Joe, Harry} } @article {Bierkens2018Piecewise, title = {Piecewise Deterministic Markov Processes for Scalable Monte Carlo on Restricted Domains}, journal = {Statistics and Probability Letters}, volume = {136}, year = {2018}, pages = {148{\textendash}154}, author = {Joris Bierkens and Alexandre Bouchard-C{\^o}t{\'e} and Arnaud Doucet and Andrew B Duncan and Paul Fearnhead and Thibaut Lienart and Gareth Roberts and Sebastian J Vollmer} } @conference {Campbell2018Probabilistic, title = {Probabilistic inference of clonal gene expression through integration of RNA \& DNA-seq at single-cell resolution}, booktitle = {HitSeq}, year = {2018}, author = {Kieran Campbell and Alexandre Bouchard-C{\^o}t{\'e} and Sohrab Shah} } @article {sadatsafavi2018relative, title = {Relative impact characteristic curve: a graphical tool to visualize and quantify the clinical utility and population-level consequences of implementing markers}, journal = {Annals of epidemiology}, year = {2018}, publisher = {Elsevier}, author = {Sadatsafavi, Mohsen and Gustafson, Paul and Zafari, Zafar and Sin, Don D} } @conference {chang2018reversible, title = {Reversible Architectures for Arbitrarily Deep Residual Neural Networks}, booktitle = {AAAI Conference on Artificial Intelligence}, year = {2018}, author = {Chang, Bo and Meng, Lili and Haber, Eldad and Ruthotto, Lars and Begert, David and Holtham, Elliot} } @book {10451, title = {Robust Statistics: Theory and Methods (with R)}, series = {Wiley Series in Probability and Statistics}, year = {2018}, pages = {464}, publisher = {John Wiley \& Sons Ltd }, organization = {John Wiley \& Sons Ltd }, edition = {2}, address = {New York}, issn = {9781119214687}, doi = {10.1002/9781119214656}, author = {Maronna, Ricardo A. and Martin, Douglas R. and Yohai, Victor J. and Salibian-Barrera, M.} } @article {9485, title = {Semiparametric inference for the dominance index under the density ratio model.}, journal = {Biometrika}, year = {2018}, author = {Zhuang, Weiwei and Hu, Boyi and Chen, Jiahua} } @article {9214, title = {Statistical challenges in assessing the engineering properties of forest products}, journal = {Annual review of statistics and its application - invitation only}, volume = {5}, year = {2018}, pages = {237-264}, author = {Zidek, James V. and LUM, CONROY} } @article {HomrighausenMcDonald2015a, title = {A study on tuning parameter selection for the high-dimensional lasso}, journal = {Journal of Statistical Computation and Simulation}, volume = {88}, year = {2018}, pages = {2865{\textendash}2892}, url = {http://dx.doi.org/10.1080/00949655.2018.1491575}, author = {Homrighausen, Darren and McDonald, Daniel J.} } @article {9985, title = {Subset selection procedures with an application to lumber strength properties}, journal = {Sanhkya Ser B}, volume = {80}, year = {2018}, pages = {146-172}, author = {Yumi Kondo and James V Zidek and Carolyn G Taylor and Constance van Eeden} } @article {9332, title = {Tail-weighted dependence measures with limit being tail dependence coefficient}, journal = {Journal of Nonparametric Statistics}, volume = {to appear}, year = {2018}, month = {2018}, author = {Lee, D. and Joe, H. and Krupskii, P.} } @article {Lee.Joe.ea2018, title = {Tail-weighted dependence measures with limit being the tail dependence coefficient}, journal = {Journal of Nonparametric Statistics}, volume = {30}, number = {2}, year = {2018}, pages = {262-290}, doi = {10.1080/10485252.2017.1407414}, author = {Lee, D and Joe, H and Krupskii, P} } @article {9660, title = {Toxic Colors: The Use of Deep Learning for Predicting Toxicity of Compounds Merely from Their Graphic Images}, journal = {Journal of Chemical Information and Modeling}, year = {2018}, abstract = {

The majority of computational methods for predicting toxicity of chemicals are typically based on {\textquotedblleft}nonmechanistic{\textquotedblright} cheminformatics solutions, relying on an arsenal of QSAR descriptors, often vaguely associated with chemical structures, and typically employing {\textquotedblleft}black-box{\textquotedblright} mathematical algorithms. Nonetheless, such machine learning models, while having lower generalization capacity and interpretability, typically achieve a very high accuracy in predicting various toxicity endpoints, as unambiguously reflected by the results of the recent Tox21 competition. In the current study, we capitalize on the power of modern AI to predict Tox21 benchmark data using merely simple 2D drawings of chemicals, without employing any chemical descriptors. In particular, we have processed rather trivial 2D sketches of molecules with a supervised 2D convolutional neural network (2DConvNet) and demonstrated that the modern image recognition technology results in prediction accuracies comparable to the state-of-the-art cheminformatics tools. Furthermore, the performance of the image-based 2DConvNet model was comparatively evaluated on an external set of compounds from the Prestwick chemical library and resulted in experimental identification of significant and previously unreported antiandrogen potentials for several well-established generic drugs.

}, author = {Michael Fernandez and Fuqiang Ban and Godwin Woo and Michael Hsing and Takeshi Yamazaki and Eric LeBlanc and Paul S. Rennie and William J. Welch and Artem Cherkasov} } @article {8959, title = {Using artificial censoring to improve extreme tail quantile estimates.}, journal = {Applied Statistics}, year = {2018}, pages = {Accepted Dec 4, 2017}, author = {Liu, Yang and Salibian-Barrera, Mat{\'\i}as and Zamar, Ruben and Zidek, James V} } @article {9333, title = {Using Artificial Censoring to Improve Extreme Tail Quantile Estimates}, journal = {Journal of the Royal Statistical Society Series C}, volume = {67}, year = {2018}, month = {08/2018}, pages = {791-812}, doi = {10.1111/rssc.12262}, url = {https://doi.org/10.1111/rssc.12262}, author = {Liu, Yang and Salibian-Barrera, Mat{\'\i}as and Zamar, Ruben H. and Zidek, James V.} } @article {9480, title = {The Validity and Efficiency of Hypothesis Testing in Observational Studies with Time-Varying Exposures}, journal = {Observational Studies}, year = {2018}, abstract = {

The fundamental obstacle of observational studies is that of unmeasured confounding. \ If all potential confounders are measured within the data, and treatment occurs at but a single time-point, conventional regression adjustment methods provide consistent estimates and allow for valid hypothesis testing in a relatively straightforward manner. \ In situations for which treatment occurs at several successive timepoints, as in many longitudinal studies, another type of confounding is also problematic: even if all confounders are known and measured in the data, time-dependent confounding may bias estimates and invalidate testing due to collider-stratification. \ While {\textquoteleft}{\textquoteleft}causal inference methods{\textquoteright}{\textquoteright} can adequately adjust for time-dependent confounding, these methods require strong and unverifiable assumptions. \ Alternatively, instrumental variable analysis can be used. \ By means of a simple illustrative scenario and simulation studies, this paper sheds light on the issues involved when considering the relative merits of these two approaches for the purpose of hypothesis testing in the presence of time-dependent confounding.

}, url = {https://obsstudies.org/validity-efficiency-hypothesis-testing-observational-studies-time-varying-exposures/}, author = {Campbell, H and Gustafson, P} } @article {9741, title = {Variation and evolution of function-valued traits}, journal = {Annual Review of Ecology, Evolution, and Systematics}, volume = {49}, year = {2018}, chapter = {139}, author = {R Gomulkiewicz and J Kingsolver and P Carter and N Heckman} } @article {gustafson2018sensitivity, title = {When Is a Sensitivity Parameter Exactly That?}, journal = {Statistical Science}, volume = {33}, number = {1}, year = {2018}, pages = {86{\textendash}95}, publisher = {Institute of Mathematical Statistics}, author = {Gustafson, Paul and McCandless, Lawrence C} } @article {8864, title = {Analysis of Aggregated Functional Data from Mixed Populations with Application to Energy Consumption}, journal = {Environmetrics}, volume = { 28}, year = {2017}, chapter = {e2414}, abstract = {

Understanding energy consumption patterns of different types of consumers is essential in any planning of energy distribution. However, obtaining individual-level consumption information is often either not possible or too expensive. Therefore, we consider data from aggregations of energy use, that is, from sums of individuals{\textquoteright} energy use, where each individual falls into one of C consumer classes. Unfortunately, the exact number of individuals of each class may be unknown due to inaccuracies in consumer registration or irregularities in consumption patterns. We develop a methodology to estimate both the expected energy use of each class as a function of time and the true number of consumers in each class. To accomplish this, we use B-splines to model both the expected consumption and the individual-level random effects. We treat the reported numbers of consumers in each category as random variables with distribution depending on the true number of consumers in each class and on the probabilities of a consumer in one class reporting as another class. We obtain maximum likelihood estimates of all parameters via a maximization algorithm. We introduce a special numerical trick for calculating the maximum likelihood estimates of the true number of consumers in each class. We apply our method to a data set and study our method via simulation.

}, author = {Amanda Lenzi and Camila P.E. de Souza and Ronaldo Dias and Nancy L. Garcia and Nancy E. Heckman} } @article {9508, title = {On the application of statistical learning approaches to construct inverse probability weights in marginal structural Cox models: Hedging against weight-model misspecification}, journal = {Communications in Statistics - Simulation and Computation}, volume = {46}, year = {2017}, pages = {7668-7697}, doi = { doi.org/10.1080/03610918.2016.1248574 }, author = {Karim, ME and Petkau, J and Gustafson, P and Tremlett, H and BeAMS Study Group} } @article {karim2017application, title = {On the application of statistical learning approaches to construct inverse probability weights in marginal structural cox models: hedging against weight-model misspecification}, journal = {Communications in Statistics-Simulation and Computation}, volume = {46}, number = {10}, year = {2017}, pages = {7668{\textendash}7697}, publisher = {Taylor \& Francis}, author = {Karim, Mohammad Ehsanul and Petkau, John and Gustafson, Paul and Tremlett, Helen and Group, The Beams Study} } @article {9510, title = {Bayesian analysis of pair-matched case-control studies subject to outcome misclassification}, journal = {Statistics in Medicine}, volume = {36}, year = {2017}, pages = {4196-4213}, doi = {10.1002/sim.7427}, author = {H{\"o}gg, T. and Petkau, J. and Zhao, Y. and Gustafson, P., and Wijnands, J.M.A. and Tremlett, H.} } @article {9221, title = {Bayesian analysis of pair-matched case-control studies subject to outcome misclassification}, journal = {Statistics in Medicine}, volume = {36}, year = {2017}, month = {08/2017}, chapter = {4196{\textendash}4213}, doi = {10.1002/sim.7427}, author = {H{\"o}gg, Tanja and Petkau, John and Zhao, Yinshan and Gustafson, Paul and Wijnands, Jos{\'e} MA and Tremlett, Helen} } @article {hogg2017bayesian, title = {Bayesian analysis of pair-matched case-control studies subject to outcome misclassification}, journal = {Statistics in medicine}, volume = {36}, number = {26}, year = {2017}, pages = {4196{\textendash}4213}, publisher = {Wiley Online Library}, author = {H{\"o}gg, Tanja and Petkau, John and Zhao, Yinshan and Gustafson, Paul and Wijnands, Jos{\'e} MA and Tremlett, Helen} } @unpublished {Park2017-kl, title = {A Bayesian approach to mediation analysis predicts 206 causal target genes in Alzheimer{\textquoteright}s disease}, journal = {bioRxiv}, year = {2017}, pages = {219428}, publisher = {bioRxiv}, abstract = {Characterizing the intermediate phenotypes, such as gene expression, that mediate genetic effects on complex diseases is a fundamental problem in human genetics. Existing methods utilize genotypic data and summary statistics to identify putative disease genes, but cannot distinguish pleiotropy from causal mediation and are limited by overly strong assumptions about the data. To overcome these limitations, we develop Causal Multivariate Mediation within Extended Linkage disequilibrium (CaMMEL), a novel Bayesian inference framework to jointly model multiple mediated and unmediated effects relying only on summary statistics. We show in simulation that CaMMEL accurately distinguishes between mediating and pleiotropic genes unlike existing methods. We applied CaMMEL to Alzheimer9s disease (AD) and found 206 causal genes in sub-threshold loci (p}, keywords = {1 CRS 2021, 1 Deconv Paper, mediation, My Papers}, author = {Park, Yongjin and Sarkar, Abhishek and He, Liang and Davila-Velderrain, Jose and De Jager, Philip L and Kellis, Manolis} } @article {Bouchard2017Bouncy, title = {The Bouncy Particle Sampler: A non-reversible rejection-free Markov chain Monte Carlo method}, journal = {Journal of the American Statistical Association}, volume = {(Accepted)}, year = {2017}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Sebastian J. Vollmer and Arnaud Doucet} } @article {mccandless2017comparison, title = {A comparison of Bayesian and Monte Carlo sensitivity analysis for unmeasured confounding}, journal = {Statistics in medicine}, volume = {36}, number = {18}, year = {2017}, pages = {2887{\textendash}2901}, publisher = {Wiley Online Library}, author = {McCandless, Lawrence C and Gustafson, Paul} } @article {9320, title = {Conditional Equivalence Testing: an alternative remedy for publication bias}, journal = {arXiv preprint arXiv:1710.01771}, year = {2017}, author = {Campbell, Harlan and Gustafson, Paul} } @article {chen2017consistency, title = {Consistency of the MLE under mixture models}, journal = {Statistical Science}, volume = {32}, number = {1}, year = {2017}, pages = {47{\textendash}63}, publisher = {Institute of Mathematical Statistics}, author = {Chen, Jiahua} } @article {Krupskii2016, title = {Copula-based measures of reflection and permutation asymmetry and statistical tests}, journal = {Statistical Papers}, volume = {58(4)}, year = {2017}, month = {2017}, pages = {1165-1187}, author = {Krupskii, Pavel} } @article {burstyn2017correction, title = {Correction of odds ratios in case-control studies for exposure misclassification with partial knowledge of the degree of agreement among experts who assessed exposures}, journal = {Occup Environ Med}, year = {2017}, pages = {oemed{\textendash}2017}, publisher = {BMJ Publishing Group Ltd}, author = {Burstyn, Igor and Gustafson, Paul and Pintos, Javier and Lavou{\'e}, J{\'e}r{\^o}me and Siemiatycki, Jack} } @article {Salehi2017ddClone, title = {ddClone: joint statistical inference of clonal populations from single-cell and bulk tumor sequencing data}, journal = {Genome Biology}, volume = {18}, year = {2017}, author = {Sohrab Salehi and Adi Steif and Andrew Roth and Samuel Aparicio and Alexandre Bouchard-C{\^o}t{\'e} and Sohrab P. Shah} } @article {9662, title = {Discussion of Random-Projection Ensemble Classification by T. I. Cannings and R. J. Samworth}, journal = {Journal of the Royal Statistical Society B}, volume = {79}, year = {2017}, pages = {1024-1025}, doi = {10.1111/rssb.12228}, url = {http://dx.doi.org/10.1111/rssb.12228}, author = {Jabed H. Tomal and William J. Welch and Ruben H. Zamar} } @article {Lindsten2017Divideandconquer, title = {Divide-and-conquer with sequential Monte Carlo}, journal = {Journal of Computational Statistics and Graphics}, volume = {26}, year = {2017}, pages = {445{\textendash}458}, author = {Fredrik Lindsten and Adam M. Johansen and Christian A. Naesseth and Bonnie Kirkpatrick and Thomas B. Schon and John Aston and Alexandre Bouchard-C{\^o}t{\'e}} } @article {Lindsten2017Divideandconquer, title = {Divide-and-conquer with sequential Monte Carlo}, journal = {Journal of Computational Statistics and Graphics}, volume = {26}, year = {2017}, pages = {445{\textendash}458}, author = {Fredrik Lindsten and ~Adam M. Johansen and ~Christian A. Naesseth and ~Bonnie Kirkpatrick and ~Thomas B. Schon and ~John Aston and Alexandre Bouchard-C{\^o}t{\'e}} } @article {9511, title = {Effects of adherence to the first-generation injectable immunomodulatory drugs on disability accumulation in multiple sclerosis: a longitudinal cohort study}, journal = {British Medical Journal Open}, volume = {7}, year = {2017}, pages = {ID e018612, 7 pages}, doi = {10.1136/bmjopen-2017-018612}, url = {https://bmjopen.bmj.com/content/7/9/e018612}, author = {Zhang, T. and Kingwell, E. and Zhu, F. and Petkau, J. and Kastrukoff, L.F. and Marrie, R.A. and Tremlett, H. and Evans, C.} } @conference {Straub17_CVPR, title = {Efficient global point cloud alignment using Bayesian nonparametric mixtures}, booktitle = {IEEE Conference on Computer Vision and Pattern Recognition}, year = {2017}, author = {Julian Straub and Trevor Campbell and Jonathan P. How and John Fisher} } @article {9487, title = {Elicitability and backtesting: Perspectives for banking regulation.}, journal = {The Annals of Applied Statistics}, volume = {11}, year = {2017}, pages = {1833--1874}, author = {Nolde, N. and Ziegel, J.} } @article {9310, title = {Evaluating the safety of beta-interferons in multiple sclerosis: A series of nested case-control studies}, journal = {Neurology}, volume = {88}, year = {2017}, pages = {2310-2320}, abstract = {

Objective: To examine the association between interferon-b (IFN-b) and potential adverse events using population-based health administrative data in British Columbia, Canada.
Methods: Patients with relapsing-remitting multiple sclerosis (RRMS) who were registered at a British Columbia Multiple Sclerosis Clinic (1995{\textendash}2004) were eligible for inclusion and were followed up until death, absence from British Columbia, exposure to a non{\textendash}IFN-b disease modifying drug, or December 31, 2008. Incidence rates were estimated for each potential adverse event (selected a priori and defined with ICD-9/10 diagnosis codes from physician and hospital claims). A nested case-control study was conducted to assess the odds of previous IFN-b exposure for each potential adverse event with at least 30 cases. Cases were matched by age (65 years), sex, and year of cohort entry, with up to 20 randomly selected (by incidence density sampling) controls. Odds ratios (ORs) with 95\% confidence intervals (95\% CIs) were estimated with conditional logistic regression adjusted for age at cohort entry.
Results: Of the 2,485 eligible patients, 77.9\% were women, and 1,031 were treated with IFN-b during follow-up. From the incidence analyses, 27 of the 47 potential adverse events had at least 30 cases. Patients with incident stroke (ORadj 1.83, 95\% CI 1.16{\textendash}2.89), migraine (ORadj 1.55, 95\%CI 1.18{\textendash}2.04), depression (ORadj 1.33, 95\%CI 1.13{\textendash}1.56), and hematologic abnormalities (ORadj 1.32, 95\% CI 1.01{\textendash}1.72) were more likely to have previous exposure to IFN-b than controls.
Conclusions: Among patients with RRMS, IFN-b was associated with a 1.8- and 1.6-fold increase in the risk of stroke and migraine and 1.3-fold increases in depression and hematologic abnormalities.

}, doi = {10.1212/WNL.0000000000004037}, author = {de Jong, HJI and Kingwell, E and Shirani, A and Cohen-Tervaert, JW and Hupperts, R.. and Zhao, Y and Zhu, F and Evans, C and van der Kop, ML and Traboulsee, A and Gustafson, P and Petkau, J and Marrie, RA and Tremlett, H} } @article {Deligiannidis2017Exponential, title = {Exponential ergodicity of the Bouncy Particle Sampler}, journal = {arXiv}, volume = {1705.04579}, year = {2017}, author = {George Deligiannidis and Alexandre Bouchard-C{\^o}t{\'e} and Arnaud Doucet} } @article {9315, title = {Factor copula models for data with spatio-temporal dependence}, journal = {Spatial Statistics}, volume = {22(1)}, year = {2017}, month = {2017}, pages = {180-195}, author = {Krupskii, P. and Genton, M.} } @article {Park2017-vv, title = {Fast and reliable inference algorithm for hierarchical stochastic block models}, year = {2017}, abstract = {Network clustering reveals the organization of a network or corresponding complex system with elements represented as vertices and interactions as edges in a (directed, weighted) graph. Although the notion of clustering can be somewhat loose, network clusters or groups are generally considered as nodes with enriched interactions and edges sharing common patterns. Statistical inference often treats groups as latent variables, with observed networks generated from latent group structure, termed a stochastic block model. Regardless of the definitions, statistical inference can be either translated to modularity maximization, which is provably an NP-complete problem. Here we present scalable and reliable algorithms that recover hierarchical stochastic block models fast and accurately. Our algorithm scales almost linearly in number of edges, and inferred models were more accurate that other scalable methods.}, keywords = {1 CRS 2021, My Papers, Network}, author = {Park, Yongjin and Bader, Joel S} } @article {chen2017finite, title = {On finite mixture models}, journal = {Statistical Theory and Related Fields}, volume = {1}, number = {1}, year = {2017}, pages = {15{\textendash}27}, publisher = {Taylor \& Francis}, author = {Chen, Jiahua} } @article {9284, title = {Flexible Correlation Structure for Accurate Prediction and Uncertainty Quantification in Bayesian Gaussian Process Emulation of a Computer Model}, journal = {SIAM/ASA Journal on Uncertainty Quantification}, volume = {5}, year = {2017}, pages = {620}, chapter = {598}, url = {http://epubs.siam.org/doi/abs/10.1137/15M1008774}, author = {Hao Chen and Jason Loeppky and William Welch} } @article {9663, title = {Flexible Correlation Structure for Accurate Prediction and Uncertainty Quantification in Bayesian Gaussian Process Emulation of a Computer Model}, journal = {SIAM/ASA Journal on Uncertainty Quantification}, volume = {5}, year = {2017}, pages = {598{\textendash}620}, doi = {https://doi.org/10.1137/15M1008774}, url = {https://doi.org/10.1137/15M1008774}, author = {Hao Chen and Jason L. Loeppky and William J. Welch} } @article {wijnands2017health, title = {Health-care use before a first demyelinating event suggestive of a multiple sclerosis prodrome: a matched cohort study}, journal = {The Lancet Neurology}, volume = {16}, number = {6}, year = {2017}, pages = {445{\textendash}451}, publisher = {Elsevier}, author = {Wijnands, Jos{\'e} MA and Kingwell, Elaine and Zhu, Feng and Zhao, Yinshan and H{\"o}gg, Tanja and Stadnyk, Karen and Ekuma, Okechukwu and Lu, Xinya and Evans, Charity and Fisk, John D and others} } @article {islam2017hepatitis, title = {Hepatitis C cross-genotype immunity and implications for vaccine development}, journal = {Scientific reports}, volume = {7}, number = {1}, year = {2017}, pages = {12326}, publisher = {Nature Publishing Group}, author = {Islam, Nazrul and Krajden, Mel and Shoveller, Jean and Gustafson, Paul and Gilbert, Mark and Wong, Jason and Tyndall, Mark W and Janjua, Naveed Zafar} } @article {cai2017hypothesis, title = {Hypothesis testing in the presence of multiple samples under density ratio models}, journal = {Statistica Sinica}, volume = {27}, year = {2017}, pages = {716{\textendash}783}, author = {Cai, Song and Chen, Jiahua and Zidek, James V} } @article {9309, title = {Identification of treatment responders based on multiple longitudinal outcomes with applications to multiple sclerosis patients}, journal = {Statistics in Medicine}, volume = {36}, year = {2017}, pages = {1862-1883}, abstract = {

Identification of treatment responders is a challenge in comparative studies where treatment efficacy is measured by multiple longitudinally collected continuous and count outcomes. Existing procedures often identify responders on the basis of only a single outcome. We propose a novel multiple longitudinal outcome mixture model that assumes that, conditionally on a cluster label, each longitudinal outcome is from a generalized linear mixed effect model. We utilize a Monte Carlo expectation-maximization algorithm to obtain the maximum likelihood estimates of our high-dimensional model and classify patients according to their estimated posterior probability of being a responder. We demonstrate the flexibility of our novel procedure on two multiple sclerosis clinical trial datasets with distinct data structures. Our simulation study shows that incorporating multiple outcomes improves the responder identification performance; this can occur even if some of the outcomes are ineffective. Our general procedure facilitates the identification of responders who are comprehensively defined by multiple outcomes from various distributions.

}, doi = {10.1002/sim.7230}, author = {Kondo, Y and Zhao, Y and Petkau, J} } @article {islam2017incidence, title = {Incidence, risk factors, and prevention of hepatitis C reinfection: a population-based cohort study}, journal = {The Lancet Gastroenterology \& Hepatology}, volume = {2}, number = {3}, year = {2017}, pages = {200{\textendash}210}, publisher = {Elsevier}, author = {Islam, Nazrul and Krajden, Mel and Shoveller, Jean and Gustafson, Paul and Gilbert, Mark and Buxton, Jane A and Wong, Jason and Tyndall, Mark W and Janjua, Naveed Zafar and Cohort, British Columbia Hepatitis Testers and others} } @article {meng2017inferring, title = {Inferring population size: extending the multiplier method to incorporate multiple traits with a likelihood-based approach}, journal = {Stat}, volume = {6}, number = {1}, year = {2017}, pages = {4{\textendash}13}, publisher = {Wiley Online Library}, author = {Meng, Vivian Yun and Gustafson, Paul} } @proceedings {McDonald2017, title = {Minimax Density Estimation for Growing Dimension}, journal = {Proceedings of the Twentieth International Conference on Artificial Intelligence and Statistics (AISTATS)}, volume = {54}, year = {2017}, pages = {194{\textendash}203}, publisher = {PMLR}, url = {http://proceedings.mlr.press/v54/mcdonald17a.html}, author = {McDonald, Daniel J.}, editor = {Singh, Aarti and Zhu, Jerry} } @article { ISI:000388061700010, title = {Model selection for discrete regular vine copulas}, journal = {COMPUTATIONAL STATISTICS \& DATA ANALYSIS}, volume = {106}, year = {2017}, month = {FEB}, pages = {138-152}, issn = {0167-9473}, doi = {10.1016/j.csda.2016.09.007}, author = {Panagiotelis, Anastasios and Czado, Claudia and Joe, Harry and Stoeber, Jakob} } @article {Park2017-cb, title = {Multi-tissue polygenic models for transcriptome-wide association studies}, journal = {bioRxiv}, year = {2017}, month = {feb}, pages = {107623}, publisher = {Cold Spring Harbor Labs Journals}, abstract = {Transcriptome-wide association studies (TWAS) have proven to be a powerful tool to identify genes associated with human diseases by aggregating cis-regulatory effects on gene expression. However, TWAS relies on building predictive models of gene expression, which are sensitive to the sample size and tissue on which they are trained. The Gene Tissue Expression Project has produced reference transcriptomes across 53 human tissues and cell types; however, the data is highly sparse, making it difficult to build polygenic models in relevant tissues for TWAS. Here, we propose \textbackslashtextquoteleftfQTL\textbackslashtextquoteright, a multi-tissue, multivariate model for mapping expression quantitative trait loci and predicting gene expression. Our model decomposes eQTL effects into SNP-specific and tissue-specific components, pooling information across relevant tissues to effectively boost sample sizes. In simulation, we demonstrate that our multi-tissue approach outperforms single-tissue approaches in identifying causal eQTLs and tissues of action. Using our method, we fit polygenic models for 13,461 genes, characterized the tissue-specificity of the learned cis-eQTLs, and performed TWAS for Alzheimer{\textquoteright}s disease and schizophrenia, identifying 107 and 382 associated genes, respectively.}, keywords = {My Papers}, author = {Park, Yongjin and Sarkar, Abhishek K and Bhutani, Kunal and Kellis, Manolis} } @article {Hua.Joe2017, title = {Multivariate dependence modeling based on comonotonic factors}, journal = {Journal of Multivariate Analysis}, volume = {155}, year = {2017}, pages = {317-333}, doi = {10.1016/j.jmva.2017.01.008}, author = {Hua, L and Joe, H} } @article {8874, title = {Multivariate Location and Scatter Matrix Estimation Under Cellwise and Casewise Contamination}, journal = {CSDA}, year = {2017}, month = {02/2017}, doi = {10.1016/j.csda.2017.02.007}, author = {Leung, A. and Yohai, V. and Zamar, R.} } @article {beliveau2017network, title = {Network meta-analysis of disconnected networks: How dangerous are random baseline treatment effects?}, journal = {Research synthesis methods}, volume = {8}, number = {4}, year = {2017}, pages = {465{\textendash}474}, publisher = {Wiley Online Library}, author = {B{\'e}liveau, Audrey and Goring, Sarah and Platt, Robert W and Gustafson, Paul} } @article {McDonaldShalizi2016, title = {Nonparametric risk bounds for time-series forecasting}, journal = {Journal of Machine Learning Research}, volume = {18}, number = {32}, year = {2017}, pages = {1{\textendash}40}, url = {http://www.jmlr.org/papers/v18/13-336.html}, author = {McDonald, D. J. and Shalizi, Cosma Rohilla and Schervish, Mark} } @inbook {Joe2017, title = {Parametric copula families for statistical models}, booktitle = {Copulas and Dependence Models with Applications: Contributions in Honor of Roger B. Nelsen}, year = {2017}, pages = {119{\textendash}134}, publisher = {Springer}, organization = {Springer}, address = {Berlin}, url = {https://link.springer.com/book/10.1007/978-3-319-64221-5}, author = {Joe, Harry}, editor = {M. Ubeda-Flores and E. de Amo-Artero and F. Durante and J. Fernandez-Sanchez} } @article {Bouchard2017Particle, title = {Particle Gibbs split-merge sampling for Bayesian inference in mixture models}, journal = {Journal of Machine Learning Research}, volume = {18}, year = {2017}, pages = {1{\textendash}39}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Arnaud Doucet and Andrew Roth} } @article {10.1371/journal.pone.0177569, title = {PGCA: An algorithm to link protein groups created from MS/MS data}, journal = {PLOS ONE}, volume = {12}, number = {5}, year = {2017}, month = {05}, pages = {1-19}, publisher = {Public Library of Science}, abstract = {The quantitation of proteins using shotgun proteomics has gained popularity in the last decades, simplifying sample handling procedures, removing extensive protein separation steps and achieving a relatively high throughput readout. The process starts with the digestion of the protein mixture into peptides, which are then separated by liquid chromatography and sequenced by tandem mass spectrometry (MS/MS). At the end of the workflow, recovering the identity of the proteins originally present in the sample is often a difficult and ambiguous process, because more than one protein identifier may match a set of peptides identified from the MS/MS spectra. To address this identification problem, many MS/MS data processing software tools combine all plausible protein identifiers matching a common set of peptides into a protein group. However, this solution introduces new challenges in studies with multiple experimental runs, which can be characterized by three main factors: i) protein groups{\textquoteright} identifiers are local, i.e., they vary run to run, ii) the composition of each group may change across runs, and iii) the supporting evidence of proteins within each group may also change across runs. Since in general there is no conclusive evidence about the absence of proteins in the groups, protein groups need to be linked across different runs in subsequent statistical analyses. We propose an algorithm, called Protein Group Code Algorithm (PGCA), to link groups from multiple experimental runs by forming global protein groups from connected local groups. The algorithm is computationally inexpensive and enables the connection and analysis of lists of protein groups across runs needed in biomarkers studies. We illustrate the identification problem and the stability of the PGCA mapping using 65 iTRAQ experimental runs. Further, we use two biomarker studies to show how PGCA enables the discovery of relevant candidate protein group markers with similar but non-identical compositions in different runs.}, doi = {10.1371/journal.pone.0177569}, url = {https://doi.org/10.1371/journal.pone.0177569}, author = {Kepplinger, David and Takhar, Mandeep and Sasaki, Mayu and Hollander, Zsuzsanna and Smith, Derek and McManus, Bruce and McMaster, W. Robert and Ng, Raymond T. and Cohen Freue, Gabriela V.} } @article {Vanetti2017Piecewise, title = {Piecewise Deterministic Markov Chain Monte Carlo}, journal = {arXiv}, volume = {1707.05296}, year = {2017}, author = {Paul Vanetti and Alexandre Bouchard-C{\^o}t{\'e} and George Deligiannidis and Arnaud Doucet} } @article {Zhai2017Poissonian, title = {A Poissonian model of indel rate variation for phylogenetic tree inference}, journal = {Systematic Biology}, volume = {66}, year = {2017}, pages = {698{\textendash}714}, author = {Yongliang Zhai and Alexandre Bouchard-C{\^o}t{\'e}} } @article {Zhai2017Poissonian, title = {A Poissonian model of indel rate variation for phylogenetic tree inference}, journal = {Systematic Biology}, volume = {(Accepted)}, year = {2017}, author = {Yongliang Zhai and Alexandre Bouchard-C{\^o}t{\'e}} } @article {3973, title = {Pre-averaged kernel estimators for the drift function of a diffusion process in the presence of microstructure noise}, journal = {Statistical Inference for Stochastic Processes}, volume = {20}, year = {2017}, month = {07/2017}, chapter = { 237}, abstract = {

We consider estimation of the drift function of a stationary diffusion process when we observe high-frequency data with microstructure noise over a long time interval. We propose to estimate the drift function at a point by a Nadaraya{\textendash}Watson estimator that uses observations that have been pre-averaged to reduce the noise. We give conditions under which our estimator is consistent and asympotically normal. Its rate and asymptotic bias and variance are the same as those without microstructure noise. To use our method in data analysis, we propose a data-based cross-validation method to determine the bandwidth in the Nadaraya{\textendash}Watson estimator. Via simulation, we study several methods of bandwidth choices, and compare our estimator to several existing estimators. In terms of mean squared error, our new estimator out- performs existing estimators.

}, author = {Wooyong Lee and Priscilla Greenwood and Nancy Heckman and Wolfgang Wefelmeyer} } @article {DingMcDonald2017, title = {Predicting phenotypes from microarrays using amplified, initially marginal, eigenvector regression}, journal = {Bioinformatics}, volume = {33}, number = {14}, year = {2017}, pages = {i350{\textendash}i358}, url = {http://dx.doi.org/10.1093/bioinformatics/btx265}, author = {Ding, Lei and McDonald, Daniel J.} } @article {9483, title = {Regularization in regime-switching Gaussian autoregressive models}, journal = {The Canadian Journal of Statistics}, volume = {45}, year = {2017}, pages = {374}, chapter = {356}, author = {Khalili, Abbas and Chen, Jiahua and Stephens, David, A} } @article {McPherson2017ReMixT, title = {ReMixT: clone-specific genomic structure estimation in cancer}, journal = {Genome Biology}, volume = {18}, year = {2017}, author = {A. McPherson and A. Roth and G. Ha and C. Chauve and A. Steif and C. P. E. de Souza and P. Eirew and A. Bouchard-C{\^o}t{\'e} and S. Aparicio and S. Sahinalp and S. Shah.} } @article {HomrighausenMcDonald2015, title = {Risk consistency of cross-validation for lasso-type procedures}, journal = {Statistica Sinica}, volume = {27}, number = {3}, year = {2017}, pages = {1017{\textendash}1036}, url = {http://dx.doi.org/10.5705/ss.202015.0355}, author = {Homrighausen, Darren and McDonald, Daniel J.} } @article {doi:10.1080/10485252.2017.1369077, title = {Robust estimators for additive models using backfitting}, journal = {Journal of Nonparametric Statistics}, volume = {29}, number = {4}, year = {2017}, pages = {744-767}, publisher = {Taylor \& Francis}, doi = {10.1080/10485252.2017.1369077}, url = {https://doi.org/10.1080/10485252.2017.1369077}, author = {Graciela Boente and Alejandra Mart{\'\i}nez and Matias Salibian-Barrera} } @article {islam2017role, title = {Role of primary T-cell immunodeficiency and hepatitis B coinfection on spontaneous clearance of hepatitis C: The BC Hepatitis Testers Cohort}, journal = {Journal of viral hepatitis}, volume = {24}, number = {5}, year = {2017}, pages = {421{\textendash}429}, publisher = {Wiley Online Library}, author = {Islam, Nazrul and Krajden, Mel and Gilbert, Mark and Gustafson, Paul and Yu, Amanda and Kuo, Margot and Chong, Mei and Alvarez, Maria and Wong, Jason and Tyndall, Mark W and others} } @article {Jun2017Sequential, title = {Sequential decision model for inference and prediction on non-uniform hypergraphs with application to knot matching from computational forestry}, journal = {arXiv}, volume = {1708.07592}, year = {2017}, author = {Seong-Hwan Jun and Samuel W. K. Wong and James V. Zidek and Alexandre Bouchard-C{\^o}t{\'e}} } @conference {Jun2017Sequential, title = {Sequential Graph Matching with Sequential Monte Carlo}, booktitle = {AISTATS}, volume = {20}, year = {2017}, pages = {1075{\textendash}1084}, author = {Seong-Hwan Jun and Samuel W.K. Wong and James V. Zidek and Alexandre Bouchard-C{\^o}t{\'e}} } @proceedings {9802, title = {Sequential graph matching with sequential monte carlo}, journal = {20th International Conference on Artificial Intelligence and Statistics}, year = {2017}, month = {2017}, publisher = {AISTATS}, address = {Fort Lauderdale, Florida}, author = {Seong-Hwan Jun and Alexandre Bouchare-Cote}, editor = {Samuel W.K. Wonlg} } @article {9396, title = {Sparse transition matrix estimation for high-dimensional and locally stationary vector autoregressive models}, journal = {Electronic Journal of Statistics}, volume = {11}, year = {2017}, pages = {3871{\textendash}3902}, author = {Ding, Xin and Qiu, Ziyi and Chen, Xiaohui} } @article {8960, title = {Spatio-temporal modelling of temperature fields in the Pacific Northwest}, journal = {Environmetrics}, year = {2017}, pages = {Resubmitted}, author = {Casquilho-Resende, Camila M. and Le, Nhu D and Zidek, James V} } @article {9349, title = {Switching nonparametric regression models for multi-curve data}, journal = {Canadian Journal of Statistics}, volume = {45}, year = {2017}, pages = {442{\textendash}460}, keywords = {EM algorithm, Functional data analysis, latent variables, machine learning, MSC 2010: Primary 62G08, nonparametric regression, power usage, secondary 62G05, switching nonparametric regression model}, issn = {1708-945X}, doi = {10.1002/cjs.11331}, url = {http://dx.doi.org/10.1002/cjs.11331}, author = {de Souza, Camila P. E. and Heckman, Nancy E. and Xu, Fan} } @unpublished {Park2017-ce, title = {Temporal expression divergence of network modules}, journal = {bioRxiv}, year = {2017}, month = {jul}, pages = {167734}, abstract = {Here we propose new module-based approaches to identify differentially regulated network sub-modules combining temporal trajectories of expression profiles with static network skeletons. Starting from modules identified by network clustering of static networks, our analysis refines pre-defined genesets by partitioning them into smaller homogeneous sets by non-paramettric Bayesian methods. Especially for case-control time series data we developed multi-time point discriminative models and identified each network module as a mixture or admixture of dynamic discriminative functions. Our results shows that our proposed approach outperformed existing geneset enrichment methods in simulation studies. Moreover we applied the methods to neural stem cell differentiation data, and discovered novel modules differentially perturbed in different developmental stages.}, keywords = {1 CRS 2021, My Papers}, author = {Park, Yongjin and Kang, Tae-Hyuk and Friedmann, Theodore and Bader, Joel} } @article {9523, title = {Two-Step and Likelihood Methods for Joint Models of Longitudinal and Survival Data}, journal = {Communication in Statistics}, volume = {46}, year = {2017}, chapter = {6019}, author = {Ye, Q and Wu, L} } @article {10393, title = {Accelerating gene discovery by phenotyping whole-genome sequenced multi-mutation strains and using the sequence kernel association test (SKAT)}, journal = {PLoS genetics}, volume = {12}, year = {2016}, pages = {e1006235}, author = {Timbers, Tiffany A and Garland, Stephanie J and Mohan, Swetha and Flibotte, Stephane and Edgley, Mark and Muncaster, Quintin and Au, Vinci and Li-Leger, Erica and Rosell, Federico I and Cai, Jerry and others} } @article {riddell_adaptive_2013, title = {An adaptive clinical trials procedure for a sensitive subgroup examined in the multiple sclerosis context}, journal = {Statistical Methods in Medical Research}, volume = {25}, year = {2016}, pages = {1330-1345}, abstract = {

The biomarker-adaptive threshold design (BATD) allows researchers to simultaneously study the efficacy of treatment in the overall group and to investigate the relationship between a hypothesized predictive biomarker and the treatment effect on the primary outcome. It was originally developed for survival outcomes for Phase III clinical trials where the biomarker of interest is measured on a continuous scale. In this paper, generalizations of the BATD to accommodate count biomarkers and outcomes are developed and then studied in the multiple sclerosis (MS) context where the number of relapses is a commonly used outcome. Through simulation studies, we find that the BATD has increased power compared with a traditional fixed procedure under varying scenarios for which there exists a sensitive patient subgroup. As an illustration, we apply the procedure for two hypothesized markers, baseline enhancing lesion count and disease duration at baseline, using data from a previously completed trial. MS duration appears to be a predictive marker relationship for this dataset, and the procedure indicates that the treatment effect is strongest for patients who have had MS for less than 7.8 years. The procedure holds promise of enhanced statistical power when the treatment effect is greatest in a sensitive patient subgroup.

}, keywords = {adaptive designs, Biomarkers, clinical trials, negative binomial regression}, doi = {10.1177/0962280213480576}, url = {http://smm.sagepub.com/content/early/2013/04/01/0962280213480576}, author = {Riddell, CA and Zhao, Y and Petkau, J} } @article {3361, title = {Adult lifetime alcohol consumption and invasive epithelial ovarian cancer risk in a population-based case-control study}, journal = {Gynecologic Oncology}, volume = {140}, year = {2016}, pages = {277-284}, author = {Linda S Cook and Andy Leung and Kenneth Swenerton and Richard P. Gallagher and Anthony Magliocco and Helen Steed and Martin Koebel and Jill Nation and Sima Eshragh and Angela Brooks-Wilson and Nhu D Le} } @article {9665, title = {Analysis Methods for Computer Experiments: How to Assess and What Counts?}, journal = {Statistical Science}, volume = {31}, year = {2016}, pages = {40{\textendash}60}, doi = {https://dx.doi.org/10.14288/1.0302078}, url = {https://dx.doi.org/10.14288/1.0302078}, author = {Hao Chen and Jason L. Loeppky and Jerome Sacks and William J. Welch} } @article {8887, title = {Analysis Methods for Computer Experiments: How to Assess and What Counts?}, journal = {Statistical Science}, volume = {31}, year = {2016}, pages = {40-60}, chapter = {40}, url = {http://projecteuclid.org/euclid.ss/1455115913}, author = {Chen, Hao and Loeppky, Jason L. and Sacks, Jerome and Welch, William J.} } @article {Falasinnu2016a, title = {An assessment of population-based screening guidelines versus clinical prediction rules for chlamydia and gonorrhea case finding}, journal = {Preventive medicine}, volume = {89}, year = {2016}, pages = {51{\textendash}56}, publisher = {Academic Press}, doi = {10.1016/j.ypmed.2016.04.001}, author = {Falasinnu, Titilola and Gilbert, Mark and Gustafson, Paul and Shoveller, Jean} } @article {Zhang2016, title = {Association between the use of selective serotonin reuptake inhibitors and multiple sclerosis disability progression}, journal = {Pharmacoepidemiology and Drug Safety}, year = {2016}, doi = {10.1002/pds.4031}, author = {Zhang, Tingting and Kingwell, Elaine and De Jong, Hilda JI and Zhu, Feng and Zhao, Yinshan and Carruthers, Robert and Petkau, John and Gustafson, Paul and Oger, Joel and Tremlett, Helen} } @article {9308, title = {Association between the use of selective serotonin reuptake inhibitors and multiple sclerosis disability progression}, journal = {Pharmacoepidemiology and Drug Safety}, volume = {25}, year = {2016}, pages = {1150-1159}, abstract = {

Background Benefits of selective serotonin reuptake inhibitors (SSRIs) in modifying the multiple sclerosis (MS) disease course have been suggested, but their ability to delay disability progression remains unknown. We examined the association between SSRI exposure and MS disability progression. Methods A nested case{\textendash}control study was conducted using the British Columbia (Canada) Multiple Sclerosis clinical data linked to health administrative data. The primary outcome was a sustained score of 6 (requires a cane to walk) on the Expanded Disability Status Scale (EDSS), and the secondary outcome was the onset of secondary progressive MS (SPMS, an advanced stage of MS). The cases were those who reached a study outcome and were matched with up to four randomly selected controls by sex, age, EDSS and calendar year at study entry using incidence density sampling. The associations between disability worsening and SSRI exposure were assessed with conditional logistic regression models, adjusted for confounders. Results A total of 3920 patients were included in the main analyses, of which 272 reached sustained EDSS 6 and 187 reached SPMS. SSRI exposure was significantly different between patients who reached sustained EDSS 6 and controls [adjusted odds ratio (adjOR):1.44; 95\% confidence interval (CI):1.03{\textendash}2.01]. However, SSRI exposure was not significantly different between those who reached SPMS and their controls (adjOR:1.35; 95\%CI:0.89{\textendash}2.04). Conclusion We found no evidence to suggest that SSRI exposure was associated with a delay in MS disability accumulation or progression.

}, doi = {10.1002/pds.4031}, author = {Zhang, T and Kingwell, E and DeJong, HJI and Zhu, F and Zhao, Y and Carruthers, R and Petkau, J and Gustafson, P and Oger, J and Tremlett, H} } @article {Liu2016, title = {Bayesian adjustment for the misclassification in both dependent and independent variables with application to a breast cancer study}, journal = {Statistics in Medicine}, year = {2016}, doi = {10.1002/sim.6996}, author = {Liu, Juxin and Gustafson, Paul and Huo, Dezheng} } @article {8957, title = {Bayesian Data Fusion Approaches to Predicting Spatial Tracks: Application to Marine Mammals.}, journal = {Annals of Applied Statistics}, year = {2016}, pages = {Accepted}, author = {Liu, Yang and Zidek, James V and Trites, Andrew and Battaile, Brian} } @article {Xia2016, title = {Bayesian regression models adjusting for unidirectional covariate misclassification}, journal = {Canadian Journal of Statistics}, volume = {44}, number = {2}, year = {2016}, pages = {198{\textendash}218}, doi = {10.1002/cjs.11284}, author = {Xia, Michelle and Gustafson, Paul} } @article {Roth2016Clonal, title = {Clonal genotype and population structure inference from single-cell tumor sequencing}, journal = {Nature Methods}, volume = {13}, year = {2016}, pages = {575{\textendash}576}, author = {A Roth and Andrew McPherson and Emma Laks and Justina Biele and Damian Yap and Adrian Wan and Maia Smith and Cydney Nielsen and Jessica N. McAlpine and Samuel Aparicio and Alexandre Bouchard-C{\^o}t{\'e} and Sohrab P. Shah} } @article {8876, title = {Combined oral contraceptive use before the first birth and epithelial ovarian cancer risk}, journal = {British Journal of Cancer }, year = {2016}, author = {Cook, L. S. and Pestak, C. and Leung, A. and Le, N.} } @article {chen_comment:_2016, title = {Comment: Expected Improvement for Efficient Blackbox Constrained Optimization}, journal = {Technometrics}, volume = {58}, number = {1}, year = {2016}, pages = {12{\textendash}15}, url = {http://www.tandfonline.com/doi/full/10.1080/00401706.2015.1044119}, author = {Chen, Hao and Welch, William J.} } @article { ISI:000366777800013, title = {Comparison of non-nested models under a general measure of distance}, journal = {Journal of Statistical Planning and Inference}, volume = {170}, year = {2016}, month = {MAR}, pages = {166-185}, publisher = {Elsevier Science BV}, type = {Article}, abstract = {As a supplement to summary statistics of information criteria, the closeness of two or more competing non-nested models can be compared under a procedure that is more general than that proposed in Vuong (1989); measures of closeness other than the Kullback-Leibler divergence are allowed. Large deviation theory is used to obtain a bound of the power of rejecting the null hypothesis that the two models are equally close to the true model. Such a bound can be expressed in terms of a constant gamma is an element of [0, 1); gamma can be computed empirically without any knowledge of the data generating mechanism. Additionally, based on the constant gamma, the procedures constructed based on different measures of distance can be compared on their abilities to conclude a difference between two models. (C) 2015 Elsevier B.V. All rights reserved.}, keywords = {Composite likelihood, Copula, Large deviation theory, Model comparison, Model misspecification}, issn = {0378-3758}, doi = {10.1016/j.jspi.2015.10.004}, author = {Ng, C. T. and Joe, Harry} } @article {karim2016comparison, title = {Comparison of Statistical Approaches for Dealing With Immortal Time Bias in Drug Effectiveness Studies}, journal = {American Journal of Epidemiology}, year = {2016}, pages = {kwv445}, publisher = {Oxford University Press}, doi = {10.1093/aje/kwv445}, author = {Karim, Mohammad Ehsanul and Gustafson, Paul and Petkau, John and Tremlett, Helen} } @article {9307, title = {Comparison of statistical approaches for dealing with immortal time bias in drug effectiveness studies}, journal = {American Journal of Epidemiology}, volume = {184}, year = {2016}, pages = {325-335}, abstract = {

In time-to-event analyses of observational studies of drug effectiveness, incorrect handling of the period between cohort entry and first treatment exposure during follow-up may result in immortal time bias. This bias can be eliminated by acknowledging a change in treatment exposure status with time-dependent analyses, such as fitting a time-dependent Cox model. The prescription time distribution matching (PTDM) method has been proposed as a simpler approach for controlling immortal time bias. Using simulation studies and theoretical quantification of bias, we compared the performance of the PTDM approach with that of the time-dependent Cox model in the presence of immortal time. Both assessments revealed that the PTDM approach did not adequately address immortal time bias. Based on our simulation results, another recently proposed observational data analysis technique, the sequential Cox approach, was found to be more useful than the PTDM approach (Cox: bias = -0.002, mean squared error = 0.025; PTDM: bias = -1.411, mean squared error = 2.011). We applied these approaches to investigate the association of β-interferon treatment with delaying disability progression in a multiple sclerosis cohort in British Columbia, Canada (Long-Term Benefits and Adverse Effects of Beta-Interferon for Multiple Sclerosis (BeAMS) Study, 1995{\textendash}2008).

}, keywords = {bias, confounding factors, epidemiologic methods, immortal time bias, Longitudinal Studies, Models, survival analysis}, doi = {10.1093/aje/kwv445}, author = {Karim, ME and Gustafson, P and Petkau, J and Tremlett, H and BeAMS Study Group} } @article {9518, title = {Comparison of statistical approaches for dealing with immortal time bias in drug effectiveness studies}, journal = {American Journal of Epidemiology}, volume = {184}, year = {2016}, pages = {857-858}, type = {Letter}, author = {Karim, M.E. and Gustafson, P. and Petkau, J. and Tremlett, T.} } @article {9183, title = {Composite likelihood under hidden Markov model}, journal = {Statistica Sinica}, volume = {26}, year = {2016}, pages = {1569{\textendash}1586}, author = {Chen, Jiahua and Huang, Yi and Wang, Peiming} } @article {chen2016composite, title = {Composite likelihood under hidden Markov model}, journal = {Statistica Sinica}, volume = {26}, number = {4}, year = {2016}, pages = {1569{\textendash}1586}, publisher = {C/O DR HC HO, INST STATISTICAL SCIENCE, ACADEMIA SINICA, TAIPEI 115, TAIWAN}, author = {Chen, Jiahua and Huang, Yi and Wang, Peiming} } @article {9184, title = {Consistency of the MLE under mixture models}, journal = {arXiv preprint arXiv:1607.01251}, year = {2016}, author = {Chen, Jiahua} } @article {chen2016consistency, title = {Consistency of the penalized MLE for two-parameter gamma mixture models}, journal = {Science China Mathematics}, volume = {59}, number = {12}, year = {2016}, pages = {2301{\textendash}2318}, publisher = {Science China Press}, author = {Chen, Jiahua and Li, Shaoting and Tan, Xianming} } @article {9180, title = {Consistency of the penalized MLE for two-parameter gamma mixture models}, journal = {Science China Mathematics}, volume = {59}, year = {2016}, pages = {2301{\textendash}2318}, author = {Chen, Jiahua and Li, Shaoting and Tan, Xianming} } @conference {Huggins16_NIPS, title = {Coresets for scalable Bayesian logistic regression}, booktitle = {Advances in Neural Information Processing Systems}, year = {2016}, author = {Jonathan Huggins and Trevor Campbell and Tamara Broderick} } @article {jung2016correction, title = {Correction: Iron Regulation of the Major Virulence Factors in the AIDS-Associated Pathogen Cryptococcus neoformans}, journal = {PLoS Biol}, volume = {14}, number = {3}, year = {2016}, pages = {e1002410}, publisher = {Public Library of Science}, author = {Jung, Won Hee and Sham, Anita and White, Rick and Kronstad, James W} } @article {Goring2016, title = {Disconnected by design: analytic approach in treatment networks having no common comparator}, journal = {Research synthesis methods}, year = {2016}, publisher = {Wiley Online Library}, doi = {10.1002/jrsm.1204}, author = {Goring, SM and Gustafson, P and Liu, Y and Saab, S and Cline, SK and Platt, RW} } @article {McPherson2016Divergent, title = {Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer}, journal = {Nature Genetics}, volume = {48}, year = {2016}, pages = {758{\textendash}767}, author = {Andrew McPherson and others} } @article {pmid26761122, title = {Early postnatal docosahexaenoic acid levels and improved preterm brain development}, journal = {Pediatr. Res.}, year = {2016}, month = {Jan}, author = {Tam, E. W. and Chau, V. and Barkovich, A. J. and Ferriero, D. M. and Miller, S. P. and Rogers, E. E. and Grunau, R. E. and Synnes, A. R. and Xu, D. and Foong, J. and Brant, R. and Innis, S. M.} } @conference {Cai16_NIPS, title = {Edge-exchangeable graphs and sparsity}, booktitle = {Advances in Neural Information Processing Systems}, year = {2016}, author = {Diana Cai and Trevor Campbell and Tamara Broderick} } @inbook {9187, title = {Empirical Likelihood Inference Under Density Ratio Models Based on Type I Censored Samples: Hypothesis Testing and Quantile Estimation}, booktitle = {Advanced Statistical Methods in Data Science}, year = {2016}, pages = {123{\textendash}151}, publisher = {Springer Singapore}, organization = {Springer Singapore}, author = {Cai, Song and Chen, Jiahua} } @article {McConechy13012016, title = {Endometrial carcinomas with POLE exonuclease domain mutations have a favorable prognosis}, journal = {Clinical Cancer Research}, year = {2016}, abstract = {Purpose: The aim of this study was to confirm the prognostic significance of POLE exonuclease domain mutations (EDM) in endometrial carcinoma (EC) patients. In addition, the effect of treatment on POLE mutated tumours was assessed. Experimental design: A retrospective patient cohort of 496 EC patients was identified for targeted sequencing of the POLE exonuclease domain, yielding 406 evaluable tumours. Univariable and multivariable analyses were performed to determine the effect of POLE mutation status on progression-free survival (PFS), disease-specific survival (DSS) and overall survival (OS). Combining results from eight studies in a meta-analysis, we computed pooled hazard ratios (HR) for PFS, DSS, and OS. Results: POLE EDMs were identified in 39 of 406 (9.6\%) ECs. Women with POLE mutated ECs were younger, with Stage 1 (92\%) tumors, grade 3 (62\%), endometrioid histology (82\%) and frequent (49\%) lymphovascular invasion. In univariable analysis, POLE mutated ECs had significantly improved outcomes compared to patients with no EDMs for PFS, DSS and OS. In multivariable analysis, POLE EDMs were only significantly associated with improved PFS. The effect of adjuvant treatment on POLE mutated cases could not be determined conclusively, however both treated and untreated patients with POLE EDMs had good outcomes. Meta-analysis revealed an association between POLE EDMs and improved PFS and DSS with pooled HRs 0.34 (95\% CI 0.15-0.73) and 0.35 (95\% CI 0.13-0.92), respectively. Conclusions: POLE EDMs are prognostic markers associated with excellent outcomes for EC patients. Further investigation is needed to conclusively determine if treatment is necessary for this group of women.}, doi = {10.1158/1078-0432.CCR-15-2233}, url = {http://clincancerres.aacrjournals.org/content/early/2016/01/13/1078-0432.CCR-15-2233.abstract}, author = {McConechy, Melissa K. and Talhouk, Aline and Leung, Samuel and Chiu, Derek S and Yang, Winnie and Senz, Janine and Reha-Krantz, Linda J. and Lee, Cheng-Han and Huntsman, David G. and Gilks, Blake and McAlpine, Jessica N.} } @article {8977, title = {Estimating the damage caused by proof loading lumber products}, number = {277}, year = {2016}, month = {11/2016}, type = {Technical Report}, author = {Yanling Cai and James V Zidek} } @article {tomal_exploiting_2016, title = {Exploiting Multiple Descriptor Sets in QSAR Studies}, journal = {Journal of chemical information and modeling}, volume = {56}, number = {3}, year = {2016}, pages = {501{\textendash}509}, url = {http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00663}, author = {Tomal, Jabed H. and Welch, William J. and Zamar, Ruben H.} } @article {Karim2016, title = {Hypothesis Testing for an Exposure{\textendash}Disease Association in Case{\textendash}Control Studies Under Nondifferential Exposure Misclassification in the Presence of Validation Data: Bayesian and Frequentist Adjustments}, journal = {Statistics in Biosciences}, year = {2016}, pages = {1{\textendash}19}, publisher = {Springer}, doi = {10.1007/s12561-015-9141-9}, author = {Karim, Mohammad Ehsanul and Gustafson, Paul} } @article {Zhai2016Inferring, title = {Inferring history of human populations using single-nucleotide polymorphism}, journal = {Annals of Applied Stat}, volume = {10}, year = {2016}, pages = {2047{\textendash}2074}, author = {Yongliang Zhai and Alexandre Bouchard-C{\^o}t{\'e}} } @article {Zhai2016Inferring, title = {Inferring history of human populations using single-nucleotide polymorphism}, journal = {Annals of Applied Statistics}, volume = {10}, year = {2016}, pages = {2047{\textendash}2074}, author = {Yongliang Zhai and Alexandre Bouchard-C{\^o}t{\'e}} } @conference {8894, title = {Initial estimators for regularized robust methods in high-dimensional settings}, booktitle = {22nd International Conference on Computational Statistics}, year = {2016}, author = {Kepplinger, D. and Salibian-Barrera, M. and Cohen Freue, G.V.} } @article {8964, title = {Mitigating the effects of preferentially selected monitoring sites for environmental policy and health risk analysis}, journal = {Spatial and Spatio-temporal epidemiology}, volume = {18}, year = {2016}, pages = {44-52}, author = {Shaddick, Gavin and Zidek, James V and Liu, Yi} } @article {8971, title = {Modulation recognition in the 868 {MHz} band using classification trees and random forests}, journal = {{AEU} - International Journal of Electronics and Communications}, volume = {70}, year = {2016}, pages = {1321 - 1328}, keywords = {random forest}, issn = {1434-8411}, doi = {10.1016/j.aeue.2016.07.001}, url = {http://www.sciencedirect.com/science/article/pii/S1434841116303430}, author = {Ken Lau and Matias Salibian-Barrera and Lutz Lampe} } @article {chen2016monitoring, title = {Monitoring test under nonparametric random effects model}, journal = {arXiv preprint arXiv:1610.05809}, year = {2016}, author = {Chen, Jiahua and Li, Pengfei and Liu, Yukun and Zidek, James V} } @article {9182, title = {Monitoring test under nonparametric random effects model}, journal = {arXiv preprint arXiv:1610.05809}, year = {2016}, author = {Chen, Jiahua and Li, Pengfei and Liu, Yukun and Zidek, James V} } @article { ISI:000369469400009, title = {Multivariate models for dependent clusters of variables with conditional independence given aggregation variables}, journal = {Computational Statistics \& Data Analysis}, volume = {97}, year = {2016}, month = {MAY}, pages = {114-132}, abstract = {A general multivariate distributional approach, with conditional independence given aggregation variables, is presented to combine group-based submodels when variables are naturally divided into several non-overlapping groups. When the distributions are all multivariate Gaussian, the dependence among different groups is parsimonious based on conditional independence given linear combinations of variables in each group. For the case of multivariate t distributions in each group, a grouped t distribution is obtained. The approach can be extended so that the copula for each group is based on a skew-t distribution, and an application of this is given to financial returns of stocks in several different sectors. Another example of the modeling approach is given with variables separated into groups based on their units of measurements. (C) 2015 Elsevier B.V. All rights reserved.}, issn = {0167-9473}, doi = {10.1016/j.csda.2015.12.001}, author = {Joe, Harry and Sang, Peijun} } @article {HomrighausenMcDonald2016, title = {On the Nystr{\"o}m and Column-Sampling Methods for the Approximate Principal Components Analysis of Large Data Sets}, journal = {Journal of Computational and Graphical Statistics}, volume = {25}, number = {2}, year = {2016}, pages = {344{\textendash}362}, url = {http://dx.doi.org/10.1080/10618600.2014.995799}, author = {Homrighausen, Darren and McDonald, Daniel J.} } @article {10369, title = {Observational studies of disease modifying therapies for multiple sclerosis: Methodological challenges and opportunities}, journal = {British Medical Journal}, volume = {354}, year = {2016}, pages = {i3518}, author = {Shirani, A and Zhao, Y and Karim, ME and Kingwell, E and Petkau, J and Gustafson, P and Tremlett, H} } @article {mostafavi2016parsing, title = {Parsing the Interferon Transcriptional Network and Its Disease Associations}, journal = {Cell}, volume = {164}, number = {3}, year = {2016}, pages = {564{\textendash}578}, publisher = {Elsevier}, author = {Mostafavi, Sara and Yoshida, Hideyuki and Moodley, Devapregasan and LeBoit{\'e}, Hugo and Rothamel, Katherine and Raj, Towfique and Ye, Chun Jimmie and Chevrier, Nicolas and Zhang, Shen-Ying and Feng, Ting and others} } @article {Bierkens2016Piecewise, title = {Piecewise Deterministic Markov Processes for Scalable Monte Carlo on Restricted Domains}, journal = {arXiv}, volume = {1701.04244}, year = {2016}, author = {Joris Bierkens and Alexandre Bouchard-C{\^o}t{\'e} and Arnaud Doucet and Andrew B. Duncan and Paul Fearnhead and Gareth Roberts and Sebastian J. Vollmer} } @article {pmid26739037, title = {Prenatal supplementation with Corn Soya Blend Plus reduces risk for maternal anemia in late gestation and lowers the preterm birth rate but does not improve maternal weight gain and birth anthropometric measurements in rural Cambodian women: RCT}, journal = {Am. J. Clin. Nutr.}, year = {2016}, month = {Jan}, author = {Janmohamed, A. and Karakochuk, C. D. and Boungnasiri, S. and Chapman, G. E. and Janssen, P. A. and Brant, R. and Green, T. J. and McLean, J.} } @article {nguyen2016prospective, title = {Prospective study of Retinal Nerve Fibre Layer Thickness in Alemtuzumab Treated Multiple Sclerosis Patients (P3. 083)}, journal = {Neurology}, volume = {86}, number = {16 Supplement}, year = {2016}, pages = {P3{\textendash}083}, publisher = {Lippincott Williams \& Wilkins}, author = {Nguyen, Ai-Lan and Lam, Janet and White, Rick and Carruthers, Robert and Traboulsee, Anthony} } @article {wong_quantifying_2016, title = {Quantifying Uncertainty in Lumber Grading and Strength Prediction: A Bayesian Approach}, journal = {Technometrics}, volume = {58}, number = {2}, year = {2016}, month = {apr}, pages = {236{\textendash}243}, abstract = {This article presents a joint distribution for the strength of a randomly selected piece of structural lumber and its observable characteristics. In the process of lumber strength testing, these characteristics are ascertained under strict grading protocols, as they have the potential to be strength reducing. However, for practical reasons, only a few such selected characteristics among the many present, are recorded. We present a data-generating mechanism that reflects the uncertainties resulting from the grading protocol. A Bayesian approach is then adopted for model fitting and construction of a predictive distribution for strength that accounts for the unrecorded characteristics. The method is validated on simulated examples, and then applied on a sample of specimens tested for bending and tensile strength. Use of the predictive distribution is demonstrated, and insights gained into the grading process are described. Details of the lumber testing experiments can be found in the online supplementary materials.}, issn = {0040-1706}, doi = {10.1080/00401706.2015.1033108}, url = {http://dx.doi.org/10.1080/00401706.2015.1033108}, author = {Wong, Samuel W. K. and LUM, CONROY and WU, LANG and Zidek, James V.} } @article {9348, title = {Rapid adaptive evolution of colour vision in the threespine stickleback radiation}, journal = {Proceedings of the Royal Society of London B: Biological Sciences}, volume = {283}, year = {2016}, issn = {0962-8452}, doi = {10.1098/rspb.2016.0242}, url = {http://rspb.royalsocietypublishing.org/content/283/1830/20160242}, author = {Rennison, Diana J. and Owens, Gregory L. and Heckman, Nancy and Schluter, Dolph and Veen, Thor} } @inbook {9188, title = {Regularization in Regime-Switching Gaussian Autoregressive Models}, booktitle = {Advanced Statistical Methods in Data Science}, year = {2016}, pages = {13{\textendash}34}, publisher = {Springer Singapore}, organization = {Springer Singapore}, author = {Khalili, Abbas and Chen, Jiahua and Stephens, David A} } @article {3358, title = {Robust regression estimation and inference in the presence of cellwise and casewise contamination}, journal = {CSDA}, volume = {99}, year = {2016}, month = {07/2016}, pages = {1-11}, author = {Andy Leung and Hongyang Zhang and Ruben Zamar} } @article {leung2016robust, title = {Robust regression estimation and inference in the presence of cellwise and casewise contamination}, journal = {Computational Statistics \& Data Analysis}, year = {2016}, publisher = {Elsevier}, author = {Leung, Andy and Zhang, Hongyang and Zamar, Ruben} } @article { ISI:000364259800035, title = {Robust tests for linear regression models based on tau-estimates}, journal = {COMPUTATIONAL STATISTICS \& DATA ANALYSIS}, volume = {93}, number = {SI}, year = {2016}, month = {JAN}, pages = {436-455}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {

ANOVA tests are the standard tests to compare nested linear models fitted by least squares. These tests are equivalent to likelihood ratio tests, so they have high power. However, least squares estimators are very vulnerable to outliers in the data, and thus the related ANOVA type tests are also extremely sensitive to outliers. Therefore, robust estimators can be considered to obtain a robust alternative to the ANOVA tests. Regression tau-estimators combine high robustness with high efficiency which makes them suitable for robust inference beyond parameter estimation. Robust likelihood ratio type test statistics based on the tau-estimates of the error scale in the linear model are a natural alternative to the classical ANOVA tests. The higher efficiency of the tau-scale estimates compared with other robust alternatives is expected to yield tests with good power. Their null distribution can be estimated using either an asymptotic approximation or the fast and robust bootstrap. The robustness and power of the resulting robust likelihood ratio type tests for nested linear models is studied. (C) 2014 Elsevier B.V. All rights reserved.

}, keywords = {linear regression, Robust statistics, Robust tests}, issn = {0167-9473}, doi = {10.1016/j.csda.2014.09.012}, author = {Salibian-Barrera, Mat{\'\i}as and Van Aelst, Stefan and Yohai, Victor J.} } @article {8970, title = {RSKC: An R Package for a Robust and Sparse K-Means Clustering Algorithm}, journal = {Journal of Statistical Software}, volume = {72}, year = {2016}, pages = {1{\textendash}26}, keywords = {K-means, robust clustering, sparse clustering, trimmed K-means}, issn = {1548-7660}, doi = {10.18637/jss.v072.i05}, url = {https://www.jstatsoft.org/index.php/jss/article/view/v072i05}, author = {Yumi Kondo and Matias Salibian-Barrera and Ruben Zamar} } @article {9186, title = {Sample-size calculation for tests of homogeneity}, journal = {Canadian Journal of Statistics}, volume = {44}, year = {2016}, pages = {82{\textendash}101}, author = {Chen, Jiahua and Li, Pengfei and Liu, Yukun} } @article {yu2016sequential, title = {Sequential design for binary dose{\textendash}response experiments}, journal = {Journal of Statistical Planning and Inference}, volume = {177}, year = {2016}, pages = {64{\textendash}73}, publisher = {North-Holland}, author = {Yu, Xiaoli and Chen, Jiahua and Brant, Rollin} } @article {9181, title = {Sequential design for binary dose{\textendash}response experiments}, journal = {Journal of Statistical Planning and Inference}, volume = {177}, year = {2016}, pages = {64{\textendash}73}, author = {Yu, Xiaoli and Chen, Jiahua and Brant, Rollin} } @article {10.1371/journal.pone.0153844, title = {Single-Patient Molecular Testing with NanoString nCounter Data Using a Reference-Based Strategy for Batch Effect Correction}, journal = {PLoS ONE}, volume = {11}, number = {4}, year = {2016}, month = {04}, pages = {1-18}, publisher = {Public Library of Science}, abstract = {

A major weakness in many high-throughput genomic studies is the lack of consideration of a clinical environment where one patient at a time must be evaluated. We examined generalizable and platform-specific sources of variation from NanoString gene expression data on both ovarian cancer and Hodgkin lymphoma patients. A reference-based strategy, applicable to single-patient molecular testing is proposed for batch effect correction. The proposed protocol improved performance in an established Hodgkin lymphoma classifier, reducing batch-to-batch misclassification while retaining accuracy and precision. We suggest this strategy may facilitate development of NanoString and similar molecular assays by accelerating prospective validation and clinical uptake of relevant diagnostics.

}, doi = {10.1371/journal.pone.0153844}, url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0153844}, author = {Talhouk, Aline and Kommoss, Stefan and Mackenzie, Robertson and Cheung, Martin and Leung, Samuel and Chiu, Derek S. and Kalloger, Steve E. and Huntsman, David G. and Chen, Stephanie and Intermaggio, Maria and Gronwald, Jacek and Chan, Fong C. and Ramus, Susan J. and Steidl, Christian and Scott, David W. and Anglesio, Michael S.} } @article {pmid26763312, title = {Smaller Cerebellar Growth and Poorer Neurodevelopmental Outcomes in Very Preterm Infants Exposed to Neonatal Morphine}, journal = {J. Pediatr.}, year = {2016}, month = {Jan}, author = {Zwicker, J. G. and Miller, S. P. and Grunau, R. E. and Chau, V. and Brant, R. and Studholme, C. and Liu, M. and Synnes, A. and Poskitt, K. J. and Stiver, M. L. and Tam, E. W.} } @article {8890, title = {Spatio-temporal Modelling of Temperature Fields in the Pacific Northwest}, journal = {arXiv:1604.00572}, year = {2016}, month = {04/2016}, keywords = {Complex terrain, environmental sciences, Gaussian process, nonstationarity, temperature}, url = {https://arxiv.org/abs/1604.00572}, author = {Casquilho-Resende, C. M. and Le, N. D. and Zidek, J.V.} } @article {3362, title = {Tea, coffee, and caffeinated beverage consumption and risk of epithelial ovarian cancers}, journal = {Cancer Epidemiology}, volume = {45}, year = {2016}, chapter = {119-125}, url = {http://dx.doi.org/10.1016/j.canep.2016.10.010}, author = {Andy Leung and Linda S Cook and Kenneth Swenerton and Nhu D Le and Blake C Gilks and Richard P Gallagher and Anthony Magliocco and Helen Steed and Martin K{\"o}bel and Jill Nation and Angela Brooks-Wilson} } @article {chen2016testing, title = {Testing the Order of a Normal Mixture in Mean}, journal = {Communications in Mathematics and Statistics}, volume = {4}, number = {1}, year = {2016}, pages = {21{\textendash}38}, publisher = {Springer Berlin Heidelberg}, author = {Chen, Jiahua and Li, Pengfei} } @article {9185, title = {Testing the Order of a Normal Mixture in Mean}, journal = {Communications in Mathematics and Statistics}, volume = {4}, year = {2016}, pages = {21{\textendash}38}, author = {Chen, Jiahua and Li, Pengfei} } @conference {Shahriari2016Unbounded, title = {Unbounded Bayesian optimization via regularization}, booktitle = {AISTATS}, volume = {19}, year = {2016}, pages = {1168{\textendash}1176}, author = {Bobak Shahriari and Alexandre Bouchard-C{\^o}t{\'e} and Nando de Freitas} } @article {9664, title = {Using a Gaussian Process as a Nonparametric Regression Model}, journal = {Quality and Reliability Engineering International}, volume = {32}, year = {2016}, pages = {673{\textendash}680}, author = {J. R. Gattiker and M. S. Hamada and D. M. Higdon and M. Schonlau and W. J. Welch} } @mastersthesis {9977, title = {Using computer model uncertainty to inform the design of physical experiments: An application in glaciology}, year = {2016}, school = {Simon Fraser University}, type = {masters}, author = {Sonja Surjanovic} } @article {Falasinnu2016, title = {A validation study of a clinical prediction rule for screening asymptomatic chlamydia and gonorrhoea infections among heterosexuals in British Columbia}, journal = {Sexually transmitted infections}, volume = {92}, number = {1}, year = {2016}, pages = {12{\textendash}18}, publisher = {BMJ Publishing Group Ltd}, doi = {10.1136/sextrans-2014-051992}, author = {Falasinnu, Titilola and Gilbert, Mark and Gustafson, Paul and Shoveller, Jean} } @article {10390, title = {Whole-organism developmental expression profiling identifies RAB-28 as a novel ciliary GTPase associated with the BBSome and intraflagellar transport}, journal = {PLoS genetics}, volume = {12}, year = {2016}, pages = {e1006469}, author = {Jensen, Victor L and Carter, Stephen and Sanders, Anna AWM and Li, Chunmei and Kennedy, Julie and Timbers, Tiffany A and Cai, Jerry and Scheidel, Noemie and Kennedy, Breand{\'a}n N and Morin, Ryan D and others} } @article {8956, title = {Wood Property Relationships and Survival Models in Reliability}, journal = {Applied Stochastic Models in Business and Industry}, volume = {32}, year = {2016}, pages = {792-803}, author = {Cheng, L and Wu, L and Lum, C and Zidek, JV and Yu, T} } @conference {Jewell2015Atomic, title = {Atomic spatial processes}, booktitle = {International Conference on Machine Learning (ICML)}, volume = {32}, year = {2015}, pages = {248{\textendash}256}, author = {Sean Jewell and Neil Spencer and Alexandre Bouchard-C{\^o}t{\'e}} } @article {pmid26186294, title = {Attenuated innate immune defenses in very premature neonates during the neonatal period}, journal = {Pediatr. Res.}, volume = {78}, number = {5}, year = {2015}, month = {Nov}, pages = {492{\textendash}497}, author = {Marchant, E. A. and Kan, B. and Sharma, A. A. and van Zanten, A. and Kollmann, T. R. and Brant, R. and Lavoie, P. M.} } @article {LiuDinsdale2015, title = {Automatic Learning of Basketball Strategy via SportVU Tracking Data: the Potential Field Approach}, journal = {Submitted to Sloan Sports Analytics Conference}, year = {2015}, author = {Liu, Yang and Dinsdale, Dinsdale.R. and Jun, Seong-Hwan and Briercliffe, Creagh and Bone, Jeffrey} } @article {Zhao2015Bayesian, title = {Bayesian analysis of continuous time Markov chains with application to phylogenetic modelling}, journal = {Bayesian Analysis}, volume = {(In Press)}, year = {2015}, author = {Tingting Zhao and Ziyu Wang and Alex Cumberworth and Joerg Gsponer and Nando de Freitas and Alexandre Bouchard-C{\^o}t{\'e}} } @article {Zhao2015Bayesian, title = {Bayesian analysis of continuous time Markov chains with application to phylogenetic modelling}, journal = {Bayesian Analysis}, volume = {11}, year = {2015}, pages = {1203{\textendash}1237}, author = {Tingting Zhao and Alex Cumberworth and Ziyu Wang and Joerg Gsponer and Nando de Freitas and Alexandre Bouchard-C{\^o}t{\'e}} } @book {gustafson2015bayesian, title = {Bayesian Inference for Partially Identified Models: Exploring the Limits of Limited Data}, year = {2015}, publisher = {Chapman and Hall / CRC Press}, organization = {Chapman and Hall / CRC Press}, author = {Gustafson, Paul} } @conference {Campbell15_ACC, title = {Bayesian nonparametric set construction for robust optimization}, booktitle = {American Control Conference}, year = {2015}, author = {Trevor Campbell and Jonathan P. How} } @article {Wang2015Bayesian, title = {Bayesian phylogenetic inference using the combinatorial sequential Monte Carlo method}, journal = {Journal of the American Statistical Association}, volume = {110}, year = {2015}, pages = {1362{\textendash}1374}, author = {Liangliang Wang and Alexandre Bouchard-C{\^o}t{\'e} and Arnaud Doucet} } @article {Zhang2015, title = {Beta-interferon exposure and onset of secondary progressive multiple sclerosis}, journal = {European Journal of Neurology}, volume = {22}, number = {6}, year = {2015}, pages = {990{\textendash}1000}, publisher = {Wiley Online Library}, doi = {10.1111/ene.12698}, author = {Zhang, T and Shirani, A and Zhao, Y and Karim, ME and Gustafson, P and Petkau, J and Evans, C and Kingwell, E and Kop, M and Zhu, F and others} } @article {zhang_beta-interferon_2015, title = {Beta-interferon exposure and onset of secondary progressive multiple sclerosis}, journal = {European Journal of Neurology}, volume = {22}, number = {6}, year = {2015}, pages = {990{\textendash}1000}, abstract = {

Background and purpose Beta-interferons (IFNβ) are the most widely prescribed drugs for patients with multiple sclerosis (MS). However, whether or not treatment with IFNβ can delay secondary progressive MS (SPMS) onset remains unknown. Our aim was to examine the association between IFNβ exposure and SPMS onset in patients with relapsing-remitting MS (RRMS). Methods A retrospective cohort study using British Columbia (Canada) population-based clinical and health administrative data (1985{\textendash}2008) was conducted. RRMS patients treated with IFNβ (n\ =\ 794) were compared with untreated contemporary (n\ =\ 933) and historical (n\ =\ 837) controls. Cohort entry was the first clinic visit during which patients became eligible for IFNβ treatment (baseline). The outcome was time from baseline to SPMS onset. Cox regression models with IFNβ as a time-dependent exposure were adjusted for sex, and baseline age, disease duration, disability, *socioeconomic status and *comorbidities (*available for the contemporary cohorts only). Additional analyses included propensity score adjustment. Results The median follow-up for the IFNβ-treated, untreated contemporary and historical controls were 5.7, 3.7 and 7.3\ years, and the proportions of patients reaching SPMS were 9.2\%, 11.8\% and 32.9\%, respectively. After adjustment for confounders, IFNβ exposure was not associated with the risk of reaching SPMS when either the contemporary or the historical untreated cohorts were considered (hazard ratio 1.07; 95\% confidence interval 0.93{\textendash}1.48, and hazard ratio 1.04; 95\% confidence interval 0.74{\textendash}1.46, respectively). Further adjustments and the propensity score yielded results consistent with the main analysis. Conclusions Amongst patients with RRMS, use of IFNβ was not associated with a delayed onset of SPMS.

}, keywords = {beta-interferon, cohort study, multiple sclerosis, progression}, doi = {10.1111/ene.12698}, url = {http://onlinelibrary.wiley.com/doi/10.1111/ene.12698/abstract}, author = {Zhang, T and Shirani, A and Zhao, Y and Karim, ME and Gustafson, P and Petkau, J and Evans, C and Kingwell, E and van der Kop, M and Zhu, F and Oger, J and Tremlett, H and BC MS Clinic Neurologists} } @article {Liu2015, title = {Bias Correction and Uncertainty Characterization of Dead-Reckoned Paths of Marine Mammals}, journal = {Animal Biotelmetry}, volume = {3}, number = {51}, year = {2015}, doi = {10.1186/s40317-015-0080-5}, author = {Liu, Yang and Battaile, Brian C. and Zidek, James V. and Trites, Andrew W} } @article {liu2015bias, title = {Bias correction and uncertainty characterization of Dead-Reckoned paths of marine mammals}, journal = {Animal Biotelemetry}, volume = {3}, number = {1}, year = {2015}, pages = {1}, publisher = {BioMed Central}, author = {Liu, Yang and Battaile, Brian C and Trites, Andrew W and Zidek, James V} } @article {pmid25474359, title = {Burkholderia species infections in patients with cystic fibrosis in British Columbia, Canada. 30 years{\textquoteright} experience}, journal = {Ann Am Thorac Soc}, volume = {12}, number = {1}, year = {2015}, month = {Jan}, pages = {70{\textendash}78}, author = {Zlosnik, J. E. and Zhou, G. and Brant, R. and Henry, D. A. and Hird, T. J. and Mahenthiralingam, E. and Chilvers, M. A. and Wilcox, P. and Speert, D. P.} } @article {9270, title = {Calibrating the Difficulty of Assessment Tools: Blooming a Statistics Exam}, journal = {Journal of Statistical Education}, volume = {23}, year = {2015}, author = {Bruce Dunham and Gaitri Yapa and Eugenia Yu} } @article {nolde2015challenging, title = {Challenging the standard dike freeboard: Methods to quantify statistical uncertainties in river flood protection}, journal = {Canadian Water Resources Journal/Revue canadienne des ressources hydriques}, year = {2015}, pages = {1{\textendash}10}, publisher = {Taylor \& Francis}, author = {Nolde, Natalia and Jakob, Matthias} } @article { ISI:000361763100007, title = {Clinical and molecular predictors of mortality in neurofibromatosis 2: a UK national analysis of 1192 patients}, journal = {Journal of Medical Genetics}, volume = {52}, number = {10}, year = {2015}, month = {OCT}, pages = {699-705}, publisher = {BMJ Publishing Group}, type = {Article}, abstract = {Background Neurofibromatosis 2 (NF2) is an autosomal-dominant tumour predisposition syndrome characterised by bilateral vestibular schwannomas, considerable morbidity and reduced life expectancy. Although genotype-phenotype correlations are well established in NF2, little is known about effects of mutation type or location within the gene on mortality. Improvements in NF2 diagnosis and management have occurred, but their effect on patient survival is unknown. Methods We evaluated clinical and molecular predictors of mortality in 1192 patients (771 with known causal mutations) identified through the UK National NF2 Registry. Kaplan-Meier survival and Cox regression analyses were used to evaluate predictors of mortality, with jackknife adjustment of parameter SEs to account for the strong intrafamilial phenotypic correlations that occur in NF2. Results The study included 241 deaths during 10 995 patient-years of follow-up since diagnosis. Early age at diagnosis and the presence of intracranial meningiomas were associated with increased mortality, and having a mosaic, rather than non-mosaic, NF2 mutation was associated with reduced mortality. Patients with splice-site or missense mutations had lower mortality than patients with truncating mutations (OR 0.459, 95\% CI 0.213 to 0.990, and OR 0.196, 95\% CI 0.213 to 0.990, respectively). Patients with splice-site mutations in exons 6-15 had lower mortality than patients with splice-site mutations in exons 1-5 (OR 0.333, 95\% CI 0.129 to 0.858). The mortality of patients with NF2 diagnosed in more recent decades was lower than that of patients diagnosed earlier. Conclusions Continuing advances in molecular diagnosis, imaging and treatment of NF2-associated tumours offer hope for even better survival in the future.}, issn = {0022-2593}, doi = {10.1136/jmedgenet-2015-103290}, author = {Hexter, Adam and Jones, Adrian and Joe, Harry and Heap, Laura and Smith, Miriam J. and Wallace, Andrew J. and Halliday, Dorothy and Parry, Allyson and Taylor, Amy and Raymond, Lucy and Shaw, Adam and Afridi, Shazia and Obholzer, Rupert and Axon, Patrick and King, Andrew T. and Friedman, Jan M. and Evans, D. Gareth R. and English Specialist NF2 Res Grp} } @article {rabkin2015comparison, title = {Comparison of reducing epicardial fat by exercise, diet or bariatric surgery weight loss strategies: a systematic review and meta-analysis}, journal = {Obesity Reviews}, volume = {16}, number = {5}, year = {2015}, pages = {406{\textendash}415}, publisher = {Wiley Online Library}, author = {Rabkin, SW and Campbell, H} } @article {Park2015-tf, title = {Deep learning for regulatory genomics}, journal = {Nat. Biotechnol.}, volume = {33}, number = {8}, year = {2015}, pages = {825{\textendash}826}, keywords = {deep learning, genomics}, author = {Park, Yongjin and Kellis, Manolis} } @article {pmid25859167, title = {Development and validation of weight, height and age bands to guide the prescription of fixed-dose dispersible tablet formulations}, journal = {J Pediatr Pharmacol Ther}, volume = {20}, number = {1}, year = {2015}, pages = {24{\textendash}32}, author = {Larson, C. P. and Sauve, L. and Senkungu, J. K. and Arifeen, S. E. and Brant, R.} } @article {gustafson2015discussion, title = {Discussion of {\textquoteleft}{\textquoteleft}On Bayesian Estimation of Marginal Structural Models{\textquoteright}{\textquoteright}}, journal = {Biometrics}, volume = {71}, number = {2}, year = {2015}, pages = {291{\textendash}293}, publisher = {Wiley-Blackwell}, doi = {10.1111/biom.12271}, author = {Gustafson, Paul} } @article {zidek2015comment, title = {Discussion of {\textquoteleft}{\textquoteleft}Optimal design in geostatistics under preferential sampling {\textquoteright}{\textquoteright} Ferreira and Gamerman}, journal = {Bayesian Analysis}, volume = {10}, number = {3}, year = {2015}, pages = {749{\textendash}752}, publisher = {International Society for Bayesian Analysis}, author = {Zidek, James V and others} } @article {LoewensteinKrishnamurti2015, title = {Does Increased Sexual Frequency Enhance Happiness?}, journal = {Journal of Economic Behavior and Organization}, volume = {116}, year = {2015}, pages = {206{\textendash}218}, url = {http://dx.doi.org/10.1016/j.jebo.2015.04.021}, author = {Loewenstein, George and Krishnamurti, Tamar and Kopsic, Jessica and McDonald, Daniel J.} } @article {pmid26531454, title = {Early neonatal pain exposure and brain microstructure interact to predict neurodevelopmental outcomes at 18 months corrected age in children born very preterm}, journal = {Int. J. Dev. Neurosci.}, volume = {47}, number = {Pt A}, year = {2015}, month = {Dec}, pages = {47}, author = {Vinall, J. and Zwicker, J. G. and Grunau, R. E. and Chau, V. and Poskitt, K. J. and Brant, R. and Synnes, A. R. and Miller, S. P.} } @article {pmid25923528, title = {Education about crying in normal infants is associated with a reduction in pediatric emergency room visits for crying complaints}, journal = {J Dev Behav Pediatr}, volume = {36}, number = {4}, year = {2015}, month = {May}, pages = {252{\textendash}257}, author = {Barr, R. G. and Rajabali, F. and Aragon, M. and Colbourne, M. and Brant, R.} } @article { ISI:000358354400004, title = {ENSEMBLING CLASSIFICATION MODELS BASED ON PHALANXES OF VARIABLES WITH APPLICATIONS IN DRUG DISCOVERY}, journal = {ANNALS OF APPLIED STATISTICS}, volume = {9}, number = {1}, year = {2015}, month = {MAR}, pages = {69-93}, publisher = {INST MATHEMATICAL STATISTICS}, type = {Article}, address = {3163 SOMERSET DR, CLEVELAND, OH 44122 USA}, abstract = {Statistical detection of a rare class of objects in a two-class classification problem can pose several challenges. Because the class of interest is rare in the training data, there is relatively little information in the known class response labels for model building. At the same time the available explanatory variables are often moderately high dimensional. In the four assays of our drug-discovery application, compounds are active or not against a specific biological target, such as lung cancer tumor cells, and active compounds are rare. Several sets of chemical descriptor variables from computational chemistry are available to classify the active versus inactive class; each can have up to thousands of variables characterizing molecular structure of the compounds. The statistical challenge is to make use of the richness of the explanatory variables in the presence of scant response information. Our algorithm divides the explanatory variables into subsets adaptively and passes each subset to a base classifier. The various base classifiers are then ensembled to produce one model to rank new objects by their estimated probabilities of belonging to the rare class of interest. The essence of the algorithm is to choose the subsets such that variables in the same group work well together; we call such groups phalanxes.}, keywords = {Clustering, Model selection, quantitative structure activity relationship, random forest, ranking, rare class}, issn = {1932-6157}, doi = {10.1214/14-AOAS778}, author = {Tomal, Jabed H. and Welch, William J. and Zamar, Ruben H.} } @article {tomal_ensembling_2015, title = {Ensembling classification models based on phalanxes of variables with applications in drug discovery}, journal = {The Annals of Applied Statistics}, volume = {9}, number = {1}, year = {2015}, pages = {69{\textendash}93}, url = {http://projecteuclid.org/euclid.aoas/1430226085}, author = {Tomal, Jabed H. and Welch, William J. and Zamar, Ruben H. and others} } @article {McDonaldShalizi2015, title = {Estimating beta-mixing coefficients via histograms}, journal = {Electronic Journal of Statistics}, volume = {9}, year = {2015}, pages = {2855{\textendash}2883}, url = {http://dx.doi.org/10.1214/15-EJS1094}, author = {McDonald, Daniel J. and Shalizi, Cosma Rohilla and Schervish, Mark} } @article { ISI:000351843300007, title = {Factor copula models for item response data}, journal = {Psychometrika}, volume = {80}, number = {1}, year = {2015}, month = {MAR}, pages = {126-150}, publisher = {Springer}, type = {Article}, abstract = {Factor or conditional independence models based on copulas are proposed for multivariate discrete data such as item responses. The factor copula models have interpretations of latent maxima/minima (in comparison with latent means) and can lead to more probability in the joint upper or lower tail compared with factor models based on the discretized multivariate normal distribution (or multidimensional normal ogive model). Details on maximum likelihood estimation of parameters for the factor copula model are given, as well as analysis of the behavior of the log-likelihood. Our general methodology is illustrated with several item response data sets, and it is shown that there is a substantial improvement on existing models both conceptually and in fit to data.}, keywords = {Conditional independence, factor model dependence structure, latent variable model, limited information, Partial correlation}, issn = {0033-3123}, doi = {10.1007/s11336-013-9387-4}, author = {Nikoloulopoulos, Aristidis K. and Joe, Harry} } @article {liu2015, title = {A flexible approach for multivariate mixed-effects models in the presence of non-ignorable missingness and measurement error}, journal = {Journal of Statistical Computation and Simulation}, year = {2015}, author = {Liu, J and Liu, W and Wu, L and Yang, G} } @article { ISI:000354249800006, title = {A flexible mixed-effect negative binomial regression model for detecting unusual increases in MRI lesion counts in individual multiple sclerosis patients}, journal = {Statistics in Medicine}, volume = {34}, number = {13}, year = {2015}, pages = {2165-2180}, publisher = {WILEY-BLACKWELL}, address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, abstract = {

We develop a new modeling approach to enhance a recently proposed method to detect increases of contrast-enhancing lesions (CELs) on repeated magnetic resonance imaging, which have been used as an indicator for potential adverse events in multiple sclerosis clinical trials. The method signals patients with unusual increases in CEL activity by estimating the probability of observing CEL counts as large as those observed on a patient{\textquoteright}s recent scans conditional on the patient{\textquoteright}s CEL counts on previous scans. This conditional probability index (CPI), computed based on a mixed-effect negative binomial regression model, can vary substantially depending on the choice of distribution for the patient-specific random effects. Therefore, we relax this parametric assumption to model the random effects with an infinite mixture of beta distributions, using the Dirichlet process, which effectively allows any form of distribution. To our knowledge, no previous literature considers a mixed-effect regression for longitudinal count variables where the random effect is modeled with a Dirichlet process mixture. As our inference is in the Bayesian framework, we adopt a meta-analytic approach to develop an informative prior based on previous clinical trials. This is particularly helpful at the early stages of trials when less data are available. Our enhanced method is illustrated with CEL data from 10 previous multiple sclerosis clinical trials. Our simulation study shows that our procedure estimates the CPI more accurately than parametric alternatives when the patient-specific random effect distribution is misspecified and that an informative prior improves the accuracy of the CPI estimates. Copyright (c) 2015 John Wiley \& Sons, Ltd.

}, keywords = {Dirichlet process, Longitudinal data, meta-analysis, Negative binomial, nonparametric Bayesian procedures, safety monitoring in clinical trials}, doi = {10.1002/sim.6484}, author = {Kondo, Y and Zhao, Y and Petkau, J} } @article { ISI:000361373800008, title = {Functional Data Model for Genetically Related Individuals With Application to Cow Growth}, journal = {JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS}, volume = {24}, number = {3}, year = {2015}, month = {JUL 3}, pages = {756-770}, publisher = {AMER STATISTICAL ASSOC}, type = {Article}, address = {732 N WASHINGTON ST, ALEXANDRIA, VA 22314-1943 USA}, abstract = {We propose a new version of functional data model for analyzing familial related individuals, where the within-subject correlation depends smoothly on a covariate such as age and the between-subject correlation follows family-wise genetic association. Our motivating example concerns measurements of weight as a function of age in sibling cows from independent families. Observations are sparsely sampled from trajectories of a phenotype contaminated with measurement error, where the phenotypic trajectory consists of a genetic component and an environmental component. By combining information across individuals, the genetic and environmental covariances are estimated via smoothing techniques. We study the genetic and environmental effects using principal component analysis, taking into account the genetic correlation to enhance the subject-level signal extraction. We show via the real data and simulations that incorporating the correlation structure improves predictions of individual phenotypic trajectories.}, keywords = {Functional principal components, Genetic relationship, Smoothing, Sparse functional data}, issn = {1061-8600}, doi = {10.1080/10618600.2014.948180}, author = {Lei, Edwin and Yao, Fang and Heckman, Nancy and Meyer, Karin} } @article {dong_further_2014, title = {Further investigation of safety monitoring guidelines based on magnetic resonance imaging lesion activity in multiple sclerosis clinical trials}, journal = {Multiple Sclerosis Journal}, volume = {21}, year = {2015}, pages = {101-104}, abstract = {

We assess two modified guidelines for monitoring patient safety in multiple sclerosis (MS) trials. These guidelines flag patients with an increase in contrast enhancing lesion (CEL) count above a threshold over the CEL level 1{\textendash}2 months earlier. We compare the new guidelines to the original guideline where the threshold is set according to the baseline by applying the guidelines to two previous studies. The odds ratios of a subsequent clinical relapse associated with meeting the CEL threshold based on the modified guidelines are similar to those based on the original guideline. There is a need for patient and cohort specific monitoring procedures.

}, keywords = {Clinical trials methodology, contrast-enhancing lesions, magnetic resonance imaging, multiple sclerosis, patient safety}, doi = {10.1177/1352458514533846}, url = {http://msj.sagepub.com/content/early/2014/05/20/1352458514533846}, author = {Dong, J and Zhao, Y and Petkau, A.John and Li, DKB and Riddehough, A and Traboulsee, A} } @article {Luo2015, title = {Gene-enviroment Independence in case-control studies: Issues of parameterization and Bayesian inference}, journal = {Statistics in Biosciences}, year = {2015}, doi = {dx.doi.org/10.1007/s12561-015-9134-8}, author = {Luo, H. and Burstyn, I. and Gustafson, P.} } @article { ISI:000354942900002, title = {Genetic Variation, Simplicity, and Evolutionary Constraints for Function-Valued Traits}, journal = {AMERICAN NATURALIST}, volume = {185}, number = {6}, year = {2015}, month = {JUN}, pages = {E166-E181}, publisher = {UNIV CHICAGO PRESS}, type = {Article}, address = {1427 E 60TH ST, CHICAGO, IL 60637-2954 USA}, abstract = {Understanding the patterns of genetic variation and constraint for continuous reaction norms, growth trajectories, and other function-valued traits is challenging. We describe and illustrate a recent analytical method, simple basis analysis (SBA), that uses the genetic variance-covariance (G) matrix to identify {\textquoteleft}{\textquoteleft}simple{\textquoteright}{\textquoteright} directions of genetic variation and genetic constraints that have straightforward biological interpretations. We discuss the parallels between the eigenvectors (principal components) identified by principal components analysis (PCA) and the simple basis (SB) vectors identified by SBA. We apply these methods to estimated G matrices obtained from 10 studies of thermal performance curves and growth curves. Our results suggest that variation in overall size across all ages represented most of the genetic variance in growth curves. In contrast, variation in overall performance across all temperatures represented less than one-third of the genetic variance in thermal performance curves in all cases, and genetic trade-offs between performance at higher versus lower temperatures were often important. The analyses also identify potential genetic constraints on patterns of early and later growth in growth curves. We suggest that SBA can be a useful complement or alternative to PCA for identifying biologically interpretable directions of genetic variation and constraint in function-valued traits.}, keywords = {continuous reaction norms, function-valued traits, genetic constraints, genetic variation, growth trajectories, simplicity, thermal performance curves, trade-offs}, issn = {0003-0147}, doi = {10.1086/681083}, author = {Kingsolver, Joel G. and Heckman, Nancy and Zhang, Jonathan and Carter, Patrick A. and Knies, Jennifer L. and Stinchcombe, John R. and Meyer, Karin} } @article { ISI:000354045700036, title = {The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans}, journal = {SCIENCE}, volume = {348}, number = {6235}, year = {2015}, month = {MAY 8}, pages = {648-660}, publisher = {AMER ASSOC ADVANCEMENT SCIENCE}, type = {Article}, address = {1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA}, abstract = {Understanding the functional consequences of genetic variation, and how it affects complex human disease and quantitative traits, remains a critical challenge for biomedicine. We present an analysis of RNA sequencing data from 1641 samples across 43 tissues from 175 individuals, generated as part of the pilot phase of the Genotype-Tissue Expression (GTEx) project. We describe the landscape of gene expression across tissues, catalog thousands of tissue-specific and shared regulatory expression quantitative trait loci (eQTL) variants, describe complex network relationships, and identify signals from genome-wide association studies explained by eQTLs. These findings provide a systematic understanding of the cellular and biological consequences of human genetic variation and of the heterogeneity of such effects among a diverse set of human tissues.}, issn = {0036-8075}, doi = {10.1126/science.1262110}, author = {Ardlie, Kristin G. and DeLuca, David S. and Segre, Ayellet V. and Sullivan, Timothy J. and Young, Taylor R. and Gelfand, Ellen T. and Trowbridge, Casandra A. and Maller, Julian B. and Tukiainen, Taru and Lek, Monkol and Ward, Lucas D. and Kheradpour, Pouya and Iriarte, Benjamin and Meng, Yan and Palmer, Cameron D. and Esko, Tonu and Winckler, Wendy and Hirschhorn, Joel N. and Kellis, Manolis and MacArthur, Daniel G. and Getz, Gad and Shabalin, Andrey A. and Li, Gen and Zhou, Yi-Hui and Nobel, Andrew B. and Rusyn, Ivan and Wright, Fred A. and Lappalainen, Tuuli and Ferreira, Pedro G. and Ongen, Halit and Rivas, Manuel A. and Battle, Alexis and Mostafavi, Sara and Monlong, Jean and Sammeth, Michael and Mele, Marta and Reverter, Ferran and Goldmann, Jakob M. and Koller, Daphne and Guigo, Roderic and McCarthy, Mark I. and Dermitzakis, Emmanouil T. and Gamazon, Eric R. and Im, Hae Kyung and Konkashbaev, Anuar and Nicolae, Dan L. and Cox, Nancy J. and Flutre, Timothee and Wen, Xiaoquan and Stephens, Matthew and Pritchard, Jonathan K. and Tu, Zhidong and Zhang, Bin and Huang, Tao and Long, Quan and Lin, Luan and Yang, Jialiang and Zhu, Jun and Liu, Jun and Brown, Amanda and Mestichelli, Bernadette and Tidwell, Denee and Lo, Edmund and Salvatore, Michael and Shad, Saboor and Thomas, Jeffrey A. and Lonsdale, John T. and Moser, Michael T. and Gillard, Bryan M. and Karasik, Ellen and Ramsey, Kimberly and Choi, Christopher and Foster, Barbara A. and Syron, John and Fleming, Johnell and Magazine, Harold and Hasz, Rick and Walters, Gary D. and Bridge, Jason P. and Miklos, Mark and Sullivan, Susan and Barker, Laura K. and Traino, Heather M. and Mosavel, Maghboeba and Siminoff, Laura A. and Valley, Dana R. and Rohrer, Daniel C. and Jewell, Scott D. and Branton, Philip A. and Sobin, Leslie H. and Barcus, Mary and Qi, Liqun and McLean, Jeffrey and Hariharan, Pushpa and Um, Ki Sung and Wu, Shenpei and Tabor, David and Shive, Charles and Smith, Anna M. and Buia, Stephen A. and Undale, Anita H. and Robinson, Karna L. and Roche, Nancy and Valentino, Kimberly M. and Britton, Angela and Burges, Robin and Bradbury, Debra and Hambright, Kenneth W. and Seleski, John and Korzeniewski, Greg E. and Erickson, Kenyon and Marcus, Yvonne and Tejada, Jorge and Taherian, Mehran and Lu, Chunrong and Basile, Margaret and Mash, Deborah C. and Volpi, Simona and Struewing, Jeffery P. and Temple, Gary F. and Boyer, Joy and Colantuoni, Deborah and Little, Roger and Koester, Susan and Carithers, Latarsha J. and Moore, Helen M. and Guan, Ping and Compton, Carolyn and Sawyer, Sherilyn J. and Demchok, Joanne P. and Vaught, Jimmie B. and Rabiner, Chana A. and Lockhart, Nicole C. and Ardlie, Kristin G. and Getz, Gad and Wright, Fred A. and Kellis, Manolis and Volpi, Simona and Dermitzakis, Emmanouil T. and GTEx Consortium} } @article {3360, title = {GSE: Robust Estimation in the Presence of Cellwise and Casewise Contamination and Missing Data}, year = {2015}, pages = {R package}, edition = {3.3}, author = {Andy Leung and Mike Danilov and Victor Yohai and Ruben Zamar} } @article {8962, title = {Hypothesis testing in the presence of multiple samples under a density ratio model.}, journal = {Statistica Sinica}, year = {2015}, pages = {Accepted}, author = {Cai, Song and Chen, Jiahua and Zidek, James V} } @conference {McPherson2015Importance, title = {The Importance of Mutation Loss in Modelling Evolution and Metastasis in Genomically Unstable Cancers}, booktitle = {HitSeq}, year = {2015}, author = {Andrew McPherson and Andrew Roth and Jessica McAlpine and Alexandre Bouchard-C{\^o}t{\'e} and Sohrab P. Shah} } @article {8963, title = {incorporating high-dimensional exposure modelling into studies of air pollution and health}, journal = {Statistics in Biosciences}, year = {2015}, pages = {Accepted}, author = {Liu, Yi and Shaddick, G and Zidek, James V} } @conference {Roth2015Inference, title = {Inference of clonal genotypes from single cell sequencing data}, booktitle = {HitSeq}, year = {2015}, author = {Andrew Roth and Andrew McPherson and Alexandre Bouchard-C{\^o}t{\'e} and Sohrab Shah} } @article {chen2015joy, title = {The joy of proofs in statistical research}, journal = {Canadian Journal of Statistics}, volume = {43}, number = {4}, year = {2015}, pages = {481{\textendash}497}, author = {Chen, Jiahua} } @article {9189, title = {Likelihood Ratio Test for Multi-Sample Mixture Model and Its Application to Genetic Imprinting}, journal = {Journal of the American Statistical Association}, volume = {110}, year = {2015}, pages = {867{\textendash}877}, author = {Li, Shaoting and Chen, Jiahua and Guo, Jianhua and Jing, Bing-Yi and Tsang, Shui-Ying and Xue, Hong} } @inbook {Joe2015, title = {Markov count time series models with covariates}, booktitle = {Handbook of Discrete-Valued Time Series}, year = {2015}, pages = {29{\textendash}49}, publisher = {Chapman \& Hall/CRC}, organization = {Chapman \& Hall/CRC}, chapter = {2}, address = {Boca Raton, FL}, url = {http://www.crcpress.com/product/isbn/9781466577732}, author = {Joe, Harry}, editor = {Davis, R. A. and Holan, S. H. and Lund, R. B. and Ravishanker, N.} } @article {pmid26001868, title = {Maternal and perinatal outcomes of pregnancies delivered at 23 weeks{\textquoteright} gestation}, journal = {J Obstet Gynaecol Can}, volume = {37}, number = {3}, year = {2015}, month = {Mar}, pages = {214{\textendash}224}, author = {Crane, J. M. and Magee, L. A. and Lee, T. and Synnes, A. and von Dadelszen, P. and Dahlgren, L. and De Silva, D. A. and Liston, R. and Magee, L. and Liston, R. and Allen, V. and Ansermino, M. and Brant, R. and Bujold, E. and Crane, J. and Demianczuk, N. and Joseph, K. S. and Moutquin, J. M. and Piedbouef, B. and Smith, G. and von Dadelszen, P. and Walker, M. and Whittle, W. and Dansereau, J. and Magee, L. and Farquharson, D. and Wood, S. and Demianczuk, N. and Olatunbosun, F. and Carson, G. and Smith, G. and Burym, C. and McDonald, S. and Natale, R. and Whittle, W. and Barrett, J. and Walker, M. and Gagnon, R. and Audibert, F. and Pasquier, J. C. and Bujold, E. and Allen, V. and Crane, J.} } @article {pmid25377762, title = {Maternal thoughts of harm in response to infant crying: an experimental analysis}, journal = {Arch Womens Ment Health}, volume = {18}, number = {3}, year = {2015}, month = {Jun}, pages = {447{\textendash}455}, author = {Fairbrother, N. and Barr, R. G. and Pauwels, J. and Brant, R. and Green, J.} } @article {qiu_moving_2015, title = {A moving blocks empirical likelihood method for longitudinal data}, journal = {Biometrics}, volume = {71}, number = {3}, year = {2015}, month = {sep}, pages = {616{\textendash}624}, abstract = {In the analysis of longitudinal or panel data, neglecting the serial correlations among the repeated measurements within subjects may lead to inefficient inference. In particular, when the number of repeated measurements is large, it may be desirable to model the serial correlations more generally. An appealing approach is to accommodate the serial correlations nonparametrically. In this article, we propose a moving blocks empirical likelihood method for general estimating equations. Asymptotic results are derived under sequential limits. Simulation studies are conducted to investigate the finite sample performances of the proposed methods and compare them with the elementwise and subject-wise empirical likelihood methods of Wang et al. (2010, Biometrika 97, 79{\textendash}93) and the block empirical likelihood method of You et al. (2006, Can. J. Statist. 34, 79{\textendash}96). An application to an AIDS longitudinal study is presented.}, keywords = {Empirical likelihood, General estimating equation, Longitudinal data, Nonparametric method, Serial correlation}, issn = {1541-0420}, doi = {10.1111/biom.12317}, url = {http://onlinelibrary.wiley.com/doi/10.1111/biom.12317/abstract}, author = {Qiu, Jin and WU, LANG} } @article { ISI:000352890400001, title = {Multiple sclerosis in older adults: the clinical profile and impact of interferon beta treatment}, journal = {BioMed Research International}, volume = {2015}, year = {2015}, pages = {ID451912, 11 pages}, publisher = {HINDAWI PUBLISHING CORPORATION}, address = {410 PARK AVENUE, 15TH FLOOR, \#287 PMB, NEW YORK, NY 10022 USA}, abstract = {

Background. We examined (1) patient characteristics and disease-modifying drug (DMD) exposure in late-onset (LOMS, \>= 50 years at symptom onset) versus adult-onset (AOMS, 18-\<50 years) MS and (2) the association between interferon-beta (IFN beta) and disability progression in older relapsing-onset MS adults (\>= 50 years). Methods. This retrospective study (1980-2004, British Columbia, Canada) included 358 LOMS and 5627 AOMS patients. IFN beta-treated relapsing-onset MS patients aged \>= 50 (regardless of onset age, 90) were compared with 171 contemporary and 106 historical controls. Times to EDSS 6 from onset and from IFN beta eligibility were examined using survival analyses. Results. LOMS patients (6\%) were more likely to be male, with motor onset and a primary-progressive course, and exhibit faster progression and were less likely to take DMDs. Nonetheless, 57\% were relapsing-onset, of which 31\% were prescribed DMDs, most commonly IFN beta. Among older relapsing-onset MS adults, no significant association between IFN beta exposure and disability progression was found when either the contemporary (hazard ratio [HR]: 0.46; 95\% CI: 0.18-1.22) or historical controls (HR: 0.54; 95\% CI: 0.20-1.42) were considered. Conclusion. LOMS differed clinically from AOMS. One-third of older relapsing-onset MS patients were prescribed a DMD. IFN beta exposure was not significantly associated with reduced disability in older MS patients.

}, doi = {10.1155/2015/451912}, author = {Shirani, A and Zhao, Y and Petkau, J and Gustafson, P and Karim, ME and Evans, C and Kingwell, E and van der Kop, ML and Oger, J and Tremlett, H} } @article {Shirani2015, title = {Multiple Sclerosis in Older Adults: The Clinical Profile and Impact of Interferon Beta Treatment}, journal = {BioMed research international}, volume = {2015}, year = {2015}, publisher = {Hindawi Publishing Corporation}, doi = {10.1155/2015/451912}, author = {Shirani, Afsaneh and Zhao, Yinshan and Petkau, John and Gustafson, Paul and Karim, Mohammad Ehsanul and Evans, Charity and Kingwell, Elaine and van der Kop, Mia L and Oger, Joel and Tremlett, Helen} } @article {pmid26054971, title = {Oral glucose during targeted neonatal echocardiography: is it useful?}, journal = {Arch. Dis. Child. Fetal Neonatal Ed.}, volume = {100}, number = {4}, year = {2015}, month = {Jul}, pages = {F374{\textendash}375}, author = {Lavoie, P. M. and Stritzke, A. and Ting, J. and Jabr, M. and Jain, A. and Kwan, E. and Chakkarapani, E. and Brooks, P. and Brant, R. and McNamara, P. J. and Holsti, L.} } @article {Bouchard2015Particle, title = {Particle Gibbs Split-Merge Sampling for Bayesian Inference in Mixture Models}, journal = {arXiv}, volume = {1508.02663}, year = {2015}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Arnaud Doucet and Andrew Roth} } @article {Bouchard2015Particle, title = {Particle Gibbs split-merge sampling for Bayesian inference in mixture models}, journal = {Journal of Machine Learning Research}, volume = {(Accepted)}, year = {2015}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Arnaud Doucet and Andrew Roth} } @article {zhao_personalized_2015, title = {Personalized activity index, a new safety monitoring tool for multiple sclerosis clinical trials}, journal = {Multiple Sclerosis Journal {\textendash} Experimental, Translational and Clinical}, volume = {1}, year = {2015}, pages = {1-15}, abstract = {

Background An abnormal increase of contrast-enhancing lesion (CEL) counts on frequent MRIs is interpreted as a signal of potential worsening in multiple sclerosis (MS) clinical trials. We demonstrate the utility of the MR personalized activity index (MR-pax) to identify such increases. Methods We analyzed a previous Phase II study in relapsing patients (n = 167) with MRIs at screening, baseline and months 1{\textendash}6. We performed five consecutive reviews at 90-day intervals. At each review, we evaluate the MR-pax for each patient and also identify those who meet the rule-of-five (an ad-hoc guideline currently in use). To evaluate its clinical relevance, we assess the relation between having a small MR-pax (<=0.05; indicating an unexpected CEL increase) and relapse status in the 12 weeks post-review. Results Of the 399 patient reviews, 35 cases met the rule-of-five; 35 had an MR-pax <= 0.05; 18 met both criteria. The proportions experiencing clinical relapse are 63\% among those meeting the rule-of-five, 61\% among those with MR-pax <=0.05, and 83\% for those meeting both criteria, more than double the rate of those meeting neither criterion (40\%). Conclusion A guideline combining this new personalized index and the existing threshold-based criterion is able to better identify patients with a higher risk of experiencing relapses.

}, keywords = {contrast-enhancing lesions, MRI, multiple sclerosis, safety monitoring in clinical trials}, doi = {10.1177/2055217315577829}, url = {http://mso.sagepub.com/content/1/2055217315577829}, author = {Zhao, Y and Kondo, Y and Traboulsee, A and Li, DKB and Riddehough, A and Petkau, A.John} } @article { ISI:000364916600010, title = {Predictors of disease activity in 857 patients with MS treated with interferon beta-1b}, journal = {Journal of Neurology}, volume = {262}, number = {11}, year = {2015}, pages = {2466-2471}, publisher = {SPRINGER HEIDELBERG}, address = {TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY}, abstract = {

Multiple sclerosis (MS) is a chronic demyelinating neurodegenerative disease of the CNS that requires long-term treatment. The identification of patient characteristics that can help predict disease outcomes could improve care for patients with MS. The objective of this study is to identify predictors of disease activity in patients from the BEYOND trial. This regression analysis of patients with relapsing-remitting MS from BEYOND examined the predictive value of patient characteristics at baseline and after 1 year of treatment with interferon beta-1b 250 mu g every other day for clinical and MRI outcomes after year 1 of the study. 857 and 765 patients were included in the analyses of clinical and MRI outcomes, respectively. In multivariate analyses of age, a higher number of relapses in the past 2 years, a parts per thousand yen3 new MRI lesions in the first year, and, especially, a higher number of relapses in year 1 predicted the future occurrence of relapses. By contrast, age, MRI activity, and the presence of neutralizing antibodies in the first year were principally predictive of future MRI activity. In patients with continued clinical disease activity or substantial MRI activity on therapy, an alternative therapeutic approach should be strongly considered.

}, keywords = {Interferon beta-1b, MRI lesion, multiple sclerosis, Predictor, Relapse}, doi = {10.1007/s00415-015-7862-9}, author = {Hartung, HP and Kappos, L and Goodin, DS and O{\textquoteright}Connor, P and Filippi, M and Arnason, B and Comi, G and Cook, S and Jeffery, D and Petkau, J and White, R and Bogumil, T and Beckmann, K and Stemper, B and Suarez, G and Sandbrink, R and Pohl, C} } @article {hartung2015predictors, title = {Predictors of disease activity in 857 patients with MS treated with interferon beta-1b}, journal = {Journal of neurology}, volume = {262}, number = {11}, year = {2015}, pages = {2466{\textendash}2471}, publisher = {Springer}, author = {Hartung, Hans-Peter and Kappos, Ludwig and Goodin, Douglas S and O{\textquoteright}Connor, Paul and Filippi, Massimo and Arnason, Barry and Comi, Giancarlo and Cook, Stuart and Jeffery, Douglas and Petkau, John and others} } @article { ISI:000355774000001, title = {Preface to special issue on high-dimensional dependence and copulas}, journal = {Journal of Multivariate Analysis}, volume = {138}, number = {SI}, year = {2015}, month = {JUN}, pages = {1-3}, publisher = {Elsevier Inc}, type = {Editorial Material}, issn = {0047-259X}, doi = {10.1016/j.jmva.2015.03.002}, author = {Joe, Harry and Cai, Jun and Czado, Claudia and Li, Haijun} } @article {wong2015quantifying, title = {Quantifying uncertainty in lumber grading and strength prediction: a Bayesian approach}, journal = {Technometrics}, volume = {58}, year = {2015}, pages = {236-243}, publisher = {Taylor and Francis}, author = {Wong, Samuel WK and LUM, CONROY and WU, LANG and Zidek, James V} } @article {pmid26567090, title = {A randomized controlled trial of an intervention for infants{\textquoteright} behavioral sleep problems}, journal = {BMC Pediatr}, volume = {15}, number = {1}, year = {2015}, pages = {181}, author = {Hall, W. A. and Hutton, E. and Brant, R. F. and Collet, J. P. and Gregg, K. and Saunders, R. and Ipsiroglu, O. and Gafni, A. and Triolet, K. and Tse, L. and Bhagat, R. and Wooldridge, J.} } @article {pmid26496361, title = {A Randomized Controlled Trial of the Use of Oral Glucose with or without Gentle Facilitated Tucking of Infants during Neonatal Echocardiography}, journal = {PLoS ONE}, volume = {10}, number = {10}, year = {2015}, pages = {e0141015}, author = {Lavoie, P. M. and Stritzke, A. and Ting, J. and Jabr, M. and Jain, A. and Kwan, E. and Chakkarapani, E. and Brooks, P. and Brant, R. and McNamara, P. J. and Holsti, L.} } @article { ISI:000359388200008, title = {Rejoinder on: Robust estimation of multivariate location and scatter in the presence of cellwise and casewise contamination}, journal = {TEST}, volume = {24}, number = {3}, year = {2015}, month = {SEP}, pages = {484-488}, publisher = {SPRINGER}, type = {Editorial Material}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {We thank the discussants, the referees, and the associate editor for their stimulating discussions and helpful remarks. We thank the editor for giving us the opportunity to discuss our paper in this journal. The rejoinder is organized in several sections, which address the main points raised by the discussants.}, issn = {1133-0686}, doi = {10.1007/s11749-015-0457-z}, author = {Agostinelli, Claudio and Leung, Andy and Yohai, Victor J. and Zamar, Ruben H.} } @article { ISI:000359388200008, title = {Rejoinder on: Robust estimation of multivariate location and scatter in the presence of cellwise and casewise contamination}, journal = {TEST}, volume = {24}, number = {3}, year = {2015}, month = {SEP}, pages = {484-488}, publisher = {SPRINGER}, type = {Editorial Material}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {We thank the discussants, the referees, and the associate editor for their stimulating discussions and helpful remarks. We thank the editor for giving us the opportunity to discuss our paper in this journal. The rejoinder is organized in several sections, which address the main points raised by the discussants.}, issn = {1133-0686}, doi = {10.1007/s11749-015-0457-z}, author = {Agostinelli, Claudio and Leung, Andy and Yohai, Victor J. and Zamar, Ruben H.} } @article {wang2015resampling, title = {Resampling calibrated adjusted empirical likelihood}, journal = {Canadian Journal of Statistics}, volume = {43}, number = {1}, year = {2015}, pages = {42{\textendash}59}, author = {Wang, Lei and Chen, Jiahua and Pu, Xiaolong} } @article {Etminan2015, title = {Risk of intracranial hypertension with intrauterine levonorgestrel}, journal = {Therapeutic advances in drug safety}, volume = {6}, number = {3}, year = {2015}, pages = {110{\textendash}113}, publisher = {SAGE Publications}, doi = {10.1177/2042098615588084}, author = {Etminan, Mahyar and Luo, Hao and Gustafson, Paul} } @article { ISI:000359388200001, title = {Robust estimation of multivariate location and scatter in the presence of cellwise and casewise contamination}, journal = {TEST}, volume = {24}, number = {3}, year = {2015}, month = {SEP}, pages = {441-461}, publisher = {SPRINGER}, type = {Article}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {Multivariate location and scatter matrix estimation is a cornerstone in multivariate data analysis. We consider this problem when the data may contain independent cellwise and casewise outliers. Flat data sets with a large number of variables and a relatively small number of cases are common place in modern statistical applications. In these cases, global down-weighting of an entire case, as performed by traditional robust procedures, may lead to poor results. We highlight the need for a new generation of robust estimators that can efficiently deal with cellwise outliers and at the same time show good performance under casewise outliers.}, keywords = {Cellwise contamination, Multivariate data analysis, Multivariate location and scatter, Robust estimation}, issn = {1133-0686}, doi = {10.1007/s11749-015-0450-6}, author = {Agostinelli, Claudio and Leung, Andy and Yohai, Victor J. and Zamar, Ruben H.} } @article {3359, title = {Robust estimation of multivariate location and scatter in the presence of cellwise and casewise contamination}, journal = {TEST}, volume = {24}, year = {2015}, month = {09/2015}, pages = {441-461}, author = {Agostinelli, C. and Leung, A. and Yohai, V J and Zamar, R H} } @article {troncoso_sage_2015, title = {The SAGE handbook of multilevel modeling}, journal = {International Journal of Research \& Method in Education}, volume = {38}, number = {1}, year = {2015}, month = {jan}, pages = {100{\textendash}101}, issn = {1743-727X}, doi = {10.1080/1743727X.2014.986027}, url = {http://dx.doi.org/10.1080/1743727X.2014.986027}, author = {Troncoso, Patricio} } @article { ISI:000364161000010, title = {Sample-size calculations for short-term proof-of-concept studies of tissue protection and repair in multiple sclerosis lesions via conventional clinical imaging}, journal = {Multiple Sclerosis Journal}, volume = {21}, number = {13}, year = {2015}, pages = {1693-1704}, publisher = {SAGE PUBLICATIONS LTD}, address = {1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND}, abstract = {

Background: New multiple sclerosis (MS) lesion activity on magnetic resonance imaging (MRI) can test immunomodulatory therapies in proof-of-concept trials. Comparably powerful endpoints to assess tissue protection or repair are lacking. Objective: The objective of this paper is to report sample-size calculations for assessment of new lesion recovery. Methods: In two sets of six active MS cases, new lesions were observed by monthly MRI for approximately 12 months. Averages and quartiles of normalized (proton density/T1/T2 weighted) and quantitative (T1/T2 and mean diffusivity maps for dataset 1, T2 and magnetization transfer ratio maps for dataset 2) measures were used to compare the lesion area before lesion appearance to afterward. A linear mixed-effects model incorporating lesion- and participant-specific random effects estimated average levels and variance components for sample-size calculations. Results: In both datasets, greatest statistical sensitivity was observed for the 25th percentile of normalized proton density-weighted signal. At 3T, using new lesions 15 mm(3), as few as nine participants/arm may be required for a six-month placebo-controlled add-on trial postulating a therapeutic effect size of 20\% and statistical power of 90\%. Conclusion: Lesion recovery is a powerful outcome measure for proof-of-concept clinical trials of tissue protection and repair in MS. The trial design requires active cases and is therefore best implemented near disease onset.

}, keywords = {clinical trial design, MRI, repair, T2 lesions}, doi = {10.1177/1352458515569098}, author = {Reich, DS and White, R and Cortese, ICM and Vuolo, L and Shea, CD and Collins, TL and Petkau, J} } @article {reich2015sample, title = {Sample-size calculations for short-term proof-of-concept studies of tissue protection and repair in multiple sclerosis lesions via conventional clinical imaging}, journal = {Multiple Sclerosis Journal}, year = {2015}, pages = {1352458515569098}, publisher = {SAGE Publications}, author = {Reich, Daniel S and White, Richard and Cortese, Irene CM and Vuolo, Luisa and Shea, Colin D and Collins, Tassie L and Petkau, John} } @article {guarna2015search, title = {A search for protein biomarkers links olfactory signal transduction to social immunity}, journal = {BMC genomics}, volume = {16}, number = {1}, year = {2015}, pages = {63}, publisher = {BioMed Central Ltd}, author = {Guarna, Maria M and Melathopoulos, Andony P and Huxter, Elizabeth and Iovinella, Immacolata and Parker, Robert and Stoynov, Nikolay and Tam, Amy and Moon, Kyung-Mee and Chan, Queenie WT and Pelosi, Paolo and others} } @article {tremlett2015serum, title = {Serum proteomics in multiple sclerosis disease progression}, journal = {Journal of proteomics}, volume = {118}, year = {2015}, pages = {2{\textendash}11*Senior Author}, publisher = {Elsevier}, author = {Tremlett, Helen and Dai, Darlene LY and Hollander, Zsuzsanna and Kapanen, Anita and Aziz, Tariq and Wilson-McManus, Janet E and Tebbutt, Scott J and Borchers, Christoph H and Oger, Joel and Freue, Gabriela V Cohen*} } @article { ISI:000365144600020, title = {S-Estimators for Functional Principal Component Analysis}, journal = {JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION}, volume = {110}, number = {511}, year = {2015}, month = {SEP}, pages = {1100-1111}, publisher = {AMER STATISTICAL ASSOC}, type = {Article}, address = {732 N WASHINGTON ST, ALEXANDRIA, VA 22314-1943 USA}, abstract = {

Principal component analysis is a widely used technique that provides an optimal lower-dimensional approximation to multivariate or functional datasets. These approximations can be very useful in identifying potential outliers among high-dimensional or functional observations. In this article, we propose a new class of estimators for principal components based on robust scale estimators. For a fixed dimension q, we robustly estimate the q-dimensional linear space that provides the best prediction for the data, in the sense of minimizing the sum of robust scale estimators of the coordinates of the residuals. We also study an extension to the infinite-dimensional case. Our method is consistent for elliptical random vectors, and is Fisher consistent for elliptically distributed random elements on arbitrary Hilbert spaces. Numerical experiments show that our proposal is highly competitive when compared with other methods. We illustrate our approach on a real dataset, where the robust estimator discovers atypical observations that would have been missed otherwise. Supplementary materials for this article are available online.

}, keywords = {Functional data analysis, Robust estimation, Sparse data}, issn = {0162-1459}, doi = {10.1080/01621459.2014.946991}, author = {Boente, Graciela and Salibian-Barrera, Mat{\'\i}as} } @article { ISI:000356700200015, title = {Sharing and Specificity of Co-expression Networks across 35 Human Tissues}, journal = {PLOS COMPUTATIONAL BIOLOGY}, volume = {11}, number = {5}, year = {2015}, month = {MAY}, pages = {e1004220}, publisher = {PUBLIC LIBRARY SCIENCE}, type = {Article}, address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA}, abstract = {To understand the regulation of tissue-specific gene expression, the GTEx Consortium generated RNA-seq expression data for more than thirty distinct human tissues. This data provides an opportunity for deriving shared and tissue specific gene regulatory networks on the basis of co-expression between genes. However, a small number of samples are available for a majority of the tissues, and therefore statistical inference of networks in this setting is highly underpowered. To address this problem, we infer tissue-specific gene co-expression networks for 35 tissues in the GTEx dataset using a novel algorithm, GNAT, that uses a hierarchy of tissues to share data between related tissues. We show that this transfer learning approach increases the accuracy with which networks are learned. Analysis of these networks reveals that tissue-specific transcription factors are hubs that preferentially connect to genes with tissue specific functions. Additionally, we observe that genes with tissue-specific functions lie at the peripheries of our networks. We identify numerous modules enriched for Gene Ontology functions, and show that modules conserved across tissues are especially likely to have functions common to all tissues, while modules that are upregulated in a particular tissue are often instrumental to tissue-specific function. Finally, we provide a web tool, available at mostafavilab.stat.ubc.ca/GNAT, which allows exploration of gene function and regulation in a tissue-specific manner.}, issn = {1553-734X}, doi = {10.1371/journal.pcbi.1004220}, author = {Pierson, Emma and Koller, Daphne and Battle, Alexis and Mostafavi, Sara and GTEx Consortium} } @conference {Straub15_CVPR, title = {Small-variance nonparametric clustering on the hypersphere}, booktitle = {IEEE Conference on Computer Vision and Pattern Recognition}, year = {2015}, author = {Julian Straub and Trevor Campbell and Jonathan P. How and John Fisher} } @book {shaddick2015spatio, title = {Spatio-Temporal Methods in Environmental Epidemiology}, year = {2015}, publisher = {CRC Press}, organization = {CRC Press}, author = {Shaddick, Gavin and Zidek, James V.} } @conference {Campbell15_NIPS, title = {Streaming, distributed variational inference for Bayesian nonparametrics}, booktitle = {Advances in Neural Information Processing Systems}, year = {2015}, author = {Trevor Campbell and Julian Straub and John Fisher and Jonathan P. How} } @article { ISI:000355774000005, title = {Structured factor copula models: Theory, inference and computation}, journal = {Journal of Multivariate Analysis}, volume = {138}, number = {SI}, year = {2015}, month = {JUN}, pages = {53-73}, publisher = {Elsevier Inc}, type = {Article}, abstract = {In factor copula models for multivariate data, dependence is explained via one or several common factors. These models are flexible in handling tail dependence and asymmetry with parsimonious dependence structures. We propose two structured factor copula models for the case where variables can be split into non-overlapping groups such that there is homogeneous dependence within each group. A typical example of such variables occurs for stock returns from different sectors. The structured models inherit most of dependence properties derived for common factor copula models. With appropriate numerical methods, efficient estimation of dependence parameters is possible for data sets with over 100 variables. We apply the structured factor copula models to analyze a financial data set, and compare with other copula models for tail inference. Using model-based interval estimates, we find that some commonly used risk measures may not be well discriminated by copula models, but tail-weighted dependence measures can discriminate copula models with different dependence and tail properties. (C) 2014 Elsevier Inc. All rights reserved.}, keywords = {Bi-factor model, Conditional independence, Dependence measure, Factor analysis, Tail asymmetry, Tail dependence, Truncated vine}, issn = {0047-259X}, doi = {10.1016/j.jmva.2014.11.002}, author = {Krupskii, Pavel and Joe, Harry} } @article {Krupskii.Joe2015b, title = {Structured factor copula models: theory, inference and computation}, journal = {Journal of Multivariate Analysis}, volume = {138}, year = {2015}, pages = {53{\textendash}73}, author = {Krupskii, P. and Joe, H.} } @article {Krupskii.Joe2015, title = {Tail-weighted measures of dependence}, journal = {Journal of Applied Statistics}, volume = {42}, number = {3}, year = {2015}, pages = {614{\textendash}629}, author = {Krupskii, Pavel and Joe, Harry} } @article { ISI:000346333600012, title = {Tail-weighted measures of dependence}, journal = {Journal of Applied Statistics}, volume = {42}, number = {3}, year = {2015}, month = {MAR 4}, pages = {614-629}, publisher = {Taylor \& Francis Ltd}, type = {Article}, abstract = {Multivariate copula models are commonly used in place of Gaussian dependence models when plots of the data suggest tail dependence and tail asymmetry. In these cases, it is useful to have simple statistics to summarize the strength of dependence in different joint tails. Measures of monotone association such as Kendall{\textquoteright}s tau and Spearman{\textquoteright}s rho are insufficient to distinguish commonly used parametric bivariate families with different tail properties. We propose lower and upper tail-weighted bivariate measures of dependence as additional scalar measures to distinguish bivariate copulas with roughly the same overall monotone dependence. These measures allow the efficient estimation of strength of dependence in the joint tails and can be used as a guide for selection of bivariate linking copulas in vine and factor models as well as for assessing the adequacy of fit of multivariate copula models. We apply the tail-weighted measures of dependence to a financial data set and show that the measures better discriminate models with different tail properties compared to commonly used risk measures - the portfolio value-at-risk and conditional tail expectation.}, keywords = {62H20, Copula, Dependence measure, factor model, intermediate tail dependence, Tail asymmetry, Tail dependence}, issn = {0266-4763}, doi = {10.1080/02664763.2014.980787}, author = {Krupskii, Pavel and Joe, Harry} } @article {xu2015thresholding, title = {A Thresholding Algorithm for Order Selection in Finite Mixture Models}, journal = {Communications in Statistics-Simulation and Computation}, volume = {44}, number = {2}, year = {2015}, pages = {433{\textendash}453}, publisher = {Taylor \& Francis}, author = {Xu, Chen and Chen, Jiahua} } @article { ISI:000355774000003, title = {Truncation of vine copulas using fit indices}, journal = {Journal of Multivariate Analysis}, volume = {138}, number = {SI}, year = {2015}, month = {JUN}, pages = {19-33}, publisher = {Elsevier Inc}, type = {Article}, abstract = {Vine copulas are flexible multivariate dependence models, which are built up from a set of bivariate copulas in different hierarchical levels. However, vine copulas have a computational complexity that is increasing quadratically in the number of variables. This complexity can be reduced by focusing on the sub-class of truncated vine copulas, which use only a limited number of hierarchical levels. We propose a new approach to select the adequate number of levels, such that the vine copula is still sufficiently flexible to provide a good fit to given data. The approach is based on fit indices, as used for structural equation models, to measure the goodness of a fitted truncated model. To select such truncated models, we propose methods to effectively explore the search space of truncated vine copulas, so that we are able to improve over previous greedy sequential approaches that optimized over one tree of the vine at each step. This new selection approach is evaluated in a simulation study as well as in two applications to data sets of financial returns. (C) 2015 Elsevier Inc. All rights reserved.}, keywords = {Fit index, Partial correlation, Truncated vine, Vine copula}, issn = {0047-259X}, doi = {10.1016/j.jmva.2015.02.012}, author = {Brechmann, Eike C. and Joe, Harry} } @inbook {shi_air_2014, title = {Air Quality Model Evaluation Using Gaussian Process Modelling and Empirical Orthogonal Function Decomposition}, booktitle = {Air Pollution Modeling and its Application XXIII}, year = {2014}, pages = {457{\textendash}462}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, url = {http://link.springer.com/chapter/10.1007/978-3-319-04379-1_75}, author = {Shi, Tianji and Steyn, Douw and Welch, William J.} } @book {jin_applied_2014, title = {Applied Multivariate Statistical Analysis and Related Topics with R(Chinese Edition)}, year = {2014}, month = {jun}, publisher = {Science Press}, organization = {Science Press}, address = {北京}, isbn = {978-7-03-041243-0}, author = {JIN, WU LANG QIU} } @conference {Campbell14_UAI, title = {Approximate decentralized Bayesian inference}, booktitle = {Uncertainty in Artificial Intelligence}, year = {2014}, author = {Trevor Campbell and Jonathan P. How} } @article { ISI:000340257900001, title = {Assessing approximate fit in categorical data analysis}, journal = {Multivariate Behavioral Research}, volume = {49}, number = {4}, year = {2014}, pages = {305-328}, publisher = {Routledge Journals, Taylor \& Francis Ltd}, type = {Article}, abstract = {A family of Root Mean Square Error of Approximation (RMSEA) statistics is proposed for assessing the goodness of approximation in discrete multivariate analysis with applications to item response theory (IRT) models. The family includes RMSEAs to assess the approximation up to any level of association of the discrete variables. Two members of this family are RMSEA(2), which uses up to bivariate moments, and the full information RMSEA(n). The RMSEA(2) is estimated using the M-2 statistic of Maydeu-Olivares and Joe (2005, 2006), whereas for maximum likelihood estimation, RMSEA(n) is estimated using Pearson{\textquoteright}s X-2 statistic. Using IRT models, we provide cutoff criteria of adequate, good, and excellent fit using the RMSEA(2). When the data are ordinal, we find a strong linear relationship between the RMSEA(2) and the Standardized Root Mean Squared Residual goodness-of-fit index. We are unable to offer cutoff criteria for the RMSEA(n) as its population values decrease as the number of variables and categories increase.}, issn = {0027-3171}, doi = {10.1080/00273171.2014.911075}, author = {Maydeu-Olivares, Alberto and Joe, Harry} } @article { ISI:000345076200013, title = {Association between beta-interferon exposure and hospital events in multiple sclerosis}, journal = {Pharmacoepidemiology and Drug Safety}, volume = {23}, number = {11}, year = {2014}, pages = {1213-1222}, publisher = {WILEY-BLACKWELL}, address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, abstract = {

Purpose A systematic evaluation of hospital events can be an important surrogate measure for drug effectiveness or adverse effects. The purpose of this study was to examine the association between beta-interferon use and hospital events in a large cohort of patients with multiple sclerosis (MS). MethodsRetrospective cohort study comparing beta-interferon exposed and unexposed patients using clinical data from the British Columbia MS (BCMS) database linked with health administrative databases, 1996-2008. For each patient, the primary outcome was the number of hospital events in each month, analyzed by quasi Poisson regression. Beta-interferon exposure was examined two ways: current and cumulative exposure. Secondary outcomes included whether a hospital event occurred in each month for each specific primary diagnoses, grouped by International Classification of Diseases categories. ResultsCurrent exposure to beta-interferon was not associated with an altered rate of hospital events (adjusted incident rate ratio 1.018; 95\% CI 0.803-1.290). Similarly, there was no association with cumulative exposure. Cumulative beta-interferon exposure was associated with a lower odds of respiratory disease-related hospital events compared to those never exposed to beta-interferon. ConclusionsExposure to beta-interferon for MS was not associated with a change in overall hospital event rates. Preliminary evidence suggests that the beta-interferons may have a protective effect against respiratory diseases requiring hospitalization in MS patients. Copyright (c) 2014 John Wiley \& Sons, Ltd.

}, keywords = {beta-interferon, hospitalization, multiple sclerosis, pharmacoepidemiology}, doi = {10.1002/pds.3667}, author = {Evans, C and Zhu, F and Kingwell, E and Shirani, A and van der Kop, ML and Petkau, J and Gustafson, P and Zhao, Y and Traboulsee, A and Oger, Joel and Tremlett, Helen} } @article {Evans2014, title = {Association between beta-interferon exposure and hospital events in multiple sclerosis}, journal = {Pharmacoepidemiology and drug safety}, volume = {23}, number = {11}, year = {2014}, pages = {1213{\textendash}1222}, publisher = {Wiley Online Library}, doi = {10.1002/pds.3667}, author = {Evans, Charity and Zhu, Feng and Kingwell, Elaine and Shirani, Afsaneh and Kop, Mia L and Petkau, John and Gustafson, Paul and Zhao, Yinshan and Oger, Joel and Tremlett, Helen} } @article {Gus2014, title = {Bayesian inference in partially identified models: Is the shape of the posterior distribution useful?}, journal = {Electronic Journal of Statistics}, volume = {8}, year = {2014}, pages = {476-496}, issn = {1935-7524}, doi = {10.1214/14-EJS891}, author = {Paul Gustafson} } @article {Liu2014, title = {Bayesian Melding of the Dead-Reckoned path and GPS measurements for an accurate and high-resolution path of marine mammals}, journal = {arXiv preprint arXiv: 1411.6683}, year = {2014}, author = {Liu, Yang and Battaile, Brian C. and Zidek, James V. and Trites, Andrew W} } @unpublished {liu2014bayesian, title = {Bayesian melding of the dead-reckoned path and GPS measurements for an accurate and high-resolution path of marine mammals}, journal = {arXiv preprint arXiv:1411.6683}, year = {2014}, author = {Liu, Yang and Battaile, Brian C and Zidek, James V and Trites, Andrew W} } @article {xia2014bayesian, title = {Bayesian sensitivity analyses for hidden sub-populations in weighted sampling}, journal = {Canadian Journal of Statistics}, volume = {42}, number = {3}, year = {2014}, pages = {436{\textendash}450}, publisher = {Wiley Online Library}, doi = {10.1002/cjs.11220}, author = {Xia, Michelle and Gustafson, Paul} } @article {Gustafson2014c, title = {Bayesian Statistical Methodology for Observational Health Sciences Data}, journal = {Statistics in Action: A Canadian Outlook}, year = {2014}, pages = {163}, publisher = {CRC Press}, doi = {10.1201/b16597-11}, author = {Gustafson, Paul} } @article {3364, title = {A Bayesian stochastic model for batting performance evaluation in one-day cricket}, journal = {Journal of Quantitative Analysis in Sports}, volume = {10}, year = {2014}, pages = {1{\textendash}13}, keywords = {Gibbs sampling, Hidden Markov model, parallel sampling, reliability analysis}, doi = {10.1515/jqas-2013-0057}, url = {http://www.degruyter.com/view/j/jqas.2014.10.issue-1/jqas-2013-0057/jqas-2013-0057.xml}, author = {Koulis, Theodoro and Muthukumarana, Saman and Briercliffe, Creagh} } @article {shaddick2014case, title = {A case study in preferential sampling: Long term monitoring of air pollution in the UK}, journal = {Spatial Statistics}, volume = {9}, year = {2014}, pages = {51{\textendash}65}, publisher = {Elsevier}, author = {Shaddick, Gavin and Zidek, James V} } @article {8972, title = {A characterization of elliptical distributions and some optimality properties of principal components for functional data}, journal = {Journal of Multivariate Analysis}, volume = {131}, year = {2014}, pages = {254 - 264}, keywords = {Principal components}, issn = {0047-259X}, doi = {10.1016/j.jmva.2014.07.006}, url = {http://www.sciencedirect.com/science/article/pii/S0047259X14001638}, author = {Graciela Boente and Mat{\'\i}as Salibi{\'a}n Barrera and David E. Tyler} } @article { ISI:000329163500002, title = {Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals}, journal = {GENOME RESEARCH}, volume = {24}, number = {1}, year = {2014}, month = {JAN}, pages = {14-24}, publisher = {COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT}, type = {Article}, address = {1 BUNGTOWN RD, COLD SPRING HARBOR, NY 11724 USA}, abstract = {Understanding the consequences of regulatory variation in the human genome remains a major challenge, with important implications for understanding gene regulation and interpreting the many disease-risk variants that fall outside of protein-coding regions. Here, we provide a direct window into the regulatory consequences of genetic variation by sequencing RNA from 922 genotyped individuals. We present a comprehensive description of the distribution of regulatory variation-by the specific expression phenotypes altered, the properties of affected genes, and the genomic characteristics of regulatory variants. We detect variants influencing expression of over ten thousand genes, and through the enhanced resolution offered by RNA-sequencing, for the first time we identify thousands of variants associated with specific phenotypes including splicing and allelic expression. Evaluating the effects of both long-range intra-chromosomal and trans (cross-chromosomal) regulation, we observe modularity in the regulatory network, with three-dimensional chromosomal configuration playing a particular role in regulatory modules within each chromosome. We also observe a significant depletion of regulatory variants affecting central and critical genes, along with a trend of reduced effect sizes as variant frequency increases, providing evidence that purifying selection and buffering have limited the deleterious impact of regulatory variation on the cell. Further, generalizing beyond observed variants, we have analyzed the genomic properties of variants associated with expression and splicing and developed a Bayesian model to predict regulatory consequences of genetic variants, applicable to the interpretation of individual genomes and disease studies. Together, these results represent a critical step toward characterizing the complete landscape of human regulatory variation.}, issn = {1088-9051}, doi = {10.1101/gr.155192.113}, author = {Battle, Alexis and Mostafavi, Sara and Zhu, Xiaowei and Potash, James B. and Weissman, Myrna M. and McCormick, Courtney and Haudenschild, Christian D. and Beckman, Kenneth B. and Shi, Jianxin and Mei, Rui and Urban, Alexander E. and Montgomery, Stephen B. and Levinson, Douglas F. and Koller, Daphne} } @article {Gustafson2014b, title = {Commentary: Priors, Parameters, and Probability: A Bayesian Perspective on Sensitivity Analysis}, journal = {Epidemiology}, volume = {25}, number = {6}, year = {2014}, pages = {910{\textendash}912}, publisher = {LWW}, author = {Gustafson, Paul and McCandless, Lawrence} } @article {campbell2014consequences, title = {The consequences of proportional hazards based model selection}, journal = {Statistics in medicine}, volume = {33}, number = {6}, year = {2014}, pages = {1042{\textendash}1056}, publisher = {Wiley Online Library}, author = {Campbell, H and Dean, CB} } @article {Falasinnu2014a, title = {A critical appraisal of risk models for predicting sexually transmitted infections}, journal = {Sexually transmitted diseases}, volume = {41}, number = {5}, year = {2014}, pages = {321{\textendash}330}, publisher = {LWW}, doi = {10.1097/olq.0000000000000120}, author = {Falasinnu, Titilola and Gustafson, Paul and Hottes, Travis Salway and Gilbert, Mark and Ogilvie, Gina and Shoveller, Jean} } @article { ISI:000340190800014, title = {Defining the clinical course of multiple sclerosis: The 2013 revisions}, journal = {Neurology}, volume = {83}, number = {3}, year = {2014}, pages = {278-286}, publisher = {LIPPINCOTT WILLIAMS \& WILKINS}, address = {TWO COMMERCE SQ, 2001 MARKET ST, PHILADELPHIA, PA 19103 USA}, abstract = {

Accurate clinical course descriptions (phenotypes) of multiple sclerosis (MS) are important for communication, prognostication, design and recruitment of clinical trials, and treatment decision-making. Standardized descriptions published in 1996 based on a survey of international MS experts provided purely clinical phenotypes based on data and consensus at that time, but imaging and biological correlates were lacking. Increased understanding of MS and its pathology, coupled with general concern that the original descriptors may not adequately reflect more recently identified clinical aspects of the disease, prompted a re-examination of MS disease phenotypes by the International Advisory Committee on Clinical Trials of MS. While imaging and biological markers that might provide objective criteria for separating clinical phenotypes are lacking, we propose refined descriptors that include consideration of disease activity (based on clinical relapse rate and imaging findings) and disease progression. Strategies for future research to better define phenotypes are also outlined.

}, author = {Lublin, FD and Reingold, SC and Cohen, JA and Cutter, GR and Soelberg-Sorensen, P and Thompson, AJ and Wolinsky, JS and Balcer, LJ and Banwell, B and Barkhof, F and Bebo, B and Calabresi, PA and Clanet, M and Comi, G and Fox, RJ and Freedman, MS and Goodman, AD and Inglese, M and Kappos, L and Kieseier, BC and Lincoln, JA and Lubetzki, C and Miller, AE and Montalban, X and O{\textquoteright}Connor, PW and Petkau, J and Pozzilli, C and Rudick, RA and Sormani, MP and Stueve, O and Waubant, E and Polman, CH} } @book {Joe2014, title = {Dependence Modeling with Copulas}, year = {2014}, publisher = {Chapman \& Hall/CRC}, organization = {Chapman \& Hall/CRC}, address = {Boca Raton, FL}, url = {http://www.crcpress.com/product/isbn/9781466583221}, author = {Joe, Harry} } @article {Falasinnu2014b, title = {Deriving and validating a risk estimation tool for screening asymptomatic chlamydia and gonorrhea}, journal = {Sexually transmitted diseases}, volume = {41}, number = {12}, year = {2014}, pages = {706{\textendash}712}, publisher = {LWW}, doi = {10.1097/olq.0000000000000205}, author = {Falasinnu, Titilola and Gilbert, Mark and Gustafson, Paul and Shoveller, Jean} } @article {bingham_design_2014, title = {Design of Computer Experiments for Optimization, Estimation of Function Contours, and Related Objectives}, journal = {Statistics in Action: A Canadian Outlook}, volume = {109}, year = {2014}, url = {http://books.google.com/books?hl=en\&lr=\&id=0GbvAgAAQBAJ\&oi=fnd\&pg=PA109\&dq=info:6iJ547N97RwJ:scholar.google.com\&ots=ZsI6ZcqMhr\&sig=xk0x1HgmPBsC7dJovZQoMtlGCJQ}, author = {Bingham, Derek and Ranjan, Pritam and Welch, William J.} } @article {zhao_detection_2014, title = {Detection of unusual increases in MRI lesion counts in individual multiple sclerosis patients}, journal = {Journal of the American Statistical Association}, volume = {109}, number = {505}, year = {2014}, pages = {119{\textendash}132}, doi = {10.1080/01621459.2013.847373}, url = {http://amstat.tandfonline.com/doi/abs/10.1080/01621459.2013.847373}, author = {Zhao, Y and Li, DKB and Petkau, A.John and Riddehough, A and Traboulsee, A} } @article {Sighoko2014, title = {Discordance in hormone receptor status among primary, metastatic, and second primary breast cancers: biological difference or misclassification?}, journal = {The oncologist}, volume = {19}, number = {6}, year = {2014}, pages = {592{\textendash}601}, publisher = {AlphaMed Press}, doi = {10.1634/theoncologist.2013-0427}, author = {Sighoko, Dominique and Liu, Juxin and Hou, Ningqi and Gustafson, Paul and Huo, Dezheng} } @article {Lindsten2014DivideandConquer, title = {Divide-and-Conquer with Sequential Monte Carlo}, journal = {arXiv}, volume = {1406.4993}, year = {2014}, author = {Fredrik Lindsten and ~Adam M. Johansen and ~Christian A. Naesseth and ~Bonnie Kirkpatrick and ~Thomas B. Schon and ~John Aston and Alexandre Bouchard-C{\^o}t{\'e}} } @article {Lindsten2014DivideandConquer, title = {Divide-and-Conquer with Sequential Monte Carlo}, journal = {arXiv}, volume = {1406.4993}, year = {2014}, author = {Fredrik Lindsten and Adam M. Johansen and Christian A. Naesseth and Bonnie Kirkpatrick and Thomas B. Schon and John Aston and Alexandre Bouchard-C{\^o}t{\'e}} } @article { ISI:000345588000005, title = {The effect of aggregation on extremes from asymptotically independent light-tailed risks}, journal = {EXTREMES}, volume = {17}, number = {4}, year = {2014}, month = {DEC}, pages = {615-631}, publisher = {SPRINGER}, type = {Article}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {Portfolio risk diversification is a well established concept in finance. While aggregation of several risky assets generally reduces the overall investment risk due to diversification, the effectiveness of diversification depends on the stochastic behaviour of the returns of the assets comprising the portfolio. The paper proposes a new approach to quantifying the effect of portfolio tail diversification by looking at the asymptotic behaviour of the ratio of the largest loss on the portfolio to the sum of the largest losses on the individual investments held on the stand-alone basis. It is assumed that independent and identically distributed random vectors from the underlying distribution, describing the behaviour of returns on the assets in the portfolio, can be scaled to converge onto a deterministic limit set. This property is satisfied by a number of distributions commonly used in finance. Several analytical examples are given to illustrate the proposed asymptotic diversification index as a measure of the effect of risk aggregation on extremes as well as to quantify the impact of dimension on the diversification and as a tool in optimal portfolio selection.}, keywords = {Asymptotic independence, Light-tailed distributions, Limit set, Risk diversification, Tail risk, Weak tail dependence coefficient}, issn = {1386-1999}, doi = {10.1007/s10687-014-0192-y}, author = {Nolde, Natalia} } @article {pmid25587344, title = {The effect of massage therapy on autonomic activity in critically ill children}, journal = {Evid Based Complement Alternat Med}, volume = {2014}, year = {2014}, pages = {656750}, author = {Guan, L. and Collet, J. P. and Yuskiv, N. and Skippen, P. and Brant, R. and Kissoon, N.} } @conference {Hajiaghayi2014Efficient, title = {Efficient continuous-time Markov chain estimation}, booktitle = {International Conference on Machine Learning (ICML)}, volume = {31}, year = {2014}, pages = {638{\textendash}646}, author = {Monir Hajiaghayi and Bonnie Kirkpatrick and Liangliang Wang and Alexandre Bouchard-C{\^o}t{\'e}} } @article {Shahriari2014Entropy, title = {An Entropy Search Portfolio for Bayesian Optimization}, journal = {arXiv}, volume = {1406.4625}, year = {2014}, author = {Bobak Shahriari and Ziyu Wang and Matthew W. Hoffman and Alexandre Bouchard-C{\^o}t{\'e} and Nando de Freitas} } @article {Shahriari2014Entropy, title = {An Entropy Search Portfolio for Bayesian Optimization}, journal = {arXiv}, volume = {1406.4625}, year = {2014}, author = {Bobak Shahriari and ~Ziyu Wang and ~Matthew W. Hoffman and ~Alexandre Bouchard-C{\^o}t{\'e} and ~Nando de Freitas} } @article { ISI:000343094000002, title = {Genetic Studies of Major Depressive Disorder: Why Are There No Genome-wide Association Study Findings and What Can We Do About It?}, journal = {BIOLOGICAL PSYCHIATRY}, volume = {76}, number = {7}, year = {2014}, month = {OCT 1}, pages = {510-512}, publisher = {ELSEVIER SCIENCE INC}, type = {Editorial Material}, address = {360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA}, issn = {0006-3223}, doi = {10.1016/j.biopsych.2014.07.029}, author = {Levinson, Douglas F. and Mostafavi, Sara and Milaneschi, Yuri and Rivera, Margarita and Ripke, Stephan and Wray, Naomi R. and Sullivan, Patrick F.} } @article { ISI:000327908200006, title = {Geometric interpretation of the residual dependence coefficient}, journal = {JOURNAL OF MULTIVARIATE ANALYSIS}, volume = {123}, year = {2014}, month = {JAN}, pages = {85-95}, publisher = {ELSEVIER INC}, type = {Article}, address = {525 B STREET, STE 1900, SAN DIEGO, CA 92101-4495 USA}, abstract = {The residual dependence coefficient was originally introduced by Ledford and Tawn (1996) [25] as a measure of residual dependence between extreme values in the presence of asymptotic independence. We present a geometric interpretation of this coefficient with the additional assumptions that the random samples from a given distribution can be scaled to converge onto a limit set and that the marginal distributions have Weibull-type tails. This result leads to simple and intuitive computations of the residual dependence coefficient for a variety of distributions. (C) 2013 Elsevier Inc. All rights reserved.}, keywords = {Asymptotic independence, Geometric approach, Limit set, Multivariate density, Residual dependence coefficient, Sample clouds}, issn = {0047-259X}, doi = {10.1016/j.jmva.2013.08.018}, author = {Nolde, Natalia} } @article {pmid24603545, title = {Hierarchical maturation of innate immune defences in very preterm neonates}, journal = {Neonatology}, volume = {106}, number = {1}, year = {2014}, pages = {1{\textendash}9}, author = {Sharma, A. A. and Jen, R. and Brant, R. and Ladd, M. and Huang, Q. and Skoll, A. and Senger, C. and Turvey, S. E. and Marr, N. and Lavoie, P. M.} } @article {Wang2014, title = {On the Impact of Misclassification in an Ordinal Exposure Variable}, journal = {Epidemiologic Methods}, volume = {3}, number = {1}, year = {2014}, pages = {97{\textendash}106}, doi = {10.1515/em-2013-0017}, author = {Wang, Dongxu and Gustafson, Paul} } @article {pmid24534406, title = {Invasive procedures in preterm children: brain and cognitive development at school age}, journal = {Pediatrics}, volume = {133}, number = {3}, year = {2014}, month = {Mar}, pages = {412{\textendash}421}, author = {Vinall, J. and Miller, S. P. and Bjornson, B. H. and Fitzpatrick, K. P. and Poskitt, K. J. and Brant, R. and Synnes, A. R. and Cepeda, I. L. and Grunau, R. E.} } @article {shirani_investigation_2014, title = {Investigation of heterogeneity in the association between interferon beta and disability progression in multiple sclerosis: an observational study}, journal = {European Journal of Neurology}, volume = {21}, number = {6}, year = {2014}, pages = {835{\textendash}844}, abstract = {

Background and purpose It was recently reported that there was no significant overall association between interferon beta exposure and disability progression in relapsing-remitting multiple sclerosis (RRMS) patients in an observational study from Canada. In the current study, the potential for heterogeneity in the association between exposure to interferon beta and disability progression across patients{\textquoteright} baseline characteristics was investigated. Methods RRMS patients treated with interferon beta (n\ =\ 868) and two cohorts of untreated patients (829 contemporary and 959 historical controls) were included. The main outcome was time from interferon beta treatment eligibility (baseline) to a confirmed and sustained Expanded Disability Status Scale (EDSS) score 6 using a multivariable Cox model, with treatment as a time-varying predictor, testing interaction effects for five pre-specified baseline characteristics: sex, age, disease duration, EDSS and annualized relapse rate (ARR) based on the previous 2\ years. Results Significant heterogeneity was found in the association of interferon beta exposure and disability progression only across ARR, and only when treated patients were compared with historical controls (P\ =\ 0.005 at a Bonferroni-adjusted alpha of 0.01). For patients with ARR\>1, treatment-exposed time was associated with a hazard ratio of 0.38 (95\%CI 0.20{\textendash}0.75) for disability progression compared with the unexposed time. Conclusions RRMS patients with more frequent relapses at baseline may be more likely to benefit from interferon beta treatment with respect to long-term disability progression.

}, keywords = {British Columbia, disability progression, interferon beta, multiple sclerosis, observational studies}, doi = {10.1111/ene.12324}, url = {http://onlinelibrary.wiley.com/doi/10.1111/ene.12324/abstract}, author = {Shirani, A and Zhao, Y and Karim, ME and Petkau, J and Gustafson, P and Evans, C and Kingwell, E and van der Kop, ML and Oger, J and Tremlett, H} } @article {Shirani2014, title = {Investigation of heterogeneity in the association between interferon beta and disability progression in multiple sclerosis: an observational study}, journal = {European Journal of Neurology}, volume = {21}, number = {6}, year = {2014}, pages = {835{\textendash}844}, publisher = {Wiley Online Library}, doi = {10.1111/ene.12324}, author = {Shirani, A and Zhao, Y and Karim, ME and Petkau, J and Gustafson, P and Evans, C and Kingwell, E and Kop, ML and Oger, J and Tremlett, H} } @article {zhang2014least, title = {Least angle regression for model selection}, journal = {Wiley Interdisciplinary Reviews: Computational Statistics}, volume = {6}, number = {2}, year = {2014}, pages = {116{\textendash}123}, publisher = {Wiley Online Library}, author = {Zhang, Hongyang and Zamar, Ruben H} } @article {HomrighausenMcDonald2014, title = {Leave-one-out cross-validation is risk consistent for lasso}, journal = {Machine Learning}, volume = {97}, number = {1{\textendash}2}, year = {2014}, pages = {65{\textendash}78}, url = {http://dx.doi.org/10.1007/s10994-014-5438-z}, author = {Homrighausen, Darren and McDonald, Daniel J.} } @article {liu2014level, title = {Level-specific correction for nonparametric likelihoods}, journal = {Journal of Nonparametric Statistics}, volume = {26}, number = {3}, year = {2014}, pages = {433{\textendash}449}, publisher = {Taylor \& Francis}, author = {Liu, Yukun and Chen, Jiahua and Li, Ting} } @article {li2014likelihood, title = {Likelihood Ratio Test for Multi-Sample Mixture Model and its Application to Genetic Imprinting}, journal = {Journal of the American Statistical Association}, number = {just-accepted}, year = {2014}, pages = {00{\textendash}00}, publisher = {Taylor \& Francis}, author = {Li, Shaoting and Chen, Jiahua and Guo, Jianhua and Jing, Bing-Yi and Tsang, Shui-Ying and Xue, Hong} } @article {karim2014marginal, title = {Marginal Structural Cox Models for Estimating the Association Between β-Interferon Exposure and Disease Progression in a Multiple Sclerosis Cohort}, journal = {American journal of epidemiology}, volume = {180}, number = {2}, year = {2014}, pages = {160{\textendash}171}, publisher = {Oxford University Press}, doi = {10.1093/aje/kwu125}, author = {Karim, Mohammad Ehsanul and Gustafson, Paul and Petkau, John and Zhao, Yinshan and Shirani, Afsaneh and Kingwell, Elaine and Evans, Charity and van der Kop, Mia and Oger, Joel and Tremlett, Helen} } @article { ISI:000339808700005, title = {Marginal structural Cox models for estimating the association between beta-interferon exposure and disease progression in a multiple sclerosis cohort}, journal = {American Journal of Epidemiology}, volume = {180}, number = {2}, year = {2014}, pages = {160-171}, publisher = {OXFORD UNIV PRESS INC}, address = {JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA}, abstract = {

Longitudinal observational data are required to assess the association between exposure to beta-interferon medications and disease progression among relapsing-remitting multiple sclerosis (MS) patients in the {\textquoteleft}{\textquoteleft}real-world{\textquoteright}{\textquoteright} clinical practice setting. Marginal structural Cox models (MSCMs) can provide distinct advantages over traditional approaches by allowing adjustment for time-varying confounders such as MS relapses, as well as baseline characteristics, through the use of inverse probability weighting. We assessed the suitability of MSCMs to analyze data from a large cohort of 1,697 relapsing-remitting MS patients in British Columbia, Canada (1995-2008). In the context of this observational study, which spanned more than a decade and involved patients with a chronic yet fluctuating disease, the recently proposed {\textquoteleft}{\textquoteleft}normalized stabilized{\textquoteright}{\textquoteright} weights were found to be the most appropriate choice of weights. Using this model, no association between beta-interferon exposure and the hazard of disability progression was found (hazard ratio = 1.36, 95\% confidence interval: 0.95, 1.94). For sensitivity analyses, truncated normalized unstabilized weights were used in additional MSCMs and to construct inverse probability weight-adjusted survival curves; the findings did not change. Additionally, qualitatively similar conclusions from approximation approaches to the weighted Cox model (i.e., MSCM) extend confidence in the findings.

}, keywords = {bias (epidemiology), causality, confounding factors (epidemiology), epidemiologic methods, inverse probability weighting, marginal structural Cox model, multiple sclerosis, survival analysis}, doi = {10.1093/aje/kwu125}, author = {Karim, ME and Gustafson, P and Petkau, J and Zhao, Y and Shirani, A and Kingwell, E and Evans, C and van der Kop, M and Oger, J and Tremlett, H} } @article {pmid25240708, title = {Maternal frustration, emotional and behavioural responses to prolonged infant crying}, journal = {Infant Behav Dev}, volume = {37}, number = {4}, year = {2014}, month = {Nov}, pages = {652{\textendash}664}, author = {Barr, R. G. and Fairbrother, N. and Pauwels, J. and Green, J. and Chen, M. and Brant, R.} } @conference {Jun2014Memory, title = {Memory (and time) efficient sequential Monte Carlo}, booktitle = {International Conference on Machine Learning (ICML)}, volume = {31}, year = {2014}, pages = {514{\textendash}522}, author = {Seong-Hwan Jun and Alexandre Bouchard-C{\^o}t{\'e}} } @inbook {Gustafson2014, title = {Misclassification}, booktitle = {Handbook of Epidemiology}, year = {2014}, pages = {639{\textendash}658}, publisher = {Springer}, organization = {Springer}, doi = {10.1007/978-0-387-09834-0_58}, author = {Gustafson, Paul and Greenland, Sander} } @article { ISI:000342542300004, title = {Model comparison with composite likelihood information criteria}, journal = {Bernoulli}, volume = {20}, number = {4}, year = {2014}, month = {NOV}, pages = {1738-1764}, publisher = {Int Statistical Inst}, type = {Article}, abstract = {Comparisons are made for the amount of agreement of the composite likelihood information criteria and their full likelihood counterparts when making decisions among the fits of different models; and some properties of penalty term for composite likelihood information criteria are obtained. Asymptotic theory is given for the case when a simpler model is nested within a bigger model, and the bigger model approaches the simpler model under a sequence of local alternatives. Composite likelihood can more or less frequently choose the bigger model, depending on the direction of local alternatives; in the former case, composite likelihood has more {\textquoteleft}{\textquoteleft}power{\textquoteright}{\textquoteright} to choose the bigger model. The behaviors of the information criteria are illustrated via theory and simulation examples of the Gaussian linear mixed-effects model.}, keywords = {Akaike information criterion, Bayesian information criterion, local alternatives, mixed-effects model, Model comparison}, issn = {1350-7265}, doi = {10.3150/13-BEJ539}, author = {Ng, C. T. and Joe, Harry} } @article { ISI:000332125300001, title = {Modeling regional impacts of climate teleconnections using functional data analysis}, journal = {ENVIRONMENTAL AND ECOLOGICAL STATISTICS}, volume = {21}, number = {1}, year = {2014}, month = {MAR}, pages = {1-26}, publisher = {SPRINGER}, type = {Article}, address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS}, abstract = {Teleconnections are quasi-periodic changes in atmospheric circulation that oscillate over long periods of time and impact climate over large regions. These patterns are often linked to long-term variations in climate and extreme weather events and may explain regional differences in climate vulnerability. We apply methods of functional data analysis to examine regional impacts of teleconnections on climate in British Columbia, Canada, between 1951 and 2000. We focus on monthly mean temperature as an overall determinant of crop growth and apply functional principal components analysis (FPCA) to study variations in the impacts of four major teleconnection indices affecting the Northern Hemisphere (the Southern Oscillation Index, the Pacific North American (PNA), Pacific Decadal Oscillation, and the North American Oscillation indices). Two challenges we consider are that the impacts of teleconnections cannot be observed directly and that fine scale data required to study regional variations may come from different sources with highly varied records. We first fit thin-plate regression splines to the raw data to construct complete series of pseudo-data at fixed grid points. Regression models incorporating Bayesian P-splines were then fit to the pseudo-data to estimate the impacts of the four teleconnections over time. Finally, FPCA was then applied to study regional variations in these effects. Our analysis identified strong variations in mean temperature associated with the PNA. The resulting spatial patterns also reveal areas of increased/decreased temperature variability that may have higher climate risk or be suitable for expansion of agricultural activity.}, keywords = {Agriculture, Climate variability, Functional data analysis, Functional principal components analysis, Teleconnections}, issn = {1352-8505}, doi = {10.1007/s10651-013-0241-8}, author = {Bonner, Simon J. and Newlands, Nathaniel K. and Heckman, Nancy E.} } @article {1621, title = {The Number of Relatively Prime Subsets of a Finite Union of Sets of Consecutive Integers}, journal = {Journal of Integer Sequences}, volume = {17}, year = {2014}, pages = {3}, author = {Ayad, Mohamed and Coia, Vincenzo and Kihel, Omar} } @article {3363, title = {Occupational exposure and ovarian cancer risk. Cancer causes Control}, journal = {Cancer causes Control}, volume = {7}, year = {2014}, pages = {829-841}, author = {Le, N. and Leung, A. and Brooks-Wilson, A. and Cook, L. and Swenerton, K., and Demers, P. and Gallagher, R} } @conference {9271, title = {On-line homework in probability and statistics: WeBWorK incorporating R.}, booktitle = {9th International Conference on Teaching Statistics}, year = {2014}, author = {Davor Cubranic and Bruce Dunham and Djun Kim} } @article { ISI:000337869500017, title = {Parsimonious parameterization of correlation matrices using truncated vines and factor analysis}, journal = {Computational Statistics \& Data Analysis}, volume = {77}, year = {2014}, month = {SEP}, pages = {233-251}, publisher = {Elsevier Science BV}, type = {Article}, abstract = {Both in classical multivariate analysis and in modern copula modeling, correlation matrices are a central concept of dependence modeling using multivariate normal distributions and copulas. Since the number of correlation parameters quadratically increases with the number of variables, parsimonious parameterizations of large correlation matrices in terms of O(d) parameters are important. While factor analysis is commonly used for this purpose, the use of vines is an attractive alternative: vines are graphical models based on a sequence of trees, and are based on the decomposition of a correlation matrix in terms of algebraically independent correlations and partial correlations. By limiting the number of trees, with the so-called truncation, parsimonious parameterizations of correlation matrices may be found. Moreover, truncated vines and factor models may be joined to define a combined model, with individual benefits from each of the two approaches. The different parameterizations and how they are estimated for data are discussed. In particular, spanning tree algorithms for truncated vines and a modified EM algorithm for the combined factor-vine model are proposed and evaluated in a simulation study. Three applications to psychometric and finance data sets illustrate the different parsimonious models. (C) 2014 Elsevier B.V. All rights reserved.}, keywords = {EM algorithm, Markov trees, Multivariate normal, Partial correlations, Regular vines}, issn = {0167-9473}, doi = {10.1016/j.csda.2014.03.002}, author = {Brechmann, Eike C. and Joe, Harry} } @article { ISI:000335157700044, title = {Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes}, journal = {SCIENCE}, volume = {344}, number = {6183}, year = {2014}, month = {MAY 2}, pages = {519-523}, publisher = {AMER ASSOC ADVANCEMENT SCIENCE}, type = {Article}, address = {1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA}, abstract = {To extend our understanding of the genetic basis of human immune function and dysfunction, we performed an expression quantitative trait locus (eQTL) study of purified CD4(+) T cells and monocytes, representing adaptive and innate immunity, in a multi-ethnic cohort of 461 healthy individuals. Context-specific cis- and trans-eQTLs were identified, and cross-population mapping allowed, in some cases, putative functional assignment of candidate causal regulatory variants for disease-associated loci. We note an over-representation of T cell-specific eQTLs among susceptibility alleles for autoimmune diseases and of monocyte-specific eQTLs among Alzheimer{\textquoteright}s and Parkinson{\textquoteright}s disease variants. This polarization implicates specific immune cell types in these diseases and points to the need to identify the cell-autonomous effects of disease susceptibility variants.}, issn = {0036-8075}, doi = {10.1126/science.1249547}, author = {Raj, Towfique and Rothamel, Katie and Mostafavi, Sara and Ye, Chun and Lee, Mark N. and Replogle, Joseph M. and Feng, Ting and Lee, Michelle and Asinovski, Natasha and Frohlich, Irene and Imboywa, Selina and Von Korff, Alina and Okada, Yukinori and Patsopoulos, Nikolaos A. and Davis, Scott and McCabe, Cristin and Paik, Hyun-il and Srivastava, Gyan P. and Raychaudhuri, Soumya and Hafler, David A. and Koller, Daphne and Regev, Aviv and Hacohen, Nir and Mathis, Diane and Benoist, Christophe and Stranger, Barbara E. and De Jager, Philip L.} } @inbook {9742, title = {Practical Suggestions for Developing as an Academic Leader}, booktitle = {Leadership and Women in Statistics}, year = {2014}, publisher = {Chapman and Hall}, organization = {Chapman and Hall}, author = {Dean, C.B. and Heckman, N. and Reid, N} } @article {Falasinnu2014, title = {Predictors identifying those at increased risk for STDs: a theory-guided review of empirical literature and clinical guidelines}, journal = {International journal of STD \& AIDS}, year = {2014}, pages = {0956462414555930}, publisher = {SAGE Publications}, doi = {10.1177/0956462414555930}, author = {Falasinnu, Titilola and Gilbert, Mark and Salway, Travis Hottes and Gustafson, Paul and Ogilvie, Gina and Shoveller, Jean} } @article { ISI:000348651700004, title = {Prinsimp}, journal = {R JOURNAL}, volume = {6}, number = {2}, year = {2014}, month = {DEC}, pages = {27-42}, publisher = {R FOUNDATION STATISTICAL COMPUTING}, type = {Article}, address = {WIRTSCHAFTSUNIVERSITAT, INST STATISTICS \& MATHEMATICS, AUGASSE 2-6, WIEN, 1090, AUSTRIA}, abstract = {Principal Components Analysis (PCA) is a common way to study the sources of variation in a high-dimensional data set. Typically, the leading principal components are used to understand the variation in the data or to reduce the dimension of the data for subsequent analysis. The remaining principal components are ignored since they explain little of the variation in the data. However, the space spanned by the low variation principal components may contain interesting structure, structure that PCA cannot find. Prinsimp is an R package that looks for interesting structure of low variability. {\textquoteleft}{\textquoteleft}Interesting{\textquoteright}{\textquoteright} is defined in terms of a simplicity measure. Looking for interpretable structure in a low variability space has particular importance in evolutionary biology, where such structure can signify the existence of a genetic constraint.}, issn = {2073-4859}, author = {Zhang, Jonathan and Heckman, Nancy and Cubranic, Davor and Kingsolver, Joel G. and Gaydos, Travis and Marron, J. S.} } @article {1528, title = {Prinsimp}, journal = {The R Journal}, volume = {6}, year = {2014}, month = {12/2014}, pages = {27{\textendash}42}, url = {http://journal.r-project.org/archive/2014-2/zhang-etal.pdf}, author = {Jonathan Zhang and Nancy Heckman and Davor Cubranic and Joel G. Kingsolver and Travis Gaydos and J. S. Marron} } @article {hollander2014proteomic, title = {Proteomic biomarkers of recovered heart function}, journal = {European journal of heart failure}, volume = {16}, number = {5}, year = {2014}, pages = {551{\textendash}559}, publisher = {Wiley Online Library}, author = {Hollander, Zsuzsanna and Laz{\'a}rov{\'a}, Marie and Lam, Karen KY and Ignaszewski, Andrew and Oudit, Gavin Y and Dyck, Jason RB and Schreiner, George and Pauwels, Julie and Chen, Virginia and Cohen Freue, Gabriela V and others} } @article {Roth2014PyClone, title = {PyClone: statistical inference of clonal population structure in cancer}, journal = {Nature Methods}, volume = {11}, year = {2014}, pages = {396{\textendash}398}, author = {A Roth and J. Khattra and D. Yap and A. Wan and E. Laks and J. Biele and G. Ha and S. Aparicio and A. Bouchard-C{\^o}t{\'e} and S. Shah} } @article {zidek2014reducing, title = {Reducing estimation bias in adaptively changing monitoring networks with preferential site selection}, journal = {The Annals of Applied Statistics}, volume = {8}, number = {3}, year = {2014}, pages = {1640{\textendash}1670}, publisher = {Institute of Mathematical Statistics}, author = {Zidek, James V and Shaddick, Gavin and Taylor, Carolyn G} } @article {zidek2014reducing, title = {Reducing estimation bias in adaptively changing monitoring networks with preferential site selection}, journal = {The Annals of Applied Statistics}, volume = {8}, year = {2014}, pages = {1640{\textendash}1670}, publisher = {Institute of Mathematical Statistics}, author = {Zidek, James V and Shaddick, Gavin and Taylor, Carolyn G and others} } @article { ISI:000334819300003, title = {Relations between hidden regular variation and the tail order of copulas}, journal = {Journal of Applied Probability}, volume = {51}, number = {1}, year = {2014}, month = {MAR}, pages = {37-57}, publisher = {Applied Probability Trust}, type = {Article}, abstract = {We study the relations between the tail order of copulas and hidden regular variation (HRV) on subcones generated by order statistics. Multivariate regular variation (MRV) and HRV deal with extremal dependence of random vectors with Pareto-like univariate margins. Alternatively, if one uses a copula to model the dependence structure of a random vector then the upper exponent and tail order functions can be used to capture the extremal dependence structure. After defining upper exponent functions on a series of subcones, we establish the relation between the tail order of a copula and the tail indexes for MRV and HRV. We show that upper exponent functions of a copula and intensity measures of MRV/HRV can be represented by each other, and the upper exponent function on subcones can be expressed by a Pickands-type integral representation. Finally, a mixture model is given with the mixing random vector leading to the finite-directional measure in a product-measure representation of HRV intensity measures.}, keywords = {intermediate tail dependence, Multivariate regular variation, Tail dependence, tail order function, upper exponent function}, issn = {0021-9002}, doi = {10.1017/S0021900200010068}, author = {Hua, Lei and Joe, Harry and Li, Haijun} } @conference {reich2014sample, title = {Sample-size calculations for short-term proof-of-concept studies of tissue protection and repair in MS lesions via conventional clinical imaging}, booktitle = {MULTIPLE SCLEROSIS JOURNAL}, volume = {20}, year = {2014}, pages = {284{\textendash}284}, publisher = {SAGE PUBLICATIONS LTD 1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND}, organization = {SAGE PUBLICATIONS LTD 1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND}, author = {Reich, DS and White, R and Cortese, ICM and Vuolo, L and Shea, CD and Collins, TL and Petkau, AJ} } @inbook {Bouchard2014Sequential, title = {Sequential Monte Carlo (SMC) for Bayesian phylogenetics}, booktitle = {Bayesian phylogenetics: methods, algorithms, and applications}, year = {2014}, pages = {163{\textendash}186}, author = {Alexandre Bouchard-C{\^o}t{\'e}}, editor = {Chen, M.-H. and Kuo, L. and Lewis, P. O. (eds.)} } @article {1620, title = {A Sieve model for extreme values}, journal = {Journal of Statistical Computation and Simulation}, volume = {84}, year = {2014}, pages = {1692{\textendash}1710}, author = {Coia, Vincenzo and Huang, Mei Ling} } @article {xu2014sparse, title = {The Sparse MLE for Ultrahigh-Dimensional Feature Screening}, journal = {Journal of the American Statistical Association}, volume = {109}, number = {507}, year = {2014}, pages = {1257{\textendash}1269}, publisher = {Taylor \& Francis}, author = {Xu, Chen and Chen, Jiahua} } @article {cai2014statistical, title = {Statistical modeling and forecasting of fruit crop phenology under climate change}, journal = {Environmetrics}, volume = {25}, number = {8}, year = {2014}, pages = {621{\textendash}629}, publisher = {Wiley Online Library}, author = {Cai, S and Zidek, James V and Newlands, Nathaniel K and Neilsen, Denise} } @article { ISI:000337852600001, title = {Stochastic analysis of life insurance surplus}, journal = {INSURANCE MATHEMATICS \& ECONOMICS}, volume = {56}, year = {2014}, month = {MAY}, pages = {1-13}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {The aim of the paper is to examine the behavior of insurance surplus over time for a portfolio of homogeneous life policies. We distinguish between stochastic and accounting surpluses and derive their first two moments. A recursive formula is proposed for calculating the distribution function of the accounting surplus. We then examine the probability that the accounting surplus becomes negative in a given insurance year. Numerical examples illustrate the results for portfolios of temporary and endowment life policies assuming a conditional AR(1) process for the rates of return. (C) 2014 Elsevier B.V. All rights reserved.}, keywords = {AR(1) process, Distribution function, Insurance surplus, Stochastic rates of return}, issn = {0167-6687}, doi = {10.1016/j.insmatheco.2014.02.006}, author = {Nolde, Natalia and Parker, Gary} } @article { ISI:000327908200010, title = {Strength of tail dependence based on conditional tail expectation}, journal = {Journal of Multivariate Analysis}, volume = {123}, year = {2014}, month = {JAN}, pages = {143-159}, publisher = {Elsevier Inc}, type = {Article}, abstract = {We use the conditional distribution and conditional expectation of one random variable given the other one being large to capture the strength of dependence in the tails of a bivariate random vector. We study the tail behavior of the boundary conditional cumulative distribution function (cdf) and two forms of conditional tail expectation (CTE) for various bivariate copula families. In general, for nonnegative dependence, there are three levels of strength of dependence in the tails according to the tail behavior of CTEs: asymptotically linear, sub-linear and constant. For each of these three levels, we investigate the tail behavior of CTEs for the marginal distributions belonging to maximum domain of attraction of Frechet and Gumbel, respectively, and for copula families with different tail behavior. (C) 2013 Elsevier Inc. All rights reserved.}, keywords = {Boundary conditional distribution, Copula, intermediate tail dependence, Maximum domain of attraction, Stochastic increasing, Tail behavior, Tail order, Tail quadrant independence}, issn = {0047-259X}, doi = {10.1016/j.jmva.2013.09.001}, author = {Hua, Lei and Joe, Harry} } @article { ISI:000343808700001, title = {Switching nonparametric regression models}, journal = {JOURNAL OF NONPARAMETRIC STATISTICS}, volume = {26}, number = {4}, year = {2014}, month = {OCT 2}, pages = {617-637}, publisher = {TAYLOR \& FRANCIS LTD}, type = {Article}, address = {4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND}, abstract = {We propose a methodology to analyse data arising from a curve that, over its domain, switches among J states. We consider a sequence of response variables, where each response y depends on a covariate x according to an unobserved state z. The states form a stochastic process and their possible values are j=1, horizontal ellipsis , J. If z equals j the expected response of y is one of J unknown smooth functions evaluated at x. We call this model a switching nonparametric regression model. We develop an Expectation-Maximisation algorithm to estimate the parameters of the latent state process and the functions corresponding to the J states. We also obtain standard errors for the parameter estimates of the state process. We conduct simulation studies to analyse the frequentist properties of our estimates. We also apply the proposed methodology to the well-known motorcycle dataset treating the data as coming from more than one simulated accident run with unobserved run labels.}, keywords = {EM algorithm, latent variables, machine learning, mixture of Gaussian processes, motorcycle data, nonparametric regression}, issn = {1048-5252}, doi = {10.1080/10485252.2014.941364}, author = {de Souza, Camila P. E. and Heckman, Nancy E.} } @article {mostafavi2014type, title = {Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing}, journal = {Molecular psychiatry}, volume = {19}, number = {12}, year = {2014}, pages = {1267{\textendash}1274}, publisher = {Nature Publishing Group}, author = {Mostafavi, S and Battle, A and Zhu, X and Potash, JB and Weissman, MM and Shi, J and Beckman, K and Haudenschild, C and McCormick, C and Mei, R and others} } @article { ISI:000344079500023, title = {Variation and Genetic Control of Gene Expression in Primary Immunocytes across Inbred Mouse Strains}, journal = {JOURNAL OF IMMUNOLOGY}, volume = {193}, number = {9}, year = {2014}, month = {NOV 1}, pages = {4485-4496}, publisher = {AMER ASSOC IMMUNOLOGISTS}, type = {Article}, address = {9650 ROCKVILLE PIKE, BETHESDA, MD 20814 USA}, abstract = {To determine the breadth and underpinning of changes in immunocyte gene expression due to genetic variation in mice, we performed, as part of the Immunological Genome Project, gene expression profiling for CD4(+) T cells and neutrophils purified from 39 inbred strains of the Mouse Phenome Database. Considering both cell types, a large number of transcripts showed significant variation across the inbred strains, with 22\% of the transcriptome varying by 2-fold or more. These included 119 loci with apparent complete loss of function, where the corresponding transcript was not expressed in some of the strains, representing a useful resource of {\textquoteleft}{\textquoteleft}natural knockouts.{\textquoteright}{\textquoteright} We identified 1222 cis-expression quantitative trait loci (cis-eQTL) that control some of this variation. Most (60\%) cis-eQTLs were shared between T cells and neutrophils, but a significant portion uniquely impacted one of the cell types, suggesting cell type-specific regulatory mechanisms. Using a conditional regression algorithm, we predicted regulatory interactions between transcription factors and potential targets, and we demonstrated that these predictions overlap with regulatory interactions inferred from transcriptional changes during immunocyte differentiation. Finally, comparison of these and parallel data from CD4(+) T cells of healthy humans demonstrated intriguing similarities in variability of a gene{\textquoteright}s expression: the most variable genes tended to be the same in both species, and there was an overlap in genes subject to strong cis-acting genetic variants. We speculate that this {\textquoteleft}{\textquoteleft}conservation of variation{\textquoteright}{\textquoteright} reflects a differential constraint on intraspecies variation in expression levels of different genes, either through lower pressure for some genes, or by favoring variability for others.}, issn = {0022-1767}, doi = {10.4049/jimmunol.1401280}, author = {Mostafavi, Sara and Ortiz-Lopez, Adriana and Bogue, Molly A. and Hattori, Kimie and Pop, Cristina and Koller, Daphne and Mathis, Diane and Benoist, Christophe and Immunological Genome Consortium} } @article {ascherio2014vitamin, title = {Vitamin D as an early predictor of multiple sclerosis activity and progression}, journal = {JAMA neurology}, volume = {71}, number = {3}, year = {2014}, pages = {306{\textendash}314}, publisher = {American Medical Association}, author = {Ascherio, Alberto and Munger, Kassandra L and White, Rick and K{\"o}chert, Karl and Simon, Kelly Claire and Polman, Chris H and Freedman, Mark S and Hartung, Hans-Peter and Miller, David H and Montalb{\'a}n, Xavier and others} } @article {ascherio2014vitamin, title = {Vitamin D As Predictor Of Multiple Sclerosis Activity And Progression In Patients With CIS Treated Early With Interferon beta-1b (P5. 016)}, journal = {Neurology}, volume = {82}, number = {10 Supplement}, year = {2014}, pages = {P5{\textendash}016}, publisher = {AAN Enterprises}, author = {Ascherio, Alberto and Munger, Kassandra and White, Rick and K{\"o}chert, Karl and Simon, Kelly Claire and Freedman, Mark and Hartung, Hans and Miller, David and Montalb{\'a}n, Xavier and Edan, Gilles and others} } @article {pmid25225279, title = {What matters most for patients, parents, and clinicians in the course of juvenile idiopathic arthritis? A qualitative study}, journal = {J. Rheumatol.}, volume = {41}, number = {11}, year = {2014}, month = {Nov}, pages = {2260{\textendash}2269}, author = {Guzman, J. and Gomez-Ramirez, O. and Jurencak, R. and Shiff, N. J. and Berard, R. A. and Duffy, C. M. and Oen, K. and Petty, R. E. and Benseler, S. M. and Brant, R. and Tucker, L. B.} } @article {pmid24444287, title = {What proportion of Canadian women will accept an intrauterine contraceptive at the time of second trimester abortion? Baseline data from a randomized controlled trial}, journal = {J Obstet Gynaecol Can}, volume = {36}, number = {1}, year = {2014}, month = {Jan}, pages = {51{\textendash}59}, author = {Norman, W. V. and Brooks, M. and Brant, R. and Soon, J. A. and Majdzadeh, A. and Kaczorowski, J.} } @article {pmid24212394, title = {Abnormal brain maturation in preterm neonates associated with adverse developmental outcomes}, journal = {Neurology}, volume = {81}, number = {24}, year = {2013}, month = {Dec}, pages = {2082{\textendash}2089}, author = {Chau, V. and Synnes, A. and Grunau, R. E. and Poskitt, K. J. and Brant, R. and Miller, S. P.} } @booklet {chen_analysis_2013, title = {Analysis Methods for Computer Experiments: How to Assess and What Counts?}, year = {2013}, publisher = {Tech. rep., University of British Columbia}, url = {http://www.stat.ubc.ca/ will/docs/whatcounts.pdf}, author = {Chen, Hao and Loeppky, J. and Sacks, Jerome and Welch, W.} } @article {Kepplinger2013754, title = {Analysis of energy intensity in manufacturing industry using mixed-effects models}, journal = {Energy}, volume = {59}, year = {2013}, pages = {754 - 763}, abstract = {

The paper makes a cross country analysis of the energy intensity in manufacturing sectors. Empirical data for this purpose is gathered from the databases of two international agencies namely the IEA\ (International Energy Agency) and the UNIDO\ (UN International Development Organization), which provide energy consumption and manufacturing output data respectively. The analyses are carried out with exploratory as well as formal statistical methods to identify the driving factors explaining energy intensity, identify trends and facilitate comparisons. The results from modeling the energy intensities with a linear mixed-effects model show\ some driving factors that explain the energy intensities. In general, the energy intensities of industrial sectors decreased around the world. In particular, industrialized countries with higher value of GDP\ (gross domestic product) per capita tend to have lower energy intensity indicating that efficiency in energy use is achieved along with the technological advancement. Countries with higher GDP\ and smaller population tend to have lower energy intensity values and a lower energy intensity index.

}, keywords = {Modeling}, issn = {0360-5442}, doi = {http://dx.doi.org/10.1016/j.energy.2013.07.003}, url = {http://www.sciencedirect.com/science/article/pii/S0360544213005768}, author = {D. Kepplinger and M. Templ and S. Upadhyaya} } @article {pmid23673247, title = {Anthropometric measures and the risk of endometrial cancer, overall and by tumor microsatellite status and histological subtype}, journal = {Am. J. Epidemiol.}, volume = {177}, number = {12}, year = {2013}, month = {Jun}, pages = {1378{\textendash}1387}, author = {Amankwah, E. K. and Friedenreich, C. M. and Magliocco, A. M. and Brant, R. and Courneya, K. S. and Speidel, T. and Rahman, W. and Langley, A. R. and Cook, L. S.} } @article {pmid23605145, title = {Association between sex hormones, glucose homeostasis, adipokines, and inflammatory markers and mammographic density among postmenopausal women}, journal = {Breast Cancer Res. Treat.}, volume = {139}, number = {1}, year = {2013}, month = {May}, pages = {255{\textendash}265}, author = {Woolcott, C. G. and Courneya, K. S. and Boyd, N. F. and Yaffe, M. J. and McTiernan, A. and Brant, R. and Jones, C. A. and Stanczyk, F. Z. and Terry, T. and Cook, L. S. and Wang, Q. and Friedenreich, C. M.} } @article {Bouchard2013Automated, title = {Automated reconstruction of ancient languages using probabilistic models of sound change}, journal = {Proceedings of the National Academy of Sciences}, volume = {110}, year = {2013}, pages = {4224{\textendash}4229}, author = {Alexandre Bouchard-C{\^o}t{\'e} and David Hall and Thomas L. Griffiths and Dan Klein} } @article {Gustafson2013b, title = {Bayesian Analysis of Frailty Models}, journal = {Handbook of Survival Analysis}, year = {2013}, pages = {475}, publisher = {CRC Press}, author = {Gustafson, Paul} } @article { ISI:000327432500062, title = {A Bayesian extreme value analysis of debris flows}, journal = {WATER RESOURCES RESEARCH}, volume = {49}, number = {10}, year = {2013}, month = {OCT}, pages = {7009-7022}, publisher = {AMER GEOPHYSICAL UNION}, type = {Article}, address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA}, abstract = {Debris flows carry a tremendous potential for physical destruction as well as a threat to human lives. Quantitative analysis of their frequency and magnitude relation is key to the development of mitigation measures to reduce hazard and risk. Yet, the data available for such analysis are typically very sparse, leading to point estimates for return levels that are too imprecise to be of practical value. The aim of the paper is to demonstrate how additional sources of information, in particular, expert judgment which uses physical causes and the size of the active area producing loose sediments, can be incorporated to produce more precise estimates with a smaller upper endpoint of interval estimates of extreme return levels. A Bayesian framework for extreme value analysis is used. We provide a rationale for the prior choice and discuss how its parameters can be elicited from the expert{\textquoteright}s knowledge. A case study of debris flows at Capricorn Creek in Western Canada is used to illustrate our methodology.}, keywords = {Bayesian statistics, debris flows, expert judgment, extreme value analysis, frequency-magnitude relation, informative prior}, issn = {0043-1397}, doi = {10.1002/wrcr.20494}, author = {Nolde, Natalia and Joe, Harry} } @article { ISI:000327432500062, title = {A Bayesian extreme value analysis of debris flows}, journal = {Water Resources Research}, volume = {49}, number = {10}, year = {2013}, month = {OCT}, pages = {7009-7022}, publisher = {Amer Geophysical Union}, type = {Article}, abstract = {Debris flows carry a tremendous potential for physical destruction as well as a threat to human lives. Quantitative analysis of their frequency and magnitude relation is key to the development of mitigation measures to reduce hazard and risk. Yet, the data available for such analysis are typically very sparse, leading to point estimates for return levels that are too imprecise to be of practical value. The aim of the paper is to demonstrate how additional sources of information, in particular, expert judgment which uses physical causes and the size of the active area producing loose sediments, can be incorporated to produce more precise estimates with a smaller upper endpoint of interval estimates of extreme return levels. A Bayesian framework for extreme value analysis is used. We provide a rationale for the prior choice and discuss how its parameters can be elicited from the expert{\textquoteright}s knowledge. A case study of debris flows at Capricorn Creek in Western Canada is used to illustrate our methodology.}, keywords = {Bayesian statistics, debris flows, expert judgment, extreme value analysis, frequency-magnitude relation, informative prior}, issn = {0043-1397}, doi = {10.1002/wrcr.20494}, author = {Nolde, Natalia and Joe, Harry} } @article {pmid23771484, title = {Brain injury and development in newborns with critical congenital heart disease}, journal = {Neurology}, volume = {81}, number = {3}, year = {2013}, month = {Jul}, pages = {241{\textendash}248}, author = {Dimitropoulos, A. and McQuillen, P. S. and Sethi, V. and Moosa, A. and Chau, V. and Xu, D. and Brant, R. and Azakie, A. and Campbell, A. and Barkovich, A. J. and Poskitt, K. J. and Miller, S. P.} } @article {1622, title = {A Cluster Truncated Pareto Distribution and Its Applications}, journal = {ISRN Probability and Statistics}, volume = {2013}, year = {2013}, author = {Huang, Mei Ling and Coia, Vincenzo and Brill, Percy} } @article {xing2013comparison, title = {A comparison of Bayesian hierarchical modeling with group-based exposure assessment in occupational epidemiology}, journal = {Statistics in medicine}, year = {2013}, publisher = {Wiley Online Library}, doi = {10.1002/sim.5791}, url = {http://onlinelibrary.wiley.com/doi/10.1002/sim.5791/abstract}, author = {Xing, Li and Burstyn, Igor and Richardson, David B and Gustafson, Paul} } @article {freue2013computational, title = {Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation}, journal = {PLoS Comput Biol}, volume = {9}, number = {4}, year = {2013}, pages = {e1002963}, publisher = {Public Library of Science}, author = {Freue, Gabriela V Cohen and Meredith, Anna and Smith, Derek and Bergman, Axel and Sasaki, Mayu and Lam, Karen KY and Hollander, Zsuzsanna and Opushneva, Nina and Takhar, Mandeep and Lin, David and others} } @conference {Campbell13_NIPS, title = {Dynamic clustering via asymptotics of the dependent Dirichlet process mixture}, booktitle = {Advances in Neural Information Processing Systems}, year = {2013}, author = {Trevor Campbell and Miao Liu and Brian Kulis and Jonathan P. How and Lawrence Carin} } @article {hsu_dynamic_2013, title = {Dynamic performance modelling and measuring for machine tools with continuous-state wear processes}, journal = {International Journal of Production Research}, volume = {51}, number = {15}, year = {2013}, pages = {4718{\textendash}4731}, abstract = {In this paper, we consider the problem of using empirical continuous-state wear data of machine tools to estimate the dynamic lifetime distribution and to measure the performance of a machining process subject to stochastic tool-wear evolution. Machining systems are dynamic processes whose performance variable is usually characterised by the amount of tool wear that advances gradually with a continuous range of values. To accurately capture the performance of these continuous-state wear processes, neither traditional models such as the binary-state models nor multi-state models are suitable. In this paper, an exponential mixed-effects (EME) model is first developed. The EME model is subsequently transformed into a linear mixed-effects (LME) model to enhance the fit and predictability of the wear process data. The LME models take into consideration the correlations among repeated wear measurements collected at different time points within each subject. We then implement the expectation-maximisation (EM) algorithm to obtain the full maximum likelihood estimates (MLEs) of the parameters of the LME models whose asymptotic normal distributions can be used to acquire approximate confidence intervals and a testing hypothesis for the parameters. In addition, to measure the dynamic performance of tools, the amount of wear over time estimated from LME models is compared with a given tool-failure threshold. Consequently, we obtain the reliability of the tool and the estimation of its residual-lifetime distribution, which is critical information for the tool replacement or maintenance strategy. Finally, the lower and upper wear prediction limits of the 95\% confidence level are presented. A practical application of the proposed methodology is illustrated throughout the paper.}, issn = {0020-7543}, doi = {10.1080/00207543.2013.793858}, url = {http://dx.doi.org/10.1080/00207543.2013.793858}, author = {Hsu, Bi-Min and Shu, Ming-Hung and WU, LANG} } @article {Hajiaghayi2013Efficient, title = {Efficient Continuous-Time Markov Chain Estimation}, journal = {arXiv}, volume = {1309.325}, year = {2013}, author = {Monir Hajiaghayi and Bonnie Kirkpatrick and Liangliang Wang and Alexandre Bouchard-C{\^o}t{\'e}} } @article {pmid23618911, title = {Evolution of pattern of injury and quantitative MRI on days 1 and 3 in term newborns with hypoxic-ischemic encephalopathy}, journal = {Pediatr. Res.}, volume = {74}, number = {1}, year = {2013}, month = {Jul}, pages = {82{\textendash}87}, author = {Gano, D. and Chau, V. and Poskitt, K. J. and Hill, A. and Roland, E. and Brant, R. and Chalmers, M. and Miller, S. P.} } @article {Bouchard2013Evolutionary, title = {Evolutionary inference via the Poisson indel process}, journal = {Proceedings of the National Academy of Sciences}, volume = {110}, year = {2013}, pages = {1160{\textendash}1166}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Michael I. Jordan} } @article {Krupskii.Joe2013, title = {Factor copula models for multivariate data}, journal = {Journal of Multivariate Analysis}, volume = {120}, year = {2013}, pages = {85{\textendash}101}, author = {Krupskii, Pavel and Joe, Harry} } @article { ISI:000322290500006, title = {Factor copula models for multivariate data}, journal = {Journal of Multivariate Analysis}, volume = {120}, year = {2013}, month = {SEP}, pages = {85-101}, publisher = {Elsevier Inc}, type = {Article}, abstract = {General conditional independence models ford observed variables, in terms of p latent variables, are presented in terms of bivariate copulas that link observed data to latent variables. The representation is called a factor copula model and the classical multivariate normal model with a correlation matrix having a factor structure is a special case. Dependence and tail properties of the model are obtained. The factor copula model can handle multivariate data with tail dependence and tail asymmetry, properties that the multivariate normal copula does not possess. It is a good choice for modeling high-dimensional data as a parametric form can be specified to have O(d) dependence parameters instead of O(d(2)) parameters. Data examples show that, based on the Akaike information criterion, the factor copula model provides a good fit to financial return data, in comparison with related truncated vine copula models. (C) 2013 Elsevier Inc. All rights reserved.}, keywords = {Conditional independence, Factor analysis, Pair-copula construction, Partial correlation, Tail asymmetry, Tail dependence, Truncated vine}, issn = {0047-259X}, doi = {10.1016/j.jmva.2013.05.001}, author = {Krupskii, Pavel and Joe, Harry} } @article {chen2013finite, title = {Finite-sample properties of the adjusted empirical likelihood}, journal = {Journal of Nonparametric Statistics}, volume = {25}, number = {1}, year = {2013}, pages = {147{\textendash}159}, publisher = {Taylor \& Francis}, author = {Chen, Jiahua and Huang, Yi} } @article { ISI:000319563900002, title = {The Genotype-Tissue Expression (GTEx) project}, journal = {NATURE GENETICS}, volume = {45}, number = {6}, year = {2013}, month = {JUN}, pages = {580-585}, publisher = {NATURE PUBLISHING GROUP}, type = {Editorial Material}, address = {75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA}, abstract = {Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not correlated with protein-coding changes, suggesting that polymorphisms in regulatory regions probably contribute to many disease phenotypes. Here we describe the Genotype-Tissue Expression (GTEx) project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.}, issn = {1061-4036}, doi = {10.1038/ng.2653}, author = {Lonsdale, John and Thomas, Jeffrey and Salvatore, Mike and Phillips, Rebecca and Lo, Edmund and Shad, Saboor and Hasz, Richard and Walters, Gary and Garcia, Fernando and Young, Nancy and Foster, Barbara and Moser, Mike and Karasik, Ellen and Gillard, Bryan and Ramsey, Kimberley and Sullivan, Susan and Bridge, Jason and Magazine, Harold and Syron, John and Fleming, Johnelle and Siminoff, Laura and Traino, Heather and Mosavel, Maghboeba and Barker, Laura and Jewell, Scott and Rohrer, Dan and Maxim, Dan and Filkins, Dana and Harbach, Philip and Cortadillo, Eddie and Berghuis, Bree and Turner, Lisa and Hudson, Eric and Feenstra, Kristin and Sobin, Leslie and Robb, James and Branton, Phillip and Korzeniewski, Greg and Shive, Charles and Tabor, David and Qi, Liqun and Groch, Kevin and Nampally, Sreenath and Buia, Steve and Zimmerman, Angela and Smith, Anna and Burges, Robin and Robinson, Karna and Valentino, Kim and Bradbury, Deborah and Cosentino, Mark and Diaz-Mayoral, Norma and Kennedy, Mary and Engel, Theresa and Williams, Penelope and Erickson, Kenyon and Ardlie, Kristin and Winckler, Wendy and Getz, Gad and DeLuca, David and MacArthur, Daniel and Kellis, Manolis and Thomson, Alexander and Young, Taylor and Gelfand, Ellen and Donovan, Molly and Meng, Yan and Grant, George and Mash, Deborah and Marcus, Yvonne and Basile, Margaret and Liu, Jun and Zhu, Jun and Tu, Zhidong and Cox, Nancy J. and Nicolae, Dan L. and Gamazon, Eric R. and Im, Hae Kyung and Konkashbaev, Anuar and Pritchard, Jonathan and Stevens, Matthew and Flutre, Timothee and Wen, Xiaoquan and Dermitzakis, Emmanouil T. and Lappalainen, Tuuli and Guigo, Roderic and Monlong, Jean and Sammeth, Michael and Koller, Daphne and Battle, Alexis and Mostafavi, Sara and McCarthy, Mark and Rivas, Manual and Maller, Julian and Rusyn, Ivan and Nobel, Andrew and Wright, Fred and Shabalin, Andrey and Feolo, Mike and Sharopova, Nataliya and Sturcke, Anne and Paschal, Justin and Anderson, James M. and Wilder, Elizabeth L. and Derr, Leslie K. and Green, Eric D. and Struewing, Jeffery P. and Temple, Gary and Volpi, Simona and Boyer, Joy T. and Thomson, Elizabeth J. and Guyer, Mark S. and Cathy Ng and Abdallah, Assya and Colantuoni, Deborah and Insel, Thomas R. and Koester, Susan E. and Little, A. Roger and Bender, Patrick K. and Lehner, Thomas and Yao, Yin and Compton, Carolyn C. and Vaught, Jimmie B. and Sawyer, Sherilyn and Lockhart, Nicole C. and Demchok, Joanne and Moore, Helen F.} } @article {pmid22826190, title = {Glucocorticoid-related changes in body mass index among children and adolescents with rheumatic diseases}, journal = {Arthritis Care Res (Hoboken)}, volume = {65}, number = {1}, year = {2013}, month = {Jan}, pages = {113{\textendash}121}, author = {Shiff, N. J. and Brant, R. and Guzman, J. and Cabral, D. A. and Huber, A. M. and Miettunen, P. and Roth, J. and Scuccimarri, R. and Alos, N. and Atkinson, S. A. and Collet, J. P. and Couch, R. and Cummings, E. A. and Dent, P. B. and Ellsworth, J. and Hay, J. and Houghton, K. and Jurencak, R. and Lang, B. and Larche, M. and Leblanc, C. and Rodd, C. and Saint-Cyr, C. and Stein, R. and Stephure, D. and Taback, S. and Rauch, F. and Ward, L. M.} } @article {pmid23677572, title = {Hormonal and reproductive risk factors for sporadic microsatellite stable and unstable endometrial tumors}, journal = {Cancer Epidemiol. Biomarkers Prev.}, volume = {22}, number = {7}, year = {2013}, month = {Jul}, pages = {1325{\textendash}1331}, author = {Amankwah, E. K. and Friedenreich, C. M. and Magliocco, A. M. and Brant, R. and Speidel, T. and Rahman, W. and Cook, L. S.} } @article {Kang2013-mw, title = {The housekeeping gene hypoxanthine guanine phosphoribosyltransferase (HPRT) regulates multiple developmental and metabolic pathways of murine embryonic stem cell neuronal differentiation}, journal = {PLoS One}, volume = {8}, number = {10}, year = {2013}, pages = {e74967}, abstract = {The mechanisms by which mutations of the purinergic housekeeping gene hypoxanthine guanine phosphoribosyltransferase (HPRT) cause the severe neurodevelopmental Lesch Nyhan Disease (LND) are poorly understood. The best recognized neural consequences of HPRT deficiency are defective basal ganglia expression of the neurotransmitter dopamine (DA) and aberrant DA neuronal function. We have reported that HPRT deficiency leads to dysregulated expression of multiple DA-related developmental functions and cellular signaling defects in a variety of HPRT-deficient cells, including human induced pluripotent stem (iPS) cells. We now describe results of gene expression studies during neuronal differentiation of HPRT-deficient murine ESD3 embryonic stem cells and report that HPRT knockdown causes a marked switch from neuronal to glial gene expression and dysregulates expression of Sox2 and its regulator, genes vital for stem cell pluripotency and for the neuronal/glial cell fate decision. In addition, HPRT deficiency dysregulates many cellular functions controlling cell cycle and proliferation mechanisms, RNA metabolism, DNA replication and repair, replication stress, lysosome function, membrane trafficking, signaling pathway for platelet activation (SPPA) multiple neurotransmission systems and sphingolipid, sulfur and glycan metabolism. We propose that the neural aberrations of HPRT deficiency result from combinatorial effects of these multi-system metabolic errors. Since some of these aberrations are also found in forms of Alzheimer{\textquoteright}s and Huntington{\textquoteright}s disease, we predict that some of these systems defects play similar neuropathogenic roles in diverse neurodevelopmental and neurodegenerative diseases in common and may therefore provide new experimental opportunities for clarifying pathogenesis and for devising new potential therapeutic targets in developmental and genetic disease.}, keywords = {My Papers}, author = {Kang, Tae Hyuk and Park, Yongjin and Bader, Joel S and Friedmann, Theodore} } @article {hennig2013find, title = {How to find an appropriate clustering for mixed-type variables with application to socio-economic stratification}, journal = {Journal of the Royal Statistical Society: Series C (Applied Statistics)}, volume = {62}, number = {3}, year = {2013}, pages = {309{\textendash}369}, publisher = {Wiley Online Library}, author = {Hennig, Christian and Liao, Tim F} } @article {cai2013hypothesis, title = {Hypothesis testing in the presence of multiple samples under density ratio models}, journal = {arXiv preprint arXiv:1309.4740}, year = {2013}, author = {Cai, Song and Chen, Jiahua and Zidek, James V} } @article {cai2013hypothesis, title = {Hypothesis testing in the presence of multiple samples under density ratio models}, journal = {Statistica Sinica}, year = {2013}, pages = {To appear}, author = {Cai, Song and Chen, Jiahua and Zidek, James V.} } @article {Gustafson2013, title = {Impact of Statistical Adjustment for Frequency of Venue Attendance in a Venue-based Survey of Men Who Have Sex With Men}, journal = {American Journal of Epidemiology}, volume = {177}, number = {10}, year = {2013}, pages = {1157{\textendash}1164}, publisher = {Oxford University Press}, doi = {10.1093/aje/kws358}, author = {Gustafson, Paul and Gilbert, Mark and Xia, Michelle and Michelow, Warren and Robert, Wayne and Trussler, Terry and McGuire, Marissa and Paquette, Dana and Moore, David M and Gustafson, Reka} } @article { ISI:000320131700021, title = {Interferon beta and long-term disability in multiple sclerosis}, journal = {JAMA Neurology}, volume = {70}, number = {5}, year = {2013}, pages = {651-652}, publisher = {AMER MEDICAL ASSOC}, type = {Letter}, address = {515 N STATE ST, CHICAGO, IL 60654-0946 USA}, doi = {doi:10.1001/jamaneurol.2013.2197}, author = {Shirani, A and Zhao, Y and Karim, ME and Evans, C and Kingwell, E and van der Kop, ML and Oger, J and Gustafson, P and Petkau, J and Tremlett, H} } @article {Shirani2013, title = {Interferon beta and long-term disability in multiple sclerosis}, journal = {JAMA neurology}, volume = {70}, number = {5}, year = {2013}, pages = {651{\textendash}653}, publisher = {American Medical Association}, doi = {10.1001/jamaneurol.2013.2197}, author = {Shirani, Afsaneh and Zhao, Yinshan and Karim, Mohammad Ehsanul and Evans, Charity and Kingwell, Elaine and van der Kop, Mia L and Oger, Joel and Gustafson, Paul and Petkau, John and Tremlett, Helen} } @conference {Hua.Joe2013, title = {Intermediate tail dependence: a review and some new results}, booktitle = {Stochastic Orders in Reliability and Risk}, series = {Lecture Notes in Statistics}, volume = {208}, year = {2013}, pages = {291-311}, publisher = {Springer}, organization = {Springer}, address = {New York}, doi = {10.1007/978-1-4614-6892-9_15}, author = {Hua, Lei and Joe, Harry}, editor = {Haijun Li and Xiaohu Li} } @article {luo2013investigations, title = {Investigations of Gene-Disease Associations: Costs and Benefits of Environmental Data}, journal = {Epidemiology}, volume = {24}, number = {4}, year = {2013}, pages = {562{\textendash}568}, publisher = {LWW}, doi = {10.1097/EDE.0b013e3182944dd5}, author = {Luo, Hao and Burstyn, Igor and Gustafson, Paul} } @conference {HomrighausenMcDonald2013, title = {The lasso, persistence, and cross-validation}, booktitle = {Proceedings of the Thirtieth International Conference on Machine Learning (ICML)}, volume = {28}, year = {2013}, pages = {1031{\textendash}1039}, publisher = {PMLR}, organization = {PMLR}, url = {http://proceedings.mlr.press/v28/homrighausen13.html}, author = {Homrighausen, D. and McDonald, D. J.}, editor = {Dasgupta, Sanjoy and McAllester, David} } @article {pmid24019394, title = {Longitudinal changes in IGF-I and IGFBP-3, and mammographic density among postmenopausal women}, journal = {Cancer Epidemiol. Biomarkers Prev.}, volume = {22}, number = {11}, year = {2013}, month = {Nov}, pages = {2116{\textendash}2120}, author = {Woolcott, C. G. and Courneya, K. S. and Boyd, N. F. and Yaffe, M. J. and McTiernan, A. and Brant, R. and Jones, C. A. and Stanczyk, F. Z. and Terry, T. and Cook, L. S. and Wang, Q. and Friedenreich, C. M.} } @article {zou2013markov, title = {A Markov regime-switching model for crude-oil markets: Comparison of composite likelihood and full likelihood}, journal = {Canadian Journal of Statistics}, volume = {41}, number = {2}, year = {2013}, pages = {353{\textendash}367}, publisher = {John Wiley \& Sons, Inc.}, author = {Zou, Wei and Chen, Jiahua} } @article { ISI:000320884400009, title = {Measures of tail asymmetry for bivariate copulas}, journal = {Statistical Papers}, volume = {54}, number = {3}, year = {2013}, month = {AUG}, pages = {709-726}, publisher = {Springer}, type = {Article}, abstract = {Three tail asymmetry measures for bivariate copulas are introduced using two different approaches-univariate skewness of a projection and distance between a copula and its survival/reflected copula. We compare the asymmetry measures based on certain desirable properties. Bounds for each measure are obtained and also copulas which attain these extreme values are identified. Two data examples show the amount of asymmetry that might be expected in practice.}, keywords = {Quantiles, Survival copula, Tail dependence, Univariate skewness}, issn = {0932-5026}, doi = {10.1007/s00362-012-0457-y}, author = {Rosco, J. F. and Joe, Harry} } @article {chen20132, title = {MixtureInf-package}, journal = {Inference for Finite Mixture Models}, year = {2013}, pages = {2}, author = {Chen, Jiahua and Li, Pengfei} } @article {jackson2013modelling, title = {Modelling factors that affect the presence of larval mosquitoes (Diptera: Culicidae) in stormwater drainage systems to improve the efficacy of control programmes}, journal = {The Canadian Entomologist}, volume = {145}, number = {06}, year = {2013}, pages = {674{\textendash}685}, publisher = {Cambridge Univ Press}, author = {Jackson, Michael J and Gow, Jennifer L and Evelyn, Michelle J and McMahon, TJ Scott and Campbell, Harlan and Sheppard, Jennifer and Howay, Tim J and Fladmark, Disa and Thielman, Aynsley} } @conference {Campbell13_ACC, title = {Multiagent allocation of Markov decision process tasks}, booktitle = {American Control Conference}, year = {2013}, author = {Trevor Campbell and Luke Johnson and Jonathan P. How} } @article {meyers2013multicenter, title = {Multicenter measurements of myelin water fraction and geometric mean T2: Intra-and intersite reproducibility}, journal = {Journal of Magnetic Resonance Imaging}, volume = {38}, number = {6}, year = {2013}, pages = {1445{\textendash}1453}, publisher = {Wiley Online Library}, author = {Meyers, Sandra M and Vavasour, Irene M and M{\"a}dler, Burkhard and Harris, Trudy and Fu, Eric and Li, David KB and Traboulsee, Anthony L and MacKay, Alex L and Laule, Cornelia} } @article {wang_multivariate_2013, title = {Multivariate one-sided tests for nonlinear mixed-effects models}, journal = {Canadian Journal of Statistics}, volume = {41}, number = {3}, year = {2013}, month = {sep}, pages = {453{\textendash}465}, abstract = {Multivariate one-sided hypotheses testing problems arise frequently in practice. Various tests have been developed, but mainly focused on multivariate normal distributions or contingency tables. In this article, motivated by HIV viral dynamic models, we study multivariate one-sided tests in nonlinear mixed-effects (NLME) models, for which no previous research has been carried out. We propose a likelihood ratio test (LRT), a Wald test, and a score test. Theoretical results are presented and computational issues are discussed. The proposed methods are evaluated using simulations. A real data example is presented to illustrate the methods. The Canadian Journal of Statistics 41: 453{\textendash}465; 2013 {\textcopyright} 2013 Statistical Society of Canada}, issn = {1708-945X}, doi = {10.1002/cjs.11180}, url = {http://onlinelibrary.wiley.com/doi/10.1002/cjs.11180/abstract}, author = {Wang, Tao and WU, LANG} } @article { ISI:000329285700012, title = {A Natural Robustification of the Ordinary Instrumental Variables Estimator}, journal = {BIOMETRICS}, volume = {69}, number = {3}, year = {2013}, month = {SEP}, pages = {641-650}, publisher = {WILEY-BLACKWELL}, type = {Article}, address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, abstract = {Instrumental variables estimators are designed to provide consistent parameter estimates for linear regression models when some covariates are correlated with the error term. We propose a new robust instrumental variables estimator (RIV) which is a natural robustification of the ordinary instrumental variables estimator (OIV). Specifically, we construct RIV using a robust multivariate location and scatter S-estimator to robustify the solution of the estimating equations that define OIV. RIV is computationally inexpensive and readily available for applications through the R-library riv. It has attractive robustness and asymptotic properties, including high resilience to outliers, bounded influence function, consistency under weak distributional assumptions, asymptotic normality under mild regularity conditions, and equivariance. We further endow RIV with an iterative algorithm which allows for the estimation of models with endogenous continuous covariates and exogenous dummy covariates. We study the performance of RIV when the data contains outliers using an extensive Monte Carlo simulation study and by applying it to a limited-access dataset from the Framingham Heart Study-Cohort to estimate the effect of long-term systolic blood pressure on left atrial size.}, keywords = {Endogenous covariate, instrumental variable, Robust estimation, S-estimator}, issn = {0006-341X}, doi = {10.1111/biom.12043}, author = {Freue, Gabriela V. Cohen and Ortiz-Molina, Hernan and Zamar, Ruben H.} } @article {freue2013natural, title = {A natural robustification of the ordinary instrumental variables estimator}, journal = {Biometrics}, volume = {69}, number = {3}, year = {2013}, pages = {641{\textendash}650}, publisher = {Wiley Online Library}, author = {Freue, Gabriela V Cohen and Ortiz-Molina, Hernan and Zamar, Ruben H} } @article {pmid24066085, title = {Neonatal pain-related stress and NFKBIA genotype are associated with altered cortisol levels in preterm boys at school age}, journal = {PLoS ONE}, volume = {8}, number = {9}, year = {2013}, pages = {e73926}, author = {Grunau, R. E. and Cepeda, I. L. and Chau, C. M. and Brummelte, S. and Weinberg, J. and Lavoie, P. M. and Ladd, M. and Hirschfeld, A. F. and Russell, E. and Koren, G. and Van Uum, S. and Brant, R. and Turvey, S. E.} } @article { ISI:000324146200013, title = {Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge}, journal = {PLOS ONE}, volume = {8}, number = {7}, year = {2013}, month = {JUL 18}, pages = {e68141}, publisher = {PUBLIC LIBRARY SCIENCE}, type = {Article}, address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA}, abstract = {Transcriptomic assays that measure expression levels are widely used to study the manifestation of environmental or genetic variations in cellular processes. RNA-sequencing in particular has the potential to considerably improve such understanding because of its capacity to assay the entire transcriptome, including novel transcriptional events. However, as with earlier expression assays, analysis of RNA-sequencing data requires carefully accounting for factors that may introduce systematic, confounding variability in the expression measurements, resulting in spurious correlations. Here, we consider the problem of modeling and removing the effects of known and hidden confounding factors from RNA-sequencing data. We describe a unified residual framework that encapsulates existing approaches, and using this framework, present a novel method, HCP (Hidden Covariates with Prior). HCP uses a more informed assumption about the confounding factors, and performs as well or better than existing approaches while having a much lower computational cost. Our experiments demonstrate that accounting for known and hidden factors with appropriate models improves the quality of RNA-sequencing data in two very different tasks: detecting genetic variations that are associated with nearby expression variations (cis-eQTLs), and constructing accurate co-expression networks.}, issn = {1932-6203}, doi = {10.1371/journal.pone.0068141}, author = {Mostafavi, Sara and Battle, Alexis and Zhu, Xiaowei and Urban, Alexander E. and Levinson, Douglas and Montgomery, Stephen B. and Koller, Daphne} } @article {Bouchard2013Probabilistic, title = {A Note on Probabilistic Models over Strings: Inference and Representation with Indexed Matrices}, journal = {arXiv}, volume = {1301.5054}, year = {2013}, author = {Alexandre Bouchard-C{\^o}t{\'e}} } @article {Bouchard2013Probabilistic, title = {A Note on Probabilistic Models over Strings: Inference and~ Representation with Indexed Matrices}, journal = {arXiv}, volume = {1301.5054}, year = {2013}, author = {Alexandre Bouchard-C{\^o}t{\'e}} } @article {Bouchard2013probabilistic, title = {A note on probabilistic models over strings: the linear algebra approach}, journal = {Bulletin of Mathematical Biology}, volume = {75}, year = {2013}, pages = {2529{\textendash}2550}, author = {Alexandre Bouchard-C{\^o}t{\'e}} } @article {chen2013partial, title = {A partial order on uncertainty and information}, journal = {Journal of Theoretical Probability}, volume = {26}, number = {2}, year = {2013}, pages = {349{\textendash}359}, publisher = {Springer US}, author = {Chen, Jiahua} } @article { ISI:000321102600001, title = {Penalized regression, mixed effects models and appropriate modelling}, journal = {ELECTRONIC JOURNAL OF STATISTICS}, volume = {7}, year = {2013}, pages = {1517-1552}, publisher = {INST MATHEMATICAL STATISTICS}, type = {Article}, address = {3163 SOMERSET DR, CLEVELAND, OH 44122 USA}, abstract = {Linear mixed effects methods for the analysis of longitudinal data provide a convenient framework for modelling within-individual correlation across time. Using spline functions allows for flexible modelling of the response as a smooth function of time. A computational connection between linear mixed effects modelling and spline smoothing has resulted in use of spline functions in longitudinal data analysis and the use of mixed effects software in smoothing analyses. However, care must be taken in exploiting this connection, as resulting estimates of the underlying population mean might not track the data well and associated standard errors might not reflect the true variability in the data. We discuss these shortcomings and suggest some easy-to-compute methods to eliminate them.}, keywords = {Linear mixed effects models, P-splines, penalized smoothing, sandwich estimator}, issn = {1935-7524}, doi = {10.1214/13-EJS809}, author = {Heckman, Nancy and Lockhart, Richard and Nielsen, Jason D.} } @article {lin2013plasma, title = {Plasma protein biosignatures for detection of cardiac allograft vasculopathy}, journal = {The Journal of Heart and Lung Transplantation}, volume = {32}, number = {7}, year = {2013}, pages = {723{\textendash}733.*Equal contributors.}, publisher = {Elsevier}, author = {Lin, David* and Freue, Gabriela Cohen* and Hollander, Zsuzsanna and Mancini, GB John and Sasaki, Mayu and Mui, Alice and Wilson-McManus, Janet and Ignaszewski, Andrew and Imai, Carol and Meredith, Anna and others} } @article { ISI:000314445800011, title = {Predicting acute cardiac rejection from donor heart and pre-transplant recipient blood gene expression}, journal = {JOURNAL OF HEART AND LUNG TRANSPLANTATION}, volume = {32}, number = {2}, year = {2013}, month = {FEB}, pages = {259-265}, publisher = {ELSEVIER SCIENCE INC}, type = {Article}, address = {360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA}, abstract = {BACKGROUND: Acute rejection in cardiac transplant patients remains a contributory factor to limited survival of implanted hearts. Currently, there are no biomarkers in clinical use that can predict, at the time of transplantation, the likelihood of post-transplant acute cellular rejection. Such a development would be of great value in personalizing immunosuppressive treatment. METHODS: Recipient age, donor age, cold ischemic time, warm ischemic time, panel-reactive antibody, gender mismatch, blood type mismatch and human leukocyte antigens (HLA-A, -B and -DR) mismatch between recipients and donors were tested in 53 heart transplant patients for their power to predict post-transplant acute cellular rejection. Donor transplant biopsy and recipient pre-transplant blood were also examined for the presence of genomic biomarkers in 7 rejection and 11 non-rejection patients, using non-targeted data mining techniques. RESULTS: The biomarker based on the 8 clinical variables had an area under the receiver operating characteristic curve (AUC) of 0.53. The pre-transplant recipient blood gene-based panel did not yield better performance, but the donor heart tissue gene-based panel had an AUC = 0.78. A combination of 25 probe sets from the transplant donor biopsy and 18 probe sets from the pre-transplant recipient whole blood had an AUC = 0.90. Biologic pathways implicated include VEGF- and EGFR-signaling, and MAPK. CONCLUSIONS: Based on this study, the best predictive biomarker panel contains genes from recipient whole blood and donor myocardial tissue. This panel provides clinically relevant prediction power and, if validated, may personalize immunosuppressive treatment and rejection monitoring. I Heart Lung Transplant 2013;32:259-265 (C) 2013 International Society for Heart and Lung Transplantation. All rights reserved.}, keywords = {acute rejection, biomarker, cardiac transplant, prediction}, issn = {1053-2498}, doi = {10.1016/j.healun.2012.11.008}, author = {Hollander, Zsuzsanna and Chen, Virginia and Sidhu, Keerat and Lin, David and Ng, Raymond T. and Balshaw, Robert and Cohen-Freue, Gabriela V. and Ignaszewski, Andrew and Imai, Carol and Kaan, Annemarie and Tebbutt, Scott J. and Wilson-McManus, Janet E. and McMaster, Robert W. and Keown, Paul. A. and McManus, Bruce M. and NCE CECR PROOF Ctr Excellence} } @article {pmid23558431, title = {Prenatal and postnatal inflammation in relation to cortisol levels in preterm infants at 18 months corrected age}, journal = {J Perinatol}, volume = {33}, number = {8}, year = {2013}, month = {Aug}, pages = {647{\textendash}651}, author = {Gover, A. and Chau, V. and Miller, S. P. and Brant, R. and McFadden, D. E. and Poskitt, K. J. and Synnes, A. and Weinberg, J. and Grunau, R. E.} } @article {wang_property_2013, title = {Property Modeling of Changbai Larch ( Larix Olgensis Henry) Veneers in Relation to Stand and Tree Variables}, journal = {Wood and Fiber Science}, volume = {45}, number = {3}, year = {2013}, month = {jul}, pages = {314{\textendash}329}, abstract = {The key objective of this work was to investigate properties of Changbai larch (Larix olgensis Henry) veneers in relation to stand and tree variables using both linear regression (LR) and linear mixed effects (LME) models. A veneer data set was formed with 36 sample trees from four stands in China. Each tree was cross-cut into six segments along the vertical stem. The results showed that tree diameter at breast height (DBH), tree height, and branch height exhibited certain degrees of association with either veneer modulus of elasticity (MOE) or ultrasonic propagation time (UPT) but not with veneer density. Both veneer MOE and UPT exhibited a polynomial pattern along the tree stem. Stem position was found to be the only significant variable affecting veneer density. The highest veneer MOE appeared to be situated between the second and third stems from the butt. LME and LR models were clearly similar with regard to parameter estimates. However, the overall standard error and p value from the LME model were smaller than those from the LR model, indicating that the LME model was more effective for stem-specific analysis. After adjusting confounders including the stem position, tree height exhibited no association with veneer MOE. This result did not occur with standard LR analysis.}, keywords = {Changbai larch, DBH, density, MOE, stand, statistical model, tree, veneer}, issn = {0735-6161}, url = {http://wfs.swst.org/index.php/wfs/article/view/2023}, author = {WANG, BRAD JIANHE and ZHANG, HONGBIN and WU, LANG and HUANG, SUYONG and LU, JIANXIONG and Zidek, James} } @booklet {wang2013university, title = {Property Modeling of Changbai Larch Veneers in Relation to Stand and Tree Variables}, number = {272}, year = {2013}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {WANG, BRAD JIANHE and ZHANG, HONGBIN and WU, LANG and HUANG, SUYONG and Zidek, James V and LU, JIANXIONG} } @article {xu2013pseudo, title = {Pseudo-likelihood-based Bayesian information criterion for variable selection in survey data}, journal = {Survey Methodology}, volume = {39}, year = {2013}, pages = {303{\textendash}322}, author = {Xu, Chen and Chen, Jiahua and Mantell, H} } @inbook {8973, title = {Qualitative Robustness of Bootstrap Approximations for Kernel Based Methods}, booktitle = {Robustness and Complex Data Structures: Festschrift in Honour of Ursula Gather}, year = {2013}, pages = {263{\textendash}278}, publisher = {Springer Berlin Heidelberg}, organization = {Springer Berlin Heidelberg}, address = {Berlin, Heidelberg}, isbn = {978-3-642-35494-6}, doi = {10.1007/978-3-642-35494-6_16}, url = {http://dx.doi.org/10.1007/978-3-642-35494-6_16}, author = {Christmann, Andreas and Salibian-Barrera, Mat{\'\i}as and Van Aelst, Stefan}, editor = {Becker, Claudia and Fried, Roland and Kuhnt, Sonja} } @article {chen2013quantile, title = {Quantile and quantile-function estimations under density ratio model}, journal = {The Annals of Statistics}, volume = {41}, number = {3}, year = {2013}, pages = {1669{\textendash}1692}, publisher = {Institute of Mathematical Statistics}, author = {Chen, Jiahua and Liu, Yukun} } @article {pmid24082311, title = {Remotely controlled mandibular protrusion during sleep predicts therapeutic success with oral appliances in patients with obstructive sleep apnea}, journal = {Sleep}, volume = {36}, number = {10}, year = {2013}, month = {Oct}, pages = {1517{\textendash}1525}, author = {Remmers, J. and Charkhandeh, S. and Grosse, J. and Topor, Z. and Brant, R. and Santosham, P. and Bruehlmann, S.} } @article {Falasinnu2013, title = {Risk prediction in sexual health contexts: Protocol}, journal = {JMIR research protocols}, volume = {2}, number = {2}, year = {2013}, publisher = {JMIR Publications Inc.}, doi = {10.2196/resprot.2971}, author = {Falasinnu, Titilola and Gustafson, Paul and Gilbert, Mark and Shoveller, Jean} } @article { ISI:000319173400020, title = {Robust and efficient estimation of the residual scale in linear regression}, journal = {JOURNAL OF MULTIVARIATE ANALYSIS}, volume = {116}, year = {2013}, month = {APR}, pages = {278-296}, publisher = {ELSEVIER INC}, type = {Article}, address = {525 B STREET, STE 1900, SAN DIEGO, CA 92101-4495 USA}, abstract = {Robustness and efficiency of the residual scale estimators in the regression model is important for robust inference. We introduce the class of robust generalized M-scale estimators for the regression model, derive their influence function and gross-error sensitivity, and study their maxbias behavior. In particular, we find overall minimax bias estimates for the general class and also for well-known subclasses. We pose and solve a Hampers-like optimality problem: we find generalized M-scale estimators with maximal efficiency subject to a lower bound on the global and local robustness of the estimators. (C) 2013 Elsevier Inc. All rights reserved.}, keywords = {Efficiency, Gross-error sensitivity, influence function, Maxbias, Robust scale}, issn = {0047-259X}, doi = {10.1016/j.jmva.2012.12.008}, author = {Van Aelst, Stefan and Willems, Gert and Zamar, Ruben H.} } @article {pmid23337005, title = {Score for neonatal acute physiology-II and neonatal pain predict corticospinal tract development in premature newborns}, journal = {Pediatr. Neurol.}, volume = {48}, number = {2}, year = {2013}, month = {Feb}, pages = {123{\textendash}129}, author = {Zwicker, J. G. and Grunau, R. E. and Adams, E. and Chau, V. and Brant, R. and Poskitt, K. J. and Synnes, A. and Miller, S. P.} } @inbook {balkema2013shape, title = {The shape of asymptotic dependence}, booktitle = {Prokhorov and Contemporary Probability Theory}, year = {2013}, pages = {43{\textendash}67}, publisher = {Springer}, organization = {Springer}, author = {Balkema, Guus and Embrechts, Paul and Nolde, Natalia} } @article { ISI:000320487800008, title = {Simplified pair copula constructions: Limitations and extensions}, journal = {Journal of Multivariate Analysis}, volume = {119}, year = {2013}, month = {AUG}, pages = {101-118}, publisher = {Elsevier Inc}, type = {Article}, abstract = {So-called pair copula constructions (PCCs), specifying multivariate distributions only in terms of bivariate building blocks (pair copulas), constitute a flexible class of dependence models. To keep them tractable for inference and model selection, the simplifying assumption, that copulas of conditional distributions do not depend on the values of the variables which they are conditioned on, is popular. We show that the only Archimedean copulas in dimension d >= 3 which are of the simplified type are those based on the Gamma Laplace transform or its extension, while the Student-t copulas are the only one arising from a scale mixture of Normals. Further, we illustrate how PCCs can be adapted for situations where conditional copulas depend on values which are conditioned on, and demonstrate a technique to assess the distance of a multivariate distribution from a nearby distribution that satisfies the simplifying assumption. (C) 2013 Published by Elsevier Inc.}, keywords = {Archimedean copula, Conditional distribution, Elliptical copula, Pair copula construction}, issn = {0047-259X}, doi = {10.1016/j.jmva.2013.04.014}, author = {Stoeber, Jakob and Joe, Harry and Czado, Claudia} } @article {pmid23325801, title = {Slower postnatal growth is associated with delayed cerebral cortical maturation in preterm newborns}, journal = {Sci Transl Med}, volume = {5}, number = {168}, year = {2013}, month = {Jan}, pages = {168ra8}, author = {Vinall, J. and Grunau, R. E. and Brant, R. and Chau, V. and Poskitt, K. J. and Synnes, A. R. and Miller, S. P.} } @article { ISI:000321085200001, title = {Special issue on robust analysis of complex data}, journal = {COMPUTATIONAL STATISTICS \& DATA ANALYSIS}, volume = {65}, number = {SI}, year = {2013}, month = {SEP}, pages = {1-3}, publisher = {ELSEVIER SCIENCE BV}, type = {Editorial Material}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, issn = {0167-9473}, doi = {10.1016/j.csda.2013.04.007}, author = {Croux, Christophe and Ronchetti, Elvezio and Salibian-Barrera, Mat{\'\i}as and Van Aelst, Stefan} } @article {pmid23466018, title = {Statistical methods for the meta-analysis of diagnostic tests must take into account the use of surrogate standards}, journal = {J Clin Epidemiol}, volume = {66}, number = {5}, year = {2013}, month = {May}, pages = {566{\textendash}574}, author = {Kang, J. and Brant, R. and Ghali, W. A.} } @conference {Jun2013Stochastic, title = {A Stochastic Map View of Sequential Monte Carlo with Applications to Memory and Network Efficiency}, booktitle = {Randomized Algorithm Workshop at Advances in Neural Information Processing Systems 26 (NIPS)}, year = {2013}, author = {Seong-Hwan Jun and Alexandre Bouchard-C{\^o}t{\'e}} } @article {ascherio2013supplementary, title = {Supplementary Online Content}, year = {2013}, author = {Ascherio, A and Munger, KL and White, R and others} } @article {8889, title = {Um modelo bayesiano para investiga{\c c}{\~a}o de sobremortalidade durante epidemia de dengue na Regi{\~a}o Metropolitana do Rio de Janeiro, Brasil, 2007-2008}, journal = {Cadernos de Sa{\'u}de P{\'u}blica}, volume = {29}, year = {2013}, month = {10}, pages = {2057 - 2070}, abstract = {

The aim of this study was to investigate excess mortality from dengue in Greater Metropolitan Rio de Janeiro, Brazil, during an epidemic in 2007-2008. A Poisson dynamic model was tested to predict the number of deaths during these epidemic years. Inference was conducted with a Bayesian approach. Excess mortality was detected in March 2008 in children\ \<\ 15 years. In addition, the highest number of reported dengue cases in Rio de Janeiro was in March and April 2008. Since the increase in mortality should be preceded by an increase in morbidity, one can hypothesize that there was excess mortality from dengue in children during the epidemic in Greater Metropolitan Rio de Janeiro in March 2008.

}, keywords = {Dengue; Communicable Diseases; Mortality; Epidemiological Surveillance}, issn = {0102-311X}, url = {http://www.scielo.br/scielo.php?script=sci_arttext\&pid=S0102-311X2013001000022\&nrm=iso}, author = {Malh{\~a}o, T. A. and Casquilho-Resende, C. M. and Gamerman, D. and Medronho, R. A.} } @article { ISI:000322829800011, title = {VISUALIZING GENETIC CONSTRAINTS}, journal = {ANNALS OF APPLIED STATISTICS}, volume = {7}, number = {2}, year = {2013}, month = {JUN}, pages = {860-882}, publisher = {INST MATHEMATICAL STATISTICS}, type = {Article}, address = {3163 SOMERSET DR, CLEVELAND, OH 44122 USA}, abstract = {Principal Components Analysis (PCA) is a common way to study the sources of variation in a high-dimensional data set. Typically, the leading principal components are used to understand the variation in the data or to reduce the dimension of the data for subsequent analysis. The remaining principal components are ignored since they explain little of the variation in the data. However, evolutionary biologists gain important insights from these low variation directions. Specifically, they are interested in directions of low genetic variability that are biologically interpretable. These directions are called genetic constraints and indicate directions in which a trait cannot evolve through selection. Here, we propose studying the subspace spanned by low variance principal components by determining vectors in this subspace that are simplest. Our method and accompanying graphical displays enhance the biologist{\textquoteright}s ability to visualize the subspace and identify interpretable directions of low genetic variability that align with simple directions.}, keywords = {evolutionary biology, genetic constraints, Principal components}, issn = {1932-6157}, doi = {10.1214/12-AOAS603}, author = {Gaydos, Travis L. and Heckman, Nancy E. and Kirkpatrick, Mark and Stinchcombe, J. R. and Schmitt, Johanna and Kingsolver, Joel and Marron, J. S.} } @article {ascherio2013vitamin, title = {Vitamin D as a predictor of multiple sclerosis activity and progression.}, year = {2013}, author = {Ascherio, A and Munger, K and White, R and Kochert, K and Simon, C and Polman, C and Freedman, MS and Hartung, HP and Miller, DH and Montalban, X and others} } @article {burstyn2013measures, title = {What do measures of agreement (${\k a}ppa$) tell us about quality of exposure assessment? Theoretical analysis and numerical simulation}, journal = {BMJ open}, volume = {3}, number = {12}, year = {2013}, pages = {e003952}, publisher = {British Medical Journal Publishing Group}, doi = {10.1136/bmjopen-2013-003952}, author = {Burstyn, Igor and de Vocht, Frank and Gustafson, Paul} } @article {chen2012adjusted, title = {Adjusted empirical likelihood with high-order one-sided coverage precision}, journal = {Statistics and its Interface}, volume = {5}, number = {3}, year = {2012}, pages = {281{\textendash}292}, author = {Chen, Jiahua and Liu, Yukun} } @article {pi2012application, title = {Application of linear discriminant analysis in performance evaluation of extractable nuclear antigen immunoassay systems in the screening and diagnosis of systemic autoimmune rheumatic diseases}, journal = {American journal of clinical pathology}, volume = {138}, number = {4}, year = {2012}, pages = {596{\textendash}603}, publisher = {American Society for Clinical Pathology}, author = {Pi, David and de Badyn, Monika Hudoba and Nimmo, Mike and White, Rick and Pal, Jason and Wong, Patrick and Phoon, Carmen and O{\textquoteright}Connor, Deidre and Pi, Steven and Shojania, Kam} } @article {shirani2012association, title = {Association between use of interferon beta and progression of disability in patients with relapsing-remitting multiple sclerosis}, journal = {JAMA: The Journal of the American Medical Association}, volume = {308}, number = {3}, year = {2012}, pages = {247{\textendash}256}, publisher = {American Medical Association}, doi = {10.1001/jama.2012.7625}, url = {http://jama.jamanetwork.com/article.aspx?articleid=1217239}, author = {Shirani, A. and Zhao, Y. and Karim, M.E. and Evans, C. and Kingwell, E. and van der Kop, M.L. and Oger, J. and Gustafson, P. and Petkau, J. and Tremlett, H.} } @article { ISI:000306477900025, title = {Association between use of interferon beta and progression of disability in patients with relapsing-remitting multiple sclerosis}, journal = {Journal of the American Medical Association}, volume = {308}, number = {3}, year = {2012}, pages = {247-256}, publisher = {AMER MEDICAL ASSOC}, address = {330 N WABASH AVE, STE 39300, CHICAGO, IL 60611-5885 USA}, abstract = {

Context Interferon beta is widely prescribed to treat multiple sclerosis (MS); however, its relationship with disability progression has yet to be established. Objective To investigate the association between interferon beta exposure and disability progression in patients with relapsing-remitting MS. Design, Setting, and Patients Retrospective cohort study based on prospectively collected data (1985-2008) from British Columbia, Canada. Patients with relapsing-remitting MS treated with interferon beta (n=868) were compared with untreated contemporary (n=829) and historical (n=959) cohorts. Main Outcome Measures The main outcome measure was time from interferon beta treatment eligibility (baseline) to a confirmed and sustained score of 6 (requiring a cane to walk 100 m; confirmed at \>150 days with no measurable improvement) on the Expanded Disability Status Scale (EDSS) (range, 0-10, with higher scores indicating higher disability). A multivariable Cox regression model with interferon beta treatment included as a time-varying covariate was used to assess the hazard of disease progression associated with interferon beta treatment. Analyses also included propensity score adjustment to address confounding by indication. Results The median active follow-up times (first to last EDSS measurement) were as follows: for the interferon beta-treated cohort, 5.1 years (interquartile range [IQR], 3.0-7.0 years); for the contemporary control cohort, 4.0 years (IQR, 2.1-6.4 years); and for the historical control cohort, 10.8 years (IQR, 6.3-14.7 years). The observed outcome rates for reaching a sustained EDSS score of 6 were 10.8\%, 5.3\%, and 23.1\% in the 3 cohorts, respectively. After adjustment for potential baseline confounders (sex, age, disease duration, and EDSS score), exposure to interferon beta was not associated with a statistically significant difference in the hazard of reaching an EDSS score of 6 when either the contemporary control cohort (hazard ratio, 1.30; 95\% CI, 0.92-1.83; P=.14) or the historical control cohort (hazard ratio, 0.77; 95\% CI, 0.58-1.02; P=.07) were considered. Further adjustment for comorbidities and socioeconomic status, where possible, did not change interpretations, and propensity score adjustment did not substantially change the results. Conclusion Among patients with relapsing-remitting MS, administration of interferon beta was not associated with a reduction in progression of disability. JAMA. 2012;308(3):247-256 www.jama.com

}, doi = {10.1001/jama.2012.7625}, author = {Shirani, A and Zhao, Y and Karim, ME and Evans, C and Kingwell, E and van der Kop, ML and Oger, J and Gustafson, P and Petkau, J and Tremlett, H} } @article { ISI:000306097600010, title = {ASYMPTOTIC DEPENDENCE FOR LIGHT-TAILED HOMOTHETIC DENSITIES}, journal = {ADVANCES IN APPLIED PROBABILITY}, volume = {44}, number = {2}, year = {2012}, month = {JUN}, pages = {506-527}, publisher = {APPLIED PROBABILITY TRUST}, type = {Article}, address = {THE UNIVERSITY, SCHOOL MATHEMATICS STATISTICS, SHEFFIELD S3 7RH, ENGLAND}, abstract = {Dependence between coordinate extremes is a key factor in any multivariate risk assessment. Hence, it is of interest to know whether the components of a given multivariate random vector exhibit asymptotic independence or asymptotic dependence. In the latter case the structure of the asymptotic dependence has to be clarified. In the multivariate setting it is common to have an explicit form of the density rather than the distribution function. In this paper we therefore give criteria for asymptotic dependence in terms of the density. We consider distributions with light tails and restrict attention to continuous unimodal densities defined on the whole space or on an open convex cone. For simplicity, the density is assumed to be homothetic: all level sets have the same shape. Balkema and Nolde (2010) contains conditions on the shape which guarantee asymptotic independence. The situation for asymptotic dependence, treated in the present paper, is more delicate.}, keywords = {Asymptotic dependence, Geometric approach, homothetic level set, light-tailed density, multivariate extreme}, issn = {0001-8678}, author = {Balkema, Guus and Nolde, Natalia} } @article { ISI:000302033200021, title = {Bandwidth choice for robust nonparametric scale function estimation}, journal = {COMPUTATIONAL STATISTICS \& DATA ANALYSIS}, volume = {56}, number = {6}, year = {2012}, month = {JUN}, pages = {1594-1608}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {We introduce and compare several robust procedures for bandwidth selection when estimating the variance function. These bandwidth selectors are to be used in combination with the robust scale estimates introduced by Boente et al. (2010a). We consider two different robust cross-validation strategies combined with two ways for measuring the cross-validation prediction error. The different proposals are compared with non robust alternatives using Monte Carlo simulation. We also derive some asymptotic results to investigate the large sample performance of the corresponding robust data-driven scale estimators. (C) 2011 Elsevier B.V. All rights reserved.}, keywords = {Cross-validation, Data-driven bandwidth, Heteroscedasticity, Local M-estimators, nonparametric regression, Robust estimation}, issn = {0167-9473}, doi = {10.1016/j.csda.2011.10.002}, author = {Boente, Graciela and Ruiz, Marcelo and Zamar, Ruben H.} } @article {xia2012bayesian, title = {A Bayesian method for estimating prevalence in the presence of a hidden sub-population}, journal = {Statistics in Medicine}, volume = {31}, number = {21}, year = {2012}, pages = {2386{\textendash}2398}, publisher = {Wiley Online Library}, doi = {10.1002/sim.5374}, author = {Xia, Michelle and Gustafson, Paul} } @conference {Bouchard2012Bayesian, title = {Bayesian pedigree analysis using measure factorization}, booktitle = {Advances in Neural Information Processing Systems 25 (NIPS)}, volume = {25}, year = {2012}, pages = {2906{\textendash}2914}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Bonnie Kirkpatrick} } @article {Gus2012, title = {On the behaviour of Bayesian credible intervals in partially identified models}, journal = {Electronic Journal of Statistics}, volume = {6}, year = {2012}, pages = {2107-2124}, issn = {1935-7524}, doi = {10.1214/12-EJS741}, url = {projecteuclid.org/euclid.ejs/1351865119}, author = {Paul Gustafson} } @article {joe2012inequalities, title = {Book Review of {\textquoteleft}{\textquoteleft}Inequalities: Theory of Majorization and Its Applications, by AW Marshall, I. Olkin and BC Arnold, Springer"}, journal = {Probability in the Engineering and Informational Sciences}, volume = {26}, number = {03}, year = {2012}, pages = {449{\textendash}453}, publisher = {Cambridge University Press}, doi = {10.1017/S0269964812000113}, author = {Joe, Harry} } @article {zidek2012combining, title = {Combining data and simulated data for space{\textendash}time fields: application to ozone}, journal = {Environmental and ecological statistics}, volume = {19}, number = {1}, year = {2012}, pages = {37{\textendash}56}, publisher = {Springer}, author = {Zidek, James V and Le, Nhu D. and Liu, Zhong} } @article { ISI:000305474400016, title = {Combining many interaction networks to predict gene function and analyze gene lists}, journal = {PROTEOMICS}, volume = {12}, number = {10}, year = {2012}, month = {MAY}, pages = {1687-1696}, publisher = {WILEY-BLACKWELL}, type = {Review}, address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, abstract = {In this article, we review how interaction networks can be used alone or in combination in an automated fashion to provide insight into gene and protein function. We describe the concept of a gene-recommender system that can be applied to any large collection of interaction networks to make predictions about gene or protein function based on a query list of proteins that share a function of interest. We discuss these systems in general and focus on one specific system, GeneMANIA, that has unique features and uses different algorithms from the majority of other systems.}, keywords = {Algorithm, Bioinformatics, Functional genomics, Molecular interaction, Web tool}, issn = {1615-9853}, doi = {10.1002/pmic.201100607}, author = {Mostafavi, Sara and Morris, Quaid} } @article {pmid22920273, title = {Comparing the effectiveness of copper intrauterine devices available in Canada. Is FlexiT non-inferior to NovaT when inserted immediately after first-trimester abortion? Study protocol for a randomized controlled trial}, journal = {Trials}, volume = {13}, year = {2012}, pages = {147}, author = {Norman, W. V. and Chiles, J. L. and Turner, C. A. and Brant, R. and Aslan, A. and Kaczorowski, J.} } @article {gunther2012computational, title = {A computational pipeline for the development of multi-marker bio-signature panels and ensemble classifiers}, journal = {BMC bioinformatics}, volume = {13}, number = {1}, year = {2012}, pages = {1}, publisher = {BioMed Central}, author = {G{\"u}nther, Oliver P and Chen, Virginia and Freue, Gabriela Cohen and Balshaw, Robert F and Tebbutt, Scott J and Hollander, Zsuzsanna and Takhar, Mandeep and McMaster, W Robert and McManus, Bruce M and Keown, Paul A and others} } @article {chen2012confidence, title = {Confidence intervals for the mean of a population containing many zero values under unequal probability sampling 511: Y}, journal = {Quality Control and Applied Statistics}, volume = {57}, number = {1}, year = {2012}, pages = {77}, author = {Chen, Hanfeng and Chen, Jiahua and Chen, Shun-Yi} } @inbook {vanEeden2012multiagent, title = {Contemporary Developments in Bayesian Analysis and Statistical Decision Theory: A Festschrift for William E. Strawderman}, volume = {8}, year = {2012}, pages = {131-153}, publisher = {Institute of Mathematical Statistics Collections}, organization = {Institute of Mathematical Statistics Collections}, chapter = {Multiagent estimators of an exponential mean}, author = {van Eeden, C. and Zidek, J.V.}, editor = {D. Forurndrinier, E. Marchand and Rukhin, A.L.} } @article {parker2012correlation, title = {Correlation of proteome-wide changes with social immunity behaviors provides insight into resistance to the parasitic mite, Varroa destructor, in the honey bee (Apis mellifera)}, journal = {Genome Biol}, volume = {13}, number = {9}, year = {2012}, pages = {R81{\textendash}2012}, author = {Parker, Robert and Guarna, M Marta and Melathopoulos, Andony P and Moon, Kyung-Mee and White, Rick and Huxter, Elizabeth and Pernal, Stephen F and Foster, Leonard J} } @article {Liu2012, title = {On the detectability of different forms of interaction in regression models}, journal = {Metrika}, volume = {75}, number = {3}, year = {2012}, pages = {347{\textendash}365}, publisher = {Springer}, doi = {10.1007/s00184-010-0330-8}, author = {Liu, Juxin and Gustafson, Paul} } @article {Gustafson2012a, title = {Double-robust estimators: slightly more Bayesian than meets the eye?}, journal = {The international journal of biostatistics}, volume = {8}, number = {2}, year = {2012}, pages = {1{\textendash}15}, doi = {10.2202/1557-4679.1349}, author = {Gustafson, Paul} } @article {Gu2012IJB, title = {Double-robust estimators: Slightly more Bayesian than meets the eye?}, journal = {International Journal of Biostatistics}, volume = {8}, year = {2012}, pages = {issue 2, article 4}, doi = {10.2202/1557-4679.1349}, author = {Gustafson, P.} } @article {bornn2012efficient, title = {Efficient stabilization of crop yield prediction in the Canadian Prairies}, journal = {Agricultural and forest meteorology}, volume = {152}, year = {2012}, pages = {223{\textendash}232}, publisher = {Elsevier}, author = {Bornn, Luke and Zidek, James V} } @conference {Jun2012Entangled, title = {Entangled Monte Carlo}, booktitle = {Advances in Neural Information Processing Systems 25 (NIPS)}, volume = {25}, year = {2012}, pages = {2735{\textendash}2743}, author = {Seong-Hwan Jun and Liangliang Wang and Alexandre Bouchard-C{\^o}t{\'e}} } @article {chen2012extended, title = {Extended BIC for small-n-large-P sparse GLM}, journal = {Statistica Sinica}, volume = {22}, number = {2}, year = {2012}, pages = {555}, author = {Chen, Jiahua and Chen, Zehua} } @mastersthesis {McDonald2012, title = {Generalization error bounds for state-space models}, year = {2012}, school = {Carnegie Mellon University}, type = {phd}, author = {McDonald, Daniel J.} } @article {pmid22898151, title = {Genetics and evolution of function-valued traits: understanding environmentally responsive phenotypes}, journal = {Trends Ecol. Evol. (Amst.)}, volume = {27}, number = {11}, year = {2012}, month = {Nov}, pages = {637{\textendash}647}, abstract = {Many central questions in ecology and evolutionary biology require characterizing phenotypes that change with time and environmental conditions. Such traits are inherently functions, and new {\textquoteright}function-valued{\textquoteright} methods use the order, spacing, and functional nature of the data typically ignored by traditional univariate and multivariate analyses. These rapidly developing methods account for the continuous change in traits of interest in response to other variables, and are superior to traditional summary-based analyses for growth trajectories, morphological shapes, and environmentally sensitive phenotypes. Here, we explain how function-valued methods make flexible use of data and lead to new biological insights. These approaches frequently offer enhanced statistical power, a natural basis of interpretation, and are applicable to many existing data sets. We also illustrate applications of function-valued methods to address ecological, evolutionary, and behavioral hypotheses, and highlight future directions.}, author = {Stinchcombe, J. R. and Kirkpatrick, M. and Beder, J. and Carter, P. A. and Gilchrist, G. W. and Gervini, D. and Gomulkiewicz, R. and Hallgrimsson, B. and Heckman, N. and Houle, D. and Kingsolver, J. G. and Marquez, E. and Marron, J. and Meyer, K. and Mio, W. and Schmitt, J. and Yao, F.} } @conference {Wang2012Harnessing, title = {Harnessing Non-Local Evolutionary Events for Tree Inference}, booktitle = {Society for Molecular Biology and Evolution}, year = {2012}, author = {Liangliang Wang and Alexandre Bouchard-C{\^o}t{\'e}} } @article {yuan_harvesting_2012, title = {Harvesting Classification Trees for Drug Discovery}, journal = {Journal of chemical information and modeling}, volume = {52}, number = {12}, year = {2012}, pages = {3169{\textendash}3180}, url = {http://pubs.acs.org/doi/abs/10.1021/ci3000216}, author = {Yuan, Yan and Chipman, Hugh A. and Welch, William J.} } @article {noh_hierarchical_2012, title = {Hierarchical likelihood methods for nonlinear and generalized linear mixed models with missing data and measurement errors in covariates}, journal = {Journal of Multivariate Analysis}, volume = {109}, year = {2012}, month = {aug}, pages = {42{\textendash}51}, abstract = {Nonlinear mixed-effects (NLME) models and generalized linear mixed models (GLMM) are popular in the analyses of longitudinal data and clustered data. Covariates are often introduced to partially explain the large between individual (cluster) variation. Many of these covariates, however, contain missing data and/or are measured with errors. In these cases, likelihood inference can be computationally very challenging since the observed data likelihood involves a high-dimensional and intractable integral. Computationally intensive methods such as Monte-Carlo EM algorithms may offer computational difficulties such as very slow convergence or even non-convergence. In this article, we consider hierarchical likelihood methods which approximate the observed-data likelihood using Laplace approximation so completely avoid the intractable integral. We evaluate the methods via simulation and illustrate the methods by two examples.}, keywords = {Generalized linear mixed models, Hierarchical likelihood, Measurement errors, Missing covariates, Nonlinear mixed effects models}, issn = {0047-259X}, doi = {10.1016/j.jmva.2012.02.011}, url = {http://www.sciencedirect.com/science/article/pii/S0047259X12000528}, author = {Noh, Maengseok and WU, LANG and Lee, Youngjo} } @article {mccandless2012hierarchical, title = {Hierarchical priors for bias parameters in Bayesian sensitivity analysis for unmeasured confounding}, journal = {Statistics in Medicine}, volume = {31}, number = {4}, year = {2012}, pages = {383{\textendash}396}, doi = {10.1002/sim.4453}, author = {McCandless, Lawrence C and Gustafson, Paul and Levy, Adrian R and Richardson, Sylvia} } @article {Park2012-fi, title = {How networks change with time}, journal = {Bioinformatics}, volume = {28}, number = {12}, year = {2012}, pages = {i40{\textendash}8}, abstract = {MOTIVATION: Biological networks change in response to genetic and environmental cues. Changes are reflected in the abundances of biomolecules, the composition of protein complexes and other descriptors of the biological state. Methods to infer the dynamic state of a cell would have great value for understanding how cells change over time to accomplish biological goals. RESULTS: A new method predicts the dynamic state of protein complexes in a cell, with protein expression inferred from transcription profile time courses and protein complexes inferred by joint analysis of protein co-expression and protein-protein interaction maps. Two algorithmic advances are presented: a new method, DHAC (Dynamical Hierarchical Agglomerative Clustering), for clustering time-evolving networks; and a companion method, MATCH-EM, for matching corresponding clusters across time points. With link prediction as an objective assessment metric, DHAC provides a substantial advance over existing clustering methods. An application to the yeast metabolic cycle demonstrates how waves of gene expression correspond to individual protein complexes. Our results suggest regulatory mechanisms for assembling the mitochondrial ribosome and illustrate dynamic changes in the components of the nuclear pore. AVAILABILITY: All source code and data are available under the Boost Software License as supplementary material, at www.baderzone.org, and at sourceforge.net/projects/dhacdist.}, keywords = {My Papers}, author = {Park, Yongjin and Bader, Joel S} } @article {pmid22105750, title = {Identification by families of pediatric adverse events and near misses overlooked by health care providers}, journal = {CMAJ}, volume = {184}, number = {1}, year = {2012}, month = {Jan}, pages = {29{\textendash}34}, author = {Daniels, J. P. and Hunc, K. and Cochrane, D. D. and Carr, R. and Shaw, N. T. and Taylor, A. and Heathcote, S. and Brant, R. and Lim, J. and Ansermino, J. M.} } @article {JuePress2012, title = {The impact of price discounts and calorie messaging on beverage consumption: A multi-site field study}, journal = {Preventive Medicine}, volume = {55}, year = {2012}, pages = {629{\textendash}633}, url = {http://dx.doi.org/10.1016/j.ypmed.2012.10.009}, author = {Jue, J. Jane S. and Press, Matthew J. and McDonald, Daniel J. and Volpp, Kevin G. and Asch, David A. and Mitra, Nandita and Stanowski, Anthony C. and Loewenstein, George} } @article {chen2012inference, title = {Inference on the order of a normal mixture}, journal = {Journal of the American Statistical Association}, volume = {107}, number = {499}, year = {2012}, pages = {1096{\textendash}1105}, publisher = {Taylor \& Francis Group}, author = {Chen, Jiahua and Li, Pengfei and Fu, Yuejiao} } @book {rizopoulos_joint_2012, title = {Joint Models for Longitudinal and Time-to-Event Data: With Applications in R}, year = {2012}, month = {jun}, publisher = {CRC Press}, organization = {CRC Press}, abstract = {In longitudinal studies it is often of interest to investigate how a marker that is repeatedly measured in time is associated with a time to an event of interest, e.g., prostate cancer studies where longitudinal PSA level measurements are collected in conjunction with the time-to-recurrence. Joint Models for Longitudinal and Time-to-Event Data: With Applications in R provides a full treatment of random effects joint models for longitudinal and time-to-event outcomes that can be utilized to analyze such data. The content is primarily explanatory, focusing on applications of joint modeling, but sufficient mathematical details are provided to facilitate understanding of the key features of these models. All illustrations put forward can be implemented in the R programming language via the freely available package JM written by the author. All the R code used in the book is available at: http://jmr.r-forge.r-project.org/}, keywords = {Mathematics / Probability \& Statistics / General, Medical / Epidemiology, Science / Life Sciences / Biology}, isbn = {978-1-4398-7286-4}, author = {Rizopoulos, Dimitris} } @article { ISI:000313051500018, title = {Labeling Nodes Using Three Degrees of Propagation}, journal = {PLOS ONE}, volume = {7}, number = {12}, year = {2012}, month = {DEC 28}, pages = {e51947}, publisher = {PUBLIC LIBRARY SCIENCE}, type = {Article}, address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA}, abstract = {The properties (or labels) of nodes in networks can often be predicted based on their proximity and their connections to other labeled nodes. So-called {\textquoteleft}{\textquoteleft}label propagation algorithms{\textquoteright}{\textquoteright} predict the labels of unlabeled nodes by propagating information about local label density iteratively through the network. These algorithms are fast, simple and scale to large networks but nonetheless regularly perform better than slower and much more complex algorithms on benchmark problems. We show here, however, that these algorithms have an intrinsic limitation that prevents them from adapting to some common patterns of network node labeling; we introduce a new algorithm, 3Prop, that retains all their advantages but is much more adaptive. As we show, 3Prop performs very well on node labeling problems ill-suited to label propagation, including predicting gene function in protein and genetic interaction networks and gender in friendship networks, and also performs slightly better on problems already well-suited to label propagation such as labeling blogs and patents based on their citation networks. 3Prop gains its adaptability by assigning separate weights to label information from different steps of the propagation. Surprisingly, we found that for many networks, the third iteration of label propagation receives a negative weight.}, issn = {1932-6203}, doi = {10.1371/journal.pone.0051947}, author = {Mostafavi, Sara and Goldenberg, Anna and Morris, Quaid} } @article {hu2012likelihood, title = {Likelihood With Applications}, journal = {Empirical Bayes and Likelihood Inference}, volume = {148}, year = {2012}, pages = {211}, publisher = {Springer Science and Business Media}, author = {Hu, F. and Zidek, J.V.} } @article {mackay_altman_longitudinal_2012, title = {A longitudinal model for magnetic resonance imaging lesion count data in multiple sclerosis patients}, journal = {Statistics in Medicine}, volume = {31}, number = {5}, year = {2012}, pages = {449{\textendash}469}, abstract = {

Magnetic resonance imaging (MRI) data are routinely collected at multiple time points during phase 2 clinical trials in multiple sclerosis. However, these data are typically summarized into a single response for each patient before analysis. Models based on these summary statistics do not allow the exploration of the trade-off between numbers of patients and numbers of scans per patient or the development of optimal schedules for MRI scanning. To address these limitations, in this paper, we develop a longitudinal model to describe one MRI outcome: the number of lesions observed on an individual MRI scan. We motivate our choice of a mixed hidden Markov model based both on novel graphical diagnostic methods applied to five real data sets and on conceptual considerations. Using this model, we compare the performance of a number of different tests of treatment effect. These include standard parametric and nonparametric tests, as well as tests based on the new model. We conduct an extensive simulation study using data generated from the longitudinal model to investigate the parameters that affect test performance and to assess size and power. We determine that the parameters of the hidden Markov chain do not substantially affect the performance of the tests. Furthermore, we describe conditions under which likelihood ratio tests based on the longitudinal model appreciably outperform the standard tests based on summary statistics. These results establish that the new model is a valuable practical tool for designing and analyzing multiple sclerosis clinical trials. Copyright {\textcopyright} 2011 John Wiley \& Sons, Ltd.

}, keywords = {clinical trials, hypothesis testing, latent variables, longitudinal count data, mixed hidden Markov model, model diagnostics}, doi = {10.1002/sim.4394}, url = {http://onlinelibrary.wiley.com/doi/10.1002/sim.4394/abstract}, author = {Altman, RM and Petkau, A.John and Vrecko, D and Smith, A} } @article {zhang_loss_2012, title = {Loss of Heterozygosity (LOH) Profiles{\textemdash}Validated Risk Predictors for Progression to Oral Cancer}, journal = {Cancer Prevention Research}, volume = {5}, number = {9}, year = {2012}, month = {sep}, pages = {1081{\textendash}1089}, abstract = {A major barrier to oral cancer prevention has been the lack of validated risk predictors for oral premalignant lesions (OPL). In 2000, we proposed a loss of heterozygosity (LOH) risk model in a retrospective study. This paper validated the previously reported LOH profiles as risk predictors and developed refined models via the largest longitudinal study to date of low-grade OPLs from a population-based patient group. Analysis involved a prospective cohort of 296 patients with primary mild/moderate oral dysplasia enrolled in the Oral Cancer Prediction Longitudinal Study. LOH status was determined in these OPLs. Patients were classified into high-risk or low-risk profiles to validate the 2000 model. Risk models were refined using recursive partitioning and Cox regression analyses. The prospective cohort validated that the high-risk lesions (3p and/or 9p LOH) had a 22.6-fold increase in risk (P = 0.002) compared with low-risk lesions (3p and 9p retention). Addition of another 2 markers (loci on 4q/17p) further improved the risk prediction, with five-year progression rates of 3.1\%, 16.3\%, and 63.1\% for the low-, intermediate-, and high-risk lesions, respectively. Compared with the low-risk group, intermediate- and high-risk groups had 11.6-fold and 52.1-fold increase in risk (P < 0.001). LOH profiles as risk predictors in the refined model were validated in the retrospective cohort. Multicovariate analysis with clinical features showed LOH models to be the most significant predictors of progression. LOH profiles can reliably differentiate progression risk for OPLs. Potential uses include increasing surveillance for patients with elevated risk, improving target intervention for high-risk patients while sparing a large number of low-risk patients from needless screening and treatment. Cancer Prev Res; 5(9); 1081{\textendash}9. {\textcopyright}2012 AACR.}, issn = {1940-6207, 1940-6215}, doi = {10.1158/1940-6207.CAPR-12-0173}, url = {http://cancerpreventionresearch.aacrjournals.org/content/5/9/1081}, author = {Zhang, Lewei and Poh, Catherine F. and Williams, Michele and Laronde, Denise M. and Berean, Ken and Gardner, Pamela J. and Jiang, Huijun and WU, LANG and Lee, J. Jack and Rosin, Miriam P.} } @article {bornn2012modeling, title = {Modeling nonstationary processes through dimension expansion}, journal = {Journal of the American Statistical Association}, volume = {107}, number = {497}, year = {2012}, pages = {281{\textendash}289}, publisher = {Taylor and Francis}, author = {Bornn, Luke and Shaddick, Gavin and Zidek, James V.} } @article { ISI:000298415000006, title = {MRI monitoring of immunomodulation in relapse-onset multiple sclerosis trials}, journal = {Nature Reviews Neurology}, volume = {8}, number = {1}, year = {2012}, pages = {13-21}, publisher = {NATURE PUBLISHING GROUP}, address = {75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA}, abstract = {

Over the past 15 years, MRI lesion activity has become the accepted surrogate primary outcome measure in proof-of-concept placebo-controlled clinical trials of new immunomodulating therapies in relapse-onset multiple sclerosis (MS). In parallel, the number of patients that are available for the placebo arm of trials has declined, and more-aggressive drugs are being developed. A critical review is warranted to ensure efficient MRI-and patient-resource utilization. Recently, an international panel reviewed the methodology for efficient use of MRI-monitored trials in relapse-onset MS. In this article, we provide up-to-date recommendations for scan acquisition, image analysis, outcome-measure definition and standards of reporting. Factors to consider for optimizing trial design, such as outcome measure selection and the unique requirements of phase II and phase III trials, including active-comparator studies, are outlined. Finally, we address safety considerations in the use of MRI in MS trials, and the safety-related responsibilities of the various parties involved in conducting such trials.

}, doi = {10.1038/nrneurol.2011.190}, author = {Barkhof, F and Simon, JH and Fazekas, F and Rovaris, M and Kappos, L and de Stefano, N and Polman, CH and Petkau, J and Radue, EW and Sormani, MP and Li, DK and O{\textquoteright}Connor, P and Montalban, X and Miller, DH and Filippi, M} } @article {altman_mri-based_2012, title = {MRI-based clinical trials in relapsing-remitting multiple sclerosis: new sample size calculations based on a longitudinal model}, journal = {Multiple Sclerosis Journal}, volume = {18}, number = {11}, year = {2012}, pages = {1600{\textendash}1608}, abstract = {

BACKGROUND: Sample sizes for magnetic resonance imaging (MRI)-based clinical trials in multiple sclerosis (MS) generally assume that lesion counts are reasonably described by the negative binomial (NB) model. OBJECTIVE: This study aimed to assess the appropriateness of the NB model for lesion count data and to provide sample sizes for placebo-controlled, MRI-based clinical trials in relapsing-remitting MS using a more realistic model. METHODS: The fit of the NB model in each arm of five MS clinical trials was assessed using Pearson{\textquoteright}s chi-squared statistic. Required sample sizes associated with various tests of treatment effect were estimated by simulating data from a new, longitudinal model for repeated lesion count data on individual patients. RESULTS: Evidence (p \< 0.05) against the NB model was found in at least one arm of four of the five trials. If a trial is designed using this model but the resulting clinical data do not follow its assumptions then this trial can be seriously under-powered for assessing differences in mean lesion counts. CONCLUSION: Sample sizes based on the longitudinal model are more realistic and often smaller than those previously reported using the NB model.

}, keywords = {Brain, Chi-Square Distribution, Computer Simulation, Controlled Clinical Trials as Topic, Endpoint Determination, Humans, Longitudinal Studies, magnetic resonance imaging, Models, multiple sclerosis, Predictive Value of Tests, Relapsing-Remitting, Sample Size, Statistical, Time Factors, Treatment Outcome}, doi = {10.1177/1352458512444326}, author = {Altman, RM and Petkau, A.John and Vrecko, D and Smith, A} } @article {domanski2012mrm, title = {MRM-based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma}, journal = {Proteomics}, volume = {12}, number = {8}, year = {2012}, pages = {1222{\textendash}1243}, publisher = {Wiley Online Library}, author = {Domanski, Dominik and Percy, Andrew J and Yang, Juncong and Chambers, Andrew G and Hill, John S and Freue, Gabriela V Cohen and Borchers, Christoph H} } @inbook {van2012multiagent, title = {Multiagent estimators of an exponential mean}, booktitle = {Contemporary Developments in Bayesian Analysis and Statistical Decision Theory: A Festschrift for William E. Strawderman}, year = {2012}, pages = {131{\textendash}153}, publisher = {Institute of Mathematical Statistics}, organization = {Institute of Mathematical Statistics}, author = {van Eeden, Constance and Zidek, James V and others} } @article {freue2012multiple, title = {Multiple Reaction Monitoring (MRM) Principles and Application to Coronary Artery Disease}, journal = {Circulation: Cardiovascular Genetics}, volume = {5}, number = {3}, year = {2012}, pages = {378{\textendash}378}, publisher = {Am Heart Assoc}, author = {Freue, Gabriela V Cohen and Borchers, Christoph H} } @article { ISI:000310480000021, title = {Multivariate inverse Gaussian and skew-normal densities}, journal = {Statistics \& Probability Letters}, volume = {82}, number = {12}, year = {2012}, month = {DEC}, pages = {2244-2251}, publisher = {Elsevier Science BV}, type = {Article}, abstract = {Based on inverse Gaussian random variables being transformations of skew-normal random variables, multivariate inverse Gaussian densities are obtained from appropriate multivariate skew-normal distributions. The new skew-normal distributions have some closure properties not satisfied by other multivariate skew-normal distributions. (C) 2012 Elsevier B.V. All rights reserved.}, keywords = {Closure under margins, t distribution, Transformed random variables}, issn = {0167-7152}, doi = {10.1016/j.spl.2012.08.004}, author = {Joe, Harry and Seshadri, Vanamamalai and Arnold, Barry C.} } @article { ISI:000309359000009, title = {Natural, innate improvements in multiple sclerosis disability}, journal = {Multiple Sclerosis Journal}, volume = {18}, number = {10}, year = {2012}, pages = {1412-1421}, publisher = {SAGE PUBLICATIONS LTD}, address = {1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND}, abstract = {

Background: Improvements in multiple sclerosis (MS) disability have recently been reported in immunomodulatory drug (IMD) clinical trials and observational studies. However, improvements have rarely been examined in natural history or IMD naive patients. We investigated annual and biennial improvements in Expanded Disability Status Scale (EDSS) scores in British Columbia, Canada. Methods: The British Columbian MS database was accessed for definite MS patients (1980-2009). Consecutive IMD-free EDSS scores one and two years apart (+/- 3 months) were examined; improvements (\>= 0.5,\>= 1,\>= 2 EDSS points) and sustained improvements (confirmed at one year) were described. The influence of patient characteristics on improvements was examined using logistic regression. Results: From 16,132 EDSS scores, 7653 yearly and 5845 biennial EDSS intervals were available for 2961 and 2382 patients respectively. Of the yearly intervals, 14.9\% showed an improvement (\>= 0.5 points), 8.3\% \>= 1 point and 2.2\% \>= 2 point improvement, with nearly half being sustained. Corresponding worsenings were observed in 32.9\%, 20.5\% and 7.9\% respectively, with stability in just over half (53\%). Biennial findings were similar. Characteristics generally associated with improvements included: female sex, younger age, shorter disease duration, relapsing-onset and presence of moderate disability (compared with mild or advanced) and a previous episode of worsening (disassociated from a relapse). However, improvements were also observed after periods of stability and in primary-progressive MS. Conclusion: Improvements in MS disability over one or two years are not unusual. We suggest the term {\textquoteleft}innate improvements{\textquoteright}. Our findings have implication for the design of clinical trials and observational studies in MS targeting improvements on the EDSS.

}, keywords = {disability, disease progression, improvement, innate improvement, multiple sclerosis, natural history}, doi = {10.1177/1352458512439119}, author = {Tremlett, H and Zhu, F and Petkau, J and Oger, J and Zhao, Y} } @article {SAM:SAM11149, title = {Nearest-neighbors medians clustering}, journal = {Statistical Analysis and Data Mining}, volume = {5}, number = {4}, year = {2012}, pages = {349{\textendash}362}, publisher = {Wiley Subscription Services, Inc., A Wiley Company}, keywords = {cluster analysis, local median, nearest neighbors, number of clusters}, issn = {1932-1872}, doi = {10.1002/sam.11149}, url = {http://dx.doi.org/10.1002/sam.11149}, author = {Pena, Daniel and Viladomat, J{\'u}lia and Zamar, Ruben} } @article { ISI:000299903700010, title = {Neutralizing antibodies to interferon beta-1b in multiple sclerosis: a clinico-radiographic paradox in the BEYOND trial}, journal = {Multiple Sclerosis Journal}, volume = {18}, number = {2}, year = {2012}, pages = {181-195}, publisher = {SAGE PUBLICATIONS LTD}, address = {1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND}, abstract = {

Background: The frequency and impact of neutralizing antibodies (NAbs) to interferon beta-1b (IFN beta-1b) on clinical and radiographic outcomes is controversial. Objective: To assess NAb impact in the BEYOND study. Methods: 2244 patients were randomized (2:2:1) to receive IFN beta-1b, either 250 or 500 mu g, or glatiramer acetate, 20 mg, and observed for 2-3.5 years. NAb titers were determined every 6 months. A titer \>= 20 NU/ml was considered NAb positive. Efficacy was compared between NAb-positive and NAb-negative patients, using comprehensive statistical analyses, taking into account the delayed appearance of NAbs, the time-dependent changes in the relapse rate, spontaneous reversions to NAb-negative status, NAb-titer level, and also adjusting for baseline factors. Results: In the IFN beta-1b 250 mu g group, NAb-positive titers were detected (\>= once) in 319 patients (37.0\%); of these, 112 (35.1\%) reverted to NAb-negative status. In the IFN beta-1b 500 mu g group, 340 patients (40.7\%) became NAb-positive and 119 (35.0\%) reverted to NAb-negative status. In both IFN beta groups, especially the 250 mu g arm, NAb-positive status was not associated with a convincing impact on any clinical outcome measure by any statistical analysis. By contrast, in both IFN beta groups, NAbs were associated with a very consistent deleterious impact on most MRI outcomes. Conclusion: There was a notable dissociation between the impact of NAbs on MRI and clinical outcomes. On MRI measures, the impact was consistent and convincing, whereas on clinical measures a negative impact of NAbs was not found. The basis for this clinico-radiographic paradox is unknown but it suggests that the relationship between NAbs and the therapeutic effects of IFN beta-1b is complex.

}, keywords = {BEYOND study, Interferon beta-1b, multiple sclerosis, neutralizing antibodies}, doi = {10.1177/1352458511418629}, author = {Goodin, DS and Hartung, HP and O{\textquoteright}Connor, P and Filippi, M and Arnason, B and Comi, G and Cook, S and Jeffery, D and Kappos, L and Bogumil, T and Knappertz, V and Sandbrink, R and Beckmann, K and White, R and Petkau, J and Pohl, C} } @article {goodin2012neutralizing, title = {Neutralizing antibodies to interferon beta-1b multiple sclerosis: a clinico-radiographic paradox in the BEYOND trial}, journal = {Multiple Sclerosis Journal}, volume = {18}, number = {2}, year = {2012}, pages = {181{\textendash}195}, publisher = {Sage Publications}, author = {Goodin, Douglas S and Hartung, Hans-Peter and O{\textquoteright}Connor, Paul and Filippi, Massimo and Arnason, Barry and Comi, Giancarlo and Cook, Stuart and Jeffery, Douglas and Kappos, Ludwig and Bogumil, Timon and others} } @article {chenorder, title = {ORDER SELECTION IN FINITE MIXTURE MODELS}, journal = {Journal of the American Statistical Association}, volume = {103}, year = {2012}, chapter = {1674-1683}, author = {Chen, Jiahua and Khalili, Abbas} } @article { ISI:000309793400023, title = {Pair copula constructions for multivariate discrete data}, journal = {Journal of the American Statistical Association}, volume = {107}, number = {499}, year = {2012}, month = {SEP}, pages = {1063-1072}, publisher = {Amer Statistical Assoc}, type = {Article}, abstract = {Multivariate discrete response data can be found in diverse fields, including econometrics, finance, biometrics, and psychometrics. Our contribution, through this study, is to introduce a new class of models for multivariate discrete data based on pair copula constructions (PCCs) that has two major advantages. First, by deriving the conditions under which any multivariate discrete distribution can be decomposed as a PCC, we show that discrete PCCs attain highly flexible dependence structures. Second, the computational burden of evaluating the likelihood for an m-dimensional discrete PCC only grows quadratically with in. This compares favorably to existing models for which computing the likelihood either requires the evaluation of 2(m) terms or slow numerical integration methods. We demonstrate the high quality of inference function for margins and maximum likelihood estimates, both under a simulated setting and for an application to a longitudinal discrete dataset on headache severity. This article has online supplementary material.}, keywords = {D-vine, Inference function for margins, Longitudinal data, Model selection, Ordered probit regression}, issn = {0162-1459}, doi = {10.1080/01621459.2012.682850}, author = {Panagiotelis, Anastasios and Czado, Claudia and Joe, Harry} } @article {Wang2012c, title = {Partial identification arising from nondifferential exposure misclassification: how informative are data on the unlikely, maybe, and likely exposed?}, journal = {The international journal of biostatistics}, volume = {8}, number = {1}, year = {2012}, doi = {10.1515/1557-4679.1397}, author = {Wang, Dongxu and Shen, Tian and Gustafson, Paul} } @article {Wang2012b, title = {Partial Identification arising from Nondifferential Exposure Misclassification: How Informative are Data on the Unlikely, Maybe, and Likely Exposed?}, journal = {International Journal of Biostatistics}, volume = {8}, year = {2012}, pages = {issue 1, article 31}, doi = {10.1515/1557-4679.1397}, url = {http://www.degruyter.com/view/j/ijb.2012.8.issue-1/1557-4679.1397/1557-4679.1397.xml?format=INT}, author = {Wang, D. and Shen, T. and Gustafson, P.} } @article {shangari2012partial, title = {Partial monotonicity of entropy measures}, journal = {Statistics \& Probability Letters}, volume = {82}, number = {11}, year = {2012}, pages = {1935{\textendash}1940}, publisher = {North-Holland}, author = {Shangari, Dhruv and Chen, Jiahua} } @article {Bouchard2012Phylogenetic, title = {Phylogenetic inference via sequential Monte Carlo}, journal = {Systematic Biology}, volume = {61}, year = {2012}, pages = {579{\textendash}593}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Sriram Sankararaman and Michael I. Jordan} } @article {pmid22992354, title = {Physical activity implementation in schools: a 4-year follow-up}, journal = {Am J Prev Med}, volume = {43}, number = {4}, year = {2012}, month = {Oct}, pages = {369{\textendash}377}, author = {Masse, L. C. and McKay, H. and Valente, M. and Brant, R. and Naylor, P. J.} } @article {singh2012plasma, title = {Plasma proteomics can discriminate isolated early from dual responses in asthmatic individuals undergoing an allergen inhalation challenge}, journal = {PROTEOMICS-Clinical Applications}, volume = {6}, number = {9-10}, year = {2012}, pages = {476{\textendash}485}, author = {Singh, Amrit and Cohen Freue, Gabriela V and Oosthuizen, Jean L and Kam, Sarah HY and Ruan, Jian and Takhar, Mandeep K and Gauvreau, Gail M and O{\textquoteright}Byrne, Paul M and FitzGerald, J Mark and Boulet, Louis-Philippe and others} } @article {Bouchard2012Poisson, title = {The Poisson Indel Process}, journal = {arXiv}, volume = {1207.6327}, year = {2012}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Michael I. Jordan} } @article {pmid22278180, title = {Postnatal infection is associated with widespread abnormalities of brain development in premature newborns}, journal = {Pediatr. Res.}, volume = {71}, number = {3}, year = {2012}, month = {Mar}, pages = {274{\textendash}279}, author = {Chau, V. and Brant, R. and Poskitt, K. J. and Tam, E. W. and Synnes, A. and Miller, S. P.} } @booklet {shaddick2012preferential, title = {Preferential sampling in long term monitoring of air pollution: a case study}, number = {267}, year = {2012}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Shaddick, Gavin and Zidek, James V.} } @article {maclehose2012probabilistic, title = {Is probabilistic bias analysis approximately Bayesian?}, journal = {Epidemiology}, volume = {23}, number = {1}, year = {2012}, pages = {151}, doi = {10.1097/EDE.0b013e31823b539c}, url = {10.1097/EDE.0b013e31823b539c}, author = {MacLehose, R.F. and Gustafson, P.} } @article {pmid22374882, title = {Procedural pain and brain development in premature newborns}, journal = {Ann. Neurol.}, volume = {71}, number = {3}, year = {2012}, month = {Mar}, pages = {385{\textendash}396}, author = {Brummelte, S. and Grunau, R. E. and Chau, V. and Poskitt, K. J. and Brant, R. and Vinall, J. and Gover, A. and Synnes, A. R. and Miller, S. P.} } @booklet {zhai2012review, title = {A review of dynamic duration of load models for lumber strength}, number = {270}, year = {2012}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {ZHAI, YONGLIANG and Heckman, Nancy and LUM, CONROY and PIRVU, CIPRIAN and WU, LANG and Zidek, James V.} } @article {kondo2012robust, title = {A robust and sparse K-means clustering algorithm}, journal = {arXiv preprint arXiv:1201.6082}, year = {2012}, author = {Kondo, Yumi and Salibian-Barrera, Mat{\'\i}as and Zamar, Ruben} } @article { ISI:000309793400033, title = {Robust Estimation of Multivariate Location and Scatter in the Presence of Missing Data}, journal = {JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION}, volume = {107}, number = {499}, year = {2012}, month = {SEP}, pages = {1178-1186}, publisher = {AMER STATISTICAL ASSOC}, type = {Article}, address = {732 N WASHINGTON ST, ALEXANDRIA, VA 22314-1943 USA}, abstract = {Two main issues regarding data quality are data contamination (outliers) and data completion (missing data). These two problems have attracted much attention and research but surprisingly, they are seldom considered together. Popular robust methods such as S-estimators of multivariate location and scatter offer protection against outliers but cannot deal with missing data, except for the obviously inefficient approach of deleting all incomplete cases. We generalize the definition of S-estimators of multivariate location and scatter to simultaneously deal with missing data and outliers. We show that the proposed estimators are strongly consistent under elliptical models when data are missing completely at random. We derive an algorithm similar to the Expectation-Maximization algorithm for computing the proposed estimators. This algorithm is initialized by an extension for missing data of the minimum volume ellipsoid. We assess the performance of our proposal by Monte Carlo simulation and give some real data examples. This article has supplementary material online.}, keywords = {Consistent, Elliptical distribution, EM algorithm, Fixed point equation}, issn = {0162-1459}, doi = {10.1080/01621459.2012.699792}, author = {Danilov, Mike and Yohai, Victor J. and Zamar, Ruben H.} } @booklet {Cubranic2012, title = {SBSA: Simplified Bayesian Sensitivity Analysis}, year = {2012}, note = {R package version 0.2.0}, url = {http://CRAN.R-project.org/package=SBSA}, author = {Davor Cubranic and Paul Gustafson} } @article { ISI:000312614700014, title = {Sensitivity of the limit shape of sample clouds from meta densities}, journal = {BERNOULLI}, volume = {18}, number = {4}, year = {2012}, month = {NOV}, pages = {1386-1404}, publisher = {INT STATISTICAL INST}, type = {Article}, address = {428 PRINSES BEATRIXLAAN, 2270 AZ VOORBURG, NETHERLANDS}, abstract = {The paper focuses on a class of light-tailed multivariate probability distributions. These are obtained via a transformation of the margins from a heavy-tailed original distribution. This class was introduced in Balkema et al. (J. Multivariate Anal. 101 (2010) 1738-1754). As shown there, for the light-tailed meta distribution the sample clouds, properly scaled, converge onto a deterministic set. The shape of the limit set gives a good description of the relation between extreme observations in different directions. This paper investigates how sensitive the limit shape is to changes in the underlying heavy-tailed distribution. Copulas fit in well with multivariate extremes. By Galambos{\textquoteright}s theorem, existence of directional derivatives in the upper endpoint of the copula is necessary and sufficient for convergence of the multivariate extremes provided the marginal maxima converge. The copula of the max-stable limit distribution does not depend on the margins. So margins seem to play a subsidiary role in multivariate extremes. The theory and examples presented in this paper cast a different light on the significance of margins. For light-tailed meta distributions, the asymptotic behaviour is very sensitive to perturbations of the underlying heavy-tailed original distribution, it may change drastically even when the asymptotic behaviour of the heavy-tailed density is not affected.}, keywords = {extremes, Limit set, limit shape, meta distribution, regular partition, sensitivity}, issn = {1350-7265}, doi = {10.3150/11-BEJ370}, author = {Balkema, Guus and Embrechts, Paul and Nolde, Natalia} } @article {ascherio2012serum, title = {Serum 25-hydroxyvitamin D concentrations among patients in BENEFIT predicts conversion to multiple sclerosis, MRI lesions, and brain volume loss}, year = {2012}, author = {Ascherio, A and Munger, K and Simon, C and Kappos, L and Polman, CH and Freedman, MS and Hartung, HP and Miller, DH and Montalban, X and Edan, G and others} } @article {pmid22313364, title = {Single course of antenatal steroids did not alter cortisol in preterm infants up to 18 months}, journal = {Acta Paediatr.}, volume = {101}, number = {6}, year = {2012}, month = {Jun}, pages = {604{\textendash}608}, author = {Gover, A. and Brummelte, S. and Synnes, A. R. and Miller, S. P. and Brant, R. and Weinberg, J. and Grunau, R. E.} } @booklet {zhai2012stochastic, title = {Stochastic models for the effects of duration of load on lumber properties}, number = {271}, year = {2012}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {ZHAI, YONGLIANG and Heckman, Nancy and LUM, CONROY and PIRVU, CIPRIAN and WU, LANG and Zidek, James V.} } @article {van2012subset, title = {Subset selection{\textendash}extended Rizvi{\textendash}Sobel for unequal sample sizes and its implementation}, journal = {Journal of Nonparametric Statistics}, volume = {24}, number = {2}, year = {2012}, pages = {299{\textendash}315}, publisher = {Taylor and Francis}, author = {van Eeden, Constance and Zidek, James V} } @article { ISI:000302254800049, title = {Synthetic Lethality of Cohesins with PARPs and Replication Fork Mediators}, journal = {PLOS GENETICS}, volume = {8}, number = {3}, year = {2012}, month = {MAR}, pages = {e1002574}, publisher = {PUBLIC LIBRARY SCIENCE}, type = {Article}, address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA}, abstract = {Synthetic lethality has been proposed as a way to leverage the genetic differences found in tumor cells to affect their selective killing. Cohesins, which tether sister chromatids together until anaphase onset, are mutated in a variety of tumor types. The elucidation of synthetic lethal interactions with cohesin mutants therefore identifies potential therapeutic targets. We used a cross-species approach to identify robust negative genetic interactions with cohesin mutants. Utilizing essential and non-essential mutant synthetic genetic arrays in Saccharomyces cerevisiae, we screened genome-wide for genetic interactions with hypomorphic mutations in cohesin genes. A somatic cell proliferation assay in Caenorhabditis elegans demonstrated that the majority of interactions were conserved. Analysis of the interactions found that cohesin mutants require the function of genes that mediate replication fork progression. Conservation of these interactions between replication fork mediators and cohesin in both yeast and C. elegans prompted us to test whether other replication fork mediators not found in the yeast were required for viability in cohesin mutants. PARP1 has roles in the DNA damage response but also in the restart of stalled replication forks. We found that a hypomorphic allele of the C. elegans SMC1 orthologue, him-1(e879), genetically interacted with mutations in the orthologues of PAR metabolism genes resulting in a reduced brood size and somatic cell defects. We then demonstrated that this interaction is conserved in human cells by showing that PARP inhibitors reduce the viability of cultured human cells depleted for cohesin components. This work demonstrates that large-scale genetic interaction screening in yeast can identify clinically relevant genetic interactions and suggests that PARP inhibitors, which are currently undergoing clinical trials as a treatment of homologous recombination-deficient cancers, may be effective in treating cancers that harbor cohesin mutations.}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1002574}, author = {McLellan, Jessica L. and O{\textquoteright}Neil, Nigel J. and Barrett, Irene and Ferree, Elizabeth and van Pel, Derek M. and Ushey, Kevin and Sipahimalani, Payal and Bryan, Jennifer and Rose, Ann M. and Hieter, Philip} } @article { ISI:000313478200008, title = {Tail comonotonicity and conservative risk measures}, journal = {ASTIN Bulletin}, volume = {42}, number = {2}, year = {2012}, month = {NOV}, pages = {601-629}, publisher = {Peeters}, type = {Article}, abstract = {Tail comonotonicity, or asymptotic full dependence, is proposed as a reasonable conservative dependence structure for modeling dependent risks. Some sufficient conditions have been obtained to justify the conservativity of tail comonotonicity. Simulation studies also suggest that, by using tail comonotonicity, one does not lose too much accuracy but gain reasonable conservative risk measures, especially when considering high scenario risks. A copula model with tail comonotonicity is applied to an auto insurance dataset. Particular models for tail comonotonicity for loss data can be based on the BB2 and BB3 copula families and their multivariate extensions.}, keywords = {Archimedean copula, asymptotic full dependence, conditional tail expectation, Copula, Dependence modeling, Laplace transform, regular variation}, issn = {0515-0361}, doi = {10.2143/AST42.2.2182810}, author = {Hua, Lei and Joe, Harry} } @article { ISI:000309028900029, title = {Tail comonotonicity: Properties, constructions, and asymptotic additivity of risk measures}, journal = {Insurance Mathematics \& Economics}, volume = {51}, number = {2}, year = {2012}, month = {SEP}, pages = {492-503}, publisher = {Elsevier Science BV}, type = {Article}, abstract = {We investigate properties of a version of tail comonotonicity that can be applied to absolutely continuous distributions, and give several methods for constructions of multivariate distributions with tail comonotonicity or strongest tail dependence. Archimedean copulas as mixtures of powers, and scale mixtures of a non-negative random vector with the mixing distribution having slowly varying tails, lead to a tail comonotonic dependence structure. For random variables that are in the maximum domain of attraction of either Frechet or Gumbel, we prove the asymptotic additivity property of Value at Risk and Conditional Tail Expectation. (C) 2012 Elsevier B.V. All rights reserved.}, keywords = {Archimedean copula, asymptotic full dependence, Copula, Elliptical distributions, Extreme value distributions, Regularly varying, Slowly varying}, issn = {0167-6687}, doi = {10.1016/j.insmatheco.2012.07.006}, author = {Hua, Lei and Joe, Harry} } @article {dou2012temporal, title = {Temporal forecasting with a Bayesian spatial predictor: Application to ozone}, journal = {Advances in Meteorology}, volume = {2012}, year = {2012}, publisher = {Hindawi Publishing Corporation}, author = {Dou, Yiping and Le, Nhu D. and Zidek, James V.} } @article {li2012testing, title = {Testing the order of a finite mixture}, journal = {Journal of the American Statistical Association}, year = {2012}, publisher = {Taylor \& Francis}, author = {Li, Pengfei and Chen, Jiahua} } @article {heckman2012, title = {The theory and application of penalized methods or Reproducing Kernel Hilbert Spaces made easy}, journal = {Statist. Surv.}, volume = {6}, year = {2012}, pages = {113{\textendash}141}, publisher = {The American Statistical Association, the Bernoulli Society, the Institute of Mathematical Statistics, and the Statistical Society of Canada}, doi = {10.1214/12-SS101}, url = {http://dx.doi.org/10.1214/12-SS101}, author = {Heckman, Nancy} } @article {hosseini2012time, title = {Time-varying markov models for binary temperature series in agrorisk management}, journal = {Journal of agricultural, biological, and environmental statistics}, volume = {17}, number = {2}, year = {2012}, pages = {283{\textendash}305}, publisher = {Springer}, author = {Hosseini, Reza and Le, Nhu D. and Zidek, James V} } @article { ISI:000310434100010, title = {Treatment with interferon beta for multiple sclerosis: reply}, journal = {Journal of the American Medical Association}, volume = {308}, number = {16}, year = {2012}, pages = {1627-1628}, publisher = {AMER MEDICAL ASSOC}, type = {Letter}, address = {330 N WABASH AVE, STE 39300, CHICAGO, IL 60611-5885 USA}, doi = {10.1001/jama.2012.13573}, author = {Shirani, A and Petkau, J and Tremlett, H} } @article {liu_two-step_2012, title = {Two-step and likelihood methods for HIV viral dynamic models with covariate measurement errors and missing data}, journal = {Journal of Applied Statistics}, volume = {39}, number = {5}, year = {2012}, month = {may}, pages = {963{\textendash}978}, abstract = {HIV viral dynamic models have received much attention in the literature. Long-term viral dynamics may be modelled by semiparametric nonlinear mixed-effect models, which incorporate large variation between subjects and autocorrelation within subjects and are flexible in modelling complex viral load trajectories. Time-dependent covariates may be introduced in the dynamic models to partially explain the between-individual variations. In the presence of measurement errors and missing data in time-dependent covariates, we show that the commonly used two-step method may give approximately unbiased estimates but may under-estimate standard errors. We propose a two-stage bootstrap method to adjust the standard errors in the two-step method and a likelihood method.}, issn = {0266-4763}, doi = {10.1080/02664763.2011.632404}, url = {http://dx.doi.org/10.1080/02664763.2011.632404}, author = {Liu, Wei and WU, LANG} } @article {zidek2012unbiasing, title = {Unbiasing estimates from preferentially sampled spatial data}, journal = {Relatorio Technico}, volume = {268}, year = {2012}, author = {Zidek, J.V. and Shaddick, G.} } @booklet {shaddick2012unbiasing, title = {Unbiasing estimates from preferentially sampled spatial data}, number = {268}, year = {2012}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Shaddick, Gavin and Zidek, James V.} } @article {poh_unique_2012, title = {Unique FISH Patterns Associated with Cancer Progression of Oral Dysplasia}, journal = {Journal of Dental Research}, volume = {91}, number = {1}, year = {2012}, month = {jan}, pages = {52{\textendash}57}, abstract = {Subgroups of patients with oral pre-malignant lesions (OPLs) are at extremely high risk for developing invasive cancer in spite of surgical excision. The objective of this study was to evaluate the utility of specific genes and their associated centromeres as markers to stratify OPLs for their cancer risk. Samples used in this study included 35 oral dysplasia with known outcome and 20 normal oral mucosa. Of the dysplasias, 20 were from an ongoing longitudinal study showing progression. The remaining 15 cases (2 of which progressed) were chosen from the population-based, provincial BC Oral Biopsy Service (OBS). Copy number alterations at EGFR, CEP7, CCND1, and CEP11 were evaluated by fluorescent in situ hybridization (FISH). There was no significant difference in demographics between progressors and non-progressors. Specific FISH profiles at these genes and their corresponding centromeres were associated with progression. High gene gain of CCND1 was associated with an 8-fold elevated risk of progression compared with those with no gain in time-to-progression analysis. Numerical alterations of EGFR and CCND1 and their centromeres might be an effective means for identifying OPLs at risk. Future studies will expand on this analysis and set the stage for application of this approach in routine clinical practice.}, keywords = {CCND1, chromosomal instability, EGFR, fluorescent in situ hybridization, oral dysplasia, progression}, issn = {0022-0345, 1544-0591}, doi = {10.1177/0022034511425676}, url = {http://jdr.sagepub.com/content/91/1/52}, author = {Poh, C. F. and Zhu, Y. and Chen, E. and Berean, K. W. and Wu, L. and Zhang, L. and Rosin, M. P.} } @article {domanski2012use, title = {The use of multiplexed MRM for the discovery of biomarkers to differentiate iron-deficiency anemia from anemia of inflammation}, journal = {Journal of proteomics}, volume = {75}, number = {12}, year = {2012}, pages = {3514{\textendash}3528.*Equal contributors.}, publisher = {Elsevier}, abstract = {

In this study we demonstrate the use of a multiplexed MRM-based assay to distinguish among normal (NL) and iron-metabolism disorder mouse models, particularly, iron-deficiency anemia (IDA), inflammation (INFL), and inflammation and anemia (INFL + IDA). Our initial panel of potential biomarkers was based on the analysis of 14 proteins expressed by candidate genes involved in iron transport and metabolism. Based on this study, we were able to identify a panel of 8 biomarker proteins: apolipoprotein {A4} (APO4), transferrin, transferrin receptor 1, ceruloplasmin, haptoglobin, lactoferrin, hemopexin, and matrix metalloproteinase-8 (MMP8) that clearly distinguish among the normal and disease models. Within this set of proteins, transferrin showed the best individual classification accuracy over all samples (72\%) and within the {NL} group (94\%). Compared to the best single-protein biomarker, transferrin, the use of the composite 8-protein biomarker panel improved the classification accuracy from 94\% to 100\% in the {NL} group, from 50\% to 72\% in the {INFL} group, from 66\% to 96\% in the {IDA} group, and from 79\% to 83\% in the {INFL} + {IDA} group. Based on these findings, validation of the utility of this potentially important biomarker panel in human samples in an effort to differentiate IDA, inflammation, and combinations thereof, is now warranted. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.\ 

}, author = {Domanski, Dominik* and Freue, Gabriela V Cohen* and Sojo, Luis and Kuzyk, Michael A and Ratkay, Leslie and Parker, Carol E and Goldberg, Y Paul and Borchers, Christoph H} } @article {pmid22813688, title = {Using International Classification of Diseases, 10th edition, codes to estimate abusive head trauma in children}, journal = {Am J Prev Med}, volume = {43}, number = {2}, year = {2012}, month = {Aug}, pages = {215{\textendash}220}, author = {Fujiwara, T. and Barr, R. G. and Brant, R. F. and Rajabali, F. and Pike, I.} } @article {pmid23093256, title = {Vaginal progesterone to prevent preterm birth in multiple pregnancy: a randomized controlled trial}, journal = {J Perinat Med}, volume = {40}, number = {6}, year = {2012}, month = {Nov}, pages = {593{\textendash}599}, author = {Wood, S. and Ross, S. and Tang, S. and Miller, L. and Sauve, R. and Brant, R.} } @article { ISI:000309785500045, title = {Vine copulas with asymmetric tail dependence and applications to financial return data}, journal = {Computational Statistics \& Data Analysis}, volume = {56}, number = {11, SI}, year = {2012}, month = {NOV}, pages = {3659-3673}, publisher = {Elsevier Science BV}, type = {Article}, abstract = {It has been shown that vine copulas constructed from bivariate t copulas can provide good fits to multivariate financial asset return data. However, there might be stronger tail dependence of returns in the joint lower tail of assets than the upper tail. To this end, vine copula models with appropriate choices of bivariate reflection asymmetric linking copulas will be used to assess such tail asymmetries. Comparisons of various vine copulas are made in terms of likelihood fit and forecasting of extreme quantiles. (C) 2010 Elsevier B.V. All rights reserved.}, keywords = {Copula-GARCH, Inference functions for margins, Reflection asymmetry, Value-at-Risk}, issn = {0167-9473}, doi = {10.1016/j.csda.2010.07.016}, author = {Nikoloulopoulos, Aristidis K. and Joe, Harry and Li, Haijun} } @article {louie2012yeast, title = {A yeast phenomic model for the gene interaction network modulating CFTR-deltaF508 protein biogenesis}, journal = {Genome Med}, volume = {4}, year = {2012}, pages = {103}, author = {Louie, Raymond J and Guo, Jingyu and Rodgers, John W and White, Rick and Shah, N and Pagant, Silvere and Kim, Peter and Livstone, Michael and Dolinski, Kara and McKinney, Brett A and others} } @article { ISI:000315598600001, title = {A yeast phenomic model for the gene interaction network modulating CFTR-Delta F508 protein biogenesis}, journal = {GENOME MEDICINE}, volume = {4}, year = {2012}, month = {DEC 27}, pages = {103}, publisher = {BIOMED CENTRAL LTD}, type = {Article}, address = {236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND}, abstract = {Background: The overall influence of gene interaction in human disease is unknown. In cystic fibrosis (CF) a single allele of the cystic fibrosis transmembrane conductance regulator (CFTR-Delta F508) accounts for most of the disease. In cell models, CFTR-Delta F508 exhibits defective protein biogenesis and degradation rather than proper trafficking to the plasma membrane where CFTR normally functions. Numerous genes function in the biogenesis of CFTR and influence the fate of CFTR-Delta F508. However it is not known whether genetic variation in such genes contributes to disease severity in patients. Nor is there an easy way to study how numerous gene interactions involving CFTR-Delta F would manifest phenotypically. Methods: To gain insight into the function and evolutionary conservation of a gene interaction network that regulates biogenesis of a misfolded ABC transporter, we employed yeast genetics to develop a {\textquoteleft}phenomic{\textquoteright} model, in which the CFTR-Delta F508-equivalent residue of a yeast homolog is mutated (Yor1-Delta F670), and where the genome is scanned quantitatively for interaction. We first confirmed that Yor1-Delta F undergoes protein misfolding and has reduced half-life, analogous to CFTR-Delta F. Gene interaction was then assessed quantitatively by growth curves for approximately 5,000 double mutants, based on alteration in the dose response to growth inhibition by oligomycin, a toxin extruded from the cell at the plasma membrane by Yor1. Results: From a comparative genomic perspective, yeast gene interactions influencing Yor1-Delta F biogenesis were representative of human homologs previously found to modulate processing of CFTR-Delta F in mammalian cells. Additional evolutionarily conserved pathways were implicated by the study, and a Delta F-specific pro-biogenesis function of the recently discovered ER membrane complex (EMC) was evident from the yeast screen. This novel function was validated biochemically by siRNA of an EMC ortholog in a human cell line expressing CFTR-Delta F508. The precision and accuracy of quantitative high throughput cell array phenotyping (Q-HTCP), which captures tens of thousands of growth curves simultaneously, provided powerful resolution to measure gene interaction on a phenomic scale, based on discrete cell proliferation parameters. Conclusion: We propose phenomic analysis of Yor1-Delta F as a model for investigating gene interaction networks that can modulate cystic fibrosis disease severity. Although the clinical relevance of the Yor1-Delta F gene interaction network for cystic fibrosis remains to be defined, the model appears to be informative with respect to human cell models of CFTR-Delta F. Moreover, the general strategy of yeast phenomics can be employed in a systematic manner to model gene interaction for other diseases relating to pathologies that result from protein misfolding or potentially any disease involving evolutionarily conserved genetic pathways.}, keywords = {ATP binding cassette (ABC) transporter, Comparative functional genomics, Cystic fibrosis transmembrane conductance regulator (CFTR), ER membrane complex (EMC), Gene interaction, Genetic buffering, Genotype-phenotype complexity, Membrane protein biogenesis, Phenomics, Quantitative high throughput cell array phenotyping (Q-HTCP), Yeast model of human disease}, issn = {1756-994X}, author = {Louie, Raymond J. and Guo, Jingyu and Rodgers, John W. and White, Rick and Shah, Najaf A. and Pagant, Silvere and Kim, Peter and Livstone, Michael and Dolinski, Kara and McKinney, Brett A. and Hong, Jeong and Sorscher, Eric J. and Bryan, Jennifer and Miller, Elizabeth A. and Hartman, John L.} } @article {louie2012yeast, title = {A yeast phenomic model for the gene interaction network modulating F508del-CFTR protein biogenesis}, journal = {Genome Medicine}, volume = {4}, number = {12}, year = {2012}, publisher = {BioMed Central Ltd}, author = {Louie, Raymond J and Guo, Jingyu and Rodgers, John W and White, Rick and Shah, Najaf A and Pagant, Silvere and Kim, Peter and Livstone, Michael and Dolinski, Kara and McKinney, Brett A and others} } @article {pmid20820172, title = {Adiposity changes after a 1-year aerobic exercise intervention among postmenopausal women: a randomized controlled trial}, journal = {Int J Obes (Lond)}, volume = {35}, number = {3}, year = {2011}, month = {Mar}, pages = {427{\textendash}435}, author = {Friedenreich, C. M. and Woolcott, C. G. and McTiernan, A. and Terry, T. and Brant, R. and Ballard-Barbash, R. and Irwin, M. L. and Jones, C. A. and Boyd, N. F. and Yaffe, M. J. and Campbell, K. L. and McNeely, M. L. and Karvinen, K. H. and Courneya, K. S.} } @article {chen2011advances, title = {Advances in EM-test for Finite Mixture Models}, journal = {International Workshop on Perspectives on High-dimensional Data Analysis}, year = {2011}, author = {Chen, Jiahua} } @conference {9222, title = {Agreeing to disagree: graphics for comparing expert classifications}, booktitle = {Proceedings of the 58th World Statistical Congress}, year = {2011}, publisher = {International Statistical Institute}, organization = {International Statistical Institute}, author = {Unwin, Antony and H{\"o}gg, Tanja and Pielh{\"o}fer, Alexander} } @article {dean2011analysis, title = {Analysis of gene expression patterns during seed coat development in Arabidopsis}, journal = {Molecular plant}, volume = {4}, number = {6}, year = {2011}, pages = {1074{\textendash}1091}, publisher = {Elsevier}, author = {Dean, Gillian and Cao, YongGuo and Xiang, DaoQuan and Provart, Nicholas J and Ramsay, Larissa and Ahad, Abdul and White, Rick and Selvaraj, Gopalan and Datla, Raju and Haughn, George} } @article {wu_analysis_2011, title = {Analysis of Longitudinal and Survival Data: Joint Modeling, Inference Methods, and Issues}, journal = {Journal of Probability and Statistics}, volume = {2012}, year = {2011}, month = {dec}, pages = {e640153}, abstract = {In the past two decades, joint models of longitudinal and survival data have received much attention in the literature. These models are often desirable in the following situations: (i) survival models with measurement errors or missing data in time-dependent covariates, (ii) longitudinal models with informative dropouts, and (iii) a survival process and a longitudinal process are associated via latent variables. In these cases, separate inferences based on the longitudinal model and the survival model may lead to biased or inefficient results. In this paper, we provide a brief overview of joint models for longitudinal and survival data and commonly used methods, including the likelihood method and two-stage methods.}, issn = {1687-952X}, doi = {10.1155/2012/640153}, url = {http://www.hindawi.com/journals/jps/2012/640153/abs/}, author = {WU, LANG and Liu, Wei and Yi, Grace Y. and Huang, Yangxin} } @article {wu_approximate2011, title = {Approximate Bounded Influence Estimation for Incompletely Observed Longitudinal Data}, journal = {Journal of Statistical Planning and Inference}, volume = {141}, year = {2011}, pages = {2321{\textendash}2330}, author = {Wu, L and Qiu, J} } @article {hossain2011assessing, title = {Assessing large sample bias in misspecified model scenarios with reference to exposure model misspecification in errors-in-variable regression: A new computational approach}, journal = {Journal of Statistical Planning and Inference}, volume = {141}, number = {3}, year = {2011}, pages = {1161{\textendash}1169}, publisher = {Elsevier}, doi = {10.1016/j.jspi.2010.09.017}, author = {Hossain, S. and Gustafson, P.} } @article {pmid20848591, title = {Associations of overall and abdominal adiposity with area and volumetric mammographic measures among postmenopausal women}, journal = {Int. J. Cancer}, volume = {129}, number = {2}, year = {2011}, month = {Jul}, pages = {440{\textendash}448}, author = {Woolcott, C. G. and Cook, L. S. and Courneya, K. S. and Boyd, N. F. and Yaffe, M. J. and Terry, T. and Brant, R. and McTiernan, A. and Bryant, H. E. and Magliocco, A. M. and Friedenreich, C. M.} } @article {pmid21599735, title = {Attitudes of the new generation of Canadian obstetricians: how do they differ from their predecessors?}, journal = {Birth}, volume = {38}, number = {2}, year = {2011}, month = {Jun}, pages = {129{\textendash}139}, author = {Klein, M. C. and Liston, R. and Fraser, W. D. and Baradaran, N. and Hearps, S. J. and Tomkinson, J. and Kaczorowski, J. and Brant, R.} } @article {espino2011bayesian, title = {Bayesian adjustment for measurement error in continuous exposures in an individually matched case-control study}, journal = {BMC Medical Research Methodology}, volume = {11}, number = {1}, year = {2011}, pages = {67}, publisher = {BioMed Central Ltd}, doi = {10.1186/1471-2288-11-67}, url = {http://www.biomedcentral.com/1471-2288/11/6}, author = {Espino-Hernandez, G. and Gustafson, P. and Burstyn, I.} } @article {Gustafson2011, title = {"Bayesian inference of gene-environment interaction from incomplete data: What happens when information on environment is disjoint from data on gene and disease?}, journal = {Statistics in Medicine}, volume = {30}, year = {2011}, pages = {877-889}, keywords = {partial identification gene environment Bayes misclassification}, doi = {10.1002/sim.4176}, url = {http://onlinelibrary.wiley.com/doi/10.1002/sim.4176/abstract}, author = {Gustafson, P. and Burstyn, I.} } @article {huang_bayesian_2011, title = {Bayesian inference on joint models of HIV dynamics for time-to-event and longitudinal data with skewness and covariate measurement errors}, journal = {Statistics in Medicine}, volume = {30}, number = {24}, year = {2011}, pages = {2930{\textendash}2946}, abstract = {Normality (symmetry) of the model random errors is a routine assumption for mixed-effects models in many longitudinal studies, but it may be unrealistically obscuring important features of subject variations. Covariates are usually introduced in the models to partially explain inter-subject variations, but some covariates such as CD4 cell count may be often measured with substantial errors. This paper formulates a class of models in general forms that considers model errors to have skew-normal distributions for a joint behavior of longitudinal dynamic processes and time-to-event process of interest. For estimating model parameters, we propose a Bayesian approach to jointly model three components (response, covariate, and time-to-event processes) linked through the random effects that characterize the underlying individual-specific longitudinal processes. We discuss in detail special cases of the model class, which are offered to jointly model HIV dynamic response in the presence of CD4 covariate process with measurement errors and time to decrease in CD4/CD8 ratio, to provide a tool to assess antiretroviral treatment and to monitor disease progression. We illustrate the proposed methods using the data from a clinical trial study of HIV treatment. The findings from this research suggest that the joint models with a skew-normal distribution may provide more reliable and robust results if the data exhibit skewness, and particularly the results may be important for HIV/AIDS studies in providing quantitative guidance to better understand the virologic responses to antiretroviral treatment. Copyright {\textcopyright} 2011 John Wiley \& Sons, Ltd.}, keywords = {Bayesian analysis, covariate measurement errors, joint mixed-effects models, Longitudinal data, skew-normal distribution, time to event}, issn = {1097-0258}, doi = {10.1002/sim.4321}, url = {http://onlinelibrary.wiley.com/doi/10.1002/sim.4321/abstract}, author = {Huang, Yangxin and Dagne, Getachew and WU, LANG} } @article {pmid21846449, title = {Birth technology and maternal roles in birth: knowledge and attitudes of canadian women approaching childbirth for the first time}, journal = {J Obstet Gynaecol Can}, volume = {33}, number = {6}, year = {2011}, month = {Jun}, pages = {598{\textendash}608}, author = {Klein, M. C. and Kaczorowski, J. and Hearps, S. J. and Tomkinson, J. and Baradaran, N. and Hall, W. A. and McNiven, P. and Brant, R. and Grant, J. and Dore, S. and Brasset-Latulippe, A. and Fraser, W. D.} } @article {pmid21352628, title = {The Canadian Perinatal Network: a national network focused on threatened preterm birth at 22 to 28 weeks{\textquoteright} gestation}, journal = {J Obstet Gynaecol Can}, volume = {33}, number = {2}, year = {2011}, month = {Feb}, pages = {111{\textendash}120}, author = {Magee, L. A. and von Dadelszen, P. and Allen, V. M. and Ansermino, J. M. and Audibert, F. and Barrett, J. and Brant, R. and Bujold, E. and Crane, J. M. and Demianczuk, N. and Joseph, K. S. and Lee, S. K. and Piedboeuf, B. and Smith, G. and Synnes, A. and Walker, M. and Whittle, W. and Wood, S. and Lee, T. and Li, J. and Payne, B. and Liston, R. M. and Burym, C. and Carson, G. and Dansereau, J. and Gratton, R. and McDonald, S. and Olatunbosun, F. and Pasquier, J. P.} } @article {pmid22408595, title = {The centre for healthy weights{\textendash}shapedown BC: a family-centered, multidisciplinary program that reduces weight gain in obese children over the short-term}, journal = {Int J Environ Res Public Health}, volume = {8}, number = {12}, year = {2011}, month = {Dec}, pages = {4662{\textendash}4678}, author = {Panagiotopoulos, C. and Ronsley, R. and Al-Dubayee, M. and Brant, R. and Kuzeljevic, B. and Rurak, E. and Cristall, A. and Marks, G. and Sneddon, P. and Hinchliffe, M. and Chanoine, J. P. and Masse, L. C.} } @article {pmid21482635, title = {Changes in insulin resistance indicators, IGFs, and adipokines in a year-long trial of aerobic exercise in postmenopausal women}, journal = {Endocr. Relat. Cancer}, volume = {18}, number = {3}, year = {2011}, month = {Jun}, pages = {357{\textendash}369}, author = {Friedenreich, C. M. and Neilson, H. K. and Woolcott, C. G. and McTiernan, A. and Wang, Q. and Ballard-Barbash, R. and Jones, C. A. and Stanczyk, F. Z. and Brant, R. F. and Yasui, Y. and Irwin, M. L. and Campbell, K. L. and McNeely, M. L. and Karvinen, K. H. and Courneya, K. S.} } @article {hughes-oliver_chemmodlab:_2011, title = {ChemModLab: A web-based cheminformatics modeling laboratory}, journal = {In silico biology}, volume = {11}, number = {1, 2}, year = {2011}, pages = {61{\textendash}81}, url = {http://content.iospress.com/articles/in-silico-biology/ci000016}, author = {Hughes-Oliver, Jacqueline M. and Brooks, Atina D. and Welch, William J. and Khaledi, Morteza G. and Hawkins, Douglas and Young, S. Stanley and Patil, Kirtesh and Howell, Gary W. and Ng, Raymond T. and Chu, Moody T.} } @conference {gu2011valencia, title = {Comment on {\textquoteleft}Transparent parameterizations of models for potential outcomes,{\textquoteright} by Richardson, Evans, and Robins}, booktitle = {Bayesian Statistics 9: Proceedings of the Ninth Valencia International Meeting}, year = {2011}, publisher = {Oxford University Press}, organization = {Oxford University Press}, author = {Gustafson, P.}, editor = {Bernardo, J. M. and Bayarri, M. J. and Berger, J. O. and Dawid, A. P. and Heckerman, D. and Smith, A. F. M. and West, M.} } @article { ISI:000287434900013, title = {Composite likelihood for time series models with a latent autoregressive process}, journal = {Statistica Sinica}, volume = {21}, number = {1, SI}, year = {2011}, month = {JAN}, pages = {279-305}, publisher = {{Statistica Sinica, TAIWAN}, abstract = {Consistency and asymptotic normality properties are proved for various composite likelihood estimators in a time series model with a latent Gaussian autoregressive process. The proofs require different techniques than for clustered data with the number of clusters going to infinity. The composite likelihood estimation method is applied to a count time series consisting of daily car accidents with weather related covariates. A simulation study for the count time series model shows that the performance of composite likelihood estimator is better than Zeger{\textquoteright}s moment-based estimator, and the relative efficiency is high with respect to approximate maximum likelihood.}, url = {http://www3.stat.sinica.edu.tw/statistica/j21n1/J21N112/J21N112.html}, author = {Ng, C. T. and Joe, Harry and Karlis, Dimitris and Liu, Juxin} } @conference {guo2011conserved, title = {A CONSERVED BIOGENESIS NETWORK FOR YEAST YOR1-Delta F AND CFTR-Delta F}, booktitle = {PEDIATRIC PULMONOLOGY}, year = {2011}, pages = {277{\textendash}277}, publisher = {WILEY-BLACKWELL COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA}, organization = {WILEY-BLACKWELL COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA}, author = {Guo, J and Louie, R and Rodgers, JW and White, R and Hong, J and Sorscher, EJ and Bryan, JA and Miller, EA and Hartman, JL} } @article {li2011constructing, title = {Constructing nonparametric likelihood confidence regions with high order precisions}, journal = {Statistica Sinica}, volume = {21}, number = {4}, year = {2011}, pages = {1767}, author = {Li, Xiao and Chen, Jiahua and Wu, Yaohua and Tu, Dongsheng} } @inbook {Joe2011a, title = {Dependence comparisons of vine copulae in four or more variables}, booktitle = {Dependence Modeling: Vine Copula Handbook}, year = {2011}, pages = {139{\textendash}164}, publisher = {World Scientific}, organization = {World Scientific}, chapter = {7}, address = {Singapore}, doi = {10.1142/9789814299886_0007}, author = {Joe, Harry}, editor = {Kurowicka, D. and Joe, H.} } @book {Kurowicka.Joe2011, title = {Dependence Modeling: Vine Copula Handbook}, year = {2011}, publisher = {World Scientific}, organization = {World Scientific}, address = {Singapore}, doi = {10.1142/9789814299886}, url = {http://www.worldscibooks.com/economics/7699.html}, author = {Kurowicka, D. and Joe, H.} } @article {pmid21963057, title = {Diagnostic performance of high-definition coronary computed tomography angiography performed with multiple radiation dose reduction strategies}, journal = {Can J Cardiol}, volume = {27}, number = {5}, year = {2011}, pages = {606{\textendash}612}, abstract = {Numerous radiation dose reduction measures have been proposed for coronary computed tomographic angiography (CCTA). Although these techniques allow for imaging with reduced radiation, it is unknown whether diagnostic performance is maintained. A new high-definition CCTA (HD-CCTA) allows higher spatial resolution, reduced image noise, and lower radiation doses.\ The aim of this study was to determine the diagnostic performance of HD-CCTA, in combination with multiple radiation dose reduction strategies, for the detection of obstructive coronary artery disease.\ Consecutive patients (N = 43, aged 60 {\^A}{\textpm} 10 years, 83\% male) with chest pain and referred for quantitative coronary angiography (QCA) underwent HD-CCTA with radiation dose reduction measures, including prospective electrocardiographic triggering, reduction of additional tube on-time, and minimization of tube voltage and current. Intraluminal diameter stenosis {\^a}{\textperthousand}{\textyen} 50\% was considered significant. QCA served as the reference standard. The area under the receiver-operating-characteristic curve (AUC) was used to evaluate diagnostic accuracy.\ All scans demonstrated diagnostic image quality, with 99\% (543/548) of included coronary segments interpretable by HD-CCTA. Median effective radiation dose was 2.8 mSv (interquartile range, 1.3-3.9). The AUC for the per-patient assessment for stenosis {\^a}{\textperthousand}{\textyen} 50\% was 0.90 (95\% confidence interval [CI], 0.77-0.96), with sensitivity of 95\% (95\% CI, 85\%-100\%), specificity of 79\% (95\% CI, 63\%-95\%), positive predictive value of 78\% (95\% CI, 61\%-95\%), and negative predictive value of 95\% (95\% CI, 85\%-100\%).\ Compared with QCA, HD-CCTA with multiple dose reduction measures resulted in low radiation doses and high diagnostic accuracy to detect and exclude obstructive coronary artery disease.}, author = {Heydari, B. and Leipsic, J. and Mancini, G. B. and Min, J. K. and Labounty, T. and Taylor, C. and Freue, G. V. and Heilbron, B.} } @article {Bouchard2011Discussion, title = {Discussion: Bayesian priors for loss matching}, journal = {International Statistical Review}, volume = {80}, year = {2011}, pages = {83{\textendash}86}, author = {Alexandre Bouchard-C{\^o}t{\'e} and James V. Zidek} } @article {Gustafson2011b, title = {Discussion of" Bayesian local influence for survival models," by Ibrahim, Zhu, and Tang}, journal = {Lifetime data analysis}, volume = {17}, number = {1}, year = {2011}, pages = {71}, publisher = {Springer Science \& Business Media}, doi = {10.1007/s10985-010-9173-x}, author = {Gustafson, Paul} } @article {pmid22014760, title = {Does breastfeeding reduce acute procedural pain in preterm infants in the neonatal intensive care unit? A randomized clinical trial}, journal = {Pain}, volume = {152}, number = {11}, year = {2011}, month = {Nov}, pages = {2575{\textendash}2581}, author = {Holsti, L. and Oberlander, T. F. and Brant, R.} } @article {shen_efficient_2011, title = {Efficient, adaptive cross-validation for tuning and comparing models, with application to drug discovery}, journal = {The Annals of Applied Statistics}, year = {2011}, pages = {2668{\textendash}2687}, url = {http://www.jstor.org/stable/23069346}, author = {Shen, Hui and Welch, William J. and Hughes-Oliver, Jacqueline M.} } @article {liu2011empirical, title = {An empirical assessment of bayesian melding for mapping ozone pollution}, journal = {Environmetrics}, volume = {22}, number = {3}, year = {2011}, pages = {340{\textendash}353}, publisher = {Wiley Online Library}, author = {Liu, Zhong and Le, Nhu D. and Zidek, James V} } @article { ISI:000291426800012, title = {Empirical development of improved diagnostic criteria for neurofibromatosis 2}, journal = {Genetics in Medicine}, volume = {13}, number = {6}, year = {2011}, month = {JUN}, pages = {576-581}, publisher = {Nature Publishing Group}, type = {article}, abstract = {Purpose: Four sets of clinical diagnostic criteria have been proposed for neurofibromatosis 2, but all have low sensitivity at the time of initial clinical assessment for the disease among patients with a negative family history who do not present with bilateral vestibular schwannomas. We have empirically developed and tested an improved set of diagnostic criteria that uses current understanding of the natural history and genetic characteristics of neurofibromatosis 2 to increase sensitivity while maintaining very high specificity. Methods: We used data from the UK Neurofibromatosis 2 Registry and Kaplan-Meier curves to estimate frequencies of clinical features at various ages among patients with or without unequivocal neurofibromatosis 2. On the basis of this analysis, we developed the Baser criteria, a new diagnostic system that incorporates genetic testing and gives more weight to the most characteristic features and to those that occur before 30 years of age. Results: In an independent validation subset of patients with unequivocal neurofibromatosis 2, the Baser criteria increased diagnostic sensitivity to 79\% (9-15\% greater than previous sets of criteria) while maintaining 100\% specificity at the age at onset of the first characteristic sign of neurofibromatosis 2. Conclusion: The Baser criteria permit early diagnosis in a greater proportion of patients with neurofibromatosis 2 than previous sets of diagnostic criteria. Genet Med 2011:13(6):576-581.}, keywords = {diagnosis, diagnostic criteria, genetic testing, neurofibromatosis 2, NF2}, issn = {1098-3600}, doi = {10.1097/GIM.0b013e318211faa9}, author = {Baser, Michael E. and Friedman, Jan M. and Joe, Harry and Shenton, Andrew and Wallace, Andrew J. and Ramsden, Richard T. and Evans, D. Gareth R.} } @conference {McDonaldShalizi2011a, title = {Estimating beta-mixing coefficients}, booktitle = {Proceedings of the Fourteenth International Conference on Artificial Intelligence and Statistics (AISTATS)}, volume = {15}, year = {2011}, pages = {516{\textendash}524}, publisher = {PMLR}, organization = {PMLR}, url = {http://proceedings.mlr.press/v15/mcdonald11a.html}, author = {McDonald, D. J. and Shalizi, C. R. and Schervish, M.}, editor = {Gordon, G. and Dunson, D. and Dud{\'\i}k, M.} } @article {riddell_evaluation_2011, title = {Evaluation of safety monitoring guidelines based on MRI lesion activity in multiple sclerosis}, journal = {Neurology}, volume = {77}, number = {24}, year = {2011}, pages = {2089{\textendash}2096}, abstract = {

Objective: We evaluate variants of a commonly used data safety monitoring guideline in clinical trials in multiple sclerosis (MS) that flags patients who, at a follow-up visit, have 5 or more contrast-enhancing lesions (CELs) above their baseline count. Methods: We apply the guideline to a relapsing cohort and a secondary progressive cohort. We assess the number of patients that meet the guideline and describe the characteristics of these patients; we also examine the value of the guideline in predicting relapse occurrence in the 28 days following that MRI. These analyses were repeated for thresholds varying from 1 to 10 CELs above baseline. Results: Between 4\% and 6\% of patients met the threshold of 5 in both cohorts; patients with higher baseline counts and higher T2 lesion burden were more apt to meet the threshold. After adjustment for other covariates, the odds ratio (OR) of relapse associated with meeting the threshold is significant (p \< 0.05) or near significant (0.05 <= p \< 0.10) for thresholds between 5 and 8 for the relapsing cohort, but not for the secondary progressive cohort. Across thresholds, the adjusted OR is consistently greater than 1, and there is an increasing trend as the threshold increases from 1 to 7. Conclusions: A guideline based on crossing a threshold CEL count above baseline may be valuable in monitoring patient safety. Further study should be conducted using different datasets to assess the generalizability of these results.

}, issn = {0028-3878, 1526-632X}, doi = {10.1212/WNL.0b013e31823d762d}, url = {http://www.neurology.org/content/77/24/2089}, author = {Riddell, C. A. and Zhao, Y. and Li, D. K. B. and Petkau, A. J. and Riddehough, A. and Cutter, G. R. and Traboulsee, A.} } @article {pmid21490345, title = {Family physicians who provide intrapartum care and those who do not: very different ways of viewing childbirth}, journal = {Can Fam Physician}, volume = {57}, number = {4}, year = {2011}, month = {Apr}, pages = {e139{\textendash}147}, author = {Klein, M. C. and Kaczorowski, J. and Tomkinson, J. and Hearps, S. and Baradaran, N. and Brant, R.} } @article {khalili2011feature, title = {Feature selection in finite mixture of sparse normal linear models in high-dimensional feature space}, journal = {Biostatistics}, volume = {12}, number = {1}, year = {2011}, pages = {156{\textendash}172}, publisher = {Oxford University Press}, author = {Khalili, Abbas and Chen, Jiahua and Lin, Shili} } @article {verne2011global, title = {Global transcriptome analysis of constitutive resistance to the white pine weevil in spruce}, journal = {Genome biology and evolution}, year = {2011}, publisher = {Oxford University Press}, author = {Verne, S{\'e}bastien and Jaquish, Barry and White, Rick and Ritland, Carol and Ritland, Kermit} } @inbook {cohen_multiple_2011, title = {The growing need for alternative clinical trial designs for multiple sclerosis}, booktitle = {Multiple Sclerosis Therapeutics}, year = {2011}, pages = {253-260}, publisher = {Cambridge University Press}, organization = {Cambridge University Press}, edition = {4}, chapter = {21}, address = {Cambridge}, abstract = {

This book comprehensively reviews the current state of clinical trial methods in multiple sclerosis treatment, providing investigators, sponsors and specialists with current knowledge of outcome measures and study designs for disease and symptom management. The status of the rapidly evolving field of disease-modifying drugs is presented, with emphasis on the most promising therapies currently being tested. Experts discuss disease and symptom management for MS subtypes, including neuromyelitis optica and pediatric MS. In addition, key scientific advances in MS pathology, genetics, immunology and epidemiology are presented. The fourth edition has been extensively revised, featuring more than 50\% new material. All chapters have been substantially updated to provide current information on rapidly evolving topics and this volume contains 15 new chapters, reflecting the growth of the field in recent years. This book is an essential reference for practitioners caring for MS patients, investigators planning or conducting clinical trials, and clinical trial sponsors.

}, author = {Reingold, Stephen C. and McFarland, Henry F. and Petkau, A.John} } @article {domanski2011high, title = {High-flow multiplexed MRM-based analysis of proteins in human plasma without depletion or enrichment}, journal = {Clinics in laboratory medicine}, volume = {31}, number = {3}, year = {2011}, pages = {371{\textendash}384}, publisher = {Elsevier}, author = {Domanski, Dominik and Smith, Derek S and Miller, Christine A and Yang, Yanan and Jackson, Angela M and Freue, Gabriela Cohen and Hill, John S and Parker, Carol E and Borchers, Christoph H} } @article {pmid21672213, title = {Immediate vs. delayed insertion of intrauterine contraception after second trimester abortion: study protocol for a randomized controlled trial}, journal = {Trials}, volume = {12}, year = {2011}, pages = {149}, author = {Norman, W. V. and Kaczorowski, J. and Soon, J. A. and Brant, R. and Bryan, S. and Trouton, K. J. and Dicus, L.} } @article {pmid21429518, title = {Infant distress at five weeks of age and caregiver frustration}, journal = {J. Pediatr.}, volume = {159}, number = {3}, year = {2011}, month = {Sep}, pages = {425{\textendash}430}, author = {Fujiwara, T. and Barr, R. G. and Brant, R. and Barr, M.} } @article {hartung2011interferon, title = {Interferon β-1b{\textendash}neutralizing antibodies 5 years after clinically isolated syndrome}, journal = {Neurology}, volume = {77}, number = {9}, year = {2011}, pages = {835{\textendash}843}, publisher = {AAN Enterprises}, author = {Hartung, H-P and Freedman, MS and Polman, CH and Edan, G and Kappos, L and Miller, DH and Montalban, X and Barkhof, F and Petkau, J and White, R and others} } @article {hartung_interferon_2011, title = {Interferon β-1b{\textendash}neutralizing antibodies 5 years after clinically isolated syndrome}, journal = {Neurology}, volume = {77}, number = {9}, year = {2011}, pages = {835{\textendash}843}, abstract = {

Objective: To determine the frequency and consequences of neutralizing antibodies (NAbs) in patients with a first event suggestive of multiple sclerosis (MS) treated with interferon β-1b (IFNβ-1b). Methods: In the Betaseron/Betaferon in Newly Emerging MS For Initial Treatment (BENEFIT) study, patients were randomly assigned to 250 μg IFNβ-1b (Betaferon) or placebo subcutaneously every other day for 2 years or until diagnosis of clinically definite MS (CDMS). Patients were then offered open-label IFNβ-1b for up to 5 years. NAb status was assessed every 6 months by the myxovirus protein A induction assay. A titer \>20 NU/mL was considered NAb-positive, with low (>=20{\textendash}100 NU/mL), medium (>=100{\textendash}400 NU/mL), and high (>=400 NU/mL) titer categories. Here we examine early-treated patients, who received IFNβ-1b for up to 5 years. Results: NAbs were measured in 277 of 292 early-treated patients and detected at least once in 88 (31.8\%) patients, with 53 (60.2\%) reverting to NAb negativity by year 5. Time to CDMS, time to confirmed disability progression, and annualized relapse rate did not differ between NAb-positive and NAb-negative patients or between periods of NAb positivity vs NAb negativity within patients. Increases in newly active lesion number and T2 lesion volume and conversion to McDonald MS were associated with NAb positivity and were more pronounced with higher titers. Conclusions: Although NAb positivity was associated with increased brain MRI activity, no discernible effects on clinical outcomes were found. This finding may reflect the greater power of MRI compared with clinical outcomes to detect the treatment effects of IFNβ-1b and may also result from temporal changes in NAb titers and biology.

}, doi = {10.1212/WNL.0b013e31822c90d7}, url = {http://www.neurology.org/content/77/9/835}, author = {Hartung, H.-P. and Freedman, M. S. and Polman, C. H. and Edan, G. and Kappos, L. and Miller, D. H. and Montalban, X. and Barkhof, F. and Petkau, J. and White, R. and Sahajpal, V. and Knappertz, V. and Beckmann, K. and Lanius, V. and Sandbrink, R. and Pohl, C.} } @article {ahmed2011international, title = {International Workshop on Perspectives on High-dimensional Data Analysis}, journal = {International Workshop on Perspectives on High-dimensional Data Analysis}, year = {2011}, author = {Ahmed, S Ejaz and Song, Peter XK and Zhu, Mu and Alquier, Pierre and Beran, Rudolf and Chen, Jiahua and Chenouri, Shojaeddin and Doksum, Kjell and Feng, Yang and Fraser, DAS and others} } @article {liu2011isomorphism, title = {Isomorphism check in fractional factorial designs via letter interaction pattern matrix}, journal = {Journal of Statistical Planning and Inference}, volume = {141}, number = {9}, year = {2011}, pages = {3055{\textendash}3062}, publisher = {Elsevier}, author = {Liu, Yang and Yang, Jian-Feng and Liu, Min-Qian} } @article {cadigan2011kernel, title = {Kernel regression estimators for non parametric model calibration in survey sampling}, journal = {Quality control and applied statistics}, volume = {56}, number = {1}, year = {2011}, pages = {59{\textendash}60}, publisher = {Executive Sciences Institute}, author = {Cadigan, NG and Chen, J} } @article {chen2011limiting, title = {The Limiting Distribution of the EM Test of the Order of a Finite Mixture}, journal = {Mixtures: Estimation and Applications}, year = {2011}, pages = {55{\textendash}75}, publisher = {John Wiley \& Sons, Ltd}, author = {Chen, Jiahua and Li, Pengfei} } @article {pmid21732049, title = {Mediators and moderators of the effects of a year-long exercise intervention on endogenous sex hormones in postmenopausal women}, journal = {Cancer Causes Control}, volume = {22}, number = {10}, year = {2011}, month = {Oct}, pages = {1365{\textendash}1373}, author = {Friedenreich, C. M. and Neilson, H. K. and Woolcott, C. G. and Wang, Q. and Yasui, Y. and Brant, R. F. and Stanczyk, F. Z. and Campbell, K. L. and Courneya, K. S.} } @inbook {Cooke.Kousky.ea2011, title = {Micro correlations and tail dependence}, booktitle = {Dependence Modeling: Vine Copula Handbook}, year = {2011}, pages = {89{\textendash}112}, publisher = {World Scientific}, organization = {World Scientific}, chapter = {5}, address = {Singapore}, doi = {10.1142/9789814299886_0005}, author = {Cooke, R. M. and Kousky, C. and Joe, H.}, editor = {Kurowicka, D. and Joe, H.} } @article { ISI:000289337100008, title = {Modelling species abundance using the Poisson-Tweedie family}, journal = {Environmetrics}, volume = {22}, number = {2}, year = {2011}, month = {MAR}, pages = {152-164}, publisher = {Wiley-Blackwell}, type = {Article}, abstract = {The distribution of an organism species in the environment deviates frequently from randomness due to natural cycles, availability of food resources and avoidance of harm. As a result, observed data can show over-dispersion, zero-inflation and even heavy tail. Models such as the negative binomial (NB), Poisson-inverse Gaussian (PIG), and zero-inflated Poisson are frequently used in applications instead of the Poisson distribution which is usually the default model. This paper uses a three-parameter discrete distribution that unifies distributions such as Poisson, NB, PIG, Neyman Type A, and Poisson-Pascal. The three-parameter family covers a wide range of tail heaviness relative to NB, and thus suitable for modelling over-dispersed count data with a shorter or longer tail. Moreover, it shows some capacity for zero-inflated data. Grouped counts of coliform bacteria from Lake Erie and counts of European corn borer larvae in field corn are used to illustrate the application of the model and the associated likelihood-based inferences. Copyright (C) 2010 John Wiley \& Sons, Ltd.}, keywords = {Count data, generalized Poisson-inverse Gaussian, Negative binomial, Neyman Type A, over-dispersion, Poisson, Poisson-Pascal, tail index, zero-inflation}, issn = {1180-4009}, doi = {10.1002/env.1036}, author = {El-Shaarawi, Abdel H. and Zhu, Rong and Joe, Harry} } @article {mayrand2011models, title = {Models for Collaborations and Computational Biology}, journal = {Collaborative Computational Technologies for Biomedical Research}, year = {2011}, pages = {39{\textendash}53}, publisher = {John Wiley \& Sons, Inc.}, author = {Mayrand-Chung, Shawnmarie and Cohen-Freue, Gabriela and Hollander, Zsuzsanna} } @article {lin2011molecular, title = {Molecular signatures of end-stage heart failure}, journal = {Journal of cardiac failure}, volume = {17}, number = {10}, year = {2011}, pages = {867{\textendash}874}, publisher = {Churchill Livingstone}, author = {Lin, David and Hollander, Zsuzsanna and Meredith, Anna and Stadnick, Ellamae and Sasaki, Mayu and Freue, Gabriela Cohen and Qasimi, Pooran and Mui, Alice and Ng, Raymond T and Balshaw, Robert and others} } @article {pmid20709823, title = {Mucoid and nonmucoid Burkholderia cepacia complex bacteria in cystic fibrosis infections}, journal = {Am. J. Respir. Crit. Care Med.}, volume = {183}, number = {1}, year = {2011}, month = {Jan}, pages = {67{\textendash}72}, author = {Zlosnik, J. E. and Costa, P. S. and Brant, R. and Mori, P. Y. and Hird, T. J. and Fraenkel, M. C. and Wilcox, P. G. and Davidson, A. G. and Speert, D. P.} } @article {wang_multiple_2011, title = {Multiple Imputation Methods for Multivariate One-Sided Tests with Missing Data}, journal = {Biometrics}, volume = {67}, number = {4}, year = {2011}, month = {dec}, pages = {1452{\textendash}1460}, abstract = {Summary Multivariate one-sided hypotheses testing problems arise frequently in practice. Various tests have been developed. In practice, there are often missing values in multivariate data. In this case, standard testing procedures based on complete data may not be applicable or may perform poorly if the missing data are discarded. In this article, we propose several multiple imputation methods for multivariate one-sided testing problem with missing data. Some theoretical results are presented. The proposed methods are evaluated using simulations. A real data example is presented to illustrate the methods.}, keywords = {Constrained inference, Multiple imputation, Order-restricted inference, Wald-type tests}, issn = {1541-0420}, doi = {10.1111/j.1541-0420.2011.01597.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1541-0420.2011.01597.x/abstract}, author = {Wang, Tao and WU, LANG} } @article { ISI:000293113300030, title = {An Outlier-Robust Fit for Generalized Additive Models With Applications to Disease Outbreak Detection}, journal = {JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION}, volume = {106}, number = {494}, year = {2011}, month = {JUN}, pages = {719-731}, publisher = {AMER STATISTICAL ASSOC}, type = {Article}, address = {732 N WASHINGTON ST, ALEXANDRIA, VA 22314-1943 USA}, abstract = {

We are interested in a class of unsupervised methods to detect possible disease outbreaks, that is, rapid increases in the number of cases of a particular disease that deviate from the pattern observed in the past. The motivating application for this article deals with detecting outbreaks using generalized additive models (GAMs) to model weekly counts of certain infectious diseases. We can use the distance between the predicted and observed counts for a specific week to determine whether an important departure has occurred. Unfortunately, this approach may not work as desired because GAMs can be very sensitive to the presence of a small proportion of observations that deviate from the assumed model. Thus, the outbreak may affect the predicted values causing these to be close to the atypical counts, and thus mask the outliers by having them appear not to be too extreme or atypical. We illustrate this phenomenon with influenza-like-illness doctor-visits data from the United States for the 2006-2008 flu seasons. One way to avoid this masking problem is to derive an algorithm to fit GAM models that can resist the effect of a small number of atypical observations. In this article we discuss such an outlier-robust fit for GAMs based on the backfitting algorithm. The basic idea is to replace the maximum likelihood based weights used in the generalized local scoring algorithm with those derived from robust quasi-likelihood equations (Cantoni and Ronchetti 2001b). These robust estimators for generalized linear models work well for the Poisson family of distributions, and also for binomial distributions with relatively large numbers of trials. We show that the resulting estimated mean function is resistant to the presence of outliers in the response variable and that it also remains close to the usual GAM estimator when the data do not contain atypical observations. We illustrate the use of this approach on the detection of the recent outbreak of H1N1 flu by looking at the weekly counts of influenza-like-illness (ILI) doctor visits, as reported through the U.S. Outpatient Influenza-like Illness Surveillance Network (ILINet), and also apply our method to the numbers of requested isolates in Canada. Weeks with a sudden increase in ILI visits or requested isolates are much more clearly identified as atypical by the robust fit because the observed counts are far from the ones predicted by the fitted GAM model.

}, keywords = {Outliers, Robust quasi-likelihood, Robustness}, issn = {0162-1459}, doi = {10.1198/jasa.2011.tm09654}, author = {Alimadad, Azadeh and Salibian-Barrera, Mat{\'\i}as} } @article {mostafavi2011predicting, title = {Predicting node characteristics from molecular networks}, journal = {Network Biology: Methods and Applications}, year = {2011}, pages = {399{\textendash}414}, publisher = {Springer}, author = {Mostafavi, Sara and Goldenberg, Anna and Morris, Quaid} } @article {brotto_predictors_2011, title = {Predictors of sexual desire disorders in women}, journal = {The Journal of Sexual Medicine}, volume = {8}, number = {3}, year = {2011}, pages = {742{\textendash}753}, abstract = {

INTRODUCTION: A historic belief was that testosterone was the "hormone of desire." However, recent data, which show either minimal or no significant correlation between testosterone levels and women{\textquoteright}s sexual desire, suggest that nonhormonal variables may play a key role. AIM: To compare women with hypoactive sexual desire disorder (HSDD) and those with the recently proposed more symptomatic desire disorder, Sexual Desire/Interest Disorder (SDID), on the relative contribution of hormonal vs. nonhormonal variables. METHODS: Women with HSDD (N = 58, mean age 52.5) or SDID (N = 52, mean age 50.9) participated in a biopsychosocial assessment in which six nonhormonal domains were evaluated for the degree of involvement in the current low desire complaints. Participants provided a serum sample of hormones analyzed by gas chromatography-mass spectrometry or liquid chromatography/mass spectrometry/mass spectrometry. MAIN OUTCOME MEASURES: Logistic regression was used to assess the ability of variables (nonhormonal: history of sexual abuse, developmental history, psychosexual history, psychiatric status, medical history, and sexual/relationship-related factors; hormonal: dehydroepiandrosterone [DHEA], 5-diol, 4-dione, testosterone, 5-α-dihydrotestosterone, androsterone glucuronide, 3α-diol-3G, 3α-diol-17G, and DHEA-S; and demographic: age, relationship length) to predict group membership. RESULTS: Women with SDID had significantly lower sexual desire and arousal scores, but the groups did not differ on relationship satisfaction or mood. Addition of the hormonal variables to the two demographic variables (age, relationship length) did not significantly increase predictive capability. However, the addition of the six nonhormonal variables to these two sets of predictors significantly increased ability to predict group status. Developmental history, psychiatric history, and psychosexual history added significantly to the predictive capability provided by the basic model when examined individually. CONCLUSIONS: Nonhormonal variables added significant predictive capability to the basic model, highlighting the importance of their assessment clinically where women commonly have SDID in addition to HSDD, and emphasizing the importance of addressing psychological factors in treatment.

}, keywords = {Affect, Case-Control Studies, Chi-Square Distribution, Female, Gonadal Steroid Hormones, Humans, Interpersonal Relations, Interviews as Topic, Libido, Logistic Models, Middle Aged, Psychological, Psychological Tests, Sexual Dysfunctions, Surveys and Questionnaires}, doi = {10.1111/j.1743-6109.2010.02146.x}, author = {Brotto, Lori A. and Basson, Rosemary and Petkau, A.John and Labrie, Fernand} } @conference {Saeedi2011Priors, title = {Priors over recurrent continuous time processes}, booktitle = {Advances in Neural Information Processing Systems 24 (NIPS)}, volume = {24}, year = {2011}, pages = {2052{\textendash}2060}, author = {Ardavan Saeedi and Alexandre Bouchard-C{\^o}t{\'e}} } @article {carrillo2011pseudo, title = {A pseudo-GEE approach to analyzing longitudinal surveys under imputation for missing responses}, journal = {Journal of Official Statistics}, volume = {27}, number = {2}, year = {2011}, pages = {255}, author = {Carrillo, Iv{\'a}n A and Chen, Jiahua and Wu, Changbao} } @article {liu2011regression, title = {Regression with fractional polynomials when interactions are erroneously omitted}, journal = {Journal of Statistical Planning and Inference}, year = {2011}, publisher = {Elsevier}, doi = {10.1016/j.jspi.2011.12.012}, author = {Liu, J. and Gustafson, P.} } @inbook {Joe.Cooke.ea2011, title = {Regular vines: generation algorithm and number of equivalence classes}, booktitle = {Dependence Modeling: Vine Copula Handbook}, year = {2011}, pages = {219{\textendash}231}, publisher = {World Scientific}, organization = {World Scientific}, chapter = {10}, address = {Singapore}, doi = {10.1142/9789814299886_0010}, author = {Joe, H. and Cooke, R. M. and Kurowicka, D.}, editor = {Kurowicka, D. and Joe, H.} } @article {Park2011-fz, title = {Resolving the structure of interactomes with hierarchical agglomerative clustering}, journal = {BMC Bioinformatics}, volume = {12 Suppl 1}, year = {2011}, month = {feb}, pages = {S44}, abstract = {BACKGROUND: Graphs provide a natural framework for visualizing and analyzing networks of many types, including biological networks. Network clustering is a valuable approach for summarizing the structure in large networks, for predicting unobserved interactions, and for predicting functional annotations. Many current clustering algorithms suffer from a common set of limitations: poor resolution of top-level clusters; over-splitting of bottom-level clusters; requirements to pre-define the number of clusters prior to analysis; and an inability to jointly cluster over multiple interaction types. RESULTS: A new algorithm, Hierarchical Agglomerative Clustering (HAC), is developed for fast clustering of heterogeneous interaction networks. This algorithm uses maximum likelihood to drive the inference of a hierarchical stochastic block model for network structure. Bayesian model selection provides a principled method for collapsing the fine-structure within the smallest groups, and for identifying the top-level groups within a network. Model scores are additive over independent interaction types, providing a direct route for simultaneous analysis of multiple interaction types. In addition to inferring network structure, this algorithm generates link predictions that with cross-validation provide a quantitative assessment of performance for real-world examples. CONCLUSIONS: When applied to genome-scale data sets representing several organisms and interaction types, HAC provides the overall best performance in link prediction when compared with other clustering methods and with model-free graph diffusion kernels. Investigation of performance on genome-scale yeast protein interactions reveals roughly 100 top-level clusters, with a long-tailed distribution of cluster sizes. These are in turn partitioned into 1000 fine-level clusters containing 5 proteins on average, again with a long-tailed size distribution. Top-level clusters correspond to broad biological processes, whereas fine-level clusters correspond to discrete complexes. Surprisingly, link prediction based on joint clustering of physical and genetic interactions performs worse than predictions based on individual data sets, suggesting a lack of synergy in current high-throughput data.}, keywords = {My Papers}, author = {Park, Yongjin and Bader, Joel S} } @article { ISI:000297832100025, title = {Second order regular variation and conditional tail expectation of multiple risks}, journal = {Insurance Mathematics \& Economics}, volume = {49}, number = {3}, year = {2011}, month = {NOV}, pages = {537-546}, publisher = {Elsevier Science BV}, type = {Article}, abstract = {For the purpose of risk management, the study of tail behavior of multiple risks is more relevant than the study of their overall distributions. Asymptotic study assuming that each marginal risk goes to infinity is more mathematically tractable and has also uncovered some interesting performance of risk measures and relationships between risk measures by their first order approximations. However, the First order approximation is only a crude way to understand tail behavior of multiple risks, and especially for sub-extremal risks. In this paper, we conduct asymptotic analysis on conditional tail expectation (CTE) under the condition of second order regular variation (2RV). First, the closed-form second order approximation of CTE is obtained for the univariate case. Then CTE of the form E vertical bar X-1 vertical bar g(X-1, ..., X-d) > t], as t -> infinity. is studied, where g is a loss aggregating function and (X-1, ..., X-d) := (RT1, ..., RTd) with R independent of (T-1, ..., T-d) and the survivor function of R satisfying the condition of 2RV. Closed-form second order approximations of CTE for this multivariate form have been derived in terms of corresponding value at risk. For both the univariate and multivariate cases, we find that the first order approximation is affected by only the regular variation index -alpha of marginal survivor functions, while the second order approximation is influenced by both the parameters for first and second order regular variation, and the rate of convergence to the first order approximation is dominated by the second order parameter only. We have also shown that the 2RV condition and the assumptions for the multivariate form are satisfied by many parametric distribution families, and thus the closed-form approximations would be useful for applications. Those closed-form results extend the study of Zhu and Li (submitted for publication). (C) 2011 Elsevier B.V. All rights reserved.}, keywords = {Asymptotic analysis, conditional tail expectation, Second order approximation, Sub-extremal multiple risk, Value at risk}, issn = {0167-6687}, doi = {10.1016/j.insmatheco.2011.08.013}, author = {Hua, Lei and Joe, Harry} } @article {yi_simultaneous_2011, title = {Simultaneous Inference and Bias Analysis for Longitudinal Data with Covariate Measurement Error and Missing Responses}, journal = {Biometrics}, volume = {67}, number = {1}, year = {2011}, month = {mar}, pages = {67{\textendash}75}, abstract = {Summary Longitudinal data arise frequently in medical studies and it is common practice to analyze such data with generalized linear mixed models. Such models enable us to account for various types of heterogeneity, including between- and within-subjects ones. Inferential procedures complicate dramatically when missing observations or measurement error arise. In the literature, there has been considerable interest in accommodating either incompleteness or covariate measurement error under random effects models. However, there is relatively little work concerning both features simultaneously. There is a need to fill up this gap as longitudinal data do often have both characteristics. In this article, our objectives are to study simultaneous impact of missingness and covariate measurement error on inferential procedures and to develop a valid method that is both computationally feasible and theoretically valid. Simulation studies are conducted to assess the performance of the proposed method, and a real example is analyzed with the proposed method.}, keywords = {Bias analysis, Longitudinal data, Measurement error, missing data, Monte Carlo EM algorithm, Random effects models}, issn = {1541-0420}, doi = {10.1111/j.1541-0420.2010.01437.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1541-0420.2010.01437.x/abstract}, author = {Yi, G. Y. and Liu, W. and WU, LANG} } @article {pmid21347278, title = {Srf1 is a novel regulator of phospholipase D activity and is essential to buffer the toxic effects of C16:0 platelet activating factor}, journal = {PLoS Genet.}, volume = {7}, number = {2}, year = {2011}, pages = {e1001299}, abstract = {During Alzheimer{\textquoteright}s Disease, sustained exposure to amyloid-{\^I}{\texttwosuperior}{\^a}{\quotesinglbase}{\quotedblbase}{\^a}{\quotesinglbase}{\quotesinglbase} oligomers perturbs metabolism of ether-linked glycerophospholipids defined by a saturated 16 carbon chain at the sn-1 position. The intraneuronal accumulation of 1-O-hexadecyl-2-acetyl-sn-glycerophosphocholine (C16:0 PAF), but not its immediate precursor 1-O-hexadecyl-sn-glycerophosphocholine (C16:0 lyso-PAF), participates in signaling tau hyperphosphorylation and compromises neuronal viability. As C16:0 PAF is a naturally occurring lipid involved in cellular signaling, it is likely that mechanisms exist to protect cells against its toxic effects. Here, we utilized a chemical genomic approach to identify key processes specific for regulating the sensitivity of Saccharomyces cerevisiae to alkyacylglycerophosphocholines elevated in Alzheimer{\textquoteright}s Disease. We identified ten deletion mutants that were hypersensitive to C16:0 PAF and five deletion mutants that were hypersensitive to C16:0 lyso-PAF. Deletion of YDL133w, a previously uncharacterized gene which we have renamed SRF1 (Spo14 Regulatory Factor 1), resulted in the greatest differential sensitivity to C16:0 PAF over C16:0 lyso-PAF. We demonstrate that Srf1 physically interacts with Spo14, yeast phospholipase D (PLD), and is essential for PLD catalytic activity in mitotic cells. Though C16:0 PAF treatment does not impact hydrolysis of phosphatidylcholine in yeast, C16:0 PAF does promote delocalization of GFP-Spo14 and phosphatidic acid from the cell periphery. Furthermore, we demonstrate that, similar to yeast cells, PLD activity is required to protect mammalian neural cells from C16:0 PAF. Together, these findings implicate PLD as a potential neuroprotective target capable of ameliorating disruptions in lipid metabolism in response to accumulating oligomeric amyloid-{\^I}{\texttwosuperior}{\^a}{\quotesinglbase}{\quotedblbase}{\^a}{\quotesinglbase}{\quotesinglbase}.}, author = {Kennedy, M. A. and Kabbani, N. and Lambert, J. P. and Swayne, L. A. and Ahmed, F. and Figeys, D. and Bennett, S. A. and Bryan, J. and Baetz, K.} } @inbook {ohlund2011standard, title = {Standard operating procedures and protocols for the preparation and analysis of plasma samples using the iTRAQ methodology}, booktitle = {Sample Preparation in Biological Mass Spectrometry}, year = {2011}, pages = {575{\textendash}624}, publisher = {Springer Netherlands}, organization = {Springer Netherlands}, author = {Ohlund, Leanne B and Hardie, Darryl B and Elliott, Monica H and Camenzind, Alexander G and Smith, Derek S and Reid, Jennifer D and Freue, Gabriela V Cohen and Bergman, Axel P and Sasaki, Mayu and Robertson, Lisa and others} } @inbook {Joe2011b, title = {Tail dependence in vine copulae}, booktitle = {Dependence Modeling: Vine Copula Handbook}, year = {2011}, pages = {165{\textendash}187}, publisher = {World Scientific}, organization = {World Scientific}, chapter = {8}, address = {Singapore}, doi = {10.1142/9789814299886_0008}, author = {Joe, Harry}, editor = {Kurowicka, D. and Joe, H.} } @article { ISI:000293048300012, title = {Tail order and intermediate tail dependence of multivariate copulas}, journal = {Journal of Multivariate Analysis}, volume = {102}, number = {10}, year = {2011}, month = {NOV}, pages = {1454-1471}, publisher = {Elsevier Inc}, type = {Article}, abstract = {In order to study copula families that have tail patterns and tail asymmetry different from multivariate Gaussian and t copulas, we introduce the concepts of tail order and tail order functions. These provide an integrated way to study both tail dependence and intermediate tail dependence. Some fundamental properties of tail order and tail order functions are obtained. For the multivariate Archimedean copula, we relate the tail heaviness of a positive random variable to the tail behavior of the Archimedean copula constructed from the Laplace transform of the random variable, and extend the results of Charpentier and Segers [7] [A. Charpentier, J. Segers, Tails of multivariate Archimedean copulas, Journal of Multivariate Analysis 100 (7)(2009) 1521-1537] for upper tails of Archimedean copulas. In addition, a new one-parameter Archimedean copula family based on the Laplace transform of the inverse Gamma distribution is proposed; it possesses patterns of upper and lower tails not seen in commonly used copula families. Finally, tail orders are studied for copulas constructed from mixtures of max-infinitely divisible copulas. (C) 2011 Elsevier Inc. All rights reserved.}, keywords = {Archimedean copula, Laplace transform, Max-infinitely divisible, Maximal moment, Reflection symmetry, regular variation, Tail asymmetry}, issn = {0047-259X}, doi = {10.1016/j.jmva.2011.05.011}, author = {Hua, Lei and Joe, Harry} } @article { ISI:000299151700002, title = {Tail risk of multivariate regular variation}, journal = {Methodology and Computing in Applied Probability}, volume = {13}, number = {4}, year = {2011}, month = {DEC}, pages = {671-693}, publisher = {Springer}, type = {Article}, abstract = {Tail risk refers to the risk associated with extreme values and is often affected by extremal dependence among multivariate extremes. Multivariate tail risk, as measured by a coherent risk measure of tail conditional expectation, is analyzed for multivariate regularly varying distributions. Asymptotic expressions for tail risk are established in terms of the intensity measure that characterizes multivariate regular variation. Tractable bounds for tail risk are derived in terms of the tail dependence function that describes extremal dependence. Various examples involving Archimedean copulas are presented to illustrate the results and quality of the bounds.}, keywords = {Coherent risk, Copula, Regularly varying, Tail conditional expectation, Tail dependence}, issn = {1387-5841}, doi = {10.1007/s11009-010-9183-x}, author = {Joe, Harry and Li, Haijun} } @article {chen2011tuning, title = {Tuning the EM-test for finite mixture models}, journal = {Canadian Journal of Statistics}, volume = {39}, number = {3}, year = {2011}, pages = {389{\textendash}404}, publisher = {John Wiley \& Sons, Inc.}, author = {Chen, Jiahua and Li, Pengfei} } @article { ISI:000296637500013, title = {Unsupervised detection of genes of influence in lung cancer using biological networks}, journal = {BIOINFORMATICS}, volume = {27}, number = {22}, year = {2011}, month = {NOV 15}, pages = {3166-3172}, publisher = {OXFORD UNIV PRESS}, type = {Article}, address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND}, abstract = {Motivation: Lung cancer is often discovered long after its onset, making identifying genes important in its initiation and progression a challenge. By the time the tumors are discovered, we only observe the final sum of changes of the few genes that initiated cancer and thousands of genes that they have influenced. Gene interactions and heterogeneity of samples make it difficult to identify genes consistent between different cohorts. Using gene and gene-product interaction networks, we propose a principled approach to identify a small subset of genes whose network neighbors exhibit consistently high expression change ( in cancerous tissue versus normal) regardless of their own expression. We hypothesize that these genes can shed light on the larger scale perturbations in the overall landscape of expression levels. Results: We benchmark our method on simulated data, and show that we can recover a true gene list in noisy measurement data. We then apply our method to four non-small cell lung cancer and two pancreatic cancer cohorts, finding several genes that are consistent within all cohorts of the same cancer type. Conclusion: Our model is flexible, robust and identifies gene sets that are more consistent across cohorts than several other approaches. Additionally, our method can be applied on a per-patient basis not requiring large cohorts of patients to find genes of influence. Our approach is generally applicable to gene expression studies where the goal is to identify a small set of influential genes that may in turn explain the much larger set of genome-wide expression changes.}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btr533}, author = {Goldenberg, Anna and Mostafavi, Sara and Quon, Gerald and Boutros, Paul C. and Morris, Quaid D.} } @inbook {Cooke.Joe.ea2011, title = {Vines arise}, booktitle = {Dependence Modeling: Vine Copula Handbook}, year = {2011}, pages = {37{\textendash}71}, publisher = {World Scientific Publishing Company}, organization = {World Scientific Publishing Company}, chapter = {3}, address = {Singapore}, doi = {10.1142/9789814299886_0003}, author = {Cooke, R. M. and Joe, H. and Aas, K.}, editor = {Kurowicka, D. and Joe, H.} } @article { ISI:000294806800005, title = {Weighted scores method for regression models with dependent data}, journal = {Biostatistics}, volume = {12}, number = {4}, year = {2011}, month = {OCT}, pages = {653-665}, publisher = {Oxford Univ Press}, type = {Article}, abstract = {

There are copula-based statistical models in the literature for regression with dependent data such as clustered and longitudinal overdispersed counts, for which parameter estimation and inference are straightforward. For situations where the main interest is in the regression and other univariate parameters and not the dependence, we propose a {\textquoteleft}{\textquoteleft}weighted scores method{\textquoteright}{\textquoteright}, which is based on weighting score functions of the univariate margins. The weight matrices are obtained initially fitting a discretized multivariate normal distribution, which admits a wide range of dependence. The general methodology is applied to negative binomial regression models. Asymptotic and small-sample efficiency calculations show that our method is robust and nearly as efficient as maximum likelihood for fully specified copula models. An illustrative example is given to show the use of our weighted scores method to analyze utilization of health care based on family characteristics.

}, keywords = {Composite likelihood, Copulas, Count data, Estimating equations, Negative binomial}, issn = {1465-4644}, doi = {10.1093/biostatistics/kxr005}, author = {Nikoloulopoulos, Aristidis K. and Joe, Harry and Chaganty, N. R.} } @article {liu2010adjusted, title = {Adjusted empirical likelihood with high-order precision}, journal = {The Annals of Statistics}, volume = {38}, number = {3}, year = {2010}, pages = {1341{\textendash}1362}, publisher = {Institute of Mathematical Statistics}, author = {Liu, Yukun and Chen, Jiahua} } @article {le2010healthcanada, title = {Air Pollution and Cancer}, journal = {Chronic Diseases in Canada}, volume = {29}, number = {2}, year = {2010}, author = {Le, N.D. and Sun, L. and Zidek, J.V.} } @article {pmid20159820, title = {Alberta physical activity and breast cancer prevention trial: sex hormone changes in a year-long exercise intervention among postmenopausal women}, journal = {J. Clin. Oncol.}, volume = {28}, number = {9}, year = {2010}, month = {Mar}, pages = {1458{\textendash}1466}, author = {Friedenreich, C. M. and Woolcott, C. G. and McTiernan, A. and Ballard-Barbash, R. and Brant, R. F. and Stanczyk, F. Z. and Terry, T. and Boyd, N. F. and Yaffe, M. J. and Irwin, M. L. and Jones, C. A. and Yasui, Y. and Campbell, K. L. and McNeely, M. L. and Karvinen, K. H. and Wang, Q. and Courneya, K. S.} } @article { ISI:000278796800008, title = {ASYMPTOTIC INDEPENDENCE FOR UNIMODAL DENSITIES}, journal = {ADVANCES IN APPLIED PROBABILITY}, volume = {42}, number = {2}, year = {2010}, month = {JUN}, pages = {411-432}, publisher = {APPLIED PROBABILITY TRUST}, type = {Article}, address = {THE UNIVERSITY, SCHOOL MATHEMATICS STATISTICS, SHEFFIELD S3 7RH, ENGLAND}, abstract = {Asymptotic independence of the components of random vectors is a concept used in many applications. The standard criteria for checking asymptotic independence are given in terms of distribution functions (DFs). DFs are rarely available in an explicit form, especially in the multivariate case. Often we are given the form of the density or, via the shape of the data clouds, we can obtain a good geometric image of the asymptotic shape of the level sets of the density. In this paper we establish a simple sufficient condition for asymptotic independence for light-tailed densities in terms of this asymptotic shape. This condition extends Sibuya{\textquoteright}s classic result on asymptotic independence for Gaussian densities.}, keywords = {Asymptotic independence, blunt, homothetic density, level set, skew normal, star shaped}, issn = {0001-8678}, author = {Balkema, Guus and Nolde, Natalia} } @article {ChGu2010statmed, title = {Bayesian adjustment for exposure misclassification in case-control studies}, journal = {Statistics in Medicine}, volume = {29}, year = {2010}, pages = {994-1003}, doi = {10.1002/sim.3829}, author = {Chu, R. and Gustafson, P. and Le, N.} } @article {Gustafson2010, title = {Bayesian inference for partially identified models}, journal = {The international journal of biostatistics}, volume = {6}, number = {2}, year = {2010}, doi = {10.2202/1557-4679.1206}, author = {Gustafson, Paul} } @article {gu2010ijbio, title = {Bayesian inference for partially identified models}, journal = {International Journal of Biostatistics}, volume = {6}, year = {2010}, pages = {issue 2 article 17}, doi = {10.2202/1557-4679.1206}, author = {Gustafson, P.} } @conference {Bouchard2010Bayesian, title = {Bayesian Phylogenetic Inference using Sequential Monte Carlo Algorithms}, booktitle = {Society for Molecular Biology and Evolution}, year = {2010}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Sriram Sankararaman and Michael I. Jordan} } @article {pmid20040606, title = {Brief report: Maternal kangaroo care for neonatal pain relief: a systematic narrative review}, journal = {J Pediatr Psychol}, volume = {35}, number = {9}, year = {2010}, month = {Oct}, pages = {975{\textendash}984}, author = {Warnock, F. F. and Castral, T. C. and Brant, R. and Sekilian, M. and Leite, A. M. and Owens, S. d. e. L. and Scochi, C. G.} } @article { ISI:000275203500001, title = {clues: An R Package for Nonparametric Clustering Based on Local Shrinking}, journal = {JOURNAL OF STATISTICAL SOFTWARE}, volume = {33}, number = {4}, year = {2010}, month = {FEB}, pages = {1-16}, publisher = {JOURNAL STATISTICAL SOFTWARE}, type = {Article}, address = {UCLA DEPT STATISTICS, 8130 MATH SCIENCES BLDG, BOX 951554, LOS ANGELES, CA 90095-1554 USA}, abstract = {Determining the optimal number of clusters appears to be a persistant and controversial issue in cluster analysis. Most existing R packages targeting clustering require the user to specify the number of clusters in advance. However, if this subjectively chosen number is far from optimal, clustering may produce seriously misleading results. In order to address this vexing problem, we develop the R package clues to automate and evaluate the selection of an optimal number of clusers, which is widely applicable in the field of clustering analysis. Package clues uses two main procedures, shrinking and partitioning, to estimate an optimal number of clusters by maximizing an index function, either the CH index or the Silhouette index, rather than relying on guessing a pre-specified number. Five agreement indices (Rand index, Hubert and Arabie{\textquoteright}s adjusted Rand index, Morey and Agresti{\textquoteright}s adjusted Rand index, Fowlkes and Mallows index and Jaccard index), which measure the degree of agreement between any two partitions, are also provided in clues. In addition to numerical evidence, clues also supplies a deeper insight into the partitioning process with trajectory plots.}, keywords = {agreement index, cluster analysis, dissimilarity measure, K-nearest neighbor}, issn = {1548-7660}, author = {Chang, Fang and Qiu, Weiliang and Zamar, Ruben H. and Lazarus, Ross and Wang, Xiaogang} } @article {chen2010confidence, title = {Confidence intervals for the mean of a population containing many zero values under unequal-probability sampling}, journal = {Canadian Journal of Statistics}, volume = {38}, number = {4}, year = {2010}, pages = {582{\textendash}597}, publisher = {John Wiley \& Sons, Inc.}, author = {Chen, Hanfeng and Chen, Jiahua and Chen, Shun-Yi} } @article { ISI:000280675100006, title = {Count data time series models based on expectation thinning}, journal = {Stochastic Models}, volume = {26}, number = {3}, year = {2010}, pages = {PII 925211404}, publisher = {Taylor \& Francis Inc}, type = {article}, abstract = {Motivated by modelling of unequally spaced count data time series, we propose the construction of a class of continuous-time first-order Markov processes based on the self-generalized expectation thinning operations. Properties of families of random variables leading to self-generalized expectation thinning operations are obtained. Characterization results are obtained for stationary marginal distributions, the innovation random variables and the infinitesimal innovation. The transition matrix and distribution of sojourn time are also derived. Particular families of self-generalized random variables are given to make the theory concrete for modelling count data that are overdispersed relative to Poisson. We also show that the self-generalizability condition is important in order to get nice properties for the Markov processes.}, keywords = {Autoregressive, Birth-death process, Continuous-time Markov process, Expectation thinning, Generalized discrete self-decomposability, overdispersion, Self-generalizability, Sojourn time}, issn = {1532-6349}, doi = {10.1080/15326349.2010.498318}, author = {Zhu, Rong and Joe, Harry} } @article {pmid20854664, title = {Designing and implementing a longitudinal study of children with neurological, genetic or metabolic conditions: charting the territory}, journal = {BMC Pediatr}, volume = {10}, year = {2010}, pages = {67}, author = {Siden, H. and Steele, R. and Brant, R. and Cadell, S. and Davies, B. and Straatman, L. and Widger, K. and Andrews, G. S.} } @article {zhao_does_2010, title = {Does MRI lesion activity regress in secondary progressive multiple sclerosis?}, journal = {Multiple Sclerosis}, volume = {16}, year = {2010}, pages = {434-442}, abstract = {

Background: The rate of new contrast-enhancing lesions (CELs) on monthly magnetic resonance imaging (MRI) scans has been shown to decrease over a 9-month period in placebo-treated patients with relapsing{\textendash}remitting (RR) multiple sclerosis (RRMS). Objective: We examined this phenomenon in placebo-treated secondary progressive MS (SPMS) patients. Methods: Patients were chosen from two clinical trials. Monthly scans were taken at screening, baseline and months 1{\textendash}9 for Cohort-1 and months 1{\textendash}6 for Cohort-2. We examined the monthly new CEL rates according to initial CEL level: 0, 1{\textendash}3, \>3 CELs at screening, and presence and absence of pre-study relapses. Results:Respectively, 59, 21 and 14 of the 94 Cohort-1 patients, and 36, 17 and 9 of the 62 Cohort-2 patients had 0, 1{\textendash}3 and \>3 initial CELs. For Cohort-1, the monthly new CEL rates did not change during follow-up, regardless of initial CEL level. For Cohort-2, the monthly rate was unchanged in the 0 initial CEL subgroup, but decreased 33\% (95\% confidence interval: 8\%, 52\%) from months 1{\textendash}3 to months 4{\textendash}6 in the other two subgroups. For the combined cohorts, a decreasing rate was observed in the 12 patients with \>3 initial CELs and pre-study relapses. Conclusions: The short-term trend of new CEL activity in placebo-treated SPMS patients may vary across cohorts.

}, doi = {10.1177/1352458509359726}, url = {http://msj.sagepub.com/content/early/2010/02/18/1352458509359726}, author = {Zhao, Y. and Petkau, A.John and Traboulsee, A. and Riddehough, A. and Li, D. K. B.} } @article {Park2010-to, title = {Dynamic networks from hierarchical bayesian graph clustering}, journal = {PLoS One}, volume = {5}, number = {1}, year = {2010}, month = {jan}, pages = {e8118}, abstract = {Biological networks change dynamically as protein components are synthesized and degraded. Understanding the time-dependence and, in a multicellular organism, tissue-dependence of a network leads to insight beyond a view that collapses time-varying interactions into a single static map. Conventional algorithms are limited to analyzing evolving networks by reducing them to a series of unrelated snapshots.Here we introduce an approach that groups proteins according to shared interaction patterns through a dynamical hierarchical stochastic block model. Protein membership in a block is permitted to evolve as interaction patterns shift over time and space, representing the spatial organization of cell types in a multicellular organism. The spatiotemporal evolution of the protein components are inferred from transcript profiles, using Arabidopsis root development (5 tissues, 3 temporal stages) as an example.The new model requires essentially no parameter tuning, out-performs existing snapshot-based methods, identifies protein modules recruited to specific cell types and developmental stages, and could have broad application to social networks and other similar dynamic systems.}, keywords = {My Papers}, author = {Park, Yongjin and Moore, Cristopher and Bader, Joel S} } @article {parker2010ecological, title = {Ecological adaptation of diverse honey bee (Apis mellifera) populations}, journal = {PloS one}, volume = {5}, number = {6}, year = {2010}, pages = {e11096}, publisher = {Public Library of Science}, author = {Parker, Robert and Melathopoulos, Andony P and White, Rick and Pernal, Stephen F and Guarna, M Marta and Foster, Leonard J} } @article {pmid19968808, title = {The effect of age on the dose of remifentanil for tracheal intubation in infants and children}, journal = {Paediatr Anaesth}, volume = {20}, number = {1}, year = {2010}, month = {Jan}, pages = {19{\textendash}27}, author = {Hume-Smith, H. and McCormack, J. and Montgomery, C. and Brant, R. and Malherbe, S. and Mehta, D. and Ansermino, J. M.} } @article {pmid20975577, title = {Electronic and paper diary recording of infant and caregiver behaviors}, journal = {J Dev Behav Pediatr}, volume = {31}, number = {9}, year = {2010}, pages = {685{\textendash}693}, author = {Lam, J. and Barr, R. G. and Catherine, N. and Tsui, H. and Hahnhaussen, C. L. and Pauwels, J. and Brant, R.} } @article {variyath2010empirical, title = {Empirical likelihood based variable selection}, journal = {Journal of Statistical Planning and Inference}, volume = {140}, number = {4}, year = {2010}, pages = {971{\textendash}981}, publisher = {Elsevier}, author = {Variyath, Asokan Mulayath and Chen, Jiahua and Abraham, Bovas} } @article {robert2010erratum, title = {Erratum: Terpenoid metabolite profiling in Sitka spruce identifies association of dehydroabietic acid,(+)-3-carene and terpinolene with resistance against white pine weevil}, journal = {Botany}, volume = {88}, number = {10}, year = {2010}, pages = {937{\textendash}937}, publisher = {NRC Research Press}, author = {Robert, Jeanne A and Madilao, Lufiani L and White, Rick and Yanchuk, Alvin and King, John and Bohlmann, J{\"o}rg} } @article {Johnston2010, title = {Expanding access to HAART: a cost-effective approach for treating and preventing HIV}, journal = {Aids}, volume = {24}, number = {12}, year = {2010}, pages = {1929{\textendash}1935}, publisher = {LWW}, doi = {10.1097/qad.0b013e32833af85d}, author = {Johnston, Karissa M and Levy, Adrian R and Lima, Viviane D and Hogg, Robert S and Tyndall, Mark W and Gustafson, Paul and Briggs, Andrew and Montaner, Julio S} } @article {pmid20598316, title = {Extreme premature birth is not associated with impaired development of brain microstructure}, journal = {J. Pediatr.}, volume = {157}, number = {5}, year = {2010}, month = {Nov}, pages = {726{\textendash}732}, author = {Bonifacio, S. L. and Glass, H. C. and Chau, V. and Berman, J. I. and Xu, D. and Brant, R. and Barkovich, A. J. and Poskitt, K. J. and Miller, S. P. and Ferriero, D. M.} } @article { ISI:000279474400012, title = {Fast integration of heterogeneous data sources for predicting gene function with limited annotation}, journal = {BIOINFORMATICS}, volume = {26}, number = {14}, year = {2010}, month = {JUL 15}, pages = {1759-1765}, publisher = {OXFORD UNIV PRESS}, type = {Article}, address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND}, abstract = {Motivation: Many algorithms that integrate multiple functional association networks for predicting gene function construct a composite network as a weighted sum of the individual networks and then use the composite network to predict gene function. The weight assigned to an individual network represents the usefulness of that network in predicting a given gene function. However, because many categories of gene function have a small number of annotations, the process of assigning these network weights is prone to overfitting. Results: Here, we address this problem by proposing a novel approach to combining multiple functional association networks. In particular, we present a method where network weights are simultaneously optimized on sets of related function categories. The method is simpler and faster than existing approaches. Further, we show that it produces composite networks with improved function prediction accuracy using five example species (yeast, mouse, fly, Esherichia coli and human).}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btq262}, author = {Mostafavi, Sara and Morris, Quaid} } @article { ISI:000281333900020, title = {Fast robust estimation of prediction error based on resampling}, journal = {COMPUTATIONAL STATISTICS \& DATA ANALYSIS}, volume = {54}, number = {12, SI}, year = {2010}, month = {DEC 1}, pages = {3121-3130}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {Robust estimators of the prediction error of a linear model are proposed. The estimators are based on the resampling techniques cross-validation and bootstrap. The robustness of the prediction error estimators is obtained by robustly estimating the regression parameters of the linear model and by trimming the largest prediction errors. To avoid the recalculation of time-consuming robust regression estimates, fast approximations for the robust estimates of the resampled data are used. This leads to time-efficient and robust estimators of prediction error. (C) 2010 Elsevier B.V. All rights reserved.}, keywords = {bootstrap, Cross-validation, Prediction error, Robustness}, issn = {0167-9473}, doi = {10.1016/j.csda.2010.01.031}, author = {Khan, Jafar A. and Van Aelst, Stefan and Zamar, Ruben H.} } @article { ISI:000273235400006, title = {Finding approximate solutions to combinatorial problems with very large data sets using BIRCH}, journal = {COMPUTATIONAL STATISTICS \& DATA ANALYSIS}, volume = {54}, number = {3}, year = {2010}, month = {MAR 1}, pages = {655-667}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {Computing estimators with good robustness properties generally requires solving highly complex optimization problems. The current state-of-the-art algorithms to find approximate solutions to these problems need to access the data set a large number to times and become unfeasible when the data do not fit in memory. In this paper the BIRCH algorithm is adapted to calculate approximate solutions to problems in this class. For data sets that fit in memory, this approach is able to find approximate Least Trimmed Squares (LTS) and Minimum Covariance Determinant (MCD) estimators that compare very well with those returned by the fast-LTS and fast-MCD algorithms, and in some cases is able to find a better solution (in terms of value of the objective function) than those returned by the fast-algorithms. This methodology can also be applied to the Linear Grouping Algorithm and its robust variant for very large datasets. Finally, results from a simulation study indicate that this algorithm performs comparably well to fast-LTS in simple situations (large data sets with a small number of covariates and small proportion of outliers) and does much better than fast-LTS in more challenging situations without requiring extra computational time. These findings seem to confirm that this approach provides the first computationally feasible and reliable approximating algorithm in the literature to compute the LTS and MCD estimators for data sets that do not fit in memory. (C) 2008 Elsevier B.V. All rights reserved.}, issn = {0167-9473}, doi = {10.1016/j.csda.2008.08.001}, author = {Harrington, Justin and Salibian-Barrera, Mat{\'\i}as} } @article { ISI:000284148900035, title = {The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function}, journal = {NUCLEIC ACIDS RESEARCH}, volume = {38}, number = {2}, year = {2010}, month = {JUL}, pages = {W214-W220}, publisher = {OXFORD UNIV PRESS}, type = {Article}, address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND}, abstract = {GeneMANIA (http://www.genemania.org) is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. Six organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens and Saccharomyces cerevisiae) and hundreds of data sets have been collected from GEO, BioGRID, Pathway Commons and I2D, as well as organism-specific functional genomics data sets. Users can select arbitrary subsets of the data sets associated with an organism to perform their analyses and can upload their own data sets to analyze. The GeneMANIA algorithm performs as well or better than other gene function prediction methods on yeast and mouse benchmarks. The high accuracy of the GeneMANIA prediction algorithm, an intuitive user interface and large database make GeneMANIA a useful tool for any biologist.}, issn = {0305-1048}, doi = {10.1093/nar/gkq537}, author = {Warde-Farley, David and Donaldson, Sylva L. and Comes, Ovi and Zuberi, Khalid and Badrawi, Rashad and Chao, Pauline and Franz, Max and Grouios, Chris and Kazi, Farzana and Lopes, Christian Tannus and Maitland, Anson and Mostafavi, Sara and Montojo, Jason and Shao, Quentin and Wright, George and Bader, Gary D. and Morris, Quaid} } @booklet {NSERC Canada; Hong Kong Polytechnic University; University of Saskatchewan}, title = {A general family of limited information goodness-of-fit statistics for multinomial data}, journal = {Dependence Modeling: Vine Copula Handbook}, volume = {75}, number = {3}, year = {2010}, month = {SEP}, pages = {393-419}, publisher = {Springer}, type = {Article}, chapter = {10}, address = {Singapore}, abstract = {Maydeu-Olivares and Joe (J. Am. Stat. Assoc. 100:1009-1020, 2005; Psychometrika 71:713-732, 2006) introduced classes of chi-square tests for (sparse) multidimensional multinomial data based on low-order marginal proportions. Our extension provides general conditions under which quadratic forms in linear functions of cell residuals are asymptotically chi-square. The new statistics need not be based on margins, and can be used for one-dimensional multinomials. We also provide theory that explains why limited information statistics have good power, regardless of sparseness. We show how quadratic-form statistics can be constructed that are more powerful than X (2) and yet, have approximate chi-square null distribution in finite samples with large models. Examples with models for truncated count data and binary item response data are used to illustrate the theory.}, keywords = {categorical data analysis, cell-focusing, discrete data, item response theory, overdispersion, overlapping cells, Poisson models, quadratic form statistics, Rasch models, score test, sparse contingency tables, zero-inflation}, issn = {0033-3123}, doi = {10.1007/s11336-010-9165-5}, url = {{http://www.worldscibooks.com/economics/7699.html doi = 10.1142/9789814299886, @InCollectionCooke.Joe.ea2011}, author = {Joe, Harry and Maydeu-Olivares, Alberto}, editor = {Kurowicka, D. and Joe, H.} } @article { ISI:000276284600019, title = {Generating random AR(p) and MA(q) Toeplitz correlation matrices}, journal = {Journal of Multivariate Analysis}, volume = {101}, number = {6}, year = {2010}, month = {JUL}, pages = {1532-1545}, publisher = {Elsevier Inc}, type = {Article}, abstract = {Methods are proposed for generating random (p+1) x (p+1) Toeplitz correlation matrices that are consistent with a causal AR(p) Gaussian time series model. The main idea is to first specify distributions for the partial autocorrelations that are algebraically independent and take values in (-1, 1), and then map to the Toeplitz matrix. Similarly, starting with pseudopartial autocorrelations, methods are proposed for generating (q+1) x (q+1) Toeplitz correlation matrices that are consistent with an invertible MA(q) Gaussian time series model. The density can be uniform or non-uniform over the space of autocorrelations up to lag p or q, or over the space of autoregressive or moving average coefficients, by making appropriate choices for the densities of the (pseudo)-partial autocorrelations. Important intermediate steps are the derivations of the Jacobians of the mappings between the (pseudo)-partial autocorrelations, autocorrelations and autoregressive/moving average coefficients. The random generating methods are useful for models with a structured Toeplitz matrix as a parameter. (C) 2010 Elsevier Inc. All rights reserved.}, keywords = {Autoregressive process, Beta distribution, Longitudinal data, Moving average process}, issn = {0047-259X}, doi = {10.1016/j.jmva.2010.01.013}, author = {Ng, C. T. and Joe, Harry} } @article { ISI:000273783100027, title = {The Genetic Landscape of a Cell}, journal = {SCIENCE}, volume = {327}, number = {5964}, year = {2010}, month = {JAN 22}, pages = {425-431}, publisher = {AMER ASSOC ADVANCEMENT SCIENCE}, type = {Article}, address = {1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA}, abstract = {A genome-scale genetic interaction map was constructed by examining 5.4 million gene-gene pairs for synthetic genetic interactions, generating quantitative genetic interaction profiles for similar to 75\% of all genes in the budding yeast, Saccharomyces cerevisiae. A network based on genetic interaction profiles reveals a functional map of the cell in which genes of similar biological processes cluster together in coherent subsets, and highly correlated profiles delineate specific pathways to define gene function. The global network identifies functional cross-connections between all bioprocesses, mapping a cellular wiring diagram of pleiotropy. Genetic interaction degree correlated with a number of different gene attributes, which may be informative about genetic network hubs in other organisms. We also demonstrate that extensive and unbiased mapping of the genetic landscape provides a key for interpretation of chemical-genetic interactions and drug target identification.}, issn = {0036-8075}, doi = {10.1126/science.1180823}, author = {Costanzo, Michael and Baryshnikova, Anastasia and Bellay, Jeremy and Kim, Yungil and Spear, Eric D. and Sevier, Carolyn S. and Ding, Huiming and Koh, Judice L. Y. and Toufighi, Kiana and Mostafavi, Sara and Prinz, Jeany and Onge, Robert P. St. and VanderSluis, Benjamin and Makhnevych, Taras and Vizeacoumar, Franco J. and Alizadeh, Solmaz and Bahr, Sondra and Brost, Renee L. and Chen, Yiqun and Cokol, Murat and Deshpande, Raamesh and Li, Zhijian and Lin, Zhen-Yuan and Liang, Wendy and Marback, Michaela and Paw, Jadine and Luis, Bryan-Joseph San and Shuteriqi, Ermira and Tong, Amy Hin Yan and van Dyk, Nydia and Wallace, Iain M. and Whitney, Joseph A. and Weirauch, Matthew T. and Zhong, Guoqing and Zhu, Hongwei and Houry, Walid A. and Brudno, Michael and Ragibizadeh, Sasan and Papp, Balazs and Pal, Csaba and Roth, Frederick P. and Giaever, Guri and Nislow, Corey and Troyanskaya, Olga G. and Bussey, Howard and Bader, Gary D. and Gingras, Anne-Claude and Morris, Quaid D. and Kim, Philip M. and Kaiser, Chris A. and Myers, Chad L. and Andrews, Brenda J. and Boone, Charles} } @article { ISI:000281333900003, title = {Globally robust confidence intervals for simple linear regression}, journal = {COMPUTATIONAL STATISTICS \& DATA ANALYSIS}, volume = {54}, number = {12, SI}, year = {2010}, month = {DEC 1}, pages = {2899-2913}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {It is well known that when the data may contain outliers or other departures from the assumed model, classical inference methods can be seriously affected and yield confidence levels much lower than the nominal ones. This paper proposes robust confidence intervals and tests for the parameters of the simple linear regression model that maintain their coverage and significance level, respectively, over whole contamination neighbourhoods. This approach can be used with any consistent regression estimator for which maximum bias curves are tabulated, and thus it is more widely applicable than previous proposals in the literature. Although the results regarding the coverage level of these confidence intervals are asymptotic in nature, simulation studies suggest that these robust inference procedures work well for small samples, and compare very favourably with earlier proposals in the literature. (C) 2009 Elsevier B.V. All rights reserved.}, issn = {0167-9473}, doi = {10.1016/j.csda.2009.05.005}, author = {Adrover, Jorge and Salibian-Barrera, Mat{\'\i}as} } @article {jung2010hapx, title = {HapX positively and negatively regulates the transcriptional response to iron deprivation in Cryptococcus neoformans}, journal = {PLoS Pathog}, volume = {6}, number = {11}, year = {2010}, pages = {e1001209{\textendash}e1001209}, author = {Jung, Won Hee and Saikia, Sanjay and Hu, Guanggan and Wang, Joyce and Fung, CK and D{\textquoteright}Souza, Cletus and White, Rick and Kronstad, James W} } @article {pmid20602512, title = {Herbivore-induced plant volatiles allow detection of Trichoplusia ni (Lepidoptera: Noctuidae) infestation on greenhouse tomato plants}, journal = {Pest Manag. Sci.}, volume = {66}, number = {8}, year = {2010}, month = {Aug}, pages = {916{\textendash}924}, abstract = {Monitoring of insect populations is an important component of integrated pest management and typically is based on the presence and number of insects in various development stages. Yet plants respond to insect herbivory and release herbivore-induced plant volatiles (HIPVs), which could be exploited in monitoring systems. The present objective was to investigate whether the information associated with HIPVs has potential to become part of advanced technologies for monitoring pest insect populations.\ In a laboratory experiment, it was determined that tomato plants, Lycopersicon esculentum Mill cv. clarence, each infested with 20 caterpillars of the cabbage looper, Trichoplusia ni (H{\"u}bner), emit HIPVs, of which (Z)-3-hexenyl acetate, (E)-beta-ocimene and beta-caryophyllene were selected as chemicals indicative of herbivory. Using an ultrafast portable gas chromatograph (zNose()) in a research greenhouse and in a commercial greenhouse, it was possible (i) to reveal differential emissions of these three indicator chemicals from plants with or without herbivory, (ii) to detect herbivory within 6 h of its onset, (iii) to track changes in indicator chemical emissions over time and (iv) to study the effect of environmental and crop-maintenance-related factors on the emission of indicator chemicals.\ HIPVs appear to be promising as reliable indicators of plant health, but further studies are needed to fully understand the potential of this concept.}, author = {Miresmailli, S. and Gries, R. and Gries, G. and Zamar, R. H. and Isman, M. B.} } @article {qiu_hiv_2010, title = {HIV Viral Dynamic Models With Censoring and Informative Dropouts}, journal = {Statistics in Biopharmaceutical Research}, volume = {2}, number = {2}, year = {2010}, pages = {220{\textendash}228}, issn = {null}, doi = {10.1198/sbr.2009.0072}, url = {http://amstat.tandfonline.com/doi/abs/10.1198/sbr.2009.0072}, author = {Qiu, Weiliang and WU, LANG} } @article {Lefebvre2010, title = {Impact of outcome model misspecification on regression and doubly-robust inverse probability weighting to estimate causal effect}, journal = {The international journal of biostatistics}, volume = {6}, number = {2}, year = {2010}, doi = {10.2202/1557-4679.1207}, author = {Lefebvre, Genevieve and Gustafson, Paul} } @article {LeGu2010ijbio, title = {Impact of outcome model misspecification on regression and doubly-robust inverse probability weighting to estimate causal effect}, journal = {International Journal of Biostatistics}, volume = {6}, year = {2010}, pages = {issue 2 article 15}, doi = {10.2202/1557-4679.1207}, author = {Lefebvre, G. and Gustafson, P.} } @article {miresmailli2010integrating, title = {Integrating plant chemical ecology, sensors and artificial intelligence for accurate pest monitoring}, journal = {Tomatoes: Agricultural Procedures, Pathogen Interactions and Health Effects}, year = {2010}, pages = {129{\textendash}146}, author = {Miresmailli, Saber and Badulescu, Dan and Mahdaviani, Maryam and Zamar, Ruben H and Isman, Murray B} } @article {wu_joint_2010, title = {Joint Inference on HIV Viral Dynamics and Immune Suppression in Presence of Measurement Errors}, journal = {Biometrics}, volume = {66}, number = {2}, year = {2010}, month = {jun}, pages = {327{\textendash}335}, abstract = {Summary: In an attempt to provide a tool to assess antiretroviral therapy and to monitor disease progression, this article studies association of human immunodeficiency virus (HIV) viral suppression and immune restoration. The data from a recent acquired immune deficiency syndrome (AIDS) study are used for illustration. We jointly model HIV viral dynamics and time to decrease in CD4/CD8 ratio in the presence of CD4 process with measurement errors, and estimate the model parameters simultaneously via a method based on a Laplace approximation and the commonly used Monte Carlo EM algorithm. The approaches and many of the points presented apply generally.}, keywords = {Laplace approximation, Longitudinal data, Mixed-effects, Nonlinear models, Time-to-event}, issn = {1541-0420}, doi = {10.1111/j.1541-0420.2009.01308.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1541-0420.2009.01308.x/abstract}, author = {Wu, L. and Liu, W. and Hu, X. J.} } @conference {Sankararaman2010Joint, title = {Joint Probabilistic Modeling of Languages and Genes}, booktitle = {Society for Molecular Biology and Evolution}, year = {2010}, author = {Sriram Sankararaman and Alexandre Bouchard-C{\^o}t{\'e} and Michael I. Jordan} } @article {cadigan2010kernel, title = {Kernel regression estimators for nonparametric model calibration in survey sampling}, journal = {Journal of Statistical Theory and Practice}, volume = {4}, number = {1}, year = {2010}, pages = {1{\textendash}25}, publisher = {Taylor \& Francis Group}, author = {Cadigan, NG and Chen, J} } @article {pmid20332266, title = {Mammographic density change with 1 year of aerobic exercise among postmenopausal women: a randomized controlled trial}, journal = {Cancer Epidemiol. Biomarkers Prev.}, volume = {19}, number = {4}, year = {2010}, month = {Apr}, pages = {1112{\textendash}1121}, author = {Woolcott, C. G. and Courneya, K. S. and Boyd, N. F. and Yaffe, M. J. and Terry, T. and McTiernan, A. and Brant, R. and Ballard-Barbash, R. and Irwin, M. L. and Jones, C. A. and Brar, S. and Campbell, K. L. and McNeely, M. L. and Karvinen, K. H. and Friedenreich, C. M.} } @article {balkema2010meta, title = {Meta densities and the shape of their sample clouds}, journal = {Journal of Multivariate Analysis}, volume = {101}, number = {7}, year = {2010}, pages = {1738{\textendash}1754}, publisher = {Elsevier}, author = {Balkema, AA and Embrechts, Paul and Nolde, N} } @booklet {hosseini2010model, title = {Model selection for the binary dichotomized temperature processes}, number = {257}, year = {2010}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Hosseini, Reza and Le, Nhu D. and Zidek, James V.} } @article {yan_model-based_2010, title = {Model-based linear clustering}, journal = {Canadian Journal of Statistics}, volume = {38}, number = {4}, year = {2010}, pages = {716{\textendash}737}, url = {http://onlinelibrary.wiley.com/doi/10.1002/cjs.10082/full}, author = {Yan, Guohua and Welch, William J. and Zamar, Ruben H.} } @article { ISI:000284674900012, title = {Model-based linear clustering}, journal = {CANADIAN JOURNAL OF STATISTICS-REVUE CANADIENNE DE STATISTIQUE}, volume = {38}, number = {4}, year = {2010}, month = {DEC}, pages = {716-737}, publisher = {WILEY-BLACKWELL}, type = {Article}, address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA}, abstract = {The authors propose a profile likelihood approach to linear clustering which explores potential linear clusters in a data set For each linear cluster an errors in variables model is assumed The optimization of the derived profile likelihood can be achieved by an EM algorithm Its asymptotic properties and its relationships with several existing clustering methods are discussed Methods to determine the number of components in a data set are adapted to this linear clustering setting Several simulated and real data sets are analyzed for comparison and illustration purposes The Canadian Journal of Statistics 38 716-737 2010 (C) 2010 Statistical Society of Canada}, keywords = {EM algorithm, errors in-variables model, linear cluster, mixture model, orthogonal regression, profile likelihood}, issn = {0319-5724}, doi = {10.1002/cjs.10082}, author = {Yan, Guohua and Welch, William J. and Zamar, Ruben H.} } @article {dou2010modeling, title = {Modeling hourly ozone concentration fields}, journal = {The Annals of Applied Statistics}, volume = {4}, number = {3}, year = {2010}, pages = {1183{\textendash}1213}, publisher = {Institute of Mathematical Statistics}, author = {Dou, Yiping and Le, Nhu D and Zidek, James V} } @article {zidek2010monitoring, title = {Monitoring network design}, journal = {Handbook of Spatial Statistics}, year = {2010}, pages = {131{\textendash}148}, publisher = {CRC Press PJ Diggle, M. Fuentes, and P. Guttorp, Boca Raton, FL}, author = {Zidek, James V and Zimmerman, Dale L} } @article { ISI:000276369000022, title = {Negative binomial time series models based on expectation thinning operators}, journal = {Journal of Statistical Planning and Inference}, volume = {140}, number = {7}, year = {2010}, month = {JUL}, pages = {1874-1888}, publisher = {Elsevier Science BV}, type = {Article}, abstract = {The study of count data time series has been active in the past decade, mainly in theory and model construction. There are different ways to construct time series models with a geometric autocorrelation function, and a given univariate margin such as negative binomial. In this paper, we investigate negative binomial time series models based on the binomial thinning and two other expectation thinning operators, and show how they differ in conditional variance or heteroscedasticity. Since the model construction is in terms of probability generating functions, typically, the relevant conditional probability mass functions do not have explicit forms. In order to do simulations, likelihood inference, graphical diagnostics and prediction, we use a numerical method for inversion of characteristic functions. We illustrate the numerical methods and compare the various negative binomial time series models for a real data example. (C) 2010 Elsevier B.V. All rights reserved.}, keywords = {Autoregressive, Binomial thinning, Generalized discrete self-decomposability, Inversion of characteristic function, Negative binomial time series, Self-generalizability}, issn = {0378-3758}, doi = {10.1016/j.jspi.2010.01.031}, author = {Zhu, Rong and Joe, Harry} } @article {pmid20147771, title = {Normal distribution of palpebral fissure lengths in Canadian school age children}, journal = {Can J Clin Pharmacol}, volume = {17}, number = {1}, year = {2010}, pages = {67{\textendash}78}, author = {Clarren, S. K. and Chudley, A. E. and Wong, L. and Friesen, J. and Brant, R.} } @article {lee_anote2010, title = {A note on the ordered means of exponential family}, journal = {Far East Journal of Theoretical Statistics}, volume = {31}, year = {2010}, pages = {69{\textendash}75}, author = {Lee, D and Liu, W and Peng, J and Wu, L} } @conference {Berg2010Painless, title = {Painless unsupervised learning with features}, booktitle = {Proceedings of the North American Chapter of the Association for Computational Linguistics (NAACL10)}, volume = {8}, year = {2010}, pages = {582{\textendash}590}, author = {Taylor Berg-Kirkpatrick and Alexandre Bouchard-C{\^o}t{\'e} and John DeNero and Dan Klein} } @article {pmid20830544, title = {Pictures worthy of a thousand words}, journal = {Can J Anaesth}, volume = {57}, number = {11}, year = {2010}, month = {Nov}, pages = {961{\textendash}965}, author = {Brasher, P. M. and Brant, R. F.} } @article {pmid20542545, title = {Pooled analysis of trials may, in the presence of heterogeneity inadvertently lead to fragile conclusions due to the importance of clinically relevant variables being either hidden or lost when the findings are pooled}, journal = {Thromb. Res.}, volume = {126}, number = {3}, year = {2010}, month = {Sep}, pages = {164{\textendash}165}, author = {Hull, R. D. and Liang, J. and Brant, R.} } @booklet {Cai:2010aa, title = {Predicting phenological events using event-history analysis}, number = {260}, year = {2010}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Cai, Song and Zidek, James V. and Newlands, Nathaniel} } @booklet {Cai:2010ab, title = {Predicting Sequences of Progressive Events Times with Time-dependent Covariates}, number = {259}, year = {2010}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Cai, Song and Zidek, James V. and Newlands, Nathaniel} } @article {Gu2010ijerph, title = {Probabilistic approaches to better quantifying the results of epidemiologic studies}, journal = {International Journal of Environmental Research and Public Health}, volume = {7}, year = {2010}, pages = {1520-1539}, doi = {10.3390/ijerph7041520}, author = {Gustafson, P. and McCandless, L. C.} } @mastersthesis {Bouchard2010Probabilistic, title = {Probabilistic Models of Evolution and Language Change}, year = {2010}, school = {UC Berkeley}, type = {phd}, author = {Alexandre Bouchard-C{\^o}t{\'e}} } @article {freue2010proteomic, title = {Proteomic signatures in plasma during early acute renal allograft rejection}, journal = {Molecular \& Cellular Proteomics}, volume = {9}, number = {9}, year = {2010}, pages = {1954{\textendash}1967}, publisher = {American Society for Biochemistry and Molecular Biology}, author = {Freue, Gabriela V Cohen and Sasaki, Mayu and Meredith, Anna and G{\"u}nther, Oliver P and Bergman, Axel and Takhar, Mandeep and Mui, Alice and Balshaw, Robert F and Ng, Raymond T and Opushneva, Nina and others} } @article {carrillo2010pseudo, title = {The pseudo-GEE approach to the analysis of longitudinal surveys}, journal = {Canadian Journal of Statistics}, volume = {38}, number = {4}, year = {2010}, pages = {540{\textendash}554}, publisher = {Wiley Online Library}, author = {Carrillo, Iv{\'a}n A and Chen, Jiahua and Wu, Changbao} } @article { ISI:000274565100016, title = {Rapid behavior-based identification of neuroactive small molecules in the zebrafish}, journal = {NATURE CHEMICAL BIOLOGY}, volume = {6}, number = {3}, year = {2010}, month = {MAR}, pages = {231-237}, publisher = {NATURE PUBLISHING GROUP}, type = {Article}, address = {75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA}, abstract = {Neuroactive small molecules are indispensable tools for treating mental illnesses and dissecting nervous system function. However, it has been difficult to discover novel neuroactive drugs. Here, we describe a high-throughput, behavior-based approach to neuroactive small molecule discovery in the zebrafish. We used automated screening assays to evaluate thousands of chemical compounds and found that diverse classes of neuroactive molecules caused distinct patterns of behavior. These {\textquoteleft}behavioral barcodes{\textquoteright} can be used to rapidly identify new psychotropic chemicals and to predict their molecular targets. For example, we identified new acetylcholinesterase and monoamine oxidase inhibitors using phenotypic comparisons and computational techniques. By combining high-throughput screening technologies with behavioral phenotyping in vivo, behavior-based chemical screens can accelerate the pace of neuroactive drug discovery and provide small-molecule tools for understanding vertebrate behavior.}, issn = {1552-4450}, doi = {10.1038/NCHEMBIO.307}, author = {Kokel, David and Bryan, Jennifer and Laggner, Christian and White, Rick and Cheung, Chung Yan J. and Mateus, Rita and Healey, David and Kim, Sonia and Werdich, Andreas A. and Haggarty, Stephen J. and MacRae, Calum A. and Shoichet, Brian and Peterson, Randall T.} } @article {kokel2010rapid, title = {Rapid behavior-based identification of neuroactive small molecules in the zebrafish}, journal = {Nature chemical biology}, volume = {6}, number = {3}, year = {2010}, pages = {231{\textendash}237}, publisher = {Nature Publishing Group}, author = {Kokel, David and Bryan, Jennifer and Laggner, Christian and White, Rick and Cheung, Chung Yan J and Mateus, Rita and Healey, David and Kim, Sonia and Werdich, Andreas A and Haggarty, Stephen J and others} } @article { ISI:000279286900018, title = {Recommendations for clinical use of data on neutralising antibodies to interferon-beta therapy in multiple sclerosis}, journal = {Lancet Neurology}, volume = {9}, number = {7}, year = {2010}, pages = {740-750}, publisher = {ELSEVIER SCIENCE INC}, address = {360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA}, abstract = {

The identification of factors that can affect the efficacy of immunomodulatory drugs in relapsing-remitting multiple sclerosis (MS) is important. For the available interferon-beta products, neutralising antibodies (NAb) have been shown to affect treatment efficacy. In June, 2009, a panel of experts in MS and NAbs to interferon-beta therapy convened in Amsterdam, Netherlands, under the auspices of the Neutralizing Antibodies on Interferon beta in Multiple Sclerosis consortium, a European-based project of the 6th Framework Programme of the European Commission, to review and discuss data on NAbs and their practical consequences for the treatment of patients with MS on interferon beta. The panel believed that information about NAbs and other markers of biological activity of interferons (ie, myxovirus resistance protein A [MxA]) can be integrated with clinical and imaging indicators to guide individual treatment decisions. In cases of sustained high-titre NAb positivity and/or lack of MxA bioactivity, a switch to a non-interferon-beta therapy should be considered. In patients who are doing poorly clinically, therapy should be switched irrespective of NAb or MxA bioactivity.

}, doi = {10.1016/S1474-4422(10)70103-4}, author = {Polman, Chris H. and Bertolotto, Antonio and Deisenhammer, Florian and Giovannoni, Gavin and Hartung, Hans-Peter and Hemmer, Bernhard and Killestein, Joep and McFarland, Henry F. and Oger, Joel and Pachner, Andrew R. and Petkau, John and Reder, Anthony T. and Reingold, Stephen C. and Schellekens, Huub and Soelberg-Sorensen, Per} } @article { ISI:000279451600006, title = {On a robust local estimator for the scale function in heteroscedastic nonparametric regression}, journal = {STATISTICS \& PROBABILITY LETTERS}, volume = {80}, number = {15-16}, year = {2010}, month = {AUG 1}, pages = {1185-1195}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {When the data used to fit an heteroscedastic nonparametric regression model are contaminated with outliers, robust estimators of the scale function are needed in order to obtain robust estimators of the regression function and to construct robust confidence bands. In this paper, local M-estimators of the scale function based on consecutive differences of the responses, for fixed designs are considered. Under mild regularity conditions, the asymptotic behavior of the local M-estimators for general weight functions is derived. (C) 2010 Elsevier B.V. All rights reserved.}, keywords = {Heteroscedasticity, Local M-estimators, nonparametric regression, Robust estimation}, issn = {0167-7152}, doi = {10.1016/j.spl.2010.03.015}, author = {Boente, Graciela and Ruiz, Marcelo and Zamar, Ruben H.} } @article { ISI:000279742601881, title = {Role of androgens in women{\textquoteright}s sexual dysfunction}, journal = {Menopause}, volume = {17}, number = {2}, year = {2010}, pages = {962-971}, publisher = {JAPAN ENDOCRINE SOC}, address = {75 YANAGINOBANBA NISHIIRU-MASUYA-CHO, SANJOU-DORI, NAKAGYOU-KU, KYOTO, 604-8111, JAPAN}, author = {Basson, Rosemary and Brotto, Lori A and Petkau, A.John and Labrie, Fernand} } @article {8877, title = {S-Estimation for Penalized Regression Splines}, journal = {Journal of Computational and Graphical Statistics}, volume = {19}, year = {2010}, pages = {609-625}, doi = {10.1198/jcgs.2010.08149}, url = {http://dx.doi.org/10.1198/jcgs.2010.08149}, author = {Kukatharmini Tharmaratnam and Gerda Claeskens and Christophe Croux and Matias Salibian-Barrera} } @article {gu2010biom, title = {Simplified Bayesian sensitivity analysis for mismeasured and unobserved confounders}, journal = {Biometrics}, volume = {66}, year = {2010}, pages = {1129-1137}, doi = {10.1111/j.1541-0420.2009.01377.x}, author = {Gustafson, P. and McCandless, L. C. and Levy, A. R. and Richardson, S.} } @article {pmid20526184, title = {Skin conductance fluctuations correlate poorly with postoperative self-report pain measures in school-aged children}, journal = {Anesthesiology}, volume = {113}, number = {1}, year = {2010}, month = {Jul}, pages = {175{\textendash}182}, author = {Choo, E. K. and Magruder, W. and Montgomery, C. J. and Lim, J. and Brant, R. and Ansermino, J. M.} } @article {pmid20880151, title = {Slower administration of propofol preserves adequate respiration in children}, journal = {Paediatr Anaesth}, volume = {20}, number = {11}, year = {2010}, month = {Nov}, pages = {1001{\textendash}1008}, author = {Dosani, M. and McCormack, J. and Reimer, E. and Brant, R. and Dumont, G. and Lim, J. and Mark Ansermino, J.} } @article {liu_asymptotic_2010, title = {Some asymptotic results for semiparametric nonlinear mixed-effects models with incomplete data}, journal = {Journal of Statistical Planning and Inference}, volume = {140}, number = {1}, year = {2010}, month = {jan}, pages = {52{\textendash}64}, abstract = {In modeling complex longitudinal data, semiparametric nonlinear mixed-effects (SNLME) models are very flexible and useful. Covariates are often introduced in the models to partially explain the inter-individual variations. In practice, data are often incomplete in the sense that there are often measurement errors and missing data in longitudinal studies. The likelihood method is a standard approach for inference for these models but it can be computationally very challenging, so computationally efficient approximate methods are quite valuable. However, the performance of these approximate methods is often based on limited simulation studies, and theoretical results are unavailable for many approximate methods. In this article, we consider a computationally efficient approximate method for a class of SNLME models with incomplete data and investigate its theoretical properties. We show that the estimates based on the approximate method are consistent and asymptotically normally distributed.}, keywords = {Approximation, Asymptotics, Longitudinal data, Measurement error}, issn = {0378-3758}, doi = {10.1016/j.jspi.2009.06.006}, url = {http://www.sciencedirect.com/science/article/pii/S0378375809001888}, author = {Liu, Wei and WU, LANG} } @article { ISI:000281333900001, title = {Special issue on variable selection and robust procedures}, journal = {COMPUTATIONAL STATISTICS \& DATA ANALYSIS}, volume = {54}, number = {12, SI}, year = {2010}, month = {DEC 1}, pages = {2879-2882}, publisher = {ELSEVIER SCIENCE BV}, type = {Editorial Material}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, issn = {0167-9473}, doi = {10.1016/j.csda.2010.07.019}, author = {Van Aelst, Stefan and Welsch, Roy and Zamar, Ruben H.} } @article { ISI:000272526200019, title = {Tail dependence functions and vine copulas}, journal = {Journal of Multivariate Analysis}, volume = {101}, number = {1}, year = {2010}, month = {JAN}, pages = {252-270}, publisher = {Elsevier Inc}, type = {Article}, abstract = {Tail dependence and conditional tail dependence functions describe, respectively, the tail probabilities and conditional tail probabilities Of a Copula at various relative scales. The properties as well as the interplay of these two functions are established based upon their homogeneous structures. The extremal dependence of a, copula, as described by its extreme Value copulas, is shown to be completely determined by its tail dependence functions. For a vine Copula built from a set of bivariate copulas, its tail dependence function can be expressed recursively by the tail dependence and conditional tail dependence functions of lower-dimensional margins. The effect of tail dependence of bivariate linking copulas on that of a vine copula is also investigated. (C) 2009 Elsevier Inc. All rights reserved.}, keywords = {Archimedean copulas, C-vine, Conditional tail, D-vine, Extreme value}, issn = {0047-259X}, doi = {10.1016/j.jmva.2009.08.002}, author = {Joe, Harry and Li, Haijun and Nikoloulopoulos, Aristidis K.} } @article {robert2010terpenoid, title = {Terpenoid metabolite profiling in Sitka spruce identifies association of dehydroabietic acid,(+)-3-carene, and terpinolene with resistance against white pine weevil}, journal = {Botany}, volume = {88}, number = {9}, year = {2010}, pages = {810{\textendash}820}, publisher = {NRC Research Press}, author = {Robert, Jeanne A and Madilao, Lufiani L and White, Rick and Yanchuk, Alvin and King, John and Bohlmann, J{\"o}rg} } @article {chen2010uncertainty, title = {Uncertainty and the conditional variance}, journal = {Statistics and probability letters}, volume = {80}, number = {23}, year = {2010}, pages = {1764{\textendash}1770}, publisher = {Elsevier}, author = {Chen, Jiahua and van Eeden, Constance and Zidek, James} } @article {chen2010uncertainty, title = {Uncertainty and the conditional variance}, journal = {Statistics \& probability letters}, volume = {80}, number = {23}, year = {2010}, pages = {1764{\textendash}1770}, publisher = {North-Holland}, author = {Chen, Jiahua and van Eeden, Constance and Zidek, James} } @article { ISI:000280072500005, title = {Uniform asymptotics for S- and MM-regression estimators}, journal = {ANNALS OF THE INSTITUTE OF STATISTICAL MATHEMATICS}, volume = {62}, number = {5}, year = {2010}, month = {OCT}, pages = {897-927}, publisher = {SPRINGER HEIDELBERG}, type = {Article}, address = {TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY}, abstract = {In this paper we find verifiable regularity conditions to ensure that S-estimators of scale and regression and MM-estimators of regression are uniformly consistent and uniformly asymptotically normally distributed over contamination neighbourhoods. Moreover, we show how to calculate the size of these neighbourhoods. In particular, we find that, for MM-estimators computed with Tukey{\textquoteright}s family of bisquare score functions, there is a trade-off between the size of these neighbourhoods and both the breakdown point of the S-estimators and the leverage of the contamination that is allowed in the neighbourhood. These results extend previous work of Salibian-Barrera and Zamar for location-scale to the linear regression model.}, keywords = {Robust inference, Robust regression, Robustness, Uniform asymptotics}, issn = {0020-3157}, doi = {10.1007/s10463-008-0189-x}, author = {Omelka, Marek and Salibian-Barrera, Mat{\'\i}as} } @conference {Bouchard2010Variational, title = {Variational inference over combinatorial spaces}, booktitle = {Advances in Neural Information Processing Systems 23 (NIPS)}, volume = {23}, year = {2010}, pages = {280{\textendash}288}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Michael I. Jordan} } @article {hollander2010whole, title = {Whole blood biomarkers of acute cardiac allograft rejection: double-crossing the biopsy}, journal = {Transplantation}, volume = {90}, number = {12}, year = {2010}, pages = {1388{\textendash}1393}, publisher = {LWW}, author = {Hollander, Zsuzsanna and Lin, David and Chen, Virginia and Ng, Raymond and Wilson-McManus, Janet and Ignaszewski, Andrew and Freue, Gabriela Cohen and Balshaw, Rob and Mui, Alice and McMaster, Robert and others} } @article {zhu2009adjusted, title = {Adjusted exponentially tilted likelihood with applications to brain morphology}, journal = {Biometrics}, volume = {65}, number = {3}, year = {2009}, pages = {919{\textendash}927}, publisher = {Blackwell Publishing Inc}, author = {Zhu, Hongtu and Zhou, Haibo and Chen, Jiahua and Li, Yimei and Lieberman, Jeffrey and Styner, Martin} } @booklet {hosseini2009analysis, title = {An analysis of Alberta{\textquoteright}s climate. Part i: Nonhomogenized data}, number = {245}, year = {2009}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Hosseini, Reza and Le, Nhu D. and Zidek, James V} } @article {ainslie2009application, title = {Application of an entropy-based Bayesian optimization technique to the redesign of an existing monitoring network for single air pollutants}, journal = {Journal of environmental management}, volume = {90}, number = {8}, year = {2009}, pages = {2715{\textendash}2729}, publisher = {Elsevier}, author = {Ainslie, B and Reuten, C and Steyn, DG and Le, Nhu D. and Zidek, James V} } @article {pmid19941707, title = {The attitudes of Canadian maternity care practitioners towards labour and birth: many differences but important similarities}, journal = {J Obstet Gynaecol Can}, volume = {31}, number = {9}, year = {2009}, month = {Sep}, pages = {827{\textendash}840}, author = {Klein, M. C. and Kaczorowski, J. and Hall, W. A. and Fraser, W. and Liston, R. M. and Eftekhary, S. and Brant, R. and Masse, L. C. and Rosinski, J. and Mehrabadi, A. and Baradaran, N. and Tomkinson, J. and Dore, S. and McNiven, P. C. and Saxell, L. and Lindstrom, K. and Grant, J. and Chamberlaine, A.} } @article {HoGu2009statmed, title = {Bayesian adjustment for covariate measurement errors: a flexible parametric approach}, journal = {Statistics in Medicine}, volume = {28}, year = {2009}, pages = {1580-1600}, doi = {10.1002/sim.3552}, author = {Hossain, S. and Gustafson, P.} } @article {LiGu2009statmed, title = {Bayesian analysis of a matched case-control study with expert prior information on both the misclassification of exposure and the exposure-disease association}, journal = {Statistics in Medicine}, volume = {28}, year = {2009}, pages = {3411-3423}, doi = {10.1002/sim.3694}, url = {http://onlinelibrary.wiley.com/doi/10.1002/sim.3694/abstract}, author = {Liu, J. and Gustafson, P. and Cherry, N. and Burstyn, I.} } @booklet {dou2009bayesian, title = {Bayesian Empirical Orthogonal Functions}, number = {242}, year = {2009}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Dou, Yiping and Le, Nhu D. and Zidek, James V.} } @article { ISI:000265170600008, title = {Bayesian likelihood robustness in linear models}, journal = {JOURNAL OF STATISTICAL PLANNING AND INFERENCE}, volume = {139}, number = {7}, year = {2009}, month = {JUL 1}, pages = {2196-2207}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {This paper deals with the problem of robustness of Bayesian regression with respect to the data. We first give a formal definition of Bayesian robustness to data contamination, prove that robustness according to the definition cannot be obtained by using heavy-tailed error distributions in linear regression models and propose a heteroscedastic approach to achieve the desired Bayesian robustness. (C) 2008 Elsevier B.V. All rights reserved.}, keywords = {Bayesian inference, Heteroscedasticity, Kullback-Leibler divergence, Robust regression}, issn = {0378-3758}, doi = {10.1016/j.jspi.2008.10.012}, author = {Pena, Daniel and Zamar, Ruben and Yan, Guohua} } @article {McGu2009statmed, title = {Bayesian propensity score analysis}, journal = {Statistics in Medicine}, volume = {28}, year = {2009}, pages = {94-112}, author = {McCandless, L. C. and Gustafson, P. and Austin, P. C.} } @article {doi:10.1198/TECH.2009.08040, title = {Choosing the Sample Size of a Computer Experiment: A Practical Guide}, journal = {Technometrics}, volume = {51}, number = {4}, year = {2009}, pages = {366-376}, abstract = {We provide reasons and evidence supporting the informal rule that the number of runs for an effective initial computer experiment should be about 10 times the input dimension. Our arguments quantify two key characteristics of computer codes that affect the sample size required for a desired level of accuracy when approximating the code via a Gaussian process (GP). The first characteristic is the total sensitivity of a code output variable to all input variables; the second corresponds to the way this total sensitivity is distributed across the input variables, specifically the possible presence of a few prominent input factors and many impotent ones (i.e., effect sparsity). Both measures relate directly to the correlation structure in the GP approximation of the code. In this way, the article moves toward a more formal treatment of sample size for a computer experiment. The evidence supporting these arguments stems primarily from a simulation study and via specific codes modeling climate and ligand activation of G-protein.}, doi = {10.1198/TECH.2009.08040}, url = {http://dx.doi.org/10.1198/TECH.2009.08040}, author = {Jason L. Loeppky and Jerome Sacks and William J. Welch} } @article {pmid19556028, title = {Comparison of the 20-hour intravenous and 72-hour oral acetylcysteine protocols for the treatment of acute acetaminophen poisoning}, journal = {Ann Emerg Med}, volume = {54}, number = {4}, year = {2009}, month = {Oct}, pages = {606{\textendash}614}, author = {Yarema, M. C. and Johnson, D. W. and Berlin, R. J. and Sivilotti, M. L. and Nettel-Aguirre, A. and Brant, R. F. and Spyker, D. A. and Bailey, B. and Chalut, D. and Lee, J. S. and Plint, A. C. and Purssell, R. A. and Rutledge, T. and Seviour, C. A. and Stiell, I. G. and Thompson, M. and Tyberg, J. and Dart, R. C. and Rumack, B. H.} } @article {McGu2009epiper, title = {Covariate balance in a Bayesian propensity score analysis of beta blocker therapy in heart failure patients}, journal = {Epidemiological Perspectives and Innovations}, volume = {6}, number = {1}, year = {2009}, pages = {article 5}, publisher = {BioMed Central Ltd}, doi = {10.1186/1742-5573-6-5}, author = {McCandless, L. C. and Gustafson, P. and Austin, P. C. and Levy, A.} } @article { ISI:000268506000005, title = {Diagnosing Multivariate Outliers Detected by Robust Estimators}, journal = {JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS}, volume = {18}, number = {1}, year = {2009}, month = {MAR}, pages = {73-91}, publisher = {AMER STATISTICAL ASSOC}, type = {Article}, address = {732 N WASHINGTON ST, ALEXANDRIA, VA 22314-1943 USA}, abstract = {We propose a number of diagnostic methods that can be used whenever multiple outliers are identified by robust estimates for multivariate location and scatter. Their main purpose is visualization of the multivariate data to help determine whether the detected outliers (a) form separate clusters or (b) are isolated or randomly scattered (such as heavy tails compared with Gaussian). We make use of Mahalanobis distances and linear projections, to check for separation and to reveal additional aspects of the data structure. Several real data examples are analyzed, and artificial examples are used to illustrate the diagnostic power of the proposed plots. Code to perform the diagnostics, datasets used as examples in the article and documention are available in the online supplements.}, keywords = {Outlier diagnostics, Robust distances, Visualization of multivariate data}, issn = {1061-8600}, doi = {10.1198/jcgs.2009.0005}, author = {Willems, Gert and Joe, Harry and Zamar, Ruben} } @article { ISI:000268506000005, title = {Diagnosing multivariate outliers detected by robust estimators}, journal = {Journal of Computational and Graphical Statistics}, volume = {18}, number = {1}, year = {2009}, month = {MAR}, pages = {73-91}, publisher = {Amer Statistical Assoc}, type = {Article}, abstract = {We propose a number of diagnostic methods that can be used whenever multiple outliers are identified by robust estimates for multivariate location and scatter. Their main purpose is visualization of the multivariate data to help determine whether the detected outliers (a) form separate clusters or (b) are isolated or randomly scattered (such as heavy tails compared with Gaussian). We make use of Mahalanobis distances and linear projections, to check for separation and to reveal additional aspects of the data structure. Several real data examples are analyzed, and artificial examples are used to illustrate the diagnostic power of the proposed plots. Code to perform the diagnostics, datasets used as examples in the article and documention are available in the online supplements.}, keywords = {Outlier diagnostics, Robust distances, Visualization of multivariate data}, issn = {1061-8600}, doi = {10.1198/jcgs.2009.0005}, author = {Willems, Gert and Joe, Harry and Zamar, Ruben} } @article {pmid19255065, title = {Do educational materials change knowledge and behaviour about crying and shaken baby syndrome? A randomized controlled trial}, journal = {CMAJ}, volume = {180}, number = {7}, year = {2009}, month = {Mar}, pages = {727{\textendash}733}, author = {Barr, R. G. and Barr, M. and Fujiwara, T. and Conway, J. and Catherine, N. and Brant, R.} } @article {pmid19584979, title = {Effect of angiotensin-converting enzyme inhibition on C-reactive protein levels: the ramipril C-reactive pRotein randomized evaluation (4R) trial results}, journal = {Can J Cardiol}, volume = {25}, number = {7}, year = {2009}, month = {Jul}, pages = {e236{\textendash}240}, author = {Verma, S. and Lonn, E. M. and Nanji, A. and Browne, K. and Ward, R. and Robertson, A. and Conradson, H. and Hildebrand, K. and Brant, R. and Anderson, T. J.} } @article {pmid19743455, title = {Effect of chorioamnionitis on brain development and injury in premature newborns}, journal = {Ann. Neurol.}, volume = {66}, number = {2}, year = {2009}, month = {Aug}, pages = {155{\textendash}164}, author = {Chau, V. and Poskitt, K. J. and McFadden, D. E. and Bowen-Roberts, T. and Synnes, A. and Brant, R. and Sargent, M. A. and Soulikias, W. and Miller, S. P.} } @article {pmid19439742, title = {Epinephrine and dexamethasone in children with bronchiolitis}, journal = {N. Engl. J. Med.}, volume = {360}, number = {20}, year = {2009}, month = {May}, pages = {2079{\textendash}2089}, author = {Plint, A. C. and Johnson, D. W. and Patel, H. and Wiebe, N. and Correll, R. and Brant, R. and Mitton, C. and Gouin, S. and Bhatt, M. and Joubert, G. and Black, K. J. and Turner, T. and Whitehouse, S. and Klassen, T. P.} } @article { ISI:000279291200002, title = {Extreme value properties of multivariate t copulas}, journal = {Extremes}, volume = {12}, number = {2}, year = {2009}, month = {JUN}, pages = {129-148}, publisher = {Springer}, type = {Article}, abstract = {The extremal dependence behavior of t copulas is examined and their extreme value limiting copulas, called the t-EV copulas, are derived explicitly using tail dependence functions. As two special cases, the Husler-Reiss and the Marshall-Olkin distributions emerge as limits of the t-EV copula as the degrees of freedom go to infinity and zero respectively. The t copula and its extremal variants attain a wide range in the set of bivariate tail dependence parameters.}, keywords = {Extreme value, t Copula, Tail dependence function}, issn = {1386-1999}, doi = {10.1007/s10687-008-0072-4}, author = {Nikoloulopoulos, Aristidis K. and Joe, Harry and Li, Haijun} } @article {gunther2009functional, title = {Functional genomic analysis of peripheral blood during early acute renal allograft rejection}, journal = {Transplantation}, volume = {88}, number = {7}, year = {2009}, pages = {942{\textendash}951}, publisher = {LWW}, author = {G{\"u}nther, Oliver P and Balshaw, Robert F and Scherer, Andreas and Hollander, Zsuzsanna and Mui, Alice and Triche, Timothy J and Freue, Gabriela Cohen and Li, Guiyun and Ng, Raymond T and Wilson-McManus, Janet and others} } @article { ISI:000275680500009, title = {Generating random correlation matrices based on vines and extended onion method}, journal = {Journal of Multivariate Analysis}, volume = {100}, number = {9}, year = {2009}, month = {OCT}, pages = {1989-2001}, publisher = {Elsevier Inc}, type = {article}, abstract = {We extend and improve two existing methods of generating random correlation matrices, the onion method of Ghosh and Henderson [S. Ghosh, S.C. Henderson, Behavior of the norta method for correlated random vector generation as the dimension increases, ACM Transactions on Modeling and Computer Simulation (TOMACS) 13 (3) (2003) 276-294] and the recently proposed method of Joe [H. Joe, Generating random correlation matrices based on partial correlations, journal of Multivariate Analysis 97 (2006) 2177-2189] based on partial correlations. The latteris based on the so-called D-vine. We extend the methodology to any regular vine and study the relationship between the multiple correlation and partial correlations on a regular vine. We explain the onion method in terms of elliptical distributions and extend it to allow generating random correlation matrices from the same joint distribution as the vine method. The methods are compared in terms of time necessary to generate 5000 random correlation matrices of given dimensions. (C) 2009 Elsevier Inc. All rights reserved.}, keywords = {Correlation matrix, Dependence vines, Onion method, Partial correlation}, issn = {0047-259X}, doi = {10.1016/j.jmva.2009.04.008}, author = {Lewandowski, Daniel and Kurowicka, Dorota and Joe, Harry} } @conference {DeNero2009Hierarchical, title = {A Hierarchical Dirichlet Process Prior for a Conditional Model of Phrase Alignment}, booktitle = {Workshop on statistical NLP at Advances in Neural Information Processing Systems 21 (NIPS)}, year = {2009}, author = {John DeNero and Alexandre Bouchard-C{\^o}t{\'e}} } @article {pmid19635277, title = {Home therapy of venous thrombosis with long-term LMWH versus usual care: patient satisfaction and post-thrombotic syndrome}, journal = {Am. J. Med.}, volume = {122}, number = {8}, year = {2009}, month = {Aug}, pages = {762{\textendash}769}, author = {Hull, R. D. and Pineo, G. F. and Brant, R. and Liang, J. and Cook, R. and Solymoss, S. and Poon, M. C. and Raskob, G.} } @article {chen2009hypothesis, title = {Hypothesis test for normal mixture models: The EM approach}, journal = {The Annals of Statistics}, year = {2009}, pages = {2523{\textendash}2542}, publisher = {Institute of Mathematical Statistics}, author = {Chen, Jiahua and Li, Pengfei} } @article {pmid19454575, title = {The impact of the Canadian Hypertension Education Programme in its first decade}, journal = {Eur. Heart J.}, volume = {30}, number = {12}, year = {2009}, month = {Jun}, pages = {1434{\textendash}1439}, author = {McAlister, F. A. and Feldman, R. D. and Wyard, K. and Brant, R. and Campbell, N. R. and McAlister, F. A. and Feldman, R. D. and Wyard, K. and Brant, R. and Campbell, N. R. and Baclic, O. and Hude, Q. and Tu, K. and Hill, M. and Hemmelgarn, B. and Joffres, M. and Tremblay, M. and Bartlett, G. and Svenson, L. and Quach, S. and Johansen, H. and Chen, G. and Amankwah, E. and Eliasziw, M. and Ghali, W. and Grover, S. and Kelly, N. and Khan, N. and Lix, L. and Maxwell, C. and Mohan, S. and Phillips, S. and Smith, M. and Taylor, G. and Wielgosz, A. and Zhang, J. and Kaczorowski, J. and Klarenbach, S. and Robinson, C. and Teare, G. and Reimer, K. and Nolan, R. and Lindsay, P. and Gwadry-Sridhar, F. and Bacej, C. and Connor-Gorber, S. and Wilkins, K. and Nichol, M. and Walker, R.} } @conference {Bouchard2009Improved, title = {Improved reconstruction of protolanguage word forms}, booktitle = {Proceedings of the North American Chapter of the Association for Computational Linguistics (NAACL09)}, volume = {7}, year = {2009}, pages = {65{\textendash}73}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Thomas L. Griffiths and Dan Klein} } @article {pmid19772665, title = {Improving outcomes for ill and injured children in emergency departments: protocol for a program in pediatric emergency medicine and knowledge translation science}, journal = {Implement Sci}, volume = {4}, year = {2009}, pages = {60}, author = {Scott, S. and Hartling, L. and Grimshaw, J. and Johnson, D. and Osmond, M. and Plint, A. and Brant, R. and Brehaut, J. C. and Graham, I. D. and Currie, G. and Shaw, N. and Bhatt, M. and Lynch, T. and Bialy, L. and Klassen, T.} } @article {pmid19114646, title = {Increases in antihypertensive prescriptions and reductions in cardiovascular events in Canada}, journal = {Hypertension}, volume = {53}, number = {2}, year = {2009}, month = {Feb}, pages = {128{\textendash}134}, author = {Campbell, N. R. and Brant, R. and Johansen, H. and Walker, R. L. and Wielgosz, A. and Onysko, J. and Gao, R. N. and Sambell, C. and Phillips, S. and McAlister, F. A.} } @article {chen2009inference, title = {Inference for multivariate normal mixtures}, journal = {Journal of Multivariate Analysis}, volume = {100}, number = {7}, year = {2009}, pages = {1367{\textendash}1383}, publisher = {Elsevier}, author = {Chen, Jiahua and Tan, Xianming} } @article {gugr2009statsci, title = {Interval estimation for messy observational data}, journal = {Statistical Science}, volume = {24}, year = {2009}, pages = {328-342}, doi = {10.1214/09-sts305}, url = {http://projecteuclid.org/euclid.ss/1270041259}, author = {Gustafson, P. and Greenland, S.} } @article {wu_longitudinal2009, title = {A Longitudinal Study of Children{\textquoteright}s Aggressive Behaviors and Their Relationships with Potential Predictors}, journal = {Canadian Journal of Statistics}, volume = {37}, year = {2009}, pages = {435{\textendash}452}, author = {Wu, L and Liu, W and Liu, J} } @book {wu_mixed_2009, title = {Mixed Effects Models for Complex Data}, year = {2009}, publisher = {CRC Press}, organization = {CRC Press}, abstract = {Although standard mixed effects models are useful in a range of studies, other approaches must often be used in correlation with them when studying complex or incomplete data. Mixed Effects Models for Complex Data discusses commonly used mixed effects models and presents appropriate approaches to address dropouts, missing data, measurement errors, censoring, and outliers. For each class of mixed effects model, the author reviews the corresponding class of regression model for cross-sectional data. An overview of general models and methods, along with motivating examples After presenting real data examples and outlining general approaches to the analysis of longitudinal/clustered data and incomplete data, the book introduces linear mixed effects (LME) models, generalized linear mixed models (GLMMs), nonlinear mixed effects (NLME) models, and semiparametric and nonparametric mixed effects models. It also includes general approaches for the analysis of complex data with missing values, measurement errors, censoring, and outliers. Self-contained coverage of specific topicsSubsequent chapters delve more deeply into missing data problems, covariate measurement errors, and censored responses in mixed effects models. Focusing on incomplete data, the book also covers survival and frailty models, joint models of survival and longitudinal data, robust methods for mixed effects models, marginal generalized estimating equation (GEE) models for longitudinal or clustered data, and Bayesian methods for mixed effects models. Background materialIn the appendix, the author provides background information, such as likelihood theory, the Gibbs sampler, rejection and importance sampling methods, numerical integration methods, optimization methods, bootstrap, and matrix algebra. Failure to properly address missing data, measurement errors, and other issues in statistical analyses can lead to severely biased or misleading results. This book explores the biases that arise when na{\"\i}ve methods are used and shows which approaches should be used to achieve accurate results in longitudinal data analysis.}, keywords = {Mathematics / Probability \& Statistics / General, Medical / Epidemiology, Science / Life Sciences / Biology}, isbn = {978-1-4200-7408-6}, author = {WU, LANG} } @article { ISI:000268567000006, title = {Modelling heavy-tailed count data using a generalised Poisson-inverse Gaussian family}, journal = {Statistics \& Probability Letters}, volume = {79}, number = {15}, year = {2009}, month = {AUG 1}, pages = {1695-1703}, publisher = {Elsevier Science BV}, type = {Article}, abstract = {We generalise the Poisson-inverse Gaussian distribution to a three-parameter family, which includes the Poisson and discrete stable distributions as boundary cases. It is flexible in modelling Count data sets with different tail heaviness. Although the family only has a closed-form probability generating function, a recursive method is developed for statistical inferences based on the likelihood. As an example, this new family is applied to data sets of citation counts of published articles. (C) 2009 Elsevier B.V. All rights reserved.}, issn = {0167-7152}, doi = {10.1016/j.spl.2009.04.011}, author = {Zhu, Rong and Joe, Harry} } @article {fu2009modified, title = {Modified likelihood ratio test for homogeneity in a two-sample problem}, journal = {Statistica Sinica}, volume = {19}, number = {4}, year = {2009}, pages = {1603}, author = {Fu, Yuejiao and Chen, Jiahua and Kalbfleisch, John D} } @article {lysenko2009multivariate, title = {Multivariate extremes of generalized skew-normal distributions}, journal = {Statistics \& Probability Letters}, volume = {79}, number = {4}, year = {2009}, pages = {525{\textendash}533}, publisher = {Elsevier}, author = {Lysenko, Natalia and Roy, Parthanil and Waeber, Rolf} } @article {li2009non, title = {Non-finite Fisher information and homogeneity: an EM approach}, journal = {Biometrika}, year = {2009}, pages = {asp011}, publisher = {Oxford University Press}, author = {Li, P and Chen, J and Marriott, P} } @article {9273, title = {Nonlinear voxel-based modelling of the haemodynamic response in fMRI}, journal = {Journal of Applied Statistics}, volume = {36}, year = {2009}, pages = {237 - 253}, chapter = {237}, author = {John Kornak and Bruce Dunham and Deborah A. Hall and Mark P. Haggard} } @conference {Bouchard2009Optimization, title = {Optimization of structured mean field objectives}, booktitle = {Proceedings of the 25th Conference on Uncertainty in Artificial Intelligence (UAI09)}, volume = {25}, year = {2009}, pages = {67{\textendash}74}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Michael I. Jordan} } @conference {4706456, title = {Personalizing entity detection and recommendation with a fusion of web log mining techniques}, booktitle = {Extending Database Technology}, year = {2009}, pages = {1100{\textendash}1103}, doi = {10.1145/1516360.1516486}, author = {Kathleen Tsoukalas and Bin Zhou and Jian Pei and Davor Cubranic} } @article {robinson2009predicting, title = {Predicting the regenerative capacity of conifer somatic embryogenic cultures by metabolomics}, journal = {Plant biotechnology journal}, volume = {7}, number = {9}, year = {2009}, pages = {952{\textendash}963}, publisher = {Wiley Online Library}, author = {Robinson, Andrew R and Dauwe, Rebecca and Ukrainetz, Nicholas K and Cullis, Ian F and White, Rick and Mansfield, Shawn D} } @article {pmid18988911, title = {Preventing brain injury in newborns with congenital heart disease: brain imaging and innovative trial designs}, journal = {Stroke}, volume = {40}, number = {1}, year = {2009}, month = {Jan}, pages = {327{\textendash}332}, author = {Sherlock, R. L. and McQuillen, P. S. and Miller, S. P. and Dyck, J. and Joynt, C. and Phillipos, E. and Massicotte, P. and Yager, J. and Brant, R. and Campbell, A. and Chau, V. and Human, D. and Poskitt, K. and Miller, S. and Shereck, E. and Synnes, A. and Ferriero, D. and Fineman, J. and Keller, R. and McQuillen, P. and Moore, P.} } @article {pmid18823874, title = {"Preventive induction" fails to demonstrate benefits for mothers or newborn infants}, journal = {Am. J. Obstet. Gynecol.}, volume = {200}, number = {4}, year = {2009}, month = {Apr}, pages = {e13{\textendash}14}, author = {Klein, M. C. and Brant, R. and Kaczorowski, J.} } @article { ISI:000263129000011, title = {PROPAGATION OF OUTLIERS IN MULTIVARIATE DATA}, journal = {ANNALS OF STATISTICS}, volume = {37}, number = {1}, year = {2009}, month = {FEB}, pages = {311-331}, publisher = {INST MATHEMATICAL STATISTICS}, type = {Article}, address = {3163 SOMERSET DR, CLEVELAND, OH 44122 USA}, abstract = {We investigate the performance of robust estimates of multivariate location under nonstandard data contamination models such as componentwise outliers (i.e., contamination in each variable is independent from the other variables). This model brings up a possible new source of statistical error that we call {\textquoteleft}{\textquoteleft}propagation of outliers.{\textquoteright}{\textquoteright} This source of error is Unusual in the sense that it is generated by the data processing itself and takes place after the data has been collected. We define and derive the influence function of robust multivariate location estimates under flexible contamination models and use it to investigate the effect of propagation of outliers. Furthermore, we show that standard high-breakdown affine equivariant estimators propagate outliers and therefore show poor breakdown behavior under componentwise contamination when the dimension d is high.}, keywords = {breakdown point, contamination model, independent contamination, influence function, Robustness}, issn = {0090-5364}, doi = {10.1214/07-AOS588}, author = {Alqallaf, Fatemah and Van Aelst, Stefan and Yohai, Victor J. and Zamar, Ruben H.} } @article {lippert2009quantitative, title = {Quantitative iTRAQ proteome and comparative transcriptome analysis of elicitor-induced Norway spruce (Picea abies) cells reveals elements of calcium signaling in the early conifer defense response}, journal = {Proteomics}, volume = {9}, number = {2}, year = {2009}, pages = {350{\textendash}367}, author = {Lippert, Dustin N and Ralph, Steven G and Phillips, Michael and White, Rick and Smith, Derek and Hardie, Darryl and Gershenzon, Jonathan and Ritland, Kermit and Borchers, Christoph H and Bohlmann, J{\"o}rg and others} } @conference {Bouchard2009Randomized, title = {Randomized pruning: efficiently calculating expectations in large dynamic programs}, booktitle = {Advances in Neural Information Processing Systems 22 (NIPS)}, volume = {22}, year = {2009}, pages = {144{\textendash}152}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Slav Petrov and Dan Klein} } @article {garcia2009robust, title = {Robust linear clustering}, journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)}, volume = {71}, number = {1}, year = {2009}, pages = {301{\textendash}318}, publisher = {Wiley Online Library}, author = {Garc{\'\i}a-Escudero, Luis Angel and Gordaliza, Alfonso and San Martin, Roberto and Van Aelst, Stefan and Zamar, Ruben} } @booklet {hosseini2009r, title = {r-th order categorical Markov chains}, number = {248}, year = {2009}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Hosseini, Reza and Zidek, James B. and Le, Nhu D.} } @conference {9272, title = {Statistics Clicks: Using Clickers in Introductory Statistics Courses}, booktitle = {Improving University Teaching}, year = {2009}, author = {Bruce Dunham} } @article { ISI:000272709800022, title = {Synthetic Lethal Genetic Interactions That Decrease Somatic Cell Proliferation in Caenorhabditis elegans Identify the Alternative RFCCTF18 as a Candidate Cancer Drug Target}, journal = {MOLECULAR BIOLOGY OF THE CELL}, volume = {20}, number = {24}, year = {2009}, month = {DEC 15}, pages = {5306-5313}, publisher = {AMER SOC CELL BIOLOGY}, type = {Article}, address = {8120 WOODMONT AVE, STE 750, BETHESDA, MD 20814-2755 USA}, abstract = {Somatic mutations causing chromosome instability (CIN) in tumors can be exploited for selective killing of cancer cells by knockdown of second-site genes causing synthetic lethality. We tested and statistically validated synthetic lethal (SL) interactions between mutations in six Saccharomyces cerevisiae CIN genes orthologous to genes mutated in colon tumors and five additional CIN genes. To identify which SL interactions are conserved in higher organisms and represent potential chemotherapeutic targets, we developed an assay system in Caenorhabditis elegans to test genetic interactions causing synthetic proliferation defects in somatic cells. We made use of postembryonic RNA interference and the vulval cell lineage of C. elegans as a readout for somatic cell proliferation defects. We identified SL interactions between members of the cohesin complex and CTF4, RAD27, and components of the alternative RFCCTF18 complex. The genetic interactions tested are highly conserved between S. cerevisiae and C. elegans and suggest that the alternative RFC components DCC1, CTF8, and CTF18 are ideal therapeutic targets because of their mild phenotype when knocked down singly in C. elegans. Furthermore, the C. elegans assay system will contribute to our knowledge of genetic interactions in a multicellular animal and is a powerful approach to identify new cancer therapeutic targets.}, issn = {1059-1524}, doi = {10.1091/mbc.E09-08-0699}, author = {McLellan, Jessica and O{\textquoteright}Neil, Nigel and Tarailo, Sanja and Stoepel, Jan and Bryan, Jennifer and Rose, Ann and Hieter, Philip} } @booklet {dou2009temporal, title = {Temporal prediction with a Bayesian spatial predictor: an application to ozone fields}, number = {249}, year = {2009}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Dou, Yiping and Le, Nhu D. and Zidek, James V} } @article {chen2009tournament, title = {Tournament screening cum EBIC for feature selection with high-dimensional feature spaces}, journal = {Science in China Series A: Mathematics}, volume = {52}, number = {6}, year = {2009}, pages = {1327{\textendash}1341}, publisher = {SP Science in China Press}, author = {Chen, Zehua and Chen, Jiahua} } @article {wuthrich2009uncertainty, title = {Uncertainty of the claims development result in the chain ladder method}, journal = {Scandinavian Actuarial Journal}, volume = {2009}, number = {1}, year = {2009}, pages = {63{\textendash}84}, publisher = {Taylor \& Francis}, author = {W{\"u}thrich, Mario V and Merz, Michael and Lysenko, Natalia} } @conference {mostafavi2009using, title = {Using the Gene Ontology hierarchy when predicting gene function}, booktitle = {Proceedings of the twenty-fifth conference on uncertainty in artificial intelligence}, year = {2009}, pages = {419{\textendash}427}, publisher = {AUAI Press}, organization = {AUAI Press}, author = {Mostafavi, Sara and Morris, Quaid} } @article {pmid19544053, title = {Visual cueing with context relevant information for reducing change blindness}, journal = {J Clin Monit Comput}, volume = {23}, number = {4}, year = {2009}, month = {Aug}, pages = {223{\textendash}232}, author = {Tappan, J. M. and Daniels, J. and Slavin, B. and Lim, J. and Brant, R. and Ansermino, J. M.} } @article { ISI:000263136700009, title = {On weighting of bivariate margins in pairwise likelihood}, journal = {Journal of Multivariate Analysis}, volume = {100}, number = {4}, year = {2009}, month = {APR}, pages = {670-685}, publisher = {Elsevier Inc}, type = {article}, abstract = {Composite and pairwise likelihood methods have recently been increasingly used. For clustered data with varying cluster sizes, we study asymptotic relative efficiencies for various weighted pairwise likelihoods, with weight being a function of cluster size. For longitudinal data, we also study weighted pairwise likelihoods with weights that can depend on lag. Good choice of weights are needed to avoid the undesirable behavior of estimators with low efficiency. Some analytic results are obtained using the multivariate normal distribution. For clustered data, a practically good choice of weight is obtained after study of relative efficiencies for an exchangeable multivariate normal model; they are different from weights that had previously been suggested. For longitudinal data, there are advantages to only include bivariate margins of adjacent or nearly adjacent pairs in the weighted pairwise likelihood. (C) 2008 Elsevier Inc. All rights reserved.}, keywords = {Binary probit, Clustered data, Composite likelihood, Longitudinal data}, issn = {0047-259X}, doi = {10.1016/j.jmva.2008.07.004}, author = {Joe, Harry and Lee, Youngjo} } @article {Gustafson2009, title = {What are the limits of posterior distributions arising from nonidentified models, and why should we care?}, journal = {Journal of the American Statistical Association}, volume = {104}, year = {2009}, pages = {1682-1695}, doi = {10.1198/jasa.2009.tm08603}, url = {http://www.tandfonline.com/doi/abs/10.1198/jasa.2009.tm08603}, author = {Gustafson, P.} } @article {lin2009whole, title = {Whole blood genomic biomarkers of acute cardiac allograft rejection}, journal = {The Journal of Heart and Lung Transplantation}, volume = {28}, number = {9}, year = {2009}, pages = {927{\textendash}935}, publisher = {Elsevier}, author = {Lin, David and Hollander, Zsuzsanna and Ng, Raymond T and Imai, Carol and Ignaszewski, Andrew and Balshaw, Robert and Freue, Gabriela Cohen and Wilson-McManus, Janet E and Qasimi, Pooran and Meredith, Anna and others} } @article {pmid18822093, title = {Accuracy of detecting changes in auditory heart rate in a simulated operating room environment}, journal = {Anaesthesia}, volume = {63}, number = {11}, year = {2008}, month = {Nov}, pages = {1181{\textendash}1186}, author = {Chou, E. and Lim, J. and Brant, R. and Ford, S. and Ansermino, J. M.} } @article { ISI:000259075900002, title = {Accuracy of Laplace approximation for discrete response mixed models}, journal = {Computational Statistics \& Data Analysis}, volume = {52}, number = {12}, year = {2008}, month = {AUG 15}, pages = {5066-5074}, publisher = {Elsevier Science BV}, type = {article}, abstract = {The Laplace approximation is amongst the computational methods used for estimation in generalized linear mixed models. it is computationally the fastest, but there hasn{\textquoteright}t been a clear analysis of when its accuracy is adequate. In this paper, for a few factors we do calculations for a variety of mixed models to show patterns in the asymptotic bias of the estimator based on the maximum of the Laplace approximation of the log-likelihood. The biggest factor for asymptotic bias is the amount of discreteness in the response variable; there is more bias for binary and ordinal responses than for a count response, and more bias for a count response when its support is mainly near 0. When there is bias, the bias decreases as the cluster size increases. Often, the Laplace approximation is adequate even for small cluster sizes. Even with bias,the Laplace approximation maybe adequate for quick assessment of competing mixed models with different random effects and covariates. (c) 2008 Elsevier B.V. All rights reserved.}, issn = {0167-9473}, doi = {10.1016/j.csda.2008.05.002}, author = {Joe, Harry} } @article {chen2008adjusted, title = {Adjusted empirical likelihood and its properties}, journal = {Journal of Computational and Graphical Statistics}, volume = {17}, number = {2}, year = {2008}, pages = {426{\textendash}443}, publisher = {Taylor \& Francis}, author = {Chen, Jiahua and Variyath, Asokan Mulayath and Abraham, Bovas} } @article {wu_approximate_2008, title = {An approximate method for nonlinear mixed-effects models with nonignorably missing covariates}, journal = {Statistics \& Probability Letters}, volume = {78}, number = {4}, year = {2008}, pages = {384{\textendash}389}, abstract = {Nonlinear mixed-effect (NLME) models are very useful in many longitudinal studies. In practice, covariates in NLME models may contain missing data, and the missing data may be nonignorable. Likelihood inference for NLME models with missing covariates can be computationally very intensive. We propose a computationally much more efficient approximate method for NLME models with nonignorably missing covariates. We illustrate the method using a real data example.}, keywords = {EM algorithm, Linearization, Longitudinal data, Taylor expansion}, issn = {0167-7152}, doi = {10.1016/j.spl.2007.07.011}, url = {http://www.sciencedirect.com/science/article/pii/S0167715207002519}, author = {WU, LANG} } @article {LiGu2008isr, title = {On Average Predictive Comparisons and Interactions}, journal = {International Statistical Review}, volume = {76}, year = {2008}, pages = {419{\"\i}{\textquestiondown}{\textonehalf}432}, doi = {10.1111/j.1751-5823.2008.00056.x}, author = {Liu, J. and Gustafson, P.} } @article {Ferrari2008, title = {A Bayesian multilevel model for estimating the diet/disease relationship in a multicenter study with exposures measured with error: the EPIC study}, journal = {Statistics in medicine}, volume = {27}, number = {29}, year = {2008}, pages = {6037{\textendash}6054}, publisher = {Wiley Online Library}, doi = {10.1002/sim.3444}, author = {Ferrari, Pietro and Carroll, Raymond J and Gustafson, Paul and Riboli, Elio} } @article {Gustafson2008, title = {Bayesian multinomial regression with class-specific predictor selection}, journal = {The Annals of Applied Statistics}, year = {2008}, pages = {1478{\textendash}1502}, publisher = {JSTOR}, doi = {10.1214/08-aoas188}, author = {Gustafson, Paul and Lefebvre, Genevieve} } @booklet {liu2008combining, title = {Combining measurements and physical model outputs for the spatial prediction of hourly ozone space-time fields}, number = {239}, year = {2008}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Liu, Zhong and Le, N.D. and Zidek, James V.} } @article { ISI:000278173500002, title = {A critical assessment of Mus musculus gene function prediction using integrated genomic evidence}, journal = {GENOME BIOLOGY}, volume = {9}, number = {1}, year = {2008}, pages = {S2}, publisher = {BIOMED CENTRAL LTD}, type = {Article}, address = {236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND}, abstract = {Background: Several years after sequencing the human genome and the mouse genome, much remains to be discovered about the functions of most human and mouse genes. Computational prediction of gene function promises to help focus limited experimental resources on the most likely hypotheses. Several algorithms using diverse genomic data have been applied to this task in model organisms; however, the performance of such approaches in mammals has not yet been evaluated. Results: In this study, a standardized collection of mouse functional genomic data was assembled; nine bioinformatics teams used this data set to independently train classifiers and generate predictions of function, as defined by Gene Ontology (GO) terms, for 21,603 mouse genes; and the best performing submissions were combined in a single set of predictions. We identified strengths and weaknesses of current functional genomic data sets and compared the performance of function prediction algorithms. This analysis inferred functions for 76\% of mouse genes, including 5,000 currently uncharacterized genes. At a recall rate of 20\%, a unified set of predictions averaged 41\% precision, with 26\% of GO terms achieving a precision better than 90\%. Conclusion: We performed a systematic evaluation of diverse, independently developed computational approaches for predicting gene function from heterogeneous data sources in mammals. The results show that currently available data for mammals allows predictions with both breadth and accuracy. Importantly, many highly novel predictions emerge for the 38\% of mouse genes that remain uncharacterized.}, issn = {1474-760X}, doi = {10.1186/gb-2008-9-s1-s2}, author = {Pena-Castillo, Lourdes and Tasan, Murat and Myers, Chad L. and Lee, Hyunju and Joshi, Trupti and Zhang, Chao and Guan, Yuanfang and Leone, Michele and Pagnani, Andrea and Kim, Wan Kyu and Krumpelman, Chase and Tian, Weidong and Obozinski, Guillaume and Qi, Yanjun and Mostafavi, Sara and Lin, Guan Ning and Berriz, Gabriel F. and Gibbons, Francis D. and Lanckriet, Gert and Qiu, Jian and Grant, Charles and Barutcuoglu, Zafer and Hill, David P. and Warde-Farley, David and Grouios, Chris and Ray, Debajyoti and Blake, Judith A. and Deng, Minghua and Jordan, Michael I. and Noble, William S. and Morris, Quaid and Klein-Seetharaman, Judith and Bar-Joseph, Ziv and Chen, Ting and Sun, Fengzhu and Troyanskaya, Olga G. and Marcotte, Edward M. and Xu, Dong and Hughes, Timothy R. and Roth, Frederick P.} } @article {pmid18359189, title = {Determination of the minimal clinically important difference for seven fatigue measures in rheumatoid arthritis}, journal = {J Clin Epidemiol}, volume = {61}, number = {7}, year = {2008}, month = {Jul}, pages = {705{\textendash}713}, author = {Pouchot, J. and Kherani, R. B. and Brant, R. and Lacaille, D. and Lehman, A. J. and Ensworth, S. and Kopec, J. and Esdaile, J. M. and Liang, M. H.} } @article { ISI:000265114100004, title = {Discovery and Expansion of Gene Modules by Seeking Isolated Groups in a Random Graph Process}, journal = {PLOS ONE}, volume = {3}, number = {10}, year = {2008}, month = {OCT 9}, pages = {e3358}, publisher = {PUBLIC LIBRARY SCIENCE}, type = {Article}, address = {185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA}, abstract = {Background: A central problem in systems biology research is the identification and extension of biological modules groups of genes or proteins participating in a common cellular process or physical complex. As a result, there is a persistent need for practical, principled methods to infer the modular organization of genes from genome-scale data. Results: We introduce a novel approach for the identification of modules based on the persistence of isolated gene groups within an evolving graph process. First, the underlying genomic data is summarized in the form of ranked gene-gene relationships, thereby accommodating studies that quantify the relevant biological relationship directly or indirectly. Then, the observed gene-gene relationship ranks are viewed as the outcome of a random graph process and candidate modules are given by the identifiable subgraphs that arise during this process. An isolation index is computed for each module, which quantifies the statistical significance of its survival time. Conclusions: The Miso (module isolation) method predicts gene modules from genomic data and the associated isolation index provides a module-specific measure of confidence. Improving on existing alternative, such as graph clustering and the global pruning of dendrograms, this index offers two intuitively appealing features: (1) the score is module-specific; and (2) different choices of threshold correlate logically with the resulting performance, i.e. a stringent cutoff yields high quality predictions, but low sensitivity. Through the analysis of yeast phenotype data, the Miso method is shown to outperform existing alternatives, in terms of the specificity and sensitivity of its predictions.}, issn = {1932-6203}, doi = {10.1371/journal.pone.0003358}, author = {Brumm, Jochen and Conibear, Elizabeth and Wasserman, Wyeth W. and Bryan, Jennifer} } @article { ISI:000253316700006, title = {Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response}, journal = {FEMS YEAST RESEARCH}, volume = {8}, number = {1}, year = {2008}, month = {FEB}, pages = {35-52}, publisher = {BLACKWELL PUBLISHING}, type = {Article}, address = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND}, abstract = {In this study, genome-wide expression analyses were used to study the response of Saccharomyces cerevisiae to stress throughout a 15-day wine fermentation. Forty per cent of the yeast genome significantly changed expression levels to mediate long-term adaptation to fermenting grape must. Among the genes that changed expression levels, a group of 223 genes was identified, which was designated as fermentation stress response (FSR) genes that were dramatically induced at various points during fermentation. FSR genes sustain high levels of induction up to the final time point and exhibited changes in expression levels ranging from four- to 80-fold. The FSR is novel; 62\% of the genes involved have not been implicated in global stress responses and 28\% of the FSR genes have no functional annotation. Genes involved in respiratory metabolism and gluconeogenesis were expressed during fermentation despite the presence of high concentrations of glucose. Ethanol, rather than nutrient depletion, seems to be responsible for entry of yeast cells into the stationary phase.}, keywords = {fermentation, gene expression, HXK2, stress response, wine}, issn = {1567-1356}, doi = {10.1111/j.1567-1364.2007.00338.x}, author = {Marks, Virginia D. and Sui, Shannan J. Ho and Erasmus, Daniel and van der Merwe, George K. and Brumm, Jochen and Wasserman, Wyeth W. and Bryan, Jennifer and van Vuuren, Hennie J. J.} } @conference {Bouchard2008Efficient, title = {Efficient inference in phylogenetic InDel trees}, booktitle = {Advances in Neural Information Processing Systems 21 (NIPS)}, volume = {21}, year = {2008}, pages = {177{\textendash}184}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Michael I. Jordan and Dan Klein} } @article {shaddick2008estimating, title = {Estimating exposure response functions using ambient pollution concentrations}, journal = {The Annals of Applied Statistics}, volume = {2}, number = {4}, year = {2008}, pages = {1249{\textendash}1270}, publisher = {Institute of Mathematical Statistics}, author = {Shaddick, Gavin and Lee, Duncan and Zidek, James V. and Salway, Ruth} } @article {polman_ethics_2008, title = {Ethics of placebo-controlled clinical trials in multiple sclerosis: a reassessment}, journal = {Neurology}, volume = {70}, number = {13 Part 2}, year = {2008}, pages = {1134{\textendash}1140}, abstract = {

The increasing number of established effective therapies for relapsing multiple sclerosis (MS) and emerging consensus for early treatment raise practical concerns and ethical dilemmas for placebo-controlled clinical trials in this disease. An international group of clinicians, ethicists, statisticians, regulators, and representatives from the pharmaceutical industry convened to reconsider prior recommendations regarding the ethics of placebo-controlled trials in MS. The group concluded that placebo-controlled trials can still be done ethically, with restrictions. For patients with relapsing MS for which established effective therapies exist, placebo-controlled trials should only be offered with rigorous informed consent if the subjects refuse to use these treatments, have not responded to them, or if these treatments are not available to them for other reasons (e.g., economics). Suggestions are provided to protect subject autonomy and improve informed consent procedures. Recommendations are tighter than previously suggested for placebo-controlled trials in {\textquotedblleft}resource-restricted{\textquotedblright} environments where established therapies may not be available. Guidance is also provided on the ethics of alternative trial designs and the balance between study subject burden and risk, scientific rationale and interpretability of trial outcomes. GLOSSARY: EET = established effective therapy; MS = multiple sclerosis; PPMS = primary progressive MS; SPMS = secondary progressive MS.

}, doi = {10.1212/01.wnl.0000306410.84794.4d}, url = {http://www.neurology.org/content/70/13_Part_2/1134}, author = {Polman, C. H. and Reingold, S. C. and Barkhof, F. and Calabresi, P. A. and Clanet, M. and Cohen, J. A. and Cutter, G. R. and Freedman, M. S. and Kappos, L. and Lublin, F. D. and McFarland, H. F. and Metz, L. M. and Miller, A. E. and Montalban, X. and O{\textquoteright}Connor, P. W. and Panitch, H. and Richert, J. R. and Petkau, J. and Schwid, S. R. and Sormani, M. P. and Thompson, A. J. and Weinshenker, B. G. and Wolinsky, J. S.} } @article {chen2008extended, title = {Extended Bayesian information criteria for model selection with large model spaces}, journal = {Biometrika}, volume = {95}, number = {3}, year = {2008}, pages = {759{\textendash}771}, publisher = {Biometrika Trust}, author = {Chen, Jiahua and Chen, Zehua} } @article { ISI:000254995100003, title = {Fast and robust bootstrap}, journal = {STATISTICAL METHODS AND APPLICATIONS}, volume = {17}, number = {1}, year = {2008}, pages = {41-71}, publisher = {SPRINGER HEIDELBERG}, type = {Article}, address = {TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY}, abstract = {

In this paper we review recent developments on a bootstrap method for robust estimators which is computationally faster and more resistant to outliers than the classical bootstrap. This fast and robust bootstrap method is, under reasonable regularity conditions, asymptotically consistent. We describe the method in general and then consider its application to perform inference based on robust estimators for the linear regression and multivariate location-scatter models. In particular, we study confidence and prediction intervals and tests of hypotheses for linear regression models, inference for location-scatter parameters and principal components, and classification error estimation for discriminant analysis.

}, keywords = {bootstrap, PCA discriminant analysis, Robust inference, Robust regression}, issn = {1618-2510}, doi = {10.1007/s10260-007-0048-6}, author = {Salibian-Barrera, Mat{\'\i}as and Van Aelst, Stefan and Willerns, Gert} } @conference { ISI:000259327700030, title = {Fast robust variable selection}, booktitle = {COMPSTAT 2008: PROCEEDINGS IN COMPUTATIONAL STATISTICS}, year = {2008}, note = {18th Symposium on Computational Statistics (COMSTAT 2008), Oporto, PORTUGAL, AUG 24-29, 2008}, pages = {359-370}, publisher = {Univ Porto, Fac Econ; PSE; FCT; FEUP; Banco Porutgal; PORTO; SPM; Caixa Geral Depositos; SPE; CLAD; ifcs}, organization = {Univ Porto, Fac Econ; PSE; FCT; FEUP; Banco Porutgal; PORTO; SPM; Caixa Geral Depositos; SPE; CLAD; ifcs}, type = {Proceedings Paper}, address = {TIERGARTENSTR 17, D-69121 HEIDELBERG, GERMANY}, abstract = {We discuss some computationally efficient procedures for robust variable selection in linear regression. A key component in these procedures is the computation of robust correlations between pairs of variables. We show that the robust variable selection procedures can easily handle missing data under the assumption that data are missing completely at random.}, keywords = {correlation, missing data, Robustness, variable selection}, isbn = {978-3-7908-2083-6}, author = {Van Aelst, Stefan and Khan, Jafar A. and Zamar, Ruben H.}, editor = {Brito, P} } @article { ISI:000259127900007, title = {The fast-tau estimator for regression}, journal = {JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS}, volume = {17}, number = {3}, year = {2008}, month = {SEP}, pages = {659-682}, publisher = {AMER STATISTICAL ASSOC}, type = {Article}, address = {732 N WASHINGTON ST, ALEXANDRIA, VA 22314-1943 USA}, abstract = {Yohai and Zamar{\textquoteright}s tau-estimators of regression have excellent statistical properties but are nevertheless rarely used in practice because of a lack of available software and the general impression that tau-estimators are difficult to approximate. We will show, however, that the computational difficulties of approximating tau-estimators are similar in nature to those of the more popular S-estimators. The main goal of this article is to compare an approximating algorithm for tau-estimators based on random resampling with some alternative heuristic search algorithms. We show that the former is not only simpler, but that when enhanced by local improvement steps it generally outperforms the considered heuristic search algorithms, even when these heuristic algorithms also incorporate local improvement steps. Additionally, we show that the random resampling algorithm for approximating tau-estimators has favorable statistical properties compared to the analogous and widely used algorithms for S- and least trimmed squares estimators.}, keywords = {random resampling, Robust regression, simulated annealing, tabu search}, issn = {1061-8600}, doi = {10.1198/106186008X343785}, author = {Salibian-Barrera, Mat{\'\i}as and Willems, Gert and Zamar, Ruben} } @article { ISI:000259127900007, title = {The fast-tau estimator for regression}, journal = {JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS}, volume = {17}, number = {3}, year = {2008}, month = {SEP}, pages = {659-682}, publisher = {AMER STATISTICAL ASSOC}, type = {Article}, address = {732 N WASHINGTON ST, ALEXANDRIA, VA 22314-1943 USA}, abstract = {

Yohai and Zamar{\textquoteright}s tau-estimators of regression have excellent statistical properties but are nevertheless rarely used in practice because of a lack of available software and the general impression that tau-estimators are difficult to approximate. We will show, however, that the computational difficulties of approximating tau-estimators are similar in nature to those of the more popular S-estimators. The main goal of this article is to compare an approximating algorithm for tau-estimators based on random resampling with some alternative heuristic search algorithms. We show that the former is not only simpler, but that when enhanced by local improvement steps it generally outperforms the considered heuristic search algorithms, even when these heuristic algorithms also incorporate local improvement steps. Additionally, we show that the random resampling algorithm for approximating tau-estimators has favorable statistical properties compared to the analogous and widely used algorithms for S- and least trimmed squares estimators.

}, keywords = {random resampling, Robust regression, simulated annealing, tabu search}, issn = {1061-8600}, doi = {10.1198/106186008X343785}, author = {Salibian-Barrera, Mat{\'\i}as and Willems, Gert and Zamar, Ruben} } @article { ISI:000278173500004, title = {GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function}, journal = {GENOME BIOLOGY}, volume = {9}, number = {1}, year = {2008}, pages = {S4}, publisher = {BIOMED CENTRAL LTD}, type = {Article}, address = {236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND}, abstract = {Background: Most successful computational approaches for protein function prediction integrate multiple genomics and proteomics data sources to make inferences about the function of unknown proteins. The most accurate of these algorithms have long running times, making them unsuitable for real-time protein function prediction in large genomes. As a result, the predictions of these algorithms are stored in static databases that can easily become outdated. We propose a new algorithm, GeneMANIA, that is as accurate as the leading methods, while capable of predicting protein function in real-time. Results: We use a fast heuristic algorithm, derived from ridge regression, to integrate multiple functional association networks and predict gene function from a single process-specific network using label propagation. Our algorithm is efficient enough to be deployed on a modern webserver and is as accurate as, or more so than, the leading methods on the MouseFunc I benchmark and a new yeast function prediction benchmark; it is robust to redundant and irrelevant data and requires, on average, less than ten seconds of computation time on tasks from these benchmarks. Conclusion: GeneMANIA is fast enough to predict gene function on-the-fly while achieving state-of-the-art accuracy. A prototype version of a GeneMANIA-based webserver is available at http://morrislab.med.utoronto.ca/prototype.}, issn = {1474-760X}, doi = {10.1186/gb-2008-9-s1-s4}, author = {Mostafavi, Sara and Ray, Debajyoti and Warde-Farley, David and Grouios, Chris and Morris, Quaid} } @article { ISI:000258951500001, title = {Global analysis of yeast endosomal transport identifies the Vps55/68 sorting complex}, journal = {MOLECULAR BIOLOGY OF THE CELL}, volume = {19}, number = {4}, year = {2008}, month = {APR}, pages = {1282-1294}, publisher = {AMER SOC CELL BIOLOGY}, type = {Article}, address = {8120 WOODMONT AVE, STE 750, BETHESDA, MD 20814-2755 USA}, abstract = {Endosomal transport is critical for cellular processes ranging from receptor down-regulation and retroviral budding to the immune response. A full understanding of endosome sorting requires a comprehensive picture of the multiprotein complexes that orchestrate vesicle formation and fusion. Here, we use unsupervised, large-scale phenotypic analysis and a novel computational approach for the global identification of endosomal transport factors. This technique effectively identifies components of known and novel protein assemblies. We report the characterization of a previously undescribed endosome sorting complex that contains two well-conserved proteins with four predicted membrane-spanning domains. Vps55p and Vps68p form a complex that acts with or downstream of ESCRT function to regulate endosomal trafficking. Loss of Vps68p disrupts recycling to the TGN as well as onward trafficking to the vacuole without preventing the formation of lumenal vesicles within the MVB. Our results suggest the Vps55/68 complex mediates a novel, conserved step in the endosomal maturation process.}, issn = {1059-1524}, doi = {10.1091/mbc.E07-07-0659}, author = {Schluter, Cayetana and Lam, Karen K. Y. and Brumm, Jochen and Wu, Bella W. and Saunders, Matthew and Stevens, Tom H. and Bryan, Jennifer and Conibear, Elizabeth} } @article {pmid18384523, title = {Hepatocellular carcinoma incidence trends in Canada: analysis by birth cohort and period of diagnosis}, journal = {Liver Int.}, volume = {28}, number = {9}, year = {2008}, month = {Nov}, pages = {1272{\textendash}1279}, author = {Pocobelli, G. and Cook, L. S. and Brant, R. and Lee, S. S.} } @article { ISI:000253390000005, title = {High breakdown point robust regression with censored data}, journal = {ANNALS OF STATISTICS}, volume = {36}, number = {1}, year = {2008}, month = {FEB}, pages = {118-146}, publisher = {INST MATHEMATICAL STATISTICS}, type = {Article}, address = {PO BOX 22718, BEACHWOOD, OH 44122 USA}, abstract = {In this paper, we propose a class of high breakdown point estimators for the linear regression model when the response variable contains censored observations. These estimators are robust against high-leverage outliers and they generalize the LMS (least median of squares), S, MM and tau-estimators for linear regression. An important contribution of this paper is that we can define consistent estimators using a bounded loss function (or equivalently, a re-descending score function). Since the calculation of these estimators can be computationally costly, we propose an efficient algorithm to compute them. We illustrate their use on an example and present simulation studies that show that these estimators also have good finite sample properties.}, keywords = {accelerated failure time models, censored data, high breakdown point estimates, linear regression model, robust estimates}, issn = {0090-5364}, doi = {10.1214/009053607000000794}, author = {Salibian-Barrera, Mat{\'\i}as and Yohai, Victor J.} } @article { ISI:000255532900018, title = {Hypothesis testing in comparative and experimental studies of function-valued traits}, journal = {EVOLUTION}, volume = {62}, number = {5}, year = {2008}, month = {MAY}, pages = {1229-1242}, publisher = {BLACKWELL PUBLISHING}, type = {Article}, address = {9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLAND}, abstract = {Many traits of evolutionary interest, when placed in their developmental, physiological, or environmental contexts, are function-valued. For instance, gene expression during development is typically a function of the age of an organism and physiological processes are often a function of environment. In comparative and experimental studies, a fundamental question is whether the function-valued trait of one group is different from another. To address this question, evolutionary biologists have several statistical methods available. These methods can be classified into one of two types: multivariate and functional. Multivariate methods, including univariate repeated-measures analysis of variance (ANOVA), treat each trait as a finite list of data. Functional methods, such as repeated-measures regression, view the data as a sample of points drawn from an underlying function. A key difference between multivariate and functional methods is that functional methods retain information about the ordering and spacing of a set of data values, information that is discarded by multivariate methods. In this study, we evaluated the importance of that discarded information in statistical analyses of function-valued traits. Our results indicate that functional methods tend to have substantially greater statistical power than multivariate approaches to detect differences in a function-valued trait between groups.}, keywords = {Functional data analysis, multivariate analysis, phenotype, power, repeated-measures ANOVA, repeated-measures regression}, issn = {0014-3820}, doi = {10.1111/j.1558-5646.2008.00340.x}, author = {Griswold, Cortland K. and Gomulkiewicz, Richard and Heckman, Nancy} } @article {chen2008inference, title = {Inference for normal mixtures in mean and variance}, journal = {Statistica Sinica}, volume = {18}, number = {2}, year = {2008}, pages = {443}, author = {Chen, Jiahua and Tan, Xianming and Zhang, Runchu} } @article { ISI:000254462600014, title = {Inferences for odds ratio with dependent pairs}, journal = {Test}, volume = {17}, number = {1}, year = {2008}, month = {MAY}, pages = {101-119}, publisher = {Springer}, type = {Article}, abstract = {In familial data analyses quantifying familial association is scientifically important. As analogies of the intraclass and interclass correlations of a normally distributed trait, we study intraclass and interclass (log) odds ratios for a binary trait. We propose non-parametric estimators of the odds ratios and derive the asymptotic variances of the estimators under the assumptions of exchangeability and closure of multivariate binary distributions under marginals. These estimators are straightforward, except for the consideration of how to weight by family size. The relative efficiencies of the non-parametric estimators are studied for some parametric models. It shows that our estimators are highly efficient, and that weighting by family size is recommended for the intraclass odds ratio. The computations of the estimators and their standard errors are illustrated with two examples.}, keywords = {binary trait, familial data, interclass and intraclass odds ratio}, issn = {1133-0686}, doi = {10.1007/s11749-006-0025-7}, author = {Zhao, Yinshan and Joe, Harry} } @article {raffa_intermediate_2008, title = {Intermediate highly active antiretroviral therapy adherence thresholds and empirical models for the development of drug resistance mutations}, journal = {Journal of Acquired Immune Deficiency Syndromes}, volume = {47}, number = {3}, year = {2008}, month = {mar}, pages = {397{\textendash}399}, doi = {10.1097/QAI.0b013e31815b0d35}, url = {http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:landingpage\&an=00126334-200803010-00020}, author = {Raffa, Jesse D and Tossonian, Harout K and Grebely, Jason and Petkau, A.John and DeVlaming, Stanley and Conway, Brian} } @article {wu_joint_2008, title = {Joint inference for nonlinear mixed-effects models and time to event at the presence of missing data}, journal = {Biostatistics}, volume = {9}, number = {2}, year = {2008}, pages = {308{\textendash}320}, abstract = {In many longitudinal studies, the individual characteristics associated with the repeated measures may be possible covariates of the time to an event of interest, and thus, it is desirable to model the time-to-event process and the longitudinal process jointly. Statistical analyses may be further complicated in such studies with missing data such as informative dropouts. This article considers a nonlinear mixed-effects model for the longitudinal process and the Cox proportional hazards model for the time-to-event process. We provide a method for simultaneous likelihood inference on the 2 models and allow for nonignorable data missing. The approach is illustrated with a recent AIDS study by jointly modeling HIV viral dynamics and time to viral rebound.}, keywords = {EM algorithm, Longitudinal data, proportional hazards model, shared parameter model}, issn = {1465-4644, 1468-4357}, doi = {10.1093/biostatistics/kxm029}, url = {http://biostatistics.oxfordjournals.org/content/9/2/308}, author = {WU, LANG and Hu, X. Joan and Wu, Hulin} } @article {petkau_magnetic_2008, title = {Magnetic resonance imaging as a surrogate outcome for multiple sclerosis relapses}, journal = {Multiple Sclerosis}, volume = {14}, year = {2008}, pages = {770-778}, abstract = {

Background Magnetic resonance imaging (MRI) of lesions in the brain may be the best current candidate for a surrogate biological marker of clinical outcomes in relapsing remitting multiple sclerosis (MS), based on its role as an objective indicator of disease pathology. No biological surrogate marker has yet been validated for MS clinical outcomes. Objective The objective of this study was to use a multi-phased study to determine if a valid surrogate relationship could be demonstrated between counts of contrast enhancing lesions (CELs) and occurrence of relapses in MS. Methods We examined correlations for the concurrent and predictive relationship between CELs over 6 months and MS relapses over the same 6 months and an additional 6 months (total: 12 months), using available data on untreated patients from a large clinical trial and natural history database. Results Concurrent and predictive correlations were inadequate to justify continuation of this study to the planned additional phases required to demonstrate a surrogate relationship between CELs and MS relapses. Conclusions Confidence intervals for correlations between CELs and MS relapses exclude the possibility that CELs can be a good surrogate for relapses over the time scales we investigated. Further exploration of surrogacy between MRI measures and MS clinical outcomes may require improved datasets, the development of MRI techniques that couple better to clinical disease, and the ability to test a wide range of imaging- and clinically-based hypotheses for surrogacy.

}, keywords = {correlations, gadolinium enhanced lesions, magnetic resonance imaging, multiple sclerosis, prognosis, surrogacy}, doi = {10.1177/1352458507088104}, url = {http://msj.sagepub.com/content/early/2008/06/05/1352458507088104}, author = {Petkau, J. and Reingold, S. C. and Held, U. and Cutter, G. R. and Fleming, T. R. and Hughes, M. D. and Miller, D. H. and McFarland, H. F. and Wolinsky, J. S.} } @article {pmid18322987, title = {Minimal clinically important difference for 7 measures of fatigue in patients with systemic lupus erythematosus}, journal = {J. Rheumatol.}, volume = {35}, number = {4}, year = {2008}, month = {Apr}, pages = {635{\textendash}642}, author = {Goligher, E. C. and Pouchot, J. and Brant, R. and Kherani, R. B. and Avina-Zubieta, J. A. and Lacaille, D. and Lehman, A. J. and Ensworth, S. and Kopec, J. and Esdaile, J. M. and Liang, M. H.} } @article {fu2008modified, title = {Modified likelihood ratio test for homogeneity in a mixture of von Mises distributions}, journal = {Journal of Statistical Planning and Inference}, volume = {138}, number = {3}, year = {2008}, pages = {667{\textendash}681}, publisher = {Elsevier}, author = {Fu, Yuejiao and Chen, Jiahua and Li, Pengfei} } @article {chen2008order, title = {Order selection in finite mixture models with a nonsmooth penalty}, journal = {Journal of the American Statistical Association}, volume = {103}, number = {484}, year = {2008}, author = {Chen, Jiahua and Khalili, Abbas} } @inbook {maydeu2008overview, title = {An overview of limited information goodness-of-fit testing in multidimensional contingency tables}, booktitle = {New Trends in Psychometrics}, year = {2008}, pages = {253{\textendash}262}, publisher = {Universal Academy Press Tokyo, Japan}, organization = {Universal Academy Press Tokyo, Japan}, author = {Maydeu-Olivares, Albert and Joe, Harry}, editor = {Shigemasu, K and Okada, A and Imaizumi, T and Hoshino, T} } @conference {4323922, title = {PLEDS: A Personalized Entity Detection System Based on Web Log Mining Techniques}, booktitle = {Web-Age Information Management}, year = {2008}, pages = {389{\textendash}396}, doi = {10.1109/WAIM.2008.62}, author = {Kathleen Tsoukalas and Bin Zhou and Jian Pei and Davor Cubranic} } @article {McDonaldThornton2008, title = {Primer on the Mortgage Market and Mortgage Finance}, journal = {The Federal Reserve Bank of St. Louis Review}, volume = {90}, number = {1}, year = {2008}, pages = {31{\textendash}46}, url = {https://files.stlouisfed.org/files/htdocs/publications/review/08/01/McDonald.pdf}, author = {McDonald, Daniel J. and Thornton, Daniel L.} } @article {pmid18451112, title = {Problems of multiplicity}, journal = {Can J Anaesth}, volume = {55}, number = {5}, year = {2008}, month = {May}, pages = {259{\textendash}261}, author = {Brasher, P. M. and Brant, R. F.} } @article {pmid18461376, title = {A randomized, controlled, crossover study of a noncustomized tongue retaining device for sleep disordered breathing}, journal = {Sleep Breath}, volume = {12}, number = {4}, year = {2008}, month = {Nov}, pages = {369{\textendash}373}, author = {Dort, L. and Brant, R.} } @booklet {liu2008university, title = {Recalibrating ozone chemical transport models}, number = {242}, year = {2008}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Liu, Zhong and Le, Nhu and Zidek, James V} } @article {zhao2008regression, title = {Regression of new gadolinium enhancing lesion activity in relapsing-remitting multiple sclerosis}, journal = {Neurology}, volume = {70}, number = {13 Part 2}, year = {2008}, pages = {1092{\textendash}1097}, publisher = {AAN Enterprises}, author = {Zhao, Yinshan and Traboulsee, Anthony and Petkau, A.John and Li, David} } @article { ISI:000258196500027, title = {Robust estimation of error scale in nonparametric regression models}, journal = {JOURNAL OF STATISTICAL PLANNING AND INFERENCE}, volume = {138}, number = {10}, year = {2008}, month = {OCT 1}, pages = {3200-3216}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {When the data used to fit a nonparametric regression model are contaminated with outliers, we need to use a robust estimator of scale in order to make robust estimation of the regression function possible. We develop a family of M-estimators of scale constructed from consecutive differences of regression responses. Estimators in our family robustify the estimator proposed by Rice [1984. Bandwidth choice for nonparametric regression. Ann. Statist. 12, 1215-1230]. Under appropriate conditions, we establish the weak consistency and asymptotic normality of all estimators in our family. Estimators in our family vary in terms of their robustness properties. We quantify the robustness of each estimator via the maxbias. We use this measure as a basis for deriving the asymptotic breakdown point of the estimator. Our theoretical results allow us to specify conditions for estimators in our family to achieve a maximum asymptotic breakdown point of 1/2. We conduct a simulation study to compare the finite sample performance of our preferred M-estimator with that of three other estimators. (C) 2008 Elsevier B.V. All rights reserved.}, keywords = {asymptotic breakdown point, consecutive differences, error scale, fixed design, M-scale estimator, M-scale functional, Maxbias, nonparametric regression, Outliers, robust}, issn = {0378-3758}, doi = {10.1016/j.jspi.2008.01.005}, author = {Ghement, Isabella Rodica and Ruiz, Marcelo and Zamar, Ruben} } @article { ISI:000259075900006, title = {Robust model selection using fast and robust bootstrap}, journal = {COMPUTATIONAL STATISTICS \& DATA ANALYSIS}, volume = {52}, number = {12}, year = {2008}, month = {AUG 15}, pages = {5121-5135}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {

Robust model selection procedures control the undue influence that outliers can have on the selection criteria by using both robust point estimators and a bounded loss function when measuring either the goodness-of-fit or the expected prediction error of each model. Furthermore, to avoid favoring over-fitting models, these two measures can be combined with a penalty term for the size of the model. The expected prediction error conditional oil the observed data may be estimated using the bootstrap. However, bootstrapping robust estimators becomes extremely time consuming on moderate to high dimensional data sets. It is shown that the expected prediction error can be estimated using a very fast and robust bootstrap method, and that this approach yields a consistent model selection method that is computationally feasible even for a relatively large number of covariates. Moreover, as opposed to other bootstrap methods, this proposal avoids the numerical problems associated with the small bootstrap samples required to obtain consistent model selection criteria. The finite-sample performance of the fast and robust bootstrap model selection method is investigated through a simulation study while its feasibility and good performance on moderately large regression models are illustrated on several real data examples. (c) 2008 Elsevier B.V. All rights reserved.

}, issn = {0167-9473}, doi = {10.1016/j.csda.2008.05.007}, author = {Salibian-Barrera, Matlas and Van Aelst, Stefan} } @conference {DeNero2008Sampling, title = {Sampling alignment structure under a Bayesian translation model}, booktitle = {Proceedings of the 2008 Conference on Empirical Methods on Natural Language Processing (EMNLP08)}, volume = {13}, year = {2008}, pages = {314{\textendash}323}, author = {John DeNero and Alexandre Bouchard-C{\^o}t{\'e} and Dan Klein} } @article {liu_semiparametric_2008, title = {A semiparametric nonlinear mixed-effects model with non-ignorable missing data and measurement errors for HIV viral data}, journal = {Computational Statistics \& Data Analysis}, volume = {53}, number = {1}, year = {2008}, month = {sep}, pages = {112{\textendash}122}, abstract = {Semiparametric nonlinear mixed-effects (NLME) models are very flexible in modeling long-term HIV viral dynamics. In practice, statistical analyses are often complicated due to measurement errors and missing data in covariates and non-ignorable missing data in the responses. We consider likelihood methods which simultaneously address measurement error and missing data problems. A real dataset is analyzed in detail, and a simulation study is conducted to evaluate the methods.}, issn = {0167-9473}, doi = {10.1016/j.csda.2008.06.018}, url = {http://www.sciencedirect.com/science/article/pii/S0167947308003290}, author = {Liu, Wei and WU, LANG} } @article {mccandetal2008jce, title = {A sensitivity analysis using information about measured confounders yielded improved assessments of uncertainty from unmeasured confounding}, journal = {Journal of Clinical Epidemiology}, volume = {61}, number = {3}, year = {2008}, pages = {247-255}, publisher = {Elsevier}, doi = {10.1016/j.jclinepi.2007.05.006}, author = {McCandless, L. C. and Gustafson, P. and Levy, A. R.} } @article {chen2008test, title = {Test for homogeneity in Hardy{\textendash}Weinberg normal mixture model}, journal = {Journal of Statistical Planning and Inference}, volume = {138}, number = {12}, year = {2008}, pages = {3774{\textendash}3788}, publisher = {North-Holland}, author = {Chen, Jiahua and Qin, Yongsong} } @article {chen2008testing, title = {Testing homogeneity in a mixture of von Mises distributions with a structural parameter}, journal = {Canadian Journal of Statistics}, volume = {36}, number = {1}, year = {2008}, pages = {129{\textendash}142}, publisher = {Wiley Online Library}, author = {Chen, Jiahua and Li, Pengfei and Fu, Yuejiao} } @article {JoGu2008statmed, title = {Use of instrumental variables in the analysis of generalized linear models in the presence of unmeasured confounding with applications to epidemiological research}, journal = {Statistics in Medicine}, volume = {27}, year = {2008}, pages = {1539-1556}, doi = {10.1002/sim.3036}, author = {Johnston, K. and Gustafson, P. and Levy, A. R. and Grootendorst, P.} } @article {pan2008u, title = {U-statistic based modified information criterion for change point problems}, journal = {Communications in Statistics{\textemdash}Theory and Methods}, volume = {37}, number = {17}, year = {2008}, pages = {2687{\textendash}2712}, publisher = {Taylor \& Francis Group}, author = {Pan, Jianmin and Chen, Jiahua} } @article { ISI:000267403600007, title = {Weighted quantile regression with nonelliptically structured covariates}, journal = {CANADIAN JOURNAL OF STATISTICS-REVUE CANADIENNE DE STATISTIQUE}, volume = {36}, number = {4}, year = {2008}, month = {DEC}, pages = {595-611}, publisher = {WILEY-BLACKWELL PUBLISHING, INC}, type = {Article}, address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA}, abstract = {Although quantile regression estimators are robust against low leverage observations with atypically large responses (Koenker \& Bassett 1978), they can be seriously affected by a few points that deviate from the majority of the sample covariates. This problem can be alleviated by downweighting observations with high leverage. Unfortunately, when the covariates are not elliptically distributed, Mahalanobis distances may not be able to correctly identify atypical points. In this paper the authors discuss the use of weights based on a new leverage measure constructed using Rosenblatt{\textquoteright}s multivariate transformation which is able to reflect nonelliptical structures in the covariate space. The resulting weighted estimators are consistent, asymptotically normal, and have a bounded influence function. In addition, the authors also discuss a selection criterion for choosing the downweighting scheme. They illustrate their approach with child growth data from Finland. Finally, their simulation studies suggest that this methodology has good finite-sample properties.}, keywords = {Nonparametric methods, quantile regression, Robustness}, issn = {0319-5724}, author = {Salibian-Barrera, Mat{\'\i}as and Wei, Ying} } @article {pmid18705947, title = {The albumin in acute stroke trial (ALIAS); design and methodology}, journal = {Int J Stroke}, volume = {2}, number = {3}, year = {2007}, month = {Aug}, pages = {214{\textendash}219}, author = {Hill, M. D. and Moy, C. S. and Palesch, Y. Y. and Martin, R. and Dillon, C. R. and Waldman, B. D. and Patterson, L. and Mendez, I. M. and Ryckborst, K. J. and Tamariz, D. and Ginsberg, M. D. and Ginsberg, M. D. and Dillon, C. and Hill, M. D. and Mendez, I. M. and Moy, C. S. and Palesch, Y. Y. and Ryckborst, K. J. and Tamariz, D. and Waldman, B. D. and Lyden, P. and Brant, R. and Coffey, C. and Di Tullio, M. and Jungreis, C. and Wijman, C. and Mayer, S. and Rabinstein, A. and Martin, R.} } @article {Walker2007, title = {The application of Bayesian analysis to issues in developmental research}, journal = {International Journal of Behavioral Development}, volume = {31}, number = {4}, year = {2007}, pages = {366{\textendash}373}, publisher = {Sage Publications}, doi = {10.1177/0165025407077763}, author = {Walker, Lawrence J and Gustafson, Paul and Frimer, Jeremy A} } @booklet {liu2007appraisal, title = {An appraisal of bayesian melding for physical-statistical modeling}, number = {233}, year = {2007}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Liu, Zhong and Le, Nhu D. and Zidek, James V and others} } @conference {levay2007archiving, title = {Archiving Community Contributed Data in MAST}, booktitle = {Astronomical Data Analysis Software and Systems XVI}, volume = {376}, year = {2007}, pages = {189}, author = {Levay, K and Kamp, I and Thompson, R and Smith, M and White, RL} } @article { ISI:000246955500029, title = {Associations of osseous abnormalities in neurofibromatosis 1}, journal = {American Journal of Medical Genetics part A}, volume = {143A}, number = {12}, year = {2007}, month = {JUN 15}, pages = {1326-1333}, abstract = {The characteristic sites of Neurofibromatosis 1-associated osseous manifestations are the long bones (usually the tibia and fibula), vertebrae and sphenoid wing. Although these focal bony lesions may cause profound clinical consequences, a minority of people with NF1 are affected. However, most people with NF1 are shorter than expected for their age, gender and family. The pathogenesis of NF1 focal osteopathy and its relationship, if any, to short stature are unknown. We examined associations between the occurrence of various osseous lesions in 3377 NF1 probands from the Children{\textquoteright}s Tumor Foundation NF International Database. Using logistic regression analysis among 260 NF1 probands who had undergone radiological examination of both the spine and skull, we found associations between the Occurrence of sphenoid wing and long bone osteopathy (conditional odds ratio [OR] = 6.1; 95\% confidence interval [CI] = 1.7-22.3; P = 0.006) and between sphenoid wing and vertebral osteopathy (OR = 16.9-1.95\% Cl = 5.3-53.3; P < 0.001) after adjusting for age and gender. Similar findings were observed from all 3377 NF1 probands using a multivariate probit regression model. in a separate analysis, we found lower age- and gender-standardized height in patients who had characteristic vertebral or sphenoid wing lesions than in people who did not (P < 0.05). We found no relationship between height and tibial osteopathy. We conclude that some people with NF1 are more likely to develop osseous manifestations than others and speculate that there may be a common pathogenetic mechanism responsible for the development of sphenoid wing osteopathy and that of the vertebrae and long bones. (c) 2007 Wiley-Liss, Inc.}, issn = {1552-4825}, doi = {10.1002/ajmg.a.31754}, author = {Alwan, S. and Armstrong, L. and Joe, H. and Birch, P. H. and Szudek, J. and Friedman, J. M.} } @article {chen2007asymptotic, title = {Asymptotic normality under two-phase sampling designs}, journal = {Statistica Sinica}, volume = {17}, number = {3}, year = {2007}, pages = {1047}, publisher = {C/O DR HC HO, INST STATISTICAL SCIENCE, ACADEMIA SINICA, TAIPEI 115, TAIWAN}, author = {Chen, Jiahua and Rao, JNK} } @article {feng2007asymptotic, title = {Asymptotic properties of likelihood ratio test statistics in affected-sib-pair analysis}, journal = {Canadian Journal of Statistics}, volume = {35}, number = {3}, year = {2007}, pages = {351{\textendash}364}, publisher = {Wiley Online Library}, author = {Feng, Zeny Z and Chen, Jiahua and Thompson, Mary E} } @article {zidek2007bath, title = {Bath Institute For Complex Systems}, year = {2007}, author = {Zidek, James V and Shaddick, Gavin and Meloche, Jean and Chatfield, Chris and White, Rick} } @article {mccandetal2007statmed, title = {Bayesian sensitivity analysis for unmeasured confounding in observational studies}, journal = {Statistics in Medicine}, volume = {26}, year = {2007}, pages = {2331-2347}, doi = {10.1002/sim.2711}, author = {McCandless, L. C. and Gustafson, P. and Levy, A. R.} } @article { ISI:000249912400020, title = {Building a robust linear model with forward selection and stepwise procedures}, journal = {COMPUTATIONAL STATISTICS \& DATA ANALYSIS}, volume = {52}, number = {1}, year = {2007}, month = {SEP 15}, pages = {239-248}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {Classical step-by-step algorithms, such as forward selection (FS) and stepwise (SW) methods, are computationally suitable, but yield poor results when the data contain outliers and other contaminations. Robust model selection procedures, on the other hand, are not computationally efficient or scalable to large dimensions, because they require the fitting of a large number of submodels. Robust and computationally efficient versions of FS and SW are proposed. Since FS and SW can be expressed in terms of sample correlations, simple robustifications are obtained by replacing these correlations by their robust counterparts. A pairwise approach is used to construct the robust correlation matrix-not only because of its computational advantages over the d-dimensional approach, but also because the pairwise approach is more consistent with the idea of step-by-step algorithms. The proposed robust methods have much better performance compared to standard FS and SW. Also, they are computationally very suitable and scalable to large high-dimensional data sets. (c) 2007 Elsevier B.V. All rights reserved.}, keywords = {computational complexity, pairwise robust correlation, robust model selection, stepwise algorithm}, issn = {0167-9473}, doi = {10.1016/j.csda.2007.01.007}, author = {Khan, Jafar A. and Van Aelst, Stefan and Zamar, Ruben H.} } @booklet {liu2007calibrating, title = {Calibrating deterministic modeling output with application of ozone fields}, number = {232}, year = {2007}, publisher = {Department of Statistics, The University of British Columbia}, author = {Liu, Zhong and Le, Nhu D. and Zidek, James V} } @article { ISI:000249912400024, title = {CLUES: A non-parametric clustering method based on local shrinking}, journal = {COMPUTATIONAL STATISTICS \& DATA ANALYSIS}, volume = {52}, number = {1}, year = {2007}, month = {SEP 15}, pages = {286-298}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {A novel non-parametric clustering method based on non-parametric local shrinking is proposed. Each data point is transformed in such a way that it moves a specific distance toward a cluster center. The direction and the associated size of each movement are determined by the median of its K-nearest neighbors. This process is repeated until a pre-defined convergence criterion is satisfied. The optimal value of the number of neighbors is determined by optimizing some commonly used index functions that measure the strengths of clusters generated by the algorithm. The number of clusters and the final partition are determined automatically without any input parameter except the stopping rule for convergence. Experiments on simulated and real data sets suggest that the proposed algorithm achieves relatively high accuracies when compared with classical clustering algorithms. (c) 2007 Elsevier B.V. All rights reserved.}, keywords = {automatic clustering, K-nearest neighbors, local shrinking, number of clusters}, issn = {0167-9473}, doi = {10.1016/j.csda.2006.12.016}, author = {Wang, Xiologang and Qiu, Weiliang and Zamar, Ruben H.} } @article {wu_computationally_2007, title = {A computationally efficient method for nonlinear mixed-effects models with nonignorable missing data in time-varying covariates}, journal = {Computational Statistics \& Data Analysis}, volume = {51}, number = {5}, year = {2007}, pages = {2410{\textendash}2419}, abstract = {Nonlinear mixed-effects (NLME) models are widely used for longitudinal data analyses. Time-dependent covariates are often introduced to partially explain inter-individual variation. These covariates often have missing data, and the missingness may be nonignorable. Likelihood inference for NLME models with nonignorable missing data in time-varying covariates can be computationally very intensive and may even offer computational difficulties such as nonconvergence. We propose a computationally very efficient method for approximate likelihood inference. The method is illustrated using a real data example.}, keywords = {EM algorithm, Linearization, Longitudinal data, Random effects model}, issn = {0167-9473}, doi = {10.1016/j.csda.2006.07.036}, url = {http://www.sciencedirect.com/science/article/pii/S0167947306002556}, author = {WU, LANG} } @article {tan2007consistency, title = {Consistency of the constrained maximum likelihood estimator in finite normal mixture models}, journal = {2007 Proceedings of the American Statistical Association, Section on Statistical Education [CD-ROM]. American Statistical Association, Alexandria, VA}, year = {2007}, pages = {2113{\textendash}2119}, author = {Tan, Xianming and Chen, Jiahua and Zhang, Runchu} } @article {nagy_correlation_2007, title = {Correlation parameterization in random function models to improve normal approximation of the likelihood or posterior}, journal = {Dept. of Statistics, The University of British Columbia, URL http://stat. ubc. ca/Research/TechReports/techreports/229. pdf, Tech. Rep}, volume = {229}, year = {2007}, url = {http://ftp.stat.ubc.ca/Research/TechReports/techreports/229.pdf}, author = {Nagy, B{\'e}la and Loeppky, Jason L. and Welch, William J.} } @article {gustafson2007describing, title = {Describing the dynamics of attention to TV commercials: A hierarchical Bayes analysis of the time to zap an ad}, journal = {Journal of Applied statistics}, volume = {34}, number = {5}, year = {2007}, pages = {585{\textendash}609}, publisher = {Taylor \& Francis}, doi = {10.1080/02664760701235279}, author = {Gustafson, P. and Siddarth, S.} } @article {chang2007designing, title = {Designing environmental monitoring networks to measure extremes}, journal = {Environmental and Ecological Statistics}, volume = {14}, number = {3}, year = {2007}, pages = {301{\textendash}321}, publisher = {Springer}, author = {Chang, Howard and Fu, Audrey Qiuyan and Le, Nhu D. and Zidek, James V} } @booklet {dou2007university, title = {A Dynamic Linear Model for Hourly Ozone Concentrations}, number = {228}, year = {2007}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Dou, Yiping and Le, Nhu D. and Zidek, James V.} } @booklet {dou2007dynamic, title = {A dynamic linear model for hourly ozone concentrations}, number = {228}, year = {2007}, publisher = {Department of Statistics, University of British Columbia}, author = {Dou, YP and Le, N.D. and Zidek, J.V.} } @article {pmid17985009, title = {Effects of an enhanced secondary prevention program for patients with heart disease: a prospective randomized trial}, journal = {Can J Cardiol}, volume = {23}, number = {13}, year = {2007}, month = {Nov}, pages = {1066{\textendash}1072}, author = {Edworthy, S. M. and Baptie, B. and Galvin, D. and Brant, R. F. and Churchill-Smith, T. and Manyari, D. and Belenkie, I.} } @article {wang_exploration_2007, title = {Exploration of cluster structure-activity relationship analysis in efficient high-throughput screening}, journal = {Journal of chemical information and modeling}, volume = {47}, number = {3}, year = {2007}, pages = {1206{\textendash}1214}, url = {http://pubs.acs.org/doi/abs/10.1021/ci600458n}, author = {Wang, X. Sunny and Salloum, G. A. and Chipman, Hugh A. and Welch, William J. and Young, S. Stanley} } @booklet {nagy_fast_2007, title = {Fast Bayesian inference for Gaussian process models}, year = {2007}, publisher = {Technical Report 230, Dept. Statistics, Univ. British Columbia}, url = {http://be.stat.ubc.ca/Research/TechReports/techreports/230.pdf}, author = {Nagy, B{\'e}la and Loeppky, Jason L. and Welch, William J.} } @article {zidek2007framework, title = {A framework for predicting personal exposures to environmental hazards}, journal = {Environmental and Ecological Statistics}, volume = {14}, number = {4}, year = {2007}, pages = {411{\textendash}431}, publisher = {Springer}, author = {Zidek, James V and Shaddick, Gavin and Meloche, Jean and Chatfield, Chris and White, Rick} } @article {zidek2007framework, title = {A framework for predicting personal exposures to environmental hazards}, journal = {Environmental and Ecological Statistics}, volume = {14}, number = {4}, year = {2007}, pages = {411{\textendash}431}, publisher = {Springer}, author = {Zidek, James V and Shaddick, Gavin and Meloche, Jean and Chatfield, Chris and White, Rick} } @article {zaharik2007genetic, title = {Genetic profiling of dendritic cells exposed to live-or ultraviolet-irradiated Chlamydia muridarum reveals marked differences in CXC chemokine profiles}, journal = {Immunology}, volume = {120}, number = {2}, year = {2007}, pages = {160{\textendash}172}, publisher = {Wiley Online Library}, author = {Zaharik, Michelle L and Nayar, Tarun and White, Rick and Ma, Caixia and Vallance, Bruce A and Straka, Nadine and Jiang, Xiaozhou and Rey-Ladino, Jose and Shen, Caixia and Brunham, Robert C} } @article { ISI:000244158100004, title = {Genomic and proteomic expression analysis of Leishmania promastigote and amastigote life stages: The Leishmania genome is constitutively expressed}, journal = {MOLECULAR AND BIOCHEMICAL PARASITOLOGY}, volume = {152}, number = {1}, year = {2007}, month = {MAR}, pages = {35-46}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {Leishinania are protozoan parasites that cause a wide spectrum of clinical diseases in humans and area major public health risk in several countries. Leishmania life cycle consists of an extracellular flagellated promastigote stage within the midgut of a sandfly vector, and a morphological distinct intracellular amastigote stage within macrophages of a mammalian host. This study reports the use of DNA oligonucleotide genome microarrays representing 8160 genes to analyze the mRNA expression profiles of L. major promastigotes and lesion derived amastigotes. Over 94\% of the genes were expressed in both life stages. Advanced statistical analysis identified a surprisingly low degree of differential mRNA expression: 1.4\% of the total genes in amastigotes and 1.5\% in promastigotes. These microarray results demonstrate that the L. major genome is essentially constitutively expressed in both life stages and suggest that Leishmania is constitutively adapted for survival and replication in either the sandfly vector or macrophage host utilizing an appropriate set of genes for each vastly different environment. Quantitative proteomics, using the isotope coded affinity tag (ICAT) technology and mass spectrometry, was used to identify L. infantum promastigote and axenic amastigote differentially expressed proteins. Of the 91 distinct proteins identified, 8\% were differentially expressed in the amastigote stage, 20\% were differentially expressed in the promastigote stage, and the remaining 72\% were considered constitutively expressed. The differential expression was validated by the identification of previously reported stage specific proteins and identified several amastigote and promastigote novel stage specific proteins. (c) 2006 Elsevier B.V. All rights reserved.}, keywords = {DNA genome microarrays, ICAT, Leishmania, quantitative proteornics}, issn = {0166-6851}, doi = {10.1016/j.molbiopara.2006.11.009}, author = {Leifso, Kirk and Cohen-Freue, Gabriela and Dogra, Nisha and Murray, Angus and McMaster, W. Robert} } @article { ISI:000248879100004, title = {Global gene expression in Leishmania}, journal = {INTERNATIONAL JOURNAL FOR PARASITOLOGY}, volume = {37}, number = {10}, year = {2007}, month = {AUG}, pages = {1077-1086}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, type = {Review}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {The completion of the genomic sequences of many protozoan pathogens of humans, including species of Leishmania, Trypanosoma and Plasmodium, provide new approaches to study the pattern of gene expression during differentiation and development. Leishmania are a major public health risk in many countries and cause a wide spectrum of clinical disease referred to as leishmaniasis. The Leishmania life cycle consists of two morphologically distinct stages: intracellular amastigotes that reside in the phagolysosome of mammalian macrophages, and extracellular promastigotes that reside within the gut of the sandfly vector. DNA microarray analysis is a powerful method to study global gene expression in terms of quantitation of mRNA levels. This review discusses the application of DNA microarray technology to study the pattern of global gene expression of Leishmania promastigote and amastigote life stages. Results from several studies show that, overall, there is a surprisingly low level of differentially expressed genes, ranging from 0.2\% to 5\% of total genes, between the amastigote and promastigote life stages. Thus, the Leishmania genome can be considered to be constitutively expressed with a limited number of genes showing stage-specific expression. Comparative genomic analyses of gene expression levels between Leishmania major and Leishmania mexicana show that the majority of differentially expressed genes between amastigotes and promastigotes are species specific with relatively few differentially expressed genes in common between these two Leishmania species. Quantitative proteomic analysis of Leishmania relative protein expression shows there is a weak correlation to gene expression. Therefore, Leishmania protein expression levels are likely regulated at the level of translation or by post transcriptional mechanisms, and differential protein modifications may be more important in development than the regulation of gene expression. (c) 2007 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.}, keywords = {comparative genomics, differential gene expression, DNA genome microarrays, Leishmania, quantitative proteomic expression analysis}, issn = {0020-7519}, doi = {10.1016/j.ijpara.2007.04.011}, author = {Cohen-Freue, Gabriela and Holzer, Timothy R. and Forney, James D. and McMaster, W. Robert} } @article {wu_hiv_2007, title = {HIV viral dynamic models with dropouts and missing covariates}, journal = {Statistics in Medicine}, volume = {26}, number = {17}, year = {2007}, pages = {3342{\textendash}3357}, abstract = {In recent years HIV viral dynamic models have received great attention in AIDS studies. Often, subjects in these studies may drop out for various reasons such as drug intolerance or drug resistance, and covariates may also contain missing data. Statistical analyses ignoring informative dropouts and missing covariates may lead to misleading results. We consider appropriate methods for HIV viral dynamic models with informative dropouts and missing covariates and evaluate these methods via simulations. A real data set is analysed, and the results show that the initial viral decay rate, which may reflect the efficacy of the anti-HIV treatment, may be over-estimated if dropout patients are ignored. We also find that the current or immediate previous viral load values may be most predictive for patients{\textquoteright} dropout. These results may be important for HIV/AIDS studies. Copyright {\textcopyright} 2007 John Wiley \& Sons, Ltd.}, keywords = {approximate method, Longitudinal data, missing data, Monte-Carlo EM, nonlinear mixed-effects model}, issn = {1097-0258}, doi = {10.1002/sim.2816}, url = {http://onlinelibrary.wiley.com/doi/10.1002/sim.2816/abstract}, author = {WU, LANG} } @article {raffa2007impact, title = {The impact of ongoing illicit drug use on methadone adherence in illicit drug users receiving treatment for HIV in a directly observed therapy program}, journal = {Drug and Alcohol Dependence}, volume = {89}, number = {2}, year = {2007}, pages = {306{\textendash}309}, publisher = {Elsevier}, author = {Raffa, Jesse D and Grebely, Jason and Tossonian, Harout and Wong, Tiffany and Viljoen, Mark and Khara, Milan and Mead, Annabel and McLean, Mark and Duncan, Fiona and Petkau, A.John and DeVlaming, S and Conway, B} } @article { ISI:000249527700043, title = {In situ analysis of living embryonic stem cells by coherent anti-stokes Raman Microscopy}, journal = {ANALYTICAL CHEMISTRY}, volume = {79}, number = {18}, year = {2007}, month = {SEP 15}, pages = {7221-7225}, publisher = {AMER CHEMICAL SOC}, type = {Letter}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {Embryonic stem cells (ESC), derived from preimplantation embryos, are defined by their ability to both self-renew and differentiate into all of the cells and tissues of a mature animal. Efforts to develop methods for in vitro culture of ESC for research or eventual therapeutic applications are hampered by the lack of rapid, nondestructive assays for distinguishing ESC from other (differentiated) cells within a growing culture. Coherent anti-Stokes Raman scattering (CARS) microscopy is shown here to be a sensitive and nondestructive method for identifying mouse ESC based on selective observation of specific molecular vibrations believed to be spectroscopic markers indicating the differentiated vs undifferentiated states of such cells. The nonlinear nature of CARS also permits imaging with subcellular resolution, potentially offering a means by which chemical changes accompanying the early stages of differentiation may be associated with certain intracellular compartments (e.g., nucleus, cytoplasm, membranes). A novel exposure/collection configuration is described, which yields high collection efficiency and low interference from nonresonant background components.}, issn = {0003-2700}, doi = {10.1021/ac070544k}, author = {Konorov, Stanislav O. and Glover, Clive H. and Piret, James M. and Bryan, Jennifer and Schulze, H. Georg and Blades, Michael W. and Turner, Robin F. B.} } @article {pmid17518305, title = {Injury mortality rates in Native and non-Native children: a population-based study}, journal = {Public Health Rep}, volume = {122}, number = {3}, year = {2007}, pages = {339{\textendash}346}, author = {Harrop, A. R. and Brant, R. F. and Ghali, W. A. and Macarthur, C.} } @article { ISI:000251334800008, title = {MDQC: a new quality assessment method for microarrays based on quality control reports}, journal = {BIOINFORMATICS}, volume = {23}, number = {23}, year = {2007}, month = {DEC 1}, pages = {3162-3169}, publisher = {OXFORD UNIV PRESS}, type = {Article}, address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND}, abstract = {Motivation: The process of producing microarray data involves multiple steps, some of which may suffer from technical problems and seriously damage the quality of the data. Thus, it is essential to identify those arrays with low quality. This article addresses two questions: (1) how to assess the quality of a microarray dataset using the measures provided in quality control (QC) reports; (2) how to identify possible sources of the quality problems. Results: We propose a novel multivariate approach to evaluate the quality of an array that examines the Mahalanobis distance of its quality attributes from those of other arrays. Thus, we call it Mahalanobis Distance Quality Control (MDQC) and examine different approaches of this method. MDQC flags problematic arrays based on the idea of outlier detection, i.e. it flags those arrays whose quality attributes jointly depart from those of the bulk of the data. Using two case studies, we show that a multivariate analysis gives substantially richer information than analyzing each parameter of the QC report in isolation. Moreover, once the QC report is produced, our quality assessment method is computationally inexpensive and the results can be easily visualized and interpreted. Finally, we show that computing these distances on subsets of the quality measures in the report may increase the methods ability to detect unusual arrays and helps to identify possible reasons of the quality problems.}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btm487}, author = {Freue, Gabriela V. Cohen and Hollander, Zsuzsanna and Shen, Enqing and Zamar, Ruben H. and Balshaw, Robert and Scherer, Andreas and McManus, Bruce and Keown, Paul and McMaster, W. Robert and Ng, Raymond T.} } @article {pmid17933854, title = {MDQC: a new quality assessment method for microarrays based on quality control reports}, journal = {Bioinformatics}, volume = {23}, number = {23}, year = {2007}, month = {Dec}, pages = {3162{\textendash}3169}, abstract = {The process of producing microarray data involves multiple steps, some of which may suffer from technical problems and seriously damage the quality of the data. Thus, it is essential to identify those arrays with low quality. This article addresses two questions: (1) how to assess the quality of a microarray dataset using the measures provided in quality control (QC) reports; (2) how to identify possible sources of the quality problems.\ We propose a novel multivariate approach to evaluate the quality of an array that examines the {\textquoteright}Mahalanobis distance{\textquoteright} of its quality attributes from those of other arrays. Thus, we call it Mahalanobis Distance Quality Control (MDQC) and examine different approaches of this method. MDQC flags problematic arrays based on the idea of outlier detection, i.e. it flags those arrays whose quality attributes jointly depart from those of the bulk of the data. Using two case studies, we show that a multivariate analysis gives substantially richer information than analyzing each parameter of the QC report in isolation. Moreover, once the QC report is produced, our quality assessment method is computationally inexpensive and the results can be easily visualized and interpreted. Finally, we show that computing these distances on subsets of the quality measures in the report may increase the method{\textquoteright}s ability to detect unusual arrays and helps to identify possible reasons of the quality problems.\ The library to implement MDQC will soon be available from Bioconductor.}, author = {Cohen Freue, G. V. and Hollander, Z. and Shen, E. and Zamar, R. H. and Balshaw, R. and Scherer, A. and McManus, B. and Keown, P. and McMaster, W. R. and Ng, R. T.} } @article {gu2007jrssb, title = {Measurement error modeling with an approximate instrumental variable}, journal = {Journal of the Royal Statistical Society, Series B}, volume = {69}, year = {2007}, pages = {797-815}, doi = {10.1111/j.1467-9868.2007.00611.x}, author = {Gustafson, P.} } @article {pmid18023448, title = {Mechanically stable porous cellulose media for affinity purification of family 9 cellulose-binding module-tagged fusion proteins}, journal = {J Chromatogr A}, volume = {1175}, number = {2}, year = {2007}, month = {Dec}, pages = {187{\textendash}196}, abstract = {A mechanically stable cellulose-based chromatography media was synthesized to permit inexpensive affinity purification of recombinant proteins containing the family 9 carbohydrate-binding module (CBM9) fused to either the N- or C-terminus of the target protein. A second-order response surface model was used to identify optimal concentrations of the primary reactants, epichlorohydrin and dimethyl sulfoxide (DMSO), required to cross-link the starting material, Perloza MT100, a compressible but inexpensive cellulose-based chromatography resin. This resulted in a mechanically stable cross-linked affinity chromatography media capable of operating at an order-of-magnitude higher linear velocity than permitted by unmodified MT100. Moments and Van Deemter analyses were used to show that rates of solute mass transfer within the column are largely unaffected by the cross-linking reaction, while the binding capacity decreased by 20\% to 7.1 micromol of protein/g resin, a value superior to most commercial affinity chromatography media. In sharp contrast to MT100, the mechanical stability and purification performance of the cross-linked media are not diminished by scale-up or repeated column use.}, author = {Kavoosi, M. and Lam, D. and Bryan, J. and Kilburn, D. G. and Haynes, C. A.} } @article {freue2007pitman, title = {The Pitman estimator of the Cauchy location parameter}, journal = {Journal of statistical planning and inference}, volume = {137}, number = {6}, year = {2007}, pages = {1900{\textendash}1913}, publisher = {North-Holland}, author = {Freue, Gabriela V Cohen} } @conference {Bouchard2007probabilistic, title = {A probabilistic approach to diachronic phonology}, booktitle = {Proceedings of the 2007 Conference on Empirical Methods on Natural Language Processing (EMNLP07)}, volume = {12}, year = {2007}, pages = {887{\textendash}896}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Percy Liang and Thomas Griffiths and Dan Klein} } @conference {Bouchard2007probabilistic, title = {A probabilistic approach to language change}, booktitle = {Advances in Neural Information Processing Systems 20 (NIPS)}, volume = {20}, year = {2007}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Percy Liang and Thomas Griffiths and Dan Klein} } @article { ISI:000251552900005, title = {Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway}, journal = {MOLECULAR \& CELLULAR PROTEOMICS}, volume = {6}, number = {11}, year = {2007}, month = {NOV}, pages = {1885-1895}, publisher = {AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC}, type = {Article}, address = {9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3996 USA}, abstract = {The ubiquitin proteasome system (UPS) comprises hundreds of different conjugation/deconjugation enzymes and multiple receptors that recognize ubiquitylated proteins. A formidable challenge to deciphering the biology of ubiquitin is to map the networks of substrates and ligands for components of the UPS. Several different receptors guide ubiquitylated substrates to the proteasome, and neither the basis for specificity nor the relative contribution of each pathway is known. To address how broad of a role the ubiquitin receptor Rpn10 (S5a) plays in turnover of proteasome substrates, we implemented a method to perform quantitative analysis of ubiquitin conjugates affinity-purified from experimentally perturbed and reference cultures of Saccharomyces cerevisiae that were differentially labeled with N-14 and N-15 isotopes. Shotgun mass spectrometry coupled with relative quantification using metabolic labeling and statistical analysis based on q values revealed ubiquitylated proteins that increased or decreased in level in response to a particular treatment. We first identified over 225 candidate UPS substrates that accumulated as ubiquitin conjugates upon proteasome inhibition. To determine which of these proteins were influenced by Rpn10, we evaluated the ubiquitin conjugate proteomes in cells lacking either the entire Rpn10 (rpn10 Delta) (or only its UIM (ubiquitininteracting motif) polyubiquitin-binding domain (uim Delta)). Twenty-seven percent of the UPS substrates accumulated as ubiquitylated species in rpn10 Delta cells, whereas only onefifth as many accumulated in uim Delta cells. These findings underscore a broad role for Rpn10 in turnover of ubiquitylated substrates but a relatively modest role for its ubiquitin-binding UIM domain. This approach illustrates the feasibility of systems-level quantitative analysis to map enzyme-substrate networks in the UPS.}, issn = {1535-9476}, doi = {10.1074/mcp.M700264-MCP200}, author = {Mayor, Thibault and Graumann, Johannes and Bryan, Jennifer and MacCoss, Michael J. and Deshaies, Raymond J.} } @article {MacNab2007, title = {Regression B-spline smoothing in Bayesian disease mapping: with an application to patient safety surveillance}, journal = {Statistics in medicine}, volume = {26}, number = {24}, year = {2007}, pages = {4455{\textendash}4474}, publisher = {Wiley Online Library}, doi = {10.1002/sim.2868}, author = {MacNab, Ying C and Gustafson, Paul} } @article { ISI:000251829200023, title = {Robust linear model selection based on least angle regression}, journal = {JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION}, volume = {102}, number = {480}, year = {2007}, month = {DEC}, pages = {1289-1299}, publisher = {AMER STATISTICAL ASSOC}, type = {Article}, address = {1429 DUKE ST, ALEXANDRIA, VA 22314 USA}, abstract = {In this article we consider the problem of building a linear prediction model when the number of candidate predictors is large and the data possibly contain anomalies that are difficult to visualize and clean. We want to predict the nonoutlying cases; therefore, we need a method that is simultaneously robust and scalable. We consider the stepwise least angle regression (LARS) algorithm which is computationally very efficient but sensitive to outliers. We introduce two different approaches to robustify LARS. The plug-in approach replaces the classical correlations in LARS by robust correlation estimates. The cleaning approach first transforms the data set by shrinking the outliers toward the bulk of the data (which we call multivariate Winsorization) and then applies LARS to the transformed data. We show that the plug in approach is time-efficient and scalable and that the bootstrap can be used to stabilize its results. We recommend using bootstrapped robustified LARS to sequence a number of candidate predictors to form a reduced set from which a more refined model can be selected.}, keywords = {bootstrap, computational complexity, robust prediction, stepwise algorithm, Winsorization}, issn = {0162-1459}, doi = {10.1198/016214507000000950}, author = {Khan, Jafar A. and Van Aelst, Stefan and Zamar, Ruben H.} } @article {gu2007biom, title = {On robustness and model flexibility in survival analysis: transformed hazards models and average effects}, journal = {Biometrics}, volume = {63}, year = {2007}, pages = {69-77}, doi = {10.1111/j.1541-0420.2006.00679.x}, author = {Gustafson, P.} } @article {pmid17272248, title = {Sample size calculations in randomized trials: common pitfalls}, journal = {Can J Anaesth}, volume = {54}, number = {2}, year = {2007}, month = {Feb}, pages = {103{\textendash}106}, author = {Brasher, P. M. and Brant, R. F.} } @article { ISI:000246559600002, title = {Seasonal confounding and residual correlation in analyses of health effects of air pollution}, journal = {ENVIRONMETRICS}, volume = {18}, number = {4}, year = {2007}, month = {JUN}, pages = {375-394}, publisher = {JOHN WILEY \& SONS LTD}, type = {Article}, address = {THE ATRIUM, SOUTHERN GATE, CHICHESTER PO19 8SQ, W SUSSEX, ENGLAND}, abstract = {To investigate the health effects of air pollution via a partially linear model, one must choose an appropriate amount of smoothing for accurate estimation of the linear pollution effects. This choice is complicated by the dependencies between the various covariates and by the potential residual correlation. Most existing approaches to making this choice are inadequate, as they neither target accurate estimation of the linear pollutant effects nor handle residual correlation. In this paper, we illustrate two new adaptive and objective methods for determining an appropriate amount of smoothing. We construct valid confidence intervals for the linear pollutant effects, intervals that account for residual correlation. We use our inferential methods to investigate the same-day effects of PM10 on daily mortality in two data sets for the period 1994 to 1996: one collected in Mexico City, an urban area with high levels of air pollution, and the other collected in Vancouver, British Columbia, an urban area with low levels of air pollution. For Mexico City, our methodology does not detect a PM10 effect. In contrast, for Vancouver, a PM10 effect corresponding to an expected 2.4\% increase (95\% confidence interval ranging from 0.0\% to 4.7\%) in daily mortality for every 10 mu g/m(3) increase in PM10 is identified. Copyright (c) 2006 John Wiley \& Sons, Ltd.}, keywords = {air pollution, bandwidth selection, generalized additive model, mortality, partially linear model, particulate matter, residual correlation, seasonal confounding, Smoothing}, issn = {1180-4009}, doi = {10.1002/env.814}, author = {Ghement, Isabella R. and Heckman, Nancy E. and Petkau, A. John} } @article {ghement2007seasonal, title = {Seasonal confounding and residual correlation in analyses of health effects of air pollution}, journal = {Environmetrics}, volume = {18}, number = {4}, year = {2007}, pages = {375{\textendash}394}, publisher = {Wiley Online Library}, author = {Ghement, Isabella R and Heckman, Nancy E and Petkau, A.John} } @article {pmid17208082, title = {Self-managed long-term low-molecular-weight heparin therapy: the balance of benefits and harms}, journal = {Am. J. Med.}, volume = {120}, number = {1}, year = {2007}, month = {Jan}, pages = {72{\textendash}82}, author = {Hull, R. D. and Pineo, G. F. and Brant, R. F. and Mah, A. F. and Burke, N. and Dear, R. and Wong, T. and Cook, R. and Solymoss, S. and Poon, M. C. and Raskob, G.} } @article {liu_simultaneous_2007, title = {Simultaneous Inference for Semiparametric Nonlinear Mixed-Effects Models with Covariate Measurement Errors and Missing Responses}, journal = {Biometrics}, volume = {63}, number = {2}, year = {2007}, month = {jun}, pages = {342{\textendash}350}, abstract = {Summary Semiparametric nonlinear mixed-effects (NLME) models are flexible for modeling complex longitudinal data. Covariates are usually introduced in the models to partially explain interindividual variations. Some covariates, however, may be measured with substantial errors. Moreover, the responses may be missing and the missingness may be nonignorable. We propose two approximate likelihood methods for semiparametric NLME models with covariate measurement errors and nonignorable missing responses. The methods are illustrated in a real data example. Simulation results show that both methods perform well and are much better than the commonly used naive method.}, keywords = {Cubic spline basis, Longitudinal data, Monte Carlo EM algorithm, Random-effects model}, issn = {1541-0420}, doi = {10.1111/j.1541-0420.2006.00687.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1541-0420.2006.00687.x/abstract}, author = {Liu, Wei and WU, LANG} } @article { ISI:000252359600010, title = {On tests for multivariate normality and associated simulation studies}, journal = {JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION}, volume = {77}, number = {11-12}, year = {2007}, month = {NOV-DEC}, pages = {1053-1068}, publisher = {TAYLOR \& FRANCIS LTD}, type = {Article}, address = {4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND}, abstract = {We study the empirical size and power of some recently proposed tests for multivariate normality (MVN) and compare them with the existing proposals that performed best in previously published studies. We show that the Royston{\textquoteright}s [Royston, J.P., 1983b, Some techniques for assessing multivariate normality based on the Shapiro-Wilk W. Applied Statistics, 32,121-133.] extension to the Shapiro and Wilk [Shapiro, S.S. and Wilk, M.B., 1965, An analysis of variance test for normality (complete samples). Biometrika, 52, 591-611.] test is unable to achieve the nominal significance level, and consider a subsequent extension proposed by Royston [Royston, J.P., 1992, Approximating the Shapiro-Wilk W-Test for non-normality. Statistics and Computing, 2, 117-119.] to correct this problem, which earlier studies appear to have ignored. A consistent and invariant test proposed by Henze and Zirkler [Henze, N. and Zirkler, B., 1990, A class of invariant consistent tests for multivariate normality. Communications in Statistics- Theory and Methods, 19, 3595-3617.] is found to have good power properties, particularly for sample sizes of 75 or more, while an approach suggested by Royston [Royston, J.P, 1992, Approximating the Shapiro-Wilk W-Test for non-normality. Statistics and Computing, 2, 117-119.] performs effectively at detecting departures from MVN for smaller sample sizes. We also compare our results to those of previous simulation studies, and discuss the challenges associated with generating multivariate data for such investigations.}, keywords = {consistent tests, goodness-of-fit, invariant test, multivariate normality, power, size}, issn = {0094-9655}, doi = {10.1080/10629360600878449}, author = {Farrell, Patrick J. and Salibian-Barrera, Mat{\'\i}as and Naczk, Katarzyna} } @article {miranda2007transcriptional, title = {The Transcriptional response of hybrid poplar (Populus trichocarpa x P. deltoids) to infection by Melampsora medusae leaf rust involves induction of flavonoid pathway genes leading to the accumulation of proanthocyanidins}, journal = {Molecular Plant-Microbe Interactions}, volume = {20}, number = {7}, year = {2007}, pages = {816{\textendash}831}, publisher = {Am Phytopath Society}, author = {Miranda, Manoela and Ralph, Steven G and Mellway, Robin and White, Rick and Heath, Michele C and Bohlmann, J{\"o}rg and Constabel, C Peter} } @article {khalili2007variable, title = {Variable selection in finite mixture of regression models}, journal = {Journal of the american Statistical association}, volume = {102}, number = {479}, year = {2007}, author = {Khalili, Abbas and Chen, Jiahua} } @article {pmid17378864, title = {The Western Canada Waiting List Project: development of a priority referral score for hip and knee arthroplasty}, journal = {J Eval Clin Pract}, volume = {13}, number = {2}, year = {2007}, month = {Apr}, pages = {192{\textendash}196}, author = {De Coster, C. and McMillan, S. and Brant, R. and McGurran, J. and Noseworthy, T.} } @article {pmid18053384, title = {Women{\textquoteright}s Pain Experience Predicts Future Surgery for Pain Associated With Endometriosis}, journal = {J Obstet Gynaecol Can}, volume = {29}, number = {12}, year = {2007}, month = {Dec}, pages = {988{\textendash}991}, author = {Jarrell, J. and Brant, R. and Leung, W. and Taenzer, P.} } @article {grgu2006aje, title = {Accounting for independent nondifferential misclassification does not increase certainty than an observed association is in the correct direction}, journal = {American Journal of Epidemiology}, volume = {164}, year = {2006}, pages = {63-68}, doi = {10.1093/aje/kwj155}, author = {Greenland, S. and Gustafson, P.} } @article {pan2006application, title = {Application of modified information criterion to multiple change point problems}, journal = {Journal of multivariate analysis}, volume = {97}, number = {10}, year = {2006}, pages = {2221{\textendash}2241}, publisher = {Elsevier}, author = {Pan, Jianmin and Chen, Jiahua} } @article {pmid17306061, title = {Assessment of mental health and illness by telephone survey: experience with an Alberta mental health survey}, journal = {Chronic Dis Can}, volume = {27}, number = {3}, year = {2006}, pages = {99{\textendash}109}, author = {Patten, S. B. and Adair, C. E. and Williams, J. V. and Brant, R. and Wang, J. L. and Casebeer, A. and Beausejour, P.} } @article {pmid16606377, title = {Association of postoperative complications with hospital costs and length of stay in a tertiary care center}, journal = {J Gen Intern Med}, volume = {21}, number = {2}, year = {2006}, month = {Feb}, pages = {177{\textendash}180}, author = {Khan, N. A. and Quan, H. and Bugar, J. M. and Lemaire, J. B. and Brant, R. and Ghali, W. A.} } @article { ISI:000241551800014, title = {On the asymptotic distribution of Pearson{\textquoteright}s $X^2$ in cross-validation samples}, journal = {Psychometrika}, volume = {71}, number = {3}, year = {2006}, month = {SEP}, pages = {587-592}, publisher = {Springer}, type = {Article}, abstract = {In categorical data analysis, two-sample cross-validation is used not only for model selection but also to obtain a realistic impression of the overall predictive effectiveness of the model. The latter is of particular importance in the case of highly parametrized models capable of capturing every idiosyncracy of the calibrating sample. We show that for maximum likelihood estimators or other asymptotically efficient estimators Pearson{\textquoteright}s X-2 is not asymptotically chi-square in the two-sample cross-validation framework due to extra variability induced by using different samples for estimation and goodness-off-it testing. We propose an alternative test statistic, X-xval(2) , obtained as a modification of X-2 which is asymptotically chi-square with C-1 degrees of freedom in cross-validation samples. Stochastically, X-xval(2) <= X-2. Furthermore, the use of X-2 instead of X-xval(2) with a chi(2)(C-1) reference distribution may provide an unduly poor impression of fit of the model in the cross-validation sample.}, keywords = {contingency tables, goodness-of-fit, item response theory modeling, latent class analysis, quadratic form statistics}, issn = {0033-3123}, doi = {10.1007/s11336-005-1284-z}, author = {Joe, Harry and Maydeu-Olivares, Albert} } @article { ISI:000237190100003, title = {The asymptotics of MM-estimators for linear regression with fixed designs}, journal = {METRIKA}, volume = {63}, number = {3}, year = {2006}, month = {JUN}, pages = {283-294}, publisher = {PHYSICA-VERLAG GMBH \& CO}, type = {Article}, address = {PO BOX 10 52 80, 69042 HEIDELBERG, GERMANY}, abstract = {MM-estimators achieve simultaneous high efficiency and high breakdown point over contamination neighborhoods. Inference based on these estimators relies on their asymptotic properties, which have been studied for the case of random covariates. In this paper we show that, under relatively mild regularity conditions, MM-estimators for linear regression models are strongly consistent when the design is fixed. Moreover, their strong consistency allows us to show that these estimators are also asymptotically normal for non-random covariates. These results justify the use of a normal approximation to the finite-sample distribution of MM-estimators for linear regression with fixed explanatory variables. Additionally, these results have been used to extend the robust bootstrap (Salibian-Barrera and Zamar in Ann Stat 30:556-582, 2002) to the case of fixed designs [see Salibian-Barrera 2004, submitted].}, keywords = {asymptotic distribution, consistency, fixed designs, MM-estimators}, issn = {0026-1335}, doi = {10.1007/s00184-005-0019-6}, author = {Salibian-Barrera, M} } @article { ISI:000238028100013, title = {Bootstrapping MM-estimators for linear regression with fixed designs}, journal = {STATISTICS \& PROBABILITY LETTERS}, volume = {76}, number = {12}, year = {2006}, month = {JUL 1}, pages = {1287-1297}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {In this paper, I study the extension of the robust bootstrap [Salibian-Barrera, M., Zarnar, R.H., 2002. Bootstrapping robust estimates of regression. Ann. Statist. 30, 556-582] to the case of fixed designs. The robust bootstrap is a computer-intensive inference method for robust regression estimators which is computationally simple (because we do not need to recompute the robust estimate with each bootstrap sample) and robust to the presence of outliers in the bootstrap samples. In this paper, I prove the consistency of this method for the case of non-random explanatory variables and illustrate its use on a real data set. Simulation results indicate that confidence intervals based on the robust bootstrap have good finite-sample coverage levels. (C) 2006 Elsevier B.V. All rights reserved.}, keywords = {bootstrap, fixed design, inference, linear regression, MM-estimators, Robustness}, issn = {0167-7152}, doi = {10.1016/j.spl.2006.01.008}, author = {Salibian-Barrera, M} } @article {pmid16722541, title = {A cluster randomized controlled trial comparing three methods of disseminating practice guidelines for children with croup [ISRCTN73394937]}, journal = {Implement Sci}, volume = {1}, year = {2006}, pages = {10}, author = {Johnson, D. W. and Craig, W. and Brant, R. and Mitton, C. and Svenson, L. and Klassen, T. P.} } @article {39232342, title = {A comparison of communication technologies to support novice team programming}, year = {2006}, pages = {695{\textendash}698}, doi = {10.1145/1134285.1134394}, author = {Davor Cubranic and Margaret-anne D. Storey and Jody Ryall} } @conference {2184581, title = {A comparison of communication technologies to support novice team programming}, booktitle = {International Conference on Software Engineering}, year = {2006}, pages = {695{\textendash}698}, doi = {10.1145/1134394}, author = {Davor Cubranic and Margaret-anne D. Storey and Jody Ryall} } @article {loeppky_computer_2006, title = {Computer model calibration or tuning in practice}, journal = {Technometrics, submitted for publication}, year = {2006}, url = {https://www.stat.ubc.ca/Research/TechReports/techreports/221.pdf}, author = {Loeppky, J. and Bingham, Derek and Welch, W.} } @article {Gustafson2006, title = {Conservative prior distributions for variance parameters in hierarchical models}, journal = {Canadian Journal of Statistics}, volume = {34}, number = {3}, year = {2006}, pages = {377{\textendash}390}, publisher = {Wiley Online Library}, doi = {10.1002/cjs.5550340302}, author = {Gustafson, Paul and Hossain, Shahadut and MacNab, Ying C} } @article {gugr2006statmed, title = {Curious phenomena in Bayesian adjustment for exposure misclassification}, journal = {Statistics in Medicine}, volume = {25}, year = {2006}, pages = {87-103}, doi = {10.1002/sim.2341}, author = {Gustafson, P. and Greenland, S.} } @article { ISI:000244258700004, title = {Discussion: Conditional growth charts}, journal = {ANNALS OF STATISTICS}, volume = {34}, number = {5}, year = {2006}, month = {OCT}, pages = {2113-2118}, publisher = {INST MATHEMATICAL STATISTICS}, type = {Editorial Material}, address = {PO BOX 22718, BEACHWOOD, OH 44122 USA}, issn = {0090-5364}, doi = {10.1214/009053606000000669}, author = {Salibian-Barrera, Mat{\'\i}as and Zamar, Ruben H.} } @article { ISI:000244258700004, title = {Discussion: Conditional growth charts}, journal = {ANNALS OF STATISTICS}, volume = {34}, number = {5}, year = {2006}, month = {OCT}, pages = {2113-2118}, publisher = {INST MATHEMATICAL STATISTICS}, type = {Editorial Material}, address = {PO BOX 22718, BEACHWOOD, OH 44122 USA}, issn = {0090-5364}, doi = {10.1214/009053606000000669}, author = {Salibian-Barrera, Mat{\'\i}as and Zamar, Ruben H.} } @article {joe2006discussion, title = {Discussion of {\textquotedblleft}Copulas: Tales and facts{\textquotedblright}, by Thomas Mikosch}, journal = {Extremes}, volume = {9}, number = {1}, year = {2006}, pages = {37{\textendash}41}, publisher = {Springer}, doi = {10.1007/s10687-006-0019-6}, author = {Joe, Harry} } @article { ISI:000242951200002, title = {Dynamic variable selection in SNP genotype autocalling from APEX microarray data}, journal = {BMC BIOINFORMATICS}, volume = {7}, year = {2006}, month = {NOV 30}, pages = {521}, publisher = {BIOMED CENTRAL LTD}, type = {Article}, address = {MIDDLESEX HOUSE, 34-42 CLEVELAND ST, LONDON W1T 4LB, ENGLAND}, abstract = {Background: Single nucleotide polymorphisms ( SNPs) are DNA sequence variations, occurring when a single nucleotide - adenine ( A), thymine ( T), cytosine ( C) or guanine ( G) - is altered. Arguably, SNPs account for more than 90\% of human genetic variation. Our laboratory has developed a highly redundant SNP genotyping assay consisting of multiple probes with signals from multiple channels for a single SNP, based on arrayed primer extension ( APEX). This mini-sequencing method is a powerful combination of a highly parallel microarray with distinctive Sanger- based dideoxy terminator sequencing chemistry. Using this microarray platform, our current genotype calling system ( known as SNP Chart) is capable of calling single SNP genotypes by manual inspection of the APEX data, which is time-consuming and exposed to user subjectivity bias. Results: Using a set of 32 Coriell DNA samples plus three negative PCR controls as a training data set, we have developed a fully- automated genotyping algorithm based on simple linear discriminant analysis ( LDA) using dynamic variable selection. The algorithm combines separate analyses based on the multiple probe sets to give a final posterior probability for each candidate genotype. We have tested our algorithm on a completely independent data set of 270 DNA samples, with validated genotypes, from patients admitted to the intensive care unit (ICU) of St. Paul{\textquoteright}s Hospital ( plus one negative PCR control sample). Our method achieves a concordance rate of 98.9\% with a 99.6\% call rate for a set of 96 SNPs. By adjusting the threshold value for the final posterior probability of the called genotype, the call rate reduces to 94.9\% with a higher concordance rate of 99.6\%. We also reversed the two independent data sets in their training and testing roles, achieving a concordance rate up to 99.8\%. Conclusion: The strength of this APEX chemistry- based platform is its unique redundancy having multiple probes for a single SNP. Our model- based genotype calling algorithm captures the redundancy in the system considering all the underlying probe features of a particular SNP, automatically down- weighting any {\textquoteleft}bad data{\textquoteright} corresponding to image artifacts on the microarray slide or failure of a specific chemistry. In this regard, our method is able to automatically select the probes which work well and reduce the effect of other so- called bad performing probes in a sample- specific manner, for any number of SNPs.}, issn = {1471-2105}, doi = {10.1186/1471-2105-7-521}, author = {Podder, Mohua and Welch, William J. and Zamar, Ruben H. and Tebbutt, Scott J.} } @article {podder_dynamic_2006, title = {Dynamic variable selection in SNP genotype autocalling from APEX microarray data}, journal = {BMC bioinformatics}, volume = {7}, number = {1}, year = {2006}, pages = {1}, url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-521}, author = {Podder, Mohua and Welch, William J. and Zamar, Ruben H. and Tebbutt, Scott J.} } @article {zidek2006editorial, title = {Editorial:(Post-normal) statistical science}, journal = {Journal of the Royal Statistical Society: Series A (Statistics in Society)}, volume = {169}, number = {1}, year = {2006}, pages = {1{\textendash}4}, publisher = {Wiley Online Library}, author = {Zidek, James V} } @conference {Liang2006endtoend, title = {An end-to-end discriminative approach to machine translation}, booktitle = {Proceedings of the 44th Annual Meeting of the Association for Computational Linguistics (ACL06)}, volume = {21}, year = {2006}, pages = {761{\textendash}768}, author = {Percy Liang and Alexandre Bouchard-C{\^o}t{\'e} and Dan Klein and Ben Taskar} } @article { ISI:000238044400008, title = {A fast algorithm for S-regression estimates}, journal = {JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS}, volume = {15}, number = {2}, year = {2006}, month = {JUN}, pages = {414-427}, publisher = {AMER STATISTICAL ASSOC}, type = {Article}, address = {1429 DUKE ST, ALEXANDRIA, VA 22314 USA}, abstract = {

Equivariant high-breakdown point regression estimates are computationally expensive, and the corresponding algorithms become unfeasible for moderately large number of regressors. One important advance to improve the computational speed of one such estimator is the fast-LTS algorithm. This article proposes an analogous algorithm for computing S-estimates. The new algorithm, that we call {\textquoteleft}{\textquoteleft}fast-S{\textquoteright}{\textquoteright}, is also based on a {\textquoteleft}{\textquoteleft}local improvement{\textquoteright}{\textquoteright} step of the resampling initial candidates. This allows for a substantial reduction of the number of candidates required to obtain a good approximation to the optimal solution. We performed a simulation study which shows that S-estimators computed with the fast-S algorithm compare favorably to the LTS-estimators computed with the fast-LTS algorithm.

}, keywords = {high breakdown point, linear regression, Robustness}, issn = {1061-8600}, doi = {10.1198/106186006X113629}, author = {Salibian-Barrera, M and Yohai, VJ} } @article {wu_generalized_2006, title = {Generalized linear mixed models with informative dropouts and missing covariates}, journal = {Metrika}, volume = {66}, number = {1}, year = {2006}, month = {aug}, pages = {1{\textendash}18}, abstract = {Generalized linear mixed models (GLMM) are useful in many longitudinal data analyses. In the presence of informative dropouts and missing covariates, however, standard complete-data methods may not be applicable. In this article, we consider a likelihood method and an approximate method for GLMM with informative dropouts and missing covariates. The methods are implemented by Monte{\textendash}Carlo EM algorithms combined with Gibbs sampler. The approximate method may lead to inconsistent estimators but is computationally more efficient than the likelihood method. The two methods are evaluated via a simulation study for longitudinal binary data, and appear to perform reasonably well. A dataset on mental distress is analyzed in details.}, keywords = {Economic Theory, general, Gibbs sampling, Linearization, Probability Theory and Stochastic Processes, PX-EM algorithm, Rejection sampling, Statistics, Statistics for Business/Economics/Mathematical Finance/Insurance}, issn = {0026-1335, 1435-926X}, doi = {10.1007/s00184-006-0083-6}, url = {http://link.springer.com/article/10.1007/s00184-006-0083-6}, author = {Wu, Kunling and WU, LANG} } @article { ISI:000241970400006, title = {Generating random correlation matrices based on partial correlations}, journal = {Journal of Multivariate Analysis}, volume = {97}, number = {10}, year = {2006}, month = {NOV}, pages = {2177-2189}, publisher = {Elsevier Inc}, type = {article}, abstract = {A d-dimensional positive definite correlation matrix R = (rho(ij)) can be parametrized in terms of the correlations rho(i,i+1) for i = 1,..., d - 1, and the partial correlations rho(ij\textbackslashi+1,.... j-1) for j - i >= 2. These ((d)(2)) parameters can independently take values in the interval (- 1, 1). Hence we can generate a random positive definite correlation matrix by choosing independent distributions F-ij, 1 <= i < j <= d, for these ((d)(2)) parameters. We obtain conditions on the F-ij so that the joint density of (rho(ij)) is proportional to a power of det(R) and hence independent of the order of indices defining the sequence of partial correlations. As a special case, we have a simple construction for generating R that is uniform over the space of positive definite correlation matrices. As a byproduct, we determine the volume of the set of correlation matrices in ((d)(2))-dimensional space. To prove our results, we obtain a simple remarkable identity which expresses det(R) as a function of rho(i,i+1) for i = 1,..., d - 1, and p(ij\textbackslashi+1,... j-1) for j - i >= 2. (C) 2005 Elsevier Inc. All rights reserved.}, keywords = {Beta distribution, determinant of correlation matrix}, issn = {0047-259X}, doi = {10.1016/j.jmva.2005.05.010}, author = {Joe, Harry} } @article { ISI:000241792300008, title = {Generation of random clusters with specified degree of separation}, journal = {Journal of Classification}, volume = {23}, number = {2}, year = {2006}, month = {SEP}, pages = {315-334}, publisher = {Springer}, type = {Article}, abstract = {We propose a random cluster generation algorithm that has the desired features: (1) the population degree of separation between clusters and the nearest neighboring clusters can be set to a specified value, based on a separation index; (2) no constraint is imposed on the isolation among clusters in each dimension; (3) the covariance matrices correspond to different shapes, diameters and orientations; (4) the full cluster structures generally could not be detected simply from pair-wise scatterplots of variables; (5) noisy variables and outliers can be imposed to make the cluster structures harder to be recovered. This algorithm is an improvement on the method used in Milligan (1985).}, keywords = {cluster generation, factorial experiment design, separation index}, issn = {0176-4268}, doi = {10.1007/s00357-006-0018-y}, author = {Qiu, Weiliang and Joe, Harry} } @article {ralph2006genomics, title = {Genomics of hybrid poplar (Populus trichocarpa [multiplication] deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-i}, journal = {Molecular ecology}, year = {2006}, publisher = {Oxford, UK: Blackwell Publishing Ltd}, author = {Ralph, Steven and Oddy, Claire and Cooper, Dawn and Yueh, Hesther and Jancsik, Sharon and Kolosova, Natalia and Philippe, Ryan N and Aeschliman, Dana and White, Rick and Huber, Dezene and others} } @article {ralph2006genomics, title = {Genomics of hybrid poplar (Populus trichocarpa$\times$ deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced de}, journal = {Molecular Ecology}, volume = {15}, number = {5}, year = {2006}, pages = {1275{\textendash}1297}, publisher = {Wiley Online Library}, author = {Ralph, Steven and Oddy, Claire and Cooper, Dawn and Yueh, Hesther and Jancsik, Sharon and Kolosova, Natalia and Philippe, Ryan N and Aeschliman, Dana and White, Rick and Huber, Dezene and others} } @article {pmid16344380, title = {The impact of the Canadian Hypertension Education Program on antihypertensive prescribing trends}, journal = {Hypertension}, volume = {47}, number = {1}, year = {2006}, month = {Jan}, pages = {22{\textendash}28}, author = {Campbell, N. R. and Tu, K. and Brant, R. and Duong-Hua, M. and McAlister, F. A.} } @article {chen2006information, title = {Information criterion and change point problem for regular models}, journal = {Sankhy\=a: The Indian Journal of Statistics}, year = {2006}, pages = {252{\textendash}282}, publisher = {JSTOR}, author = {Chen, Jiahua and Gupta, AK and Pan, Jianmin} } @article {MacNab2006, title = {An innovative application of Bayesian disease mapping methods to patient safety research: A Canadian adverse medical event study}, journal = {Statistics in medicine}, volume = {25}, number = {23}, year = {2006}, pages = {3960{\textendash}3980}, publisher = {Wiley Online Library}, doi = {10.1002/sim.2507}, author = {MacNab, Ying C and Kmetic, Andrew and Gustafson, Paul and Sheps, Sam} } @article {jung2006iron, title = {Iron regulation of the major virulence factors in the AIDS-associated pathogen Cryptococcus neoformans}, journal = {PLoS Biol}, volume = {4}, number = {12}, year = {2006}, pages = {e410}, author = {Jung, Won Hee and Sham, Anita and White, Rick and Kronstad, James W} } @article {pmid16980152, title = {Kaplan-Meier methods yielded misleading results in competing risk scenarios}, journal = {J Clin Epidemiol}, volume = {59}, number = {10}, year = {2006}, month = {Oct}, pages = {1110{\textendash}1114}, author = {Southern, D. A. and Faris, P. D. and Brant, R. and Galbraith, P. D. and Norris, C. M. and Knudtson, M. L. and Ghali, W. A.} } @article { ISI:000245010700005, title = {Limited information goodness-of-fit testing in multidimensional contingency tables}, journal = {Psychometrika}, volume = {71}, number = {4}, year = {2006}, month = {DEC}, pages = {713-732}, publisher = {Springer}, type = {Article}, abstract = {We introduce a family of goodness-of-fit statistics for testing composite null hypotheses in multidimensional contingency tables. These statistics are quadratic forms in marginal residuals up to order r. They are asymptotically chi-square under the null hypothesis when parameters are estimated using any asymptotically normal consistent estimator. For a widely used item response model, when r is small and multidimensional tables are sparse, the proposed statistics have accurate empirical Type I errors, unlike Pearson{\textquoteright}s X-2. For this model in nonsparse situations, the proposed statistics are also more powerful than X-2. In addition, the proposed statistics are asymptotically chi-square when applied to subtables, and can be used for a piecewise goodness-of-fit assessment to determine the source of misfit in poorly fitting models.}, keywords = {categorical data analysis, Composite likelihood, item response theory, Lisrel, multivariate discrete data, multivariate multinomial distribution}, issn = {0033-3123}, doi = {10.1007/s11336-005-1295-9}, author = {Maydeu-Olivares, Albert and Joe, Harry} } @article {van2006linear, title = {Linear grouping using orthogonal regression}, journal = {Computational Statistics \& Data Analysis}, volume = {50}, number = {5}, year = {2006}, pages = {1287{\textendash}1312}, publisher = {Elsevier}, author = {Van Aelst, Stefan and Wang, Xiaogang Steven and Zamar, Ruben H and Zhu, Rong} } @article {tremlett2006liver, title = {Liver test abnormalities in multiple sclerosis: Findings from placebo-treated patients}, journal = {Neurology}, volume = {67}, number = {7}, year = {2006}, pages = {1291{\textendash}1293}, publisher = {AAN Enterprises}, author = {Tremlett, H and Seem{\"u}ller, S and Zhao, Y and Yoshida, EM and Oger, J and Petkau, J} } @article {pmid17145251, title = {Long-term low-molecular-weight heparin versus usual care in proximal-vein thrombosis patients with cancer}, journal = {Am. J. Med.}, volume = {119}, number = {12}, year = {2006}, month = {Dec}, pages = {1062{\textendash}1072}, author = {Hull, R. D. and Pineo, G. F. and Brant, R. F. and Mah, A. F. and Burke, N. and Dear, R. and Wong, T. and Cook, R. and Solymoss, S. and Poon, M. C. and Raskob, G.} } @article {kibria2006matrix, title = {The matrix-t distribution and its applications in predictive inference}, journal = {Journal of Multivariate Analysis}, volume = {97}, year = {2006}, pages = {785{\textendash}795}, publisher = {Elsevier}, author = {Kibria, BM Golam} } @article { ISI:000242375200014, title = {Meta-analysis of differentiating mouse embryonic stem cell gene expression kinetics reveals early change of a small gene set}, journal = {PLOS COMPUTATIONAL BIOLOGY}, volume = {2}, number = {11}, year = {2006}, month = {NOV}, pages = {e158}, publisher = {PUBLIC LIBRARY SCIENCE}, type = {Article}, address = {185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA}, abstract = {Stem cell differentiation involves critical changes in gene expression. Identification of these should provide endpoints useful for optimizing stem cell propagation as well as potential clues about mechanisms governing stem cell maintenance. Here we describe the results of a new meta-analysis methodology applied to multiple gene expression datasets from three mouse embryonic stem cell (ESC) lines obtained at specific time points during the course of their differentiation into various lineages. We developed methods to identify genes with expression changes that correlated with the altered frequency of functionally defined, undifferentiated ESC in culture. In each dataset, we computed a novel statistical confidence measure for every gene which captured the certainty that a particular gene exhibited an expression pattern of interest within that dataset. This permitted a joint analysis of the datasets, despite the different experimental designs. Using a ranking scheme that favored genes exhibiting patterns of interest, we focused on the top 88 genes whose expression was consistently changed when ESC were induced to differentiate. Seven of these (103728_at, 8430410A17Rik, Klf2, Nr0b1, Sox2, Tcl1, and Zfp42) showed a rapid decrease in expression concurrent with a decrease in frequency of undifferentiated cells and remained predictive when evaluated in additional maintenance and differentiating protocols. Through a novel meta-analysis, this study identifies a small set of genes whose expression is useful for identifying changes in stem cell frequencies in cultures of mouse ESC. The methods and findings have broader applicability to understanding the regulation of self-renewal of other stem cell types.}, issn = {1553-734X}, doi = {10.1371/journal.pcbi.0020158}, author = {Glover, Clive H. and Marin, Michael and Eaves, Connie J. and Helgason, Cheryl D. and Piret, James M. and Bryan, Jennifer} } @article { ISI:000239509800005, title = {Modelling count data time series with Markov processes based on binomial thinning}, journal = {Journal of Time Series Analysis}, volume = {27}, number = {5}, year = {2006}, month = {SEP}, pages = {725-738}, publisher = {Blackwell Publishing}, type = {Article}, abstract = {We obtain new models and results for count data time series based on binomial thinning. Count data time series may have non-stationarity from trends or covariates, so we propose an extension of stationary time series based on binomial thinning such that the univariate marginal distributions are always in the same parametric family, such as negative binomial. We propose a recursive algorithm to calculate the probability mass functions for the innovation random variable associated with binomial thinning. This simplifies numerical calculations and estimation for the classes of time series models that we consider. An application with real data is used to illustrate the models.}, keywords = {Binomial thinning, count data time series, discrete self-decomposability, higher order Markov dependence, overdispersion, time-varying mean}, issn = {0143-9782}, doi = {10.1111/j.1467-9892.2006.00485.x}, author = {Zhu, Rong and Joe, Harry} } @article {pmid16456005, title = {Modulation of the TLR-mediated inflammatory response by the endogenous human host defense peptide LL-37}, journal = {J. Immunol.}, volume = {176}, number = {4}, year = {2006}, month = {Feb}, pages = {2455{\textendash}2464}, abstract = {The sole human cathelicidin peptide, LL-37, has been demonstrated to protect animals against endotoxemia/sepsis. Low, physiological concentrations of LL-37 (< or =1 microg/ml) were able to modulate inflammatory responses by inhibiting the release of the proinflammatory cytokine TNF-alpha in LPS-stimulated human monocytic cells. Microarray studies established a temporal transcriptional profile and identified differentially expressed genes in LPS-stimulated monocytes in the presence or absence of LL-37. LL-37 significantly inhibited the expression of specific proinflammatory genes up-regulated by NF-kappaB in the presence of LPS, including NFkappaB1 (p105/p50) and TNF-alpha-induced protein 2 (TNFAIP2). In contrast, LL-37 did not significantly inhibit LPS-induced genes that antagonize inflammation, such as TNF-alpha-induced protein 3 (TNFAIP3) and the NF-kappaB inhibitor, NFkappaBIA, or certain chemokine genes that are classically considered proinflammatory. Nuclear translocation, in LPS-treated cells, of the NF-kappaB subunits p50 and p65 was reduced > or =50\% in the presence of LL-37, demonstrating that the peptide altered gene expression in part by acting directly on the TLR-to-NF-kappaB pathway. LL-37 almost completely prevented the release of TNF-alpha and other cytokines by human PBMC following stimulation with LPS and other TLR2/4 and TLR9 agonists, but not with cytokines TNF-alpha or IL-1beta. Biochemical and inhibitor studies were consistent with a model whereby LL-37 modulated the inflammatory response to LPS/endotoxin and other agonists of TLR by a complex mechanism involving multiple points of intervention. We propose that the natural human host defense peptide LL-37 plays roles in the delicate balancing of inflammatory responses in homeostasis as well as in combating sepsis induced by certain TLR agonists.}, author = {Mookherjee, N. and Brown, K. L. and Bowdish, D. M. and Doria, S. and Falsafi, R. and Hokamp, K. and Roche, F. M. and Mu, R. and Doho, G. H. and Pistolic, J. and Powers, J. P. and Bryan, J. and Brinkman, F. S. and Hancock, R. E.} } @article {li2006mri, title = {MRI T2 lesion burden in multiple sclerosis: A plateauing relationship with clinical disability}, journal = {Neurology}, volume = {66}, number = {9}, year = {2006}, pages = {1384{\textendash}1389}, publisher = {AAN Enterprises}, author = {Li, DKB and Held, U and Petkau, J and Daumer, M and Barkhof, F and Fazekas, F and Frank, JA and Kappos, L and Miller, DH and Simon, JH and Wolinsky, J and Filippi, M} } @article {Synnes2006, title = {Neonatal intensive care unit characteristics affect the incidence of severe intraventricular hemorrhage}, journal = {Medical care}, volume = {44}, number = {8}, year = {2006}, pages = {754{\textendash}759}, publisher = {LWW}, doi = {10.1097/01.mlr.0000218780.16064.df}, author = {Synnes, Anne R and MacNab, Ying C and Qiu, Zhenguo and Ohlsson, Arne and Gustafson, Paul and Dean, Charmaine B and Lee, Shoo K and Canadian Neonatal Network and others} } @article {berrendero2006note, title = {A note on the uniform asymptotic normality of location M-estimates}, journal = {Metrika}, volume = {63}, number = {1}, year = {2006}, pages = {55{\textendash}69}, publisher = {Springer}, author = {Berrendero, Jos{\'e} R and Zamar, Ruben H} } @article {pmid17142525, title = {A novel imaging technique to measure capillary-refill time: improving diagnostic accuracy for dehydration in young children with gastroenteritis}, journal = {Pediatrics}, volume = {118}, number = {6}, year = {2006}, month = {Dec}, pages = {2402{\textendash}2408}, author = {Shavit, I. and Brant, R. and Nijssen-Jordan, C. and Galbraith, R. and Johnson, D. W.} } @article {pmid16632132, title = {Ordinal regression model and the linear regression model were superior to the logistic regression models}, journal = {J Clin Epidemiol}, volume = {59}, number = {5}, year = {2006}, month = {May}, pages = {448{\textendash}456}, author = {Norris, C. M. and Ghali, W. A. and Saunders, L. D. and Brant, R. and Galbraith, D. and Faris, P. and Knudtson, M. L.} } @article {chilson2006parallel, title = {Parallel computation of high-dimensional robust correlation and covariance matrices}, journal = {Algorithmica}, volume = {45}, number = {3}, year = {2006}, pages = {403{\textendash}431}, publisher = {Springer}, author = {Chilson, James and Ng, Raymond and Wagner, Alan and Zamar, Ruben} } @article {chilson2006parallel, title = {Parallel computation of high-dimensional robust correlation and covariance matrices}, journal = {Algorithmica}, volume = {45}, number = {3}, year = {2006}, pages = {403{\textendash}431}, publisher = {Springer}, author = {Chilson, James and Ng, Raymond and Wagner, Alan and Zamar, Ruben} } @article {gugr2006biom, title = {The performance of random coefficient regression in accounting for residual confounding}, journal = {Biometrics}, volume = {62}, year = {2006}, pages = {760-768}, doi = {10.1111/j.1541-0420.2005.00510.x}, author = {Gustafson, P. and Greenland, S.} } @article {pmid16848912, title = {Periodontal disease and spontaneous preterm birth: a case control study}, journal = {BMC Pregnancy Childbirth}, volume = {6}, year = {2006}, pages = {24}, author = {Wood, S. and Frydman, A. and Cox, S. and Brant, R. and Needoba, S. and Eley, B. and Sauve, R.} } @article {pmid16580292, title = {Peripartum myocardial ischemia: a review of Canadian deliveries from 1970 to 1998}, journal = {Am. J. Obstet. Gynecol.}, volume = {194}, number = {4}, year = {2006}, month = {Apr}, pages = {1027{\textendash}1033}, author = {Macarthur, A. and Cook, L. and Pollard, J. K. and Brant, R.} } @article { ISI:000240158700035, title = {Principal components analysis based on multivariate MM estimators with fast and robust bootstrap}, journal = {JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION}, volume = {101}, number = {475}, year = {2006}, month = {SEP}, pages = {1198-1211}, publisher = {AMER STATISTICAL ASSOC}, type = {Article}, address = {1429 DUKE ST, ALEXANDRIA, VA 22314 USA}, abstract = {We consider robust principal components analysis (PCA) based on multivariate MM estimators. We first study the robustness and efficiency of these estimators, particularly in terms of eigenvalues and eigenvectors. We then focus on inference procedures based on a fast and robust bootstrap for MM estimators. This method is an alternative to the approach based on the asymptotic distribution of the estimators and can also be used to assess the stability of the principal components. A formal consistency proof for the bootstrap method is given, and its finite-sample performance is investigated through simulations. We illustrate the use of the robust PCA and the bootstrap inference on a real dataset.}, keywords = {bootstrap, inference, MM-estimators, Principal components, Robustness}, issn = {0162-1459}, doi = {10.1198/016214506000000096}, author = {Salibian-Barrera, Mat{\'\i}as and Van Aelst, Stefan and Willems, Gert} } @article { ISI:000235921600015, title = {Range of correlation matrices for dependent Bernoulli random variables}, journal = {Biometrika}, volume = {93}, number = {1}, year = {2006}, month = {MAR}, pages = {197-206}, abstract = {We say that a pair (p, R) is compatible if there exists a multivariate binary distribution with mean vector p and correlation matrix R. In this paper we study necessary and sufficient conditions for compatibility for structured and unstructured correlation matrices. We give examples of correlation matrices that are incompatible with any p. Using our results we show that the parametric binary models of Emrich \& Piedmonte (1991) and Qaqish (2003) allow a good range of correlations between the binary variables. We also obtain necessary and sufficient conditions for a matrix of odds ratios to be compatible with a given p. Our findings support the popular belief that the odds ratios are less constrained and more flexible than the correlations.}, issn = {0006-3444}, doi = {10.1093/biomet/93.1.197}, author = {Chaganty, N R and Joe, H} } @conference { ISI:000238122900008, title = {Range of correlation matrices for dependent random variables with given marginal distributions}, booktitle = {Advances in Distribution Theory, Order Statistics, and Inference}, series = {Statistics for Industry and Technology}, year = {2006}, note = {International Conference on Distribution Theory, Order Statistics, and Inference, Univ Cantabria, Santander, SPAIN, JUN 16-18, 2004}, pages = {125-142}, publisher = {Birkhauser Boston}, organization = {Birkhauser Boston}, type = {Proceedings Paper}, abstract = {Let X-1, center dot center dot center dot, X-d be d (d >= 3) dependent random variables with finite variances such that X-j similar to F-j. Results on the set S-d(F-1, center dot center dot center dot, F-d) of possible correlation matrices with given margins are obtained; this set is relevant for simulating dependent random variables with given marginal distributions and a given correlation matrix. When F-1 = (...) = F-d = F, we let S-d(F) denote the set of possible correlation matrices. Of interest is the set of F for which Sd(F) is the same as the set of all non-negative definite correlation matrices; using a construction with conditional distributions, we show that this property holds only if F is a (location-scale shift of a) margin of a (d-1)-dimensional spherical distribution.}, keywords = {Copula, elliptically contoured, Frechet bounds, Partial correlation, spherically symmetric}, isbn = {0-8176-4361-3}, doi = {10.1007/0-8176-4487-3_8}, author = {Joe, Harry}, editor = {Balakrishnan, N and Castillo, E and Sarabia, J. M.} } @article {brunham2006reply, title = {Reply to Hagdu and to Moss et al.}, journal = {Journal of Infectious Diseases}, volume = {193}, number = {9}, year = {2006}, pages = {1338{\textendash}1339}, publisher = {Oxford University Press}, author = {Brunham, Robert C and Pourbohloul, Babak and Mak, Sunny and White, Rick and Rekart, Michael L} } @conference { ISI:000242170000004, title = {A robust linear grouping algorithm}, booktitle = {COMPSTAT 2006: Proceedings in Computational Statistics}, year = {2006}, note = {17th Symposium on Computational Statistics (COMSTAT 2006), Rome, ITALY, AUG 28-SEP 01, 2006}, pages = {43-53}, publisher = {PHYSICA-VERLAG GMBH \& CO}, organization = {PHYSICA-VERLAG GMBH \& CO}, type = {Proceedings Paper}, address = {TIERGARTENSTR 17, D-69121 HEIDELBERG, GERMANY}, abstract = {Recently, an algorithm to detect groups in a dataset that follow different linear patterns was proposed in [VWZ06]. The algorithm is flexible in the sense that it does not require the specification of a response variable. On the other hand, the algorithm requires that each observation follows one of the linear patterns in the data. However, it often occurs in practice that part of the data does not follow any of the linear patterns. Therefore, we introduce a robust linear grouping algorithm based on trimming that can still find the linear structures even if part of the data does not belong to any of the groups.}, keywords = {linear grouping, Robustness, trimming}, isbn = {3-7908-1708-2}, doi = {10.1007/978-3-7908-1709-6_4}, author = {Pison, Greet and Van Aelst, Stefan and Zamar, Ruben H.}, editor = {Rizzi, A and Vichi, M} } @article {gu2006jrssa, title = {Sample size implications when biases are modelled rather than ignored}, journal = {Journal of the Royal Statistical Society, Series A}, volume = {169}, year = {2006}, pages = {883-902}, doi = {10.1111/j.1467-985X.2006.00436.x}, author = {Gustafson, P.} } @inbook {schonlau_screening_2006, title = {Screening the input variables to a computer model via analysis of variance and visualization}, booktitle = {Screening}, year = {2006}, pages = {308{\textendash}327}, publisher = {Springer New York}, organization = {Springer New York}, url = {http://link.springer.com/chapter/10.1007/0-387-28014-6_14}, author = {Schonlau, Matthias and Welch, William J.} } @article { ISI:000232738400001, title = {Separation index and partial membership for clustering}, journal = {Computational Statistics \& Data Analysis}, volume = {50}, number = {3}, year = {2006}, month = {FEB 10}, pages = {585-603}, abstract = {We propose a new separation index that measures the magnitude of gaps between any two Clusters in a partition, by projecting the data in a pair of clusters into a one-dimensional space in which they have the maximum separation. The resulting projections can also be used to determine partial membership for points near the boundaries between two or more clusters. The matrix of separation indexes is helpful in deciding whether too many or too few clusters are specified in the clustering method. (c) 2004 Elsevier B.V. All rights reserved.}, issn = {0167-9473}, doi = {10.1016/j.csda.2004.09.009}, author = {Qiu, W and Joe, H} } @article {perlman_improved_2006, title = {Some Improved Tests for Multivariate One-Sided Hypotheses}, journal = {Metrika}, volume = {64}, number = {1}, year = {2006}, month = {feb}, pages = {23{\textendash}39}, abstract = {Multivariate one-sided hypothesis-testing problems are very common in clinical trials with multiple endpoints. The likelihood ratio test (LRT) and union-intersection test (UIT) are widely used for testing such problems. It is argued that, for many important multivariate one-sided testing problems, the LRT and UIT fail to adapt to the presence of subregions of varying dimensionalities on the boundary of the null parameter space and thus give undesirable results. Several improved tests are proposed that do adapt to the varying dimensionalities and hence reflect the evidence provided by the data more accurately than the LRT and UIT. Moreover, the proposed tests are often less biased and more powerful than the LRT and UIT.}, keywords = {Economic Theory, general, likelihood ratio test, Multiple endpoints, One-sided hypothesis, p-value, Probability Theory and Stochastic Processes, Statistics, Statistics for Business/Economics/Mathematical Finance/Insurance, Union-intersection test}, issn = {0026-1335, 1435-926X}, doi = {10.1007/s00184-006-0028-0}, url = {http://link.springer.com/article/10.1007/s00184-006-0028-0}, author = {Perlman, Michael D. and WU, LANG} } @book {le2006statistical, title = {Statistical analysis of environmental space-time processes}, year = {2006}, publisher = {Springer Science and Business Media}, organization = {Springer Science and Business Media}, author = {Le, Nhu D. and Zidek, James V.} } @article {fu2006testing, title = {Testing for homogeneity in genetic linkage analysis}, journal = {Statistica Sinica}, volume = {16}, number = {3}, year = {2006}, pages = {805}, publisher = {C/O DR HC HO, INST STATISTICAL SCIENCE, ACADEMIA SINICA, TAIPEI 115, TAIWAN}, author = {Fu, Yuejiao and Chen, Jiahua and Kalbfleisch, John D} } @booklet {chen2006tournament, title = {A tournament approach to the detection of multiple associations in genome-wide studies with pedigree data}, year = {2006}, publisher = {Working Paper 2006-09, www. stats. uwaterloo. ca. Department of Statistics \& Actuarial Sciences, University of Waterloo}, author = {Chen, Zehua and Chen, Jiahua and Liu, Jianjun and Chen, Zehua} } @article {shaddick2006using, title = {Using a probabilistic model (pCNEM) to estimate personal exposure to air pollution in a study of the short-term effect of PM10 on mortality}, journal = {Epidemiology}, volume = {17}, number = {6}, year = {2006}, pages = {S158}, publisher = {LWW}, author = {Shaddick, G and Zidek, J and Lee, D and White, R and Meloche, J and Chatfield, C} } @article {shaddick2006using, title = {Using estimated personal exposures to assess the short-term effects of air pollution on health}, journal = {University of Bath, Department of Mathematical Sciecnes Technical Report}, year = {2006}, author = {Shaddick, G. and Lee, D. and Zidek, J.V.} } @article {zaharik2006yoshinobu, title = {Yoshinobu Takakura, Yasuda Kei, Owawa Yoshiyuki, Nishikaawa Makiya: DNA and its cationic lipid complexes induce CpG motif-dependent activation of murine dendritic cells Hui Huang, Fang Li, Zhenmin Ye, Junbao Yang, Jim Xiang: CD4+ Th1 cells promote CD8+ Tc}, year = {2006}, publisher = {Wiley Online Library}, author = {Zaharik, Michelle and Nayar, Tarun and White, Rick and Ma, Caixia and Vallance, Bruce and Straka, Nadine and Jiang, Xiaozhou and Rey-Ladino, Jose and Choi, Jung-Hwa and Choi, Eun and others} } @article {variyath2005analysis, title = {Analysis of performance measures in experimental designs using jackknife}, journal = {Journal of quality technology}, volume = {37}, number = {2}, year = {2005}, pages = {91{\textendash}100}, publisher = {American Society for Quality}, author = {Variyath, Asokan Mulayath and Abraham, Bovas and Chen, Jiahua} } @article {pmid15876915, title = {Antidepressant pharmacoepidemiology in a general population sample}, journal = {J Clin Psychopharmacol}, volume = {25}, number = {3}, year = {2005}, month = {Jun}, pages = {285{\textendash}287}, author = {Patten, S. B. and Williams, J. V. and Wang, J. and Adair, C. E. and Brant, R. and Casebeer, A. and Barbui, C.} } @article {altman2005application, title = {Application of hidden Markov models to multiple sclerosis lesion count data}, journal = {Statistics in Medicine}, volume = {24}, number = {15}, year = {2005}, pages = {2335{\textendash}2344}, publisher = {Wiley Online Library}, author = {Altman, Rachel M and Petkau, A.John} } @conference {Bouchard2005approximation, title = {An approximation algorithm for labelled Markov processes: towards realistic approximation}, booktitle = {Proceedings of the International Conference on Quantitative Evaluation of Systems}, volume = {2}, year = {2005}, pages = {54{\textendash}62}, author = {Alexandre Bouchard-C{\^o}t{\'e} and Norm Ferns and Prakash Panangaden and Doina Precup} } @article { ISI:000229653000010, title = {Asymptotic efficiency of the two-stage estimation method for copula-based models}, journal = {Journal of Multivariate Analysis}, volume = {94}, number = {2}, year = {2005}, month = {JUN}, pages = {401-419}, abstract = {For multivariate copula-based models for which maximum likelihood is computationally difficult, a two-stage estimation procedure has been proposed previously; the first stage involves maximum likelihood from univariate margins, and the second stage involves maximum likelihood of the dependence parameters with the univariate parameters held fixed from the first stage. Using the theory of inference functions, a partitioned matrix in a form amenable to analysis is obtained for the asymptotic covariance matrix of the two-stage estimator. The asymptotic relative efficiency of the two-stage estimation procedure compared with maximum likelihood estimation is studied. Analysis of the limiting cases of the independence copula and Frechet upper bound help to determine common patterns in the efficiency as the dependence in the model increases. For the Frechet upper bound, the two-stage estimation procedure can sometimes be equivalent to maximum likelihood estimation for the univariate parameters. Numerical results are shown for some models, including multivariate ordinal probit and bivariate extreme value distributions, to indicate the typical level of asymptotic efficiency for discrete and continuous data. (c) 2004 Elsevier Inc. All rights reserved.}, issn = {0047-259X}, doi = {10.1016/j.jmva.2004.06.003}, author = {Joe, H} } @article {pmid15694889, title = {Atrial flutter and the risk of thromboembolism: a systematic review and meta-analysis}, journal = {Am. J. Med.}, volume = {118}, number = {2}, year = {2005}, month = {Feb}, pages = {101{\textendash}107}, author = {Ghali, W. A. and Wasil, B. I. and Brant, R. and Exner, D. V. and Cornuz, J.} } @article {pmid16205444, title = {Automated assessment of blood pressure using BpTRU compared with assessments by a trained technician and a clinic nurse}, journal = {Blood Press Monit}, volume = {10}, number = {5}, year = {2005}, month = {Oct}, pages = {257{\textendash}262}, author = {Campbell, N. R. and Conradson, H. E. and Kang, J. and Brant, R. and Anderson, T.} } @article {tu2005bartlett, title = {A Bartlett type correction for Rao{\textquoteright}s score test in Cox regression model}, journal = {Sankhy\=a: The Indian Journal of Statistics}, year = {2005}, pages = {722{\textendash}735}, publisher = {JSTOR}, author = {Tu, Dongsheng and Chen, Jiahua and Shi, Peide and Wu, Yaohua} } @article {pmid15486338, title = {Clinical usefulness of home oximetry compared with polysomnography for assessment of sleep apnea}, journal = {Am. J. Respir. Crit. Care Med.}, volume = {171}, number = {2}, year = {2005}, month = {Jan}, pages = {188{\textendash}193}, author = {Whitelaw, W. A. and Brant, R. F. and Flemons, W. W.} } @conference {1825951, title = {Collaboration support for novice team programming}, booktitle = {International Conference on Supporting Group Work}, year = {2005}, pages = {136{\textendash}139}, doi = {10.1145/1099203.1099229}, author = {Davor Cubranic and Margaret-anne D. Storey} } @article {Hanson2005, title = {Comment on {\textquoteleft}On model expansion, model contraction, identifiability and prior information: Two illustrative scenarios involving mismeasured variables,{\textquoteright} by Gustafson}, journal = {Statistical Science}, volume = {20}, year = {2005}, pages = {131-134}, author = {Hanson, T. and Johnson, W.} } @article { ISI:000232749700003, title = {Composite likelihood estimation in multivariate data analysis}, journal = {Canadian Journal of Statistics {\textendash}- Revue Canadienne de Statistique}, volume = {33}, number = {3}, year = {2005}, note = {International Conference on Dependence Modelling - Statistical Theory and Applications in Finance and Insurance (DeMoSTAFI), Quebec City, CANADA, MAY 20-22, 2004}, month = {SEP}, pages = {335-356}, abstract = {The authors propose two composite likelihood estimation procedures for multivariate models with regression/univariate and dependence parameters. One is a two-stage method based on both univariate and bivariate margins. The other estimates all the parameters simultaneously based on bivariate margins. For some special cases, the authors compare their asymptotic efficiencies with the maximum likelihood method. The performance of the two methods is reasonable, except that the first procedure is inefficient for the regression parameters under strong dependence. The second approach is generally better for the regression parameters, but less efficient for the dependence parameters under weak dependence.}, issn = {0319-5724}, doi = {10.1002/cjs.5540330303}, author = {Zhao, Y and Joe, H} } @article { ISI:000232133200005, title = {Computations for the familial analysis of binary traits}, journal = {Computational Statistics}, volume = {20}, number = {3}, year = {2005}, pages = {439-448}, abstract = {

For familial aggregation of a binary trait, one method that has been used is the GEE2 (generalized estimating equation) method corresponding to a multivariate logit model. We solve the complex estimating equations for the GEE2 method using an automatic differentiation software which computes the derivatives of a function numerically using the chain rule of the calculus repeatedly on the elementary operations of the function. Based on this, we are able to show in a simulation study that the GEE2 estimates are quite close to the maximum likelihood estimates assuming a multivariate logit model, and that the GEE2 method is computationally faster when the dimension or family size is larger than four.

}, issn = {0943-4062}, doi = {10.1007/BF02741307}, author = {Joe, H and Latif, A H M M} } @conference {regier2005data, title = {Data mining in end-of-life care research: a case study using a novel methodology}, booktitle = {JOURNAL OF PALLIATIVE CARE}, volume = {21}, number = {3}, year = {2005}, pages = {215{\textendash}215}, publisher = {CENTER BIOETHICS CLIN RES INST MONTREAL 110 PINE AVE W, MONTREAL, QUEBEC H2W 1R7, CANADA}, organization = {CENTER BIOETHICS CLIN RES INST MONTREAL 110 PINE AVE W, MONTREAL, QUEBEC H2W 1R7, CANADA}, author = {Regier, M and Barroetavena, MC and Zamer, R} } @article {wang2005derivation, title = {Derivation of mixture distributions and weighted likelihood function as minimizers of KL-divergence subject to constraints}, journal = {Annals of the Institute of Statistical Mathematics}, volume = {57}, number = {4}, year = {2005}, pages = {687{\textendash}701}, publisher = {Springer}, author = {Wang, Xiaogang and Zidek, James V} } @book {1824116, title = {The Emergent Structure of Development Tasks}, series = {European Conference on Object-Oriented Programming}, year = {2005}, pages = {33{\textendash}48}, doi = {10.1007/11531142_2}, author = {Gail C. Murphy and Mik Kersten and Martin P. Robillard and Davor Cubranic} } @article { ISI:000225197800015, title = {Estimating the p-values of robust tests for the linear model}, journal = {JOURNAL OF STATISTICAL PLANNING AND INFERENCE}, volume = {128}, number = {1}, year = {2005}, month = {JAN 15}, pages = {241-257}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {In this paper, we study the estimation of p-values for robust tests for the linear regression model. The asymptotic distribution of these tests has only been studied under the restrictive assumption of errors with known scale Or symmetric distribution. Since these robust tests are based on robust regression estimates, Efron{\textquoteright}s bootstrap (1979) presents a number of problems. In particular, it is computationally very expensive, and it is not resistant to outliers in the data. In other words, the tails of the bootstrap distribution estimates obtained by re-sampling the data may be severely affected by outliers. We show how to adapt the Robust Bootstrap (Ann. Statist 30 (2002) 556; Bootstrapping MM-estimators for linear regression with fixed designs, http://mathstat.carleton.ca/similar tomatias/pubs. html) to this problem. This method is very fast to compute, resistant to outliers in the data, and asymptotically correct under weak regularity assumptions. In this paper, we show that the Robust Bootstrap can be used to obtain asymptotically correct, computationally simple p-value estimates. A simulation study indicates that the tests whose p-values are estimated with the Robust Bootstrap have better finite sample significance levels than those obtained from the asymptotic theory based on the symmetry assumption. Although this paper is focussed on robust scores-type tests (in: Directions in Robust Statistics and Diagnostics, Part 1, Springer, New York), our approach can be applied to other robust tests (for example, Wald- and dispersion-type also discussed in Markatou et a]., 1991). (C) 2003 Elsevier B.V. All rights reserved.}, keywords = {bootstrap, Robust inference, Robust regression, scores test, Wald test}, issn = {0378-3758}, doi = {10.1016/j.jspi.2003.09.033}, author = {Salibian-Barrera, M} } @article {clayton2005evaluation, title = {Evaluation of asymptotic approximations for a two-stage Bernoulli bandit}, journal = {Journal of Statistical Planning and Inference}, volume = {130}, number = {1}, year = {2005}, pages = {133{\textendash}148}, publisher = {Elsevier}, author = {Clayton, Murray K and Petkau, A.John} } @article {pmid16299586, title = {Evidence of a large novel gene pool associated with prokaryotic genomic islands}, journal = {PLoS Genet.}, volume = {1}, number = {5}, year = {2005}, month = {Nov}, pages = {e62}, abstract = {Microbial genes that are "novel" (no detectable homologs in other species) have become of increasing interest as environmental sampling suggests that there are many more such novel genes in yet-to-be-cultured microorganisms. By analyzing known microbial genomic islands and prophages, we developed criteria for systematic identification of putative genomic islands (clusters of genes of probable horizontal origin in a prokaryotic genome) in 63 prokaryotic genomes, and then characterized the distribution of novel genes and other features. All but a few of the genomes examined contained significantly higher proportions of novel genes in their predicted genomic islands compared with the rest of their genome (Paired t test = 4.43E-14 to 1.27E-18, depending on method). Moreover, the reverse observation (i.e., higher proportions of novel genes outside of islands) never reached statistical significance in any organism examined. We show that this higher proportion of novel genes in predicted genomic islands is not due to less accurate gene prediction in genomic island regions, but likely reflects a genuine increase in novel genes in these regions for both bacteria and archaea. This represents the first comprehensive analysis of novel genes in prokaryotic genomic islands and provides clues regarding the origin of novel genes. Our collective results imply that there are different gene pools associated with recently horizontally transmitted genomic regions versus regions that are primarily vertically inherited. Moreover, there are more novel genes within the gene pool associated with genomic islands. Since genomic islands are frequently associated with a particular microbial adaptation, such as antibiotic resistance, pathogen virulence, or metal resistance, this suggests that microbes may have access to a larger "arsenal" of novel genes for adaptation than previously thought.}, author = {Hsiao, W. W. and Ung, K. and Aeschliman, D. and Bryan, J. and Finlay, B. B. and Brinkman, F. S.} } @article {GuKa2005statmed, title = {Extending logistic regression to model diffuse interactions}, journal = {Statistics in Medicine}, volume = {24}, year = {2005}, pages = {2089-2104}, doi = {10.1002/sim.2093}, author = {Gustafson, P. and Kazi, A. M. R. and Levy, A. R.} } @article {39220579, title = {A framework for describing and understanding mining tools in software development}, journal = {ACM Sigsoft Software Engineering Notes}, year = {2005}, pages = {1{\textendash}5}, doi = {10.1145/1082983.1083160}, author = {Daniel M. German and Davor Cubranic and Margaret-anne D. Storey} } @article {2206148, title = {A framework for describing and understanding mining tools in software development}, journal = {ACM Sigsoft Software Engineering Notes}, volume = {30}, year = {2005}, pages = {1{\textendash}5}, doi = {10.1145/1083142.1083160}, author = {Daniel M. German and Davor Cubranic and Margaret-anne D. Storey} } @article { ISI:000228796400015, title = {Generalized Poisson distribution: the property of mixture of Poisson and comparison with negative binomial distribution}, journal = {Biometrical Journal}, volume = {47}, number = {2}, year = {2005}, month = {APR}, pages = {219-229}, abstract = {We prove that the generalized Poisson distribution GP(theta, eta) (eta >= 0) is a mixture of Poisson distributions; this is a new property for a distribution which is the topic of the book by Consul (1989). Because we find that the fits to count data of the generalized Poisson and negative binomial distributions are often similar, to understand their differences, we compare the probability mass functions and skewnesses of the generalized Poisson and negative binomial distributions with the first two moments fixed. They have slight differences in many situations, but their zero-inflated distributions, with masses at zero, means and variances fixed, can differ more. These probabilistic comparisons are helpful in selecting a better fitting distribution for modelling count data with long right tails. Through a real example of count data with large zero fraction, we illustrate how the generalized Poisson and negative binomial distributions as well as their zero-inflated distributions can be discriminated.}, issn = {0323-3847}, doi = {10.1002/bimj.200410102}, author = {Joe, H and Zhu, R} } @article {1420161, title = {Hipikat: A Project Memory for Software Development}, journal = {IEEE Transactions on Software Engineering}, volume = {31}, year = {2005}, pages = {446{\textendash}465}, doi = {10.1109/TSE.2005.71}, author = {Davor Cubranic and Gail C. Murphy and Janice Singer and Kellogg S. Booth} } @article {Gustafson2005c, title = {Innovative Bayesian methods for biostatistics and epidemiology}, journal = {Handbook of Statistics}, volume = {25}, year = {2005}, pages = {763{\textendash}792}, publisher = {Elsevier}, doi = {10.1016/s0169-7161(05)25026-5}, author = {Gustafson, Paul and Hossain, Shahadut and McCandless, Lawrence} } @article {pmid16100643, title = {Laparoscopy and reported pain among patients with endometriosis}, journal = {J Obstet Gynaecol Can}, volume = {27}, number = {5}, year = {2005}, month = {May}, pages = {477{\textendash}485}, author = {Jarrell, J. and Mohindra, R. and Ross, S. and Taenzer, P. and Brant, R.} } @article { ISI:000233311400030, title = {Limited- and full-information estimation and goodness-of-fit testing in $2^n$ contingency tables: A unified framework}, journal = {Journal of the American Statistical Association}, volume = {100}, number = {471}, year = {2005}, month = {SEP}, pages = {1009-1020}, abstract = {High-dimensional contingency tables tend to be sparse, and standard goodness-of-fit statistics such as X-2 cannot be used without pooling categories. As an improvement on arbitrary pooling, for goodness of fit of large 2(n) contingency tables, we propose classes of quadratic form statistics based on the residuals of margins or multivariate moments up to order r. These classes of test statistics are asymptotically chi-squared distributed under the null hypothesis. Further, the marginal residuals are useful for diagnosing lack of fit of parametric models. We show that when r is small (r = 2, 3), the proposed statistics have better small-sample properties and are asymptotically more powerful than X-2 for some useful multivariate binary models. Related to these test statistics is a class of limited-information estimators based on low-dimensional margins. We show that these estimators have high efficiency for one commonly used latent trait model for binary data.}, issn = {0162-1459}, doi = {10.1198/016214504000002069}, author = {Maydeu-Olivares, A and Joe, H} } @article { ISI:000230235800002, title = {The location of constitutional neurofibromatosis 2 (NF2) splice site mutations is associated with the severity of NF2}, journal = {Journal of Medical Genetics}, volume = {42}, number = {7}, year = {2005}, month = {JUL}, pages = {540-546}, abstract = {Neurofibromatosis 2 ( NF2) patients with constitutional splice site NF2 mutations have greater variability in disease severity than NF2 patients with other types of mutations; the cause of this variability is unknown. We evaluated genotype-phenotype correlations, with particular focus on the location of splice site mutations, using mutation and clinical information on 831 patients from 528 NF2 families with identified constitutional NF2 mutations. The clinical characteristics examined were age at onset of symptoms of NF2 and number of intracranial meningiomas, which are the primary indices of the severity of NF2. Two regression models were used to analyse genotype-phenotype correlations. People with splice site mutations in exons 1 - 5 had more severe disease than those with splice site mutations in exons 11 - 15. This result is compatible with studies showing that exons 2 and 3 are required for self-association of the amino terminal of the NF2 protein in vitro, and that deletions of exons 2 and 3 in transgenic and knockout mouse models of NF2 cause a high prevalence of Schwann cell derived tumours.}, issn = {0022-2593}, doi = {10.1136/jmg.2004.029504}, author = {Baser, M E and Kuramoto, L and Woods, R and Joe, H and Friedman, J M and Wallace, A J and Ramsden, R T and Olschwang, S and Bijlsma, E and Kalamarides, M and Papi, L and Kato, R and Carroll, J and Lazaro, C and Joncourt, F and Parry, D M and Rouleau, G A and Evans, D G R} } @article {gu2005statsci, title = {On model expansion, model contraction, identifiability, and prior information: two illustrative scenarios involving mismeasured variables (with discussion)}, journal = {Statistical Science}, volume = {20}, year = {2005}, pages = {111-140}, author = {Gustafson, P.} } @article {chen2005modified, title = {Modified likelihood ratio test in finite mixture models with a structural parameter}, journal = {Journal of statistical Planning and Inference}, volume = {129}, number = {1}, year = {2005}, pages = {93{\textendash}107}, publisher = {North-Holland}, author = {Chen, Jiahua and Kalbfleisch, John D} } @booklet {van2005multi, title = {Multi-agent predictors of an exponential interevent time}, number = {215}, year = {2005}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {van Eeden, Constance and Zidek, James V} } @article {barkhof2005predicting, title = {Predicting gadolinium enhancement status in MS patients eligible for randomized clinical trials}, journal = {Neurology}, volume = {65}, number = {9}, year = {2005}, pages = {1447{\textendash}1454}, publisher = {AAN Enterprises}, author = {Barkhof, F and Held, U and Simon, JH and Daumer, M and Fazekas, F and Filippi, M and Frank, JA and Kappos, L and Li, D and Menzler, S and Miller, DH and Petkau, J and Wolinsky, J} } @article {pmid15866245, title = {Quantitative assessment of thrombus burden predicts the outcome of treatment for venous thrombosis: a systematic review}, journal = {Am. J. Med.}, volume = {118}, number = {5}, year = {2005}, month = {May}, pages = {456{\textendash}464}, author = {Hull, R. D. and Marder, V. J. and Mah, A. F. and Biel, R. K. and Brant, R. F.} } @article {shaddick2005results, title = {Results of using a probabilistic model to estimate personal exposure to air pollution on a study of the short term effect of PM10 on mortality.}, journal = {Epidemiology}, volume = {16}, number = {5}, year = {2005}, pages = {S90}, publisher = {LWW}, author = {Shaddick, G and Zidek, J and White, R and Meloche, J and Chatfield, C} } @article {wang2005selecting, title = {Selecting likelihood weights by cross-validation}, journal = {The Annals of Statistics}, volume = {33}, number = {2}, year = {2005}, pages = {463{\textendash}500}, publisher = {Institute of Mathematical Statistics}, author = {Wang, Xiaogang and Zidek, James V.} } @proceedings {12906828, title = {Teaching Requirements Engineering in Global Software Development: A report on a three-University collaboration}, journal = {Workshop on Requirements Engineering Education and Training}, year = {2005}, month = {08/2005}, pages = {685-690}, address = {Paris}, url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.88.6786\&rep=rep1\&type=pdf}, author = {Daniela Damian and Ban Al-Ani and Davor Cubranic and Lizveth Robles} } @article {brunham2005unexpected, title = {The unexpected impact of a Chlamydia trachomatis infection control program on susceptibility to reinfection}, journal = {Journal of Infectious Diseases}, volume = {192}, number = {10}, year = {2005}, pages = {1836{\textendash}1844}, publisher = {Oxford University Press}, author = {Brunham, Robert C and Pourbohloul, Babak and Mak, Sunny and White, Rick and Rekart, Michael L} } @article {feng2005universal, title = {The universal validity of the possible triangle constraint for affected sib pairs}, journal = {Canadian Journal of Statistics}, volume = {33}, number = {2}, year = {2005}, pages = {297{\textendash}310}, publisher = {Wiley Online Library}, author = {Feng, Zeny Z and Chen, Jiahua and Thompson, Mary E} } @conference {1846424, title = {On the use of visualization to support awareness of human activities in software development: a survey and a framework}, booktitle = {Software Visualization}, year = {2005}, pages = {193{\textendash}202}, doi = {10.1145/1056018.1056045}, author = {Margaret-anne D. Storey and Davor Cubranic and Daniel M. German} } @article {zidek2005using, title = {Using a probabilistic model (pCNEM) to estimate personal exposure to air pollution}, journal = {Environmetrics}, volume = {16}, number = {5}, year = {2005}, pages = {481{\textendash}493}, publisher = {Wiley Online Library}, author = {Zidek, James V and Shaddick, Gavin and White, Rick and Meloche, Jean and Chatfield, Chris} } @article {zidek2005using, title = {Using a probabilistic model (pCNEM) to estimate personal exposure to air pollution}, journal = {Environmetrics}, volume = {16}, number = {5}, year = {2005}, pages = {481{\textendash}493}, publisher = {Wiley Online Library}, author = {Zidek, James V and Shaddick, Gavin and White, Rick and Meloche, Jean and Chatfield, Chris} } @article {gu2005statmed, title = {The utility of prior information and stratification for parameter estimation with two screening tests but no gold standard}, journal = {Statistics in Medicine}, volume = {24}, year = {2005}, pages = {1203-1217}, doi = {10.1002/sim.2002}, author = {Gustafson, P.} } @article {vedal2004air, title = {Air pollution and cardiac arrhythmias in patients with implantable cardioverter defibrillators}, journal = {Inhalation toxicology}, volume = {16}, number = {6-7}, year = {2004}, pages = {353{\textendash}362}, publisher = {Taylor \& Francis}, author = {Vedal, Sverre and Rich, Kira and Brauer, Michael and White, Rick and Petkau, John} } @article {vedal2004air, title = {Air pollution and cardiac arrhythmias in patients with implantable cardioverter defibrillators}, journal = {Inhalation Toxicology}, volume = {16}, number = {6-7}, year = {2004}, pages = {353{\textendash}362}, publisher = {Taylor \& Francis}, author = {Vedal, Sverre and Rich, Kira and Brauer, Michael and White, Rick and Petkau, John} } @article {pmid15208200, title = {Analysis of longitudinal marginal structural models}, journal = {Biostatistics}, volume = {5}, number = {3}, year = {2004}, month = {Jul}, pages = {361{\textendash}380}, abstract = {In this article we construct and study estimators of the causal effect of a time-dependent treatment on survival in longitudinal studies. We employ a particular marginal structural model (MSM), proposed by Robins (2000), and follow a general methodology for constructing estimating functions in censored data models. The inverse probability of treatment weighted (IPTW) estimator of Robins et al. (2000) is used as an initial estimator and forms the basis for an improved, one-step estimator that is consistent and asymptotically linear when the treatment mechanism is consistently estimated. We extend these methods to handle informative censoring. The proposed methodology is employed to estimate the causal effect of exercise on mortality in a longitudinal study of seniors in Sonoma County. A simulation study demonstrates the bias of naive estimators in the presence of time-dependent confounders and also shows the efficiency gain of the IPTW estimator, even in the absence such confounding. The efficiency gain of the improved, one-step estimator is demonstrated through simulation.}, author = {Bryan, J. and Yu, Z. and Van Der Laan, M. J.} } @article { ISI:000220007800007, title = {Analysis of neurofibromatosis 1 (NF1) lesions by body segment}, journal = {American Journal of Medical Genetics Part A}, volume = {125A}, number = {2}, year = {2004}, month = {MAR 1}, pages = {157-161}, abstract = {

Cafe-au-lait spots and neurofibromas are defining features of neurofibromatosis 1 (NF1), but they vary greatly in number, size, and clinical importance from patient to patient. The cause of this variability is unknown. We tested the hypotheses that development of these lesions is influenced by local or familial factors. The presence or absence of cafe-au-lait spots, cutaneous neurofibromas, and diffuse plexiform neurofibromas was recorded for each of 10 divisions of the body surface in 547 NF1 patients, including 117 affected individuals in 52 families. We used stratified Mantel-Haenszel tests to look for local associations between the presence of diffuse plexiform neurofibromas, cutaneous neurofibromas, and cafe-au-lait spots in individual body segments of NF1 patients. We used a random effects model to obtain intrafamilial correlation coefficients for the age-adjusted number of body divisions affected with each of the three lesions. No significant association was observed between the occurrence of cutaneous and diffuse plexiform neurofibromas, between cafe-au-lait spots and cutaneous neurofibromas, or between cafe-au-lait spots and plexiform neurofibromas in the same body segment. The correlation among relatives in the number of body segments affected with cafe-au-lait spots was 0.45 (95\% confidence interval [CI] = 0.18-0.71), with cutaneous neurofibromas, 0.37 (95\% CI = 0.15-0.55), and with plexiform neurofibromas, 0.35 (95\% CI = 0.15-0.57). We conclude that the development of cafe-au-lait spots, cutaneous neurofibromas, and plexiform neurofibromas are spatially independent in NF1 patients but that the development of all three lesions is influenced by familial factors. (C) 2003 Wiley-Liss, Inc.

}, issn = {1552-4825}, doi = {10.1002/ajmg.a.20354}, author = {Palmer, C and Szudek, J and Joe, H and Riccardi, V M and Friedman, J M} } @article {pmid15215429, title = {ArrayPipe: a flexible processing pipeline for microarray data}, journal = {Nucleic Acids Res.}, volume = {32}, number = {Web Server issue}, year = {2004}, month = {Jul}, pages = {W457{\textendash}459}, abstract = {A number of microarray analysis software packages exist already; however, none combines the user-friendly features of a web-based interface with potential ability to analyse multiple arrays at once using flexible analysis steps. The ArrayPipe web server (freely available at www.pathogenomics.ca/arraypipe) allows the automated application of complex analyses to microarray data which can range from single slides to large data sets including replicates and dye-swaps. It handles output from most commonly used quantification software packages for dual-labelled arrays. Application features range from quality assessment of slides through various data visualizations to multi-step analyses including normalization, detection of differentially expressed genes, andcomparison and highlighting of gene lists. A highly customizable action set-up facilitates unrestricted arrangement of functions, which can be stored as action profiles. A unique combination of web-based and command-line functionality enables comfortable configuration of processes that can be repeatedly applied to large data sets in high throughput. The output consists of reports formatted as standard web pages and tab-delimited lists of calculated values that can be inserted into other analysis programs. Additional features, such as web-based spreadsheet functionality, auto-parallelization and password protection make this a powerful tool in microarray research for individuals and large groups alike.}, author = {Hokamp, K. and Roche, F. M. and Acab, M. and Rousseau, M. E. and Kuo, B. and Goode, D. and Aeschliman, D. and Bryan, J. and Babiuk, L. A. and Hancock, R. E. and Brinkman, F. S.} } @article {wang2004asymptotic, title = {Asymptotic properties of maximum weighted likelihood estimators}, journal = {Journal of Statistical Planning and Inference}, volume = {119}, number = {1}, year = {2004}, pages = {37{\textendash}54}, publisher = {Elsevier}, author = {Wang, Xiaogang and van Eeden, Constance and Zidek, James V} } @conference {1814517, title = {Automatic bug triage using text categorization}, booktitle = {Software Engineering and Knowledge Engineering}, year = {2004}, pages = {92{\textendash}97}, author = {Davor Cubranic and Gail C. Murphy} } @booklet {kondo2004university, title = {Bayesian nonparametric subset selection procedures with Weibull components}, number = {273}, year = {2004}, publisher = {Department of Statistics, University of British Columbia.}, address = {Vancouver, BC}, author = {Kondo, Yumi and Zidek, James V.} } @article {adrover2004bias, title = {Bias robustness of three median-based regression estimates}, journal = {Journal of statistical planning and inference}, volume = {122}, number = {1}, year = {2004}, pages = {203{\textendash}227}, publisher = {Elsevier}, author = {Adrover, Jorge and Zamar, Ruben H} } @article {rich2004case, title = {A case-crossover analysis of particulate air pollution and cardiac arrhythmia in patients with implantable cardioverter defibrillators}, journal = {Inhalation Toxicology}, volume = {16}, number = {6-7}, year = {2004}, pages = {363{\textendash}372}, publisher = {Taylor \& Francis}, author = {Rich, Kira E and Petkau, John and Vedal, Sverre and Brauer, Michael} } @article {van2004combining, title = {Combining the data from two normal populations to estimate the mean of one when their means difference is bounded}, journal = {Journal of Multivariate Analysis}, volume = {88}, number = {1}, year = {2004}, pages = {19{\textendash}46}, publisher = {Elsevier}, author = {van Eeden, Constance and Zidek, James V} } @inbook {lam_comparison_2004, title = {Comparison of methods based on diversity and similarity for molecule selection and the analysis of drug discovery data}, booktitle = {Chemoinformatics}, year = {2004}, pages = {301{\textendash}315}, publisher = {Springer}, organization = {Springer}, url = {http://link.springer.com/protocol/10.1385/1-59259-802-1:301}, author = {Lam, Raymond LH and Welch, William J.} } @article {pmid15096330, title = {D-dimer for the exclusion of acute venous thrombosis and pulmonary embolism: a systematic review}, journal = {Ann. Intern. Med.}, volume = {140}, number = {8}, year = {2004}, month = {Apr}, pages = {589{\textendash}602}, author = {Stein, P. D. and Hull, R. D. and Patel, K. C. and Olson, R. E. and Ghali, W. A. and Brant, R. and Biel, R. K. and Bharadia, V. and Kalra, N. K.} } @article {gustafson2004decomposing, title = {Decomposing posterior variance}, journal = {Journal of statistical planning and inference}, volume = {119}, number = {2}, year = {2004}, pages = {311{\textendash}327}, publisher = {Elsevier}, doi = {10.1016/s0378-3758(02)00491-3}, author = {Gustafson, P. and Clarke, B.} } @article {park2004detection, title = {The Detection and Testing of Multiple Outliers in Linear Regression}, journal = {Journal of the Korean Data and Information Science Society}, volume = {15}, number = {4}, year = {2004}, pages = {921{\textendash}934}, publisher = {Korean Data and Information Science Society}, author = {Park, Jin-Pyo and Zamar, Ruben H} } @article {pmid15453909, title = {Effect of time of administration on cholesterol-lowering by psyllium: a randomized cross-over study in normocholesterolemic or slightly hypercholesterolemic subjects}, journal = {Nutr J}, volume = {3}, year = {2004}, month = {Sep}, pages = {17}, author = {Van Rosendaal, G. M. and Shaffer, E. A. and Edwards, A. L. and Brant, R.} } @article { ISI:000224444900003, title = {Efficiency of generalized estimating equations for binary responses}, journal = {Journal of the Royal Statistical Society Series B {\textendash}- Statistical Methodology}, volume = {66}, number = {Part 4}, year = {2004}, pages = {851-860}, abstract = {

Using standard correlation bounds, we show that in generalized estimation equations (GEEs) the so-called {\textquoteleft}working correlation matrix{\textquoteright}R(alpha) for analysing binary data cannot in general be the true correlation matrix of the data. Methods for estimating the correlation param-eter in current GEE software for binary responses disregard these bounds. To show that the GEE applied on binary data has high efficiency, we use a multivariate binary model so that the covariance matrix from estimating equation theory can be compared with the inverse Fisher information matrix. But R(alpha) should be viewed as the weight matrix, and it should not be confused with the correlation matrix of the binary responses. We also do a comparison with more general weighted estimating equations by using a matrix Cauchy-Schwarz inequality. Our analysis leads to simple rules for the choice of alpha in an exchangeable or autoregressive AR(1) weight matrix R(alpha), based on the strength of dependence between the binary variables. An example is given to illustrate the assessment of dependence and choice of alpha.

}, issn = {1369-7412}, doi = {10.1111/j.1467-9868.2004.05741.x}, author = {Chaganty, N R and Joe, H} } @article {MacNab2004, title = {Estimation in Bayesian disease mapping}, journal = {Biometrics}, volume = {60}, number = {4}, year = {2004}, pages = {865{\textendash}873}, publisher = {Wiley Online Library}, doi = {10.1111/j.0006-341x.2004.00241.x}, author = {MacNab, Ying C and Farrell, Patrick J and Gustafson, Paul and Wen, Sijin} } @article {chen2004estimation, title = {Estimation of fish abundance indices based on scientific research trawl surveys}, journal = {Biometrics}, volume = {60}, number = {1}, year = {2004}, pages = {116{\textendash}123}, publisher = {Wiley Online Library}, author = {Chen, Jiahua and Thompson, Mary E and Wu, Changbao} } @article {wu_exact_2004, title = {Exact and Approximate Inferences for Nonlinear Mixed-Effects Models With Missing Covariates}, journal = {Journal of the American Statistical Association}, volume = {99}, number = {467}, year = {2004}, month = {sep}, pages = {700{\textendash}709}, abstract = {Nonlinear mixed-effects (NLME) models are popular in many longitudinal studies, including human immunodeficiency virus (HIV) viral dynamics, pharmacokinetic analyses, and studies of growth and decay. In practice, covariates in these studies often contain missing data, and so standard complete-data methods are not directly applicable. In this article we propose Monte Carlo parameter-expanded (PX)-EM algorithms for exact and approximate likelihood inferences for NLME models with missing covariates when the missing-data mechanism is ignorable. We allow arbitrary missing-data patterns and allow the covariates to be categorical, continuous, and mixed. The PX-EM algorithm maintains the simplicity and stability of the standard EM algorithm and may converge much faster than EM. The approximate method is computationally more efficient and may be preferable to the exact method when the exact method exhibits convergence problems, such as slow convergence or nonconvergence. It becomes an exact method for linear mixed-effects models and certain NLME models with missing covariates. We also discuss several sampling methods and convergence of the Monte Carlo (PX) EM algorithms. We illustrate the methods using a real data example from the study of HIV viral dynamics and compare the methods via a simulation study.}, issn = {0162-1459}, doi = {10.1198/016214504000001006}, url = {http://dx.doi.org/10.1198/016214504000001006}, author = {WU, LANG} } @mastersthesis {zhang2004extracting, title = {Extracting XML data from HTML repositories}, year = {2004}, school = {The University of British Columbia}, type = {phd}, author = {Zhang, Ruth Yuee} } @article {hu2004forecasting, title = {Forecasting NBA basketball playoff outcomes using the weighted likelihood}, journal = {Lecture Notes-Monograph Series}, year = {2004}, pages = {385{\textendash}395}, author = {Hu, F.eifang and Zidek, James V} } @article { ISI:000222702000007, title = {Genotype-phenotype correlations for nervous system tumors in neurofibromatosis 2: A population-based study}, journal = {American Journal of Human Genetics}, volume = {75}, number = {2}, year = {2004}, month = {AUG}, pages = {231-239}, abstract = {Neurofibromatosis 2 (NF2) is an autosomal dominant disease that is characterized by tumors on the vestibular branch of the VIII cranial nerve, but other types of nervous system tumors usually occur as well. Genotype-phenotype correlations are well documented for overall NF2 disease severity but have not been definitively evaluated for specific types of non - VIII nerve tumors. We evaluated genotype-phenotype correlations for various types of non - VIII nerve tumors in 406 patients from the population-based United Kingdom NF2 registry, using regression models with the additional covariates of current age and type of treatment center (specialty or nonspecialty). The models also permitted consideration of intrafamilial correlation. We found statistically significant genotype-phenotype correlations for intracranial meningiomas, spinal tumors, and peripheral nerve tumors. People with constitutional NF2 missense mutations, splice-site mutations, large deletions, or somatic mosaicism had significantly fewer tumors than did people with constitutional nonsense or frameshift NF2 mutations. In addition, there were significant intrafamilial correlations for intracranial meningiomas and spinal tumors, after adjustment for the type of constitutional NF2 mutation. The type of constitutional NF2 mutation is an important determinant of the number of NF2-associated intracranial meningiomas, spinal tumors, and peripheral nerve tumors.}, issn = {0002-9297}, doi = {10.1086/422700}, author = {Baser, ME and Kuramoto, L and Joe, H and Friedman, JM and Wallace, AJ and Gillespie, JE and Ramsden, RT and Evans, DGR} } @article { ISI:000186911900009, title = {Globally robust inference for the location and simple linear regression models}, journal = {JOURNAL OF STATISTICAL PLANNING AND INFERENCE}, volume = {119}, number = {2}, year = {2004}, month = {FEB 1}, pages = {353-375}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {We define globally robust confidence intervals and p-values for the location and simple linear regression models. The need for robust inference has been noticed and partially addressed in the statistical literature (see for example the book by Barnett and Lewis, Outliers in Statistical Data, Wiley, New York, 1994 and references therein). We construct intervals that are stable in the sense of achieving coverages near the nominal ones even in the presence of outliers and other departures from the parametric model. Moreover, our intervals are informative in the sense of having relatively short lengths. These globally robust confidence intervals constitute an improvement over previous robust intervals which do not take into account the potential bias of the estimates. (C) 2002 Elsevier B.V. All rights reserved.}, keywords = {linear regerssion, maximum bias, robust confidence intervals, robust interference, Robustness}, issn = {0378-3758}, doi = {10.1016/S0378-3758(02)00490-1}, author = {Adrover, J and Salibian-Barrera, M and Zamar, R} } @article {adrover2004globally, title = {Globally robust inference for the location and simple linear regression models}, journal = {Journal of statistical planning and inference}, volume = {119}, number = {2}, year = {2004}, pages = {353{\textendash}375}, publisher = {Elsevier}, author = {Adrover, Jorge and Salibian-Barrera, Mat{\'\i}as and Zamar, Ruben} } @article {pmid15494780, title = {Health-related quality of life outcomes of patients with coronary artery disease treated with cardiac surgery, percutaneous coronary intervention or medical management}, journal = {Can J Cardiol}, volume = {20}, number = {12}, year = {2004}, month = {Oct}, pages = {1259{\textendash}1266}, author = {Norris, C. M. and Saunders, L. D. and Ghali, W. A. and Brant, R. and Galbraith, P. D. and Graham, M. and Faris, P. and Dzavik, V. and Knudtson, M. L.} } @article {MacNab2004a, title = {Hierarchical Bayes analysis of multilevel health services data: a Canadian neonatal mortality study}, journal = {Health Services and Outcomes Research Methodology}, volume = {5}, number = {1}, year = {2004}, pages = {5{\textendash}26}, publisher = {Springer}, doi = {10.1007/s10742-005-5561-1}, author = {MacNab, Ying C and Qiu, Zhenguo and Gustafson, Paul and Dean, Charmaine B and Ohlsson, Arne and Lee, Shoo K} } @conference {1787923, title = {Learning from project history: a case study for software development}, booktitle = {Conference on Computer Supported Cooperative Work}, year = {2004}, pages = {82{\textendash}91}, doi = {10.1145/1031607.1031622}, author = {Davor Cubranic and Gail C. Murphy and Janice Singer and Kellogg S. Booth} } @article {9517, title = {Longitudinal analyses of the effects of neutralizing antibodies on interferon beta-1b in relapsing/remitting multiple sclerosis}, journal = {Multiple Sclerosis}, volume = {10}, year = {2004}, pages = {715}, type = {Letter}, author = {Petkau, A.John and Ebers, G.C. and Reder, A.T.} } @article {petkau2004longitudinal, title = {Longitudinal analyses of the effects of neutralizing antibodies on interferon beta-1b in relapsing-remitting multiple sclerosis}, journal = {Multiple Sclerosis}, volume = {10}, number = {2}, year = {2004}, pages = {126{\textendash}138}, publisher = {Sage Publications}, author = {Petkau, A.John and White, Richard A and Ebers, George C and Reder, Anthony T and Sibley, William A and Lublin, Fred D and Paty, Donald W and IFNB Multiple Sclerosis Study Group} } @article {petkau2004longitudinal, title = {Longitudinal analyses of the effects of neutralizing antibodies on interferon beta-1b in relapsing-remitting multiple sclerosis}, journal = {Multiple sclerosis}, volume = {10}, number = {2}, year = {2004}, pages = {126{\textendash}138}, publisher = {Sage Publications}, author = {Petkau, A John and White, Richard A and Ebers, George C and Reder, Anthony T and Sibley, William A and Lublin, Fred D and Paty, Donald W and IFNB Multiple Sclerosis Study Group and others} } @book {gustafson2004, title = {Measurement Error and Misclassification in Statistics and Epidemiology: Impact and Bayesian Adjustments}, year = {2004}, publisher = {Chapman \& Hall, CRC Press}, organization = {Chapman \& Hall, CRC Press}, doi = {10.1198/tech.2004.s239}, author = {Gustafson, P.} } @article {wu_nonlinear_2004, title = {Nonlinear mixed-effect models with nonignorably missing covariates}, journal = {Canadian Journal of Statistics}, volume = {32}, number = {1}, year = {2004}, month = {mar}, pages = {27{\textendash}37}, abstract = {Nonlinear mixed-effect models are often used in the analysis of longitudinal data. However, it sometimes happens that missing values for some of the model covariates are not purely random. Motivated by an application to HTV viral dynamics, where this situation occurs, the author considers likelihood inference for this type of problem. His approach involves a Monte Carlo EM algorithm, along with a Gibbs sampler and rejection/importance sampling methods. A concrete application is provided.}, keywords = {EM algorithm, Gibbs sampling, Longitudinal data, missing data, Rejection sampling}, issn = {1708-945X}, doi = {10.2307/3315997}, url = {http://onlinelibrary.wiley.com/doi/10.2307/3315997/abstract}, author = {WU, LANG} } @article { ISI:000221761700010, title = {Nonparametric testing for a monotone hazard function via normalized spacings}, journal = {JOURNAL OF NONPARAMETRIC STATISTICS}, volume = {16}, number = {3-4, SI}, year = {2004}, note = {International Conference on Recent Advances and Trends in NonParametric Statistics, IRAKLION, GREECE, JUL 15-19, 2002}, month = {JUN-AUG}, pages = {463-477}, publisher = {TAYLOR \& FRANCIS LTD}, type = {Article; Proceedings Paper}, address = {4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND}, abstract = {We study the problem of testing whether a hazard function is monotonic or not. The proposed test statistics, a global test and four localized tests, are all based on normalized spacings. The global test is in fact just the test statistic [Proschan, F. and Pyke, R. (1967). Tests for monotone failure rate. Fifth Berkeley Symposium, 3, 293-313], introduced for testing a constant hazard function versus a nondecreasing nonconstant hazard function. This global test is powerful for detecting global departures of the null hypothesis, but lacks power when there are local departures from the null hypothesis. By localizing the global test, we obtain tests that respond to this drawback. We also show how the testing procedures can be used when dealing with Type II censored data. We evaluate the performance of the test statistics via simulation studies and illustrate them on some data sets.}, keywords = {monotone hazard function, order statistics, spacings, Type II censoring}, issn = {1048-5252}, doi = {10.1080/10485250310001622668}, author = {Gijbels, I and Heckman, N} } @article {perlman_note_2004, title = {A Note on One-Sided Tests with Multiple Endpoints}, journal = {Biometrics}, volume = {60}, number = {1}, year = {2004}, month = {mar}, pages = {276{\textendash}280}, abstract = {Summary.~ Testing problems with multivariate one-sided alternative hypotheses are common in clinical trials with multiple endpoints. In the case of comparing two treatments, treatment 1 is often preferred if it is superior for at least one of the endpoints and not biologically inferior for the remaining endpoints. Bloch et al. (2001, Biometrics57, 1039{\textendash}1047) propose an intersection{\textendash}union test (IUT) for this testing problem, but their test does not utilize the appropriate multivariate one-sided test. In this note we modify their test by an alternative IUT that does utilize the appropriate one-sided test. Empirical and graphical evidence show that the proposed test is more appropriate for this testing problem.}, keywords = {Hotelling{\textquoteright}s T~2, Intersection-union test, Likelihood ratio tests, Multiple endpoints, Multivariate one-sided test}, issn = {1541-0420}, doi = {10.1111/j.0006-341X.2004.00159.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0006-341X.2004.00159.x/abstract}, author = {Perlman, Michael D. and WU, LANG} } @article { ISI:000221387400007, title = {A probabilistic method for detecting multivariate extreme outliers}, journal = {INTERNATIONAL JOURNAL OF NONLINEAR SCIENCES AND NUMERICAL SIMULATION}, volume = {5}, number = {2}, year = {2004}, pages = {157-170}, publisher = {FREUND PUBLISHING HOUSE LTD}, type = {Article}, address = {STE 500, CHESHAM HOUSE, 150 REGENT ST, LONDON W1R 5FA, ENGLAND}, abstract = {Given a data set arising from a series of observations, an outlier is a value that deviates substantially from the natural variability of the data set as to arouse suspicions that it was generated by a different mechanism. We call an observation an extreme outlier if it lies at an abnormal distance from the {\textquoteleft}{\textquoteleft}center{\textquoteright}{\textquoteright} of the data set. We introduce the Monte Carlo SCD algorithm for detecting extreme outliers. The algorithm finds extreme outliers in terms of a subset of the data set called the outer shell. Each iteration of the algorithm is polynomial. This could be reduced by preprocessing the data to reduce its size. This approach has an interesting new feature. It estimates a relative measure of the degree to which a data point on the outer shell is an outlier (its {\textquoteleft}{\textquoteleft}outlierness{\textquoteright}{\textquoteright}). This measure has potential for serendipitous discoveries in data mining where unusual or special behavior is of interest. Other applications include spatial filtering and smoothing in digital image processing. We apply this method to baseball data and identify the ten most exceptional pitchers of the 1998 American League. To illustrate another useful application, we also show that the SCD can be used to reduce the solution time of the D-optimal experimental design problem.}, keywords = {D-optimal design, extreme outliers, Monte Carlo, outlierness, redundancy, semidefinite programming}, issn = {1565-1339}, author = {Jibrin, S and Pressman, IS and Salibian-Barrera, M} } @article {Bryan200444, title = {Problems in gene clustering based on gene expression data}, journal = {Journal of Multivariate Analysis}, volume = {90}, number = {1}, year = {2004}, note = {Special Issue on Multivariate Methods in Genomic Data Analysis}, pages = {44 - 66}, abstract = {In this work, we assess the suitability of cluster analysis for the gene grouping problem confronted with microarray data. Gene clustering is the exercise of grouping genes based on attributes, which are generally the expression levels over a number of conditions or subpopulations. The hope is that similarity with respect to expression is often indicative of similarity with respect to much more fundamental and elusive qualities, such as function. By formally defining the true gene-specific attributes as parameters, such as expected expression across the conditions, we obtain a well-defined gene clustering parameter of interest, which greatly facilitates the statistical treatment of gene clustering. We point out that genome-wide collections of expression trajectories often lack natural clustering structure, prior to ad hoc gene filtering. The gene filters in common use induce a certain circularity to most gene cluster analyses: genes are points in the attribute space, a filter is applied to depopulate certain areas of the space, and then clusters are sought (and often found!) in the {\textquotedblleft}cleaned{\textquotedblright} attribute space. As a result, statistical investigations of cluster number and clustering strength are just as much a study of the stringency and nature of the filter as they are of any biological gene clusters. In the absence of natural clusters, gene clustering may still be a worthwhile exercise in data segmentation. In this context, partitions can be fruitfully encoded in adjacency matrices and the sampling distribution of such matrices can be studied with a variety of bootstrapping techniques.}, keywords = {bootstrap}, issn = {0047-259X}, doi = {http://dx.doi.org/10.1016/j.jmva.2004.02.011}, url = {http://www.sciencedirect.com/science/article/pii/S0047259X04000211}, author = {Jenny Bryan} } @article {2378983, title = {Project History as a Group Memory: Learning From the Past}, year = {2004}, author = {D Cubrani{\textquoteright}c} } @article {pmid15385657, title = {A randomized trial of a single dose of oral dexamethasone for mild croup}, journal = {N. Engl. J. Med.}, volume = {351}, number = {13}, year = {2004}, month = {Sep}, pages = {1306{\textendash}1313}, author = {Bjornson, C. L. and Klassen, T. P. and Williamson, J. and Brant, R. and Mitton, C. and Plint, A. and Bulloch, B. and Evered, L. and Johnson, D. W.} } @article {pmid15294459, title = {Retention of basic science knowledge: a comparison between body system-based and clinical presentation curricula}, journal = {Teach Learn Med}, volume = {16}, number = {2}, year = {2004}, pages = {116{\textendash}122}, author = {Woloschuk, W. and Mandin, H. and Harasym, P. and Lorscheider, F. and Brant, R.} } @article {yohai2004robust, title = {Robust nonparametric inference for the median}, journal = {Annals of statistics}, year = {2004}, pages = {1841{\textendash}1857}, publisher = {JSTOR}, author = {Yohai, V{\'\i}ctor J and Zamar, Ruben H} } @article {wu_simultaneous_2004, title = {Simultaneous inference for longitudinal data with detection limits and covariates measured with errors, with application to AIDS studies}, journal = {Statistics in Medicine}, volume = {23}, number = {11}, year = {2004}, month = {jun}, pages = {1715{\textendash}1731}, abstract = {In AIDS studies such as HIV viral dynamics, statistical inference is often complicated because the viral load measurements may be subject to left censoring due to a detection limit and time-varying covariates such as CD4 counts may be measured with substantial errors. Mixed-effects models are often used to model the response and the covariate processes in these studies. We propose a unified approach which addresses the censoring and measurement errors simultaneously. We estimate the model parameters by a Monte-Carlo EM algorithm via the Gibbs sampler. A simulation study is conducted to compare the proposed method with the usual two-step method and a naive method. We find that the proposed method produces approximately unbiased estimates with more reliable standard errors. A real data set from an AIDS study is analysed using the proposed method. Copyright {\textcopyright} 2004 John Wiley \& Sons, Ltd.}, keywords = {EM algorithm, Gibbs sampler, HIV, mixed-effects model}, issn = {1097-0258}, doi = {10.1002/sim.1748}, url = {http://onlinelibrary.wiley.com/doi/10.1002/sim.1748/abstract}, author = {WU, LANG} } @article {le2004statistical, title = {[Statistical Issues in Studies of the Long-Term Effects of Air Pollution: The Southern California Children{\textquoteright}s Health Study]: Comment}, journal = {Statistical Science}, volume = {19}, number = {3}, year = {2004}, pages = {442{\textendash}443}, author = {Le, Nhu D. and Zidek, James V} } @article {pmid15603606, title = {Successes and challenges in a field-based, multi-method study of home telehealth}, journal = {J Telemed Telecare}, volume = {10 Suppl 1}, year = {2004}, pages = {41{\textendash}44}, author = {Hebert, M. A. and Jansen, J. J. and Brant, R. and Hailey, D. and van der Pol, M.} } @article {pmid15010742, title = {Systematic review of statistical methods used to analyze Seattle Angina Questionnaire scores}, journal = {Can J Cardiol}, volume = {20}, number = {2}, year = {2004}, month = {Feb}, pages = {187{\textendash}193}, author = {Norris, C. M. and Ghali, W. A. and Saunders, L. D. and Brant, R. and Galbraith, P. D.} } @article {chen66kalbfleisch, title = {Testing for a finite mixture model with two components}, journal = {JR Stat. Soc. Ser. B Stat. Methodol}, volume = {66}, number = {95}, year = {2004}, pages = {115}, author = {Chen, Hangfeng and Chen, Jiahua and Kalbfleisch, John D} } @article { ISI:000223519100004, title = {Uniform asymptotics for robust location estimates when the scale is unknown}, journal = {ANNALS OF STATISTICS}, volume = {32}, number = {4}, year = {2004}, month = {AUG}, pages = {1434-1447}, publisher = {INST MATHEMATICAL STATISTICS}, type = {Article}, address = {PO BOX 22718, BEACHWOOD, OH 44122 USA}, abstract = {Most asymptotic results for robust estimates rely on regularity conditions that are difficult to verily in practice. Moreover, these results apply to fixed distribution functions. In the robustness context the distribution of the data remains largely unspecified and hence results that hold uniformly over a set of possible distribution functions are of theoretical and practical interest. Also, it is desirable to be able to determine the size of the set of distribution functions where the uniform properties hold. In this paper we study the problem of obtaining verifiable regularity conditions that suffice to yield uniform consistency and uniform asymptotic normality for location robust estimates when the scale of the errors is unknown. We study M-location estimates calculated with an S-scale and we obtain uniform asymptotic results over contamination neighborhoods. Moreover, we show how to calculate the maximum size of the contamination neighborhoods where these uniform results hold. There is a trade-off between the size of these neighborhoods and the breakdown point of the scale estimate.}, keywords = {M-estimates, Robust inference, robust location and scale models, Robustness}, issn = {0090-5364}, doi = {10.1214/009053604000000544}, author = {Salibian-Barrera, M and Zamar, RH} } @article {salibian2004uniform, title = {Uniform asymptotics for robust location estimates when the scale is unknown}, journal = {Annals of statistics}, year = {2004}, pages = {1434{\textendash}1447}, publisher = {JSTOR}, author = {Salibian-Barrera, Mat{\'\i}as and Zamar, Ruben H} } @article {ghosh2004use, title = {The use of the weighted likelihood in the natural exponential families with quadratic variance}, journal = {Canadian Journal of Statistics}, volume = {32}, number = {2}, year = {2004}, pages = {139{\textendash}157}, publisher = {Wiley Online Library}, author = {Ghosh, Malay and Zidek, James V and Maiti, Tapabrata and White, Rick} } @article {gustafson2004value, title = {On the value of derivative evaluations and random walk suppression in Markov chain Monte Carlo algorithms}, journal = {Statistics and Computing}, volume = {14}, number = {1}, year = {2004}, pages = {23{\textendash}38}, publisher = {Springer}, doi = {10.1023/b:stco.0000009413.87656.ef}, author = {Gustafson, P. and Macnab, Y.C. and Wen, S.} } @article {ghoshweighted, title = {Weighted Likelihoods for the NEF-QVF Family with Application}, journal = {Can Jour Statist}, volume = {32}, year = {2004}, pages = {139-157}, publisher = {Citeseer}, author = {Ghosh, Malay and Zidek, James V and Maiti, Tapabrata and White, Rick and Hall, Snedecor} } @article {pmid15070751, title = {Yeast genome-wide drug-induced haploinsufficiency screen to determine drug mode of action}, journal = {Proc. Natl. Acad. Sci. U.S.A.}, volume = {101}, number = {13}, year = {2004}, month = {Mar}, pages = {4525{\textendash}4530}, abstract = {Methods to systematically test drugs against all possible proteins in a cell are needed to identify the targets underlying their therapeutic action and unwanted effects. Here, we show that a genome-wide drug-induced haploinsufficiency screen by using yeast can reveal drug mode of action in yeast and can be used to predict drug mode of action in human cells. We demonstrate that dihydromotuporamine C, a compound in preclinical development that inhibits angiogenesis and metastasis by an unknown mechanism, targets sphingolipid metabolism. The systematic, unbiased and genome-wide nature of this technique makes it attractive as a general approach to identify cellular pathways affected by drugs.}, author = {Baetz, K. and McHardy, L. and Gable, K. and Tarling, T. and Reberioux, D. and Bryan, J. and Andersen, R. J. and Dunn, T. and Hieter, P. and Roberge, M.} } @article {vedal2003air, title = {Air pollution and daily mortality in a city with low levels of pollution.}, journal = {Environmental health perspectives}, volume = {111}, number = {1}, year = {2003}, pages = {45}, publisher = {National Institute of Environmental Health Science}, author = {Vedal, Sverre and Brauer, Michael and White, Richard and Petkau, John} } @article {vedal2003air, title = {Air pollution and daily mortality in a city with low levels of pollution}, journal = {Environmental Health Perspectives}, volume = {111}, number = {1}, year = {2003}, pages = {45-51}, publisher = {National Institute of Environmental Health Science}, author = {Vedal, Sverre and Brauer, Michael and White, Richard and Petkau, John} } @article {petkau2003air, title = {Air Pollution and Daily Mortality in a City with Low Levels of Pollution}, year = {2003}, author = {Petkau, John and Brauer, Michael and White, Richard and Vedal, Sverre} } @conference {Carbonetto2003, title = {Bayesian feature weighting for unsupervised learning, with application to object recognition}, booktitle = {Artificial Intelligence and Statistics (AI \& Statistics{\textquoteright} 03)}, year = {2003}, publisher = {Society for Artificial Intelligence and Statistics}, organization = {Society for Artificial Intelligence and Statistics}, author = {Carbonetto, Peter and De Freitas, Nando and Gustafson, Paul and Thompson, Natalie} } @article {murphy_bereaved_2003, title = {Bereaved Parents{\textquoteright} Outcomes 4 to 60 Months After Their Children{\textquoteright}s Deaths by Accident, Suicide, or Homicide: A Comparative Study Demonstrating Differences}, journal = {Death Studies}, volume = {27}, number = {1}, year = {2003}, pages = {39{\textendash}61}, abstract = {In this article, the authors revisit a controversial issue in the bereavement field: Does one violent cause of death of a child influence parents{\textquoteright} outcomes more than another? To address this question, we observed 173 parents prospectively 4, 12, 24, and 60 months after their children{\textquoteright}s deaths by accident, suicide, or homicide. Quantitative and qualitative research methods were used to examine the influence of three types of a child{\textquoteright}s violent death and timesince death upon 4 parent outcomes (mental distress, post-tramatic stress disorder [PTSD], acceptance of the child{\textquoteright}s death, and marital satisfaction). The results showed a significant interaction for the bereavement Group 2 Time effect for acceptance of death, a significant main effect for time for all four outcomes, and a significant main effect for group (homicide) for PTSD. Nearly 70\% of the parents reported that it took either 3 or 4 years to put their children{\textquoteright}s death into perspective and continue with their own lives; however the child{\textquoteright}s cause of death did not significantly influence parents{\textquoteright} sense of timing in this regard. Clinical and research implications of the findings are discussed.}, issn = {0748-1187}, doi = {10.1080/07481180302871}, url = {http://dx.doi.org/10.1080/07481180302871}, author = {MURPHY, SHIRLEY A. and JOHNSON, L. CLARK and WU, LANG and FAN, JUAN JUAN and LOHAN, JANET} } @article {pmid12873650, title = {Bias in estimates of confidence intervals for health outcome report cards}, journal = {J Clin Epidemiol}, volume = {56}, number = {6}, year = {2003}, month = {Jun}, pages = {553{\textendash}558}, author = {Faris, P. D. and Ghali, W. A. and Brant, R.} } @article {wang_classification_2003, title = {Classification for Ranking in Drug Discovery: Identifying and Aggregating Relevant Subsets of Variables}, journal = {Proceedings of the ISI Conference on Environmental Statistics and Health, Santiago de Compostela, Spain}, year = {2003}, pages = {173{\textendash}181}, url = {http://books.google.com/books?hl=en\&lr=\&id=xBll4aQqxKAC\&oi=fnd\&pg=PA173\&dq=info:yaGcD_7a4fgJ:scholar.google.com\&ots=uvxgHFyu46\&sig=PaTT5DK4PYIZjdia_dlDMsOQCwI}, author = {Wang, M. and Chipman, Hugh and Welch, W. J.} } @booklet {zidek2003compmod, title = {A Computational Model for Estimating Personal Exposure to Air Pollutants with Application to London{\textquoteright}s PM10 in 1997}, number = {2003-3}, year = {2003}, publisher = {Statistical and Applied Mathematical Sciences Institute}, author = {Zidek, J.V. and Meloche, J. and Shaddick, G. and Chatfield, C. and White, R} } @article {zidek2003computational, title = {A computational model for estimating personal exposure to air pollutants with application to London{\textquoteright}s PM10 in 1997}, journal = {2003 Technical Report of the Statistical and Applied Mathematical Sciences Institute}, year = {2003}, author = {Zidek, James V and Meloche, Jean and Shaddick, Gavin and Chatfield, Chris and White, Rick} } @booklet {zidek2003computational, title = {A computational model for estimating personal exposure to air pollutants with application to London’s PM10 in 1997}, journal = {Department of Statistics, University of British Columbia}, number = {205}, year = {2003}, author = {Zidek, James V and Meloche, Jean and Shaddick, Gavin and Chatfield, Chris and White, Rick} } @booklet {zidek2003computational, title = {A Computational Model for Estimating Personal Exposure to Air Pollutants with Application to London{\textquoteright}s PM}, year = {2003}, publisher = {PM10}, author = {Zidek, James V and Meloche, Jean and Shaddick, Gavin and Chatfield, Chris and White, Rick} } @article {shaddick2003computational, title = {A COMPUTATIONAL MODEL FOR ESTIMATING PERSONAL EXPOSURE TO AIR POLLUTANTS FOR USE IN STUDIES EXAMINING THE RELATIONSHIP BETWEEN AIR POLLUTION AND HEALTH: ISEE-495.}, journal = {Epidemiology}, volume = {14}, number = {5}, year = {2003}, pages = {S98}, publisher = {LWW}, author = {Shaddick, G and Zidek, J and Meloche, J and Chatfield, C and White, RF} } @article {pmid12738600, title = {A decision rule for diagnostic testing in obstructive sleep apnea}, journal = {Am. J. Respir. Crit. Care Med.}, volume = {167}, number = {10}, year = {2003}, month = {May}, pages = {1427{\textendash}1432}, author = {Tsai, W. H. and Remmers, J. E. and Brant, R. and Flemons, W. W. and Davies, J. and Macarthur, C.} } @booklet {wang2002derivation, title = {Derivation of Mixture Distributions and Weighted Likelihood Function}, number = {207}, year = {2003}, publisher = {Department of Statistics, University of British Columbia}, author = {Wang, Xiaogang and Zidek, James V} } @booklet {le2003designing, title = {Designing networks for monitoring multivariate environmental fields using data with monotone pattern}, number = {2003-5}, year = {2003}, publisher = {Statistical and Applied Mathematical Sciences Institute, RTP, NC}, author = {Le, Nhu D. and Sun, Li and Zidek, James V} } @booklet {zidek2003designing, title = {Designing Networks for Monitoring Multivariate Environmental Fields Using Data with Monotone Pattern}, number = {2003-5}, year = {2003}, publisher = {Statistical and Applied Mathematical Sciences Institute}, address = {North Carolina}, author = {Zidek, J.V. and Sun, L and Le, N.D.} } @article {wei2003empirical, title = {Empirical Bayes estimation and its superiority for two-way classification model}, journal = {Statistics \& probability letters}, volume = {63}, number = {2}, year = {2003}, pages = {165{\textendash}175}, publisher = {Elsevier}, author = {Wei, Laisheng and Chen, Jiahua} } @article {chen2003empirical, title = {Empirical likelihood confidence intervals for the mean of a population containing many zero values}, journal = {The Canadian Journal of Statistics/La Revue Canadienne de Statistique}, year = {2003}, pages = {53{\textendash}68}, publisher = {Statistical Society of Canada}, author = {Chen, Jiahua and Chen, Shun-Yi and Rao, JNK} } @article { ISI:000182480900003, title = {Exploring the {\textquoteleft}{\textquoteleft}Two-Hit hypothesis{\textquoteright}{\textquoteright} in NF2: Tests of two-hit and three-hit models of vestibular schwannoma development}, journal = {Genetic Epidemiology}, volume = {24}, number = {4}, year = {2003}, month = {MAY}, pages = {265-272}, abstract = {Neurofibromatosis 2 (NF2) is a genetic disease that occurs in approximately 1 in 40,000 live births. Almost all affected individuals develop bilateral tumors of Schwann cells that surround the vestibular nerves; these tumors are known as vestibular schwannomas (VS). Evidence from molecular genetic studies suggests that at least two mutations are involved in formation of VS in patients with NF2. Several authors proposed probabilistic models for this process in other tumors, and showed that such models are consistent with incidence data. We evaluated two different probabilistic models for a {\textquoteleft}{\textquoteleft}2-hit{\textquoteright}{\textquoteright} hypothesis for VS development in NF2 patients, and we present results from fitting these models to incidence data. Molecular evidence does not exclude the possibility that additional hits are necessary for the development of VS, and we also assessed a {\textquoteleft}{\textquoteleft}3-hit{\textquoteright}{\textquoteright} model for tumor formation. The {\textquoteleft}{\textquoteleft}3-hit{\textquoteright}{\textquoteright} model fits the data marginally better than one of the {\textquoteleft}{\textquoteleft}2-hit{\textquoteright}{\textquoteright} models and much better than the other {\textquoteleft}{\textquoteleft}2-hit{\textquoteright}{\textquoteright} model. Our findings suggest that more than two mutations may be necessary for VS development in NF2 patients. (C) 2003 Wiley-Liss, Inc.}, issn = {0741-0395}, doi = {10.1002/gepi.10238}, author = {Woods, R and Friedman, J M and Evans, D G R and Baser, M E and Joe, H} } @article {gustafson2003extension, title = {An extension of the Dirichlet prior for the analysis of longitudinal multinomial data}, journal = {Journal of Applied Statistics}, volume = {30}, number = {3}, year = {2003}, pages = {293{\textendash}310}, publisher = {Taylor \& Francis}, doi = {10.1080/0266476022000030075}, author = {Gustafson, P. and Walker, L.} } @article {pmid12605204, title = {The frequency of complications associated with the use of multiple-dose activated charcoal}, journal = {Ann Emerg Med}, volume = {41}, number = {3}, year = {2003}, month = {Mar}, pages = {370{\textendash}377}, author = {Dorrington, C. L. and Johnson, D. W. and Brant, R.} } @conference { ISI:000188793600004, title = {Functional data analysis in evolutionary biology}, booktitle = {RECENT ADVANCES AND TRENDS IN NONPARAMETRIC STATISTICS}, year = {2003}, note = {International Conference on Recent Advances and Trends in NonParametric Statistics, IRAKLION, GREECE, JUL 15-19, 2002}, pages = {49-60}, publisher = {ELSEVIER SCIENCE BV}, organization = {ELSEVIER SCIENCE BV}, type = {Proceedings Paper}, address = {SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {The evolution of physical traits from one generation to the next depends on a selection mechanism and the existence of genetic variability in the parent population. The modelling and statistical analysis of this evolution is well-developed for qualitative traits and for real or vector valued traits. The methodology can be found in quantitative genetics textbooks, as well as in evolutionary biology and animal breeding literature. The development of methodology for function-valued traits is just beginning. I will explain, in statistician{\textquoteright}s terms, some basic concepts of quantitative genetics, and discuss connections to functional data analysis.}, isbn = {0-444-51378-7}, doi = {10.1016/B978-044451378-6/50004-1}, author = {Heckman, NE}, editor = {Akritas, MG and Politis, DN} } @conference {540082, title = {Hipikat: recommending pertinent software development artifacts}, booktitle = {International Conference on Software Engineering}, year = {2003}, pages = {408{\textendash}418}, doi = {10.1109/ICSE.2003.1201219}, author = {Davor Cubranic and Gail C. Murphy} } @article {pmid12815482, title = {Incidence, survival and risk factors for the development of veno-occlusive disease in pediatric hematopoietic stem cell transplant recipients}, journal = {Bone Marrow Transplant.}, volume = {32}, number = {1}, year = {2003}, month = {Jul}, pages = {79{\textendash}87}, author = {Barker, C. C. and Butzner, J. D. and Anderson, R. A. and Brant, R. and Sauve, R. S.} } @article {chen2003information, title = {Information-theoretic approach for detecting change in the parameters of a normal model}, journal = {Mathematical methods of statistics}, volume = {12}, number = {1}, year = {2003}, pages = {116}, publisher = {New York: Allerton Press, c1992-}, author = {Chen, Jiahua and Gupta, AK} } @article { ISI:000186756300013, title = {Local linear extrapolation}, journal = {JOURNAL OF NONPARAMETRIC STATISTICS}, volume = {15}, number = {4-5}, year = {2003}, month = {AUG-OCT}, pages = {565-578}, publisher = {TAYLOR \& FRANCIS LTD}, type = {Article}, address = {4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND}, abstract = {A local linear estimator is proposed for extrapolating beyond the range of independent regression data. The asymptotic bias and variance of the local linear extrapolant are presented and used to calculate the asymptotic mean squared error. Three procedures are considered for choice of the bandwidth: a plug-in procedure. a forward cross-validation procedure and a procedure that combines the two. All of these are, in some sense. based on minimizing the asymptotic mean squared error. A simulation study shows that the forward cross-validation procedure outperforms the other two procedures both in terms of choosing a bandwidth and in terms of accurate extrapolation. The techniques are applied to two data sets.}, keywords = {bandwidth selection, local linear estimation, prediction}, issn = {1048-5252}, doi = {10.1080/10485250310001605432}, author = {Li, XC and Heckman, NE} } @article {9516, title = {Neutralising antibodies during treatment of secondary progressive multiple sclerosis with interferon beta-1b}, journal = {Neurology}, volume = {61}, year = {2003}, pages = {1025}, type = {Letter}, author = {Polman, C. and Kappos, L. and White, R. and Dahlke, F. and Beckmann, K. and Pozzilli, C. and Thompson, A. and Petkau, J. and Miller, D.} } @article {9515, title = {Neutralising antibodies to interferon beta during the treatment of multiple sclerosis}, journal = {Journal of Neurology, Neurosurgery and Psychiatry}, volume = {74}, year = {2003}, pages = {1162}, type = {Letter}, author = {Polman, C.H. and Kappos, L. and Petkau, J. and Thompson, A.} } @article {polman2003neutralizing, title = {Neutralizing antibodies during treatment of secondary progressive MS with interferon β-1b}, journal = {Neurology}, volume = {60}, number = {1}, year = {2003}, pages = {37{\textendash}43}, publisher = {Lippincott Williams \& Wilkins}, author = {Polman, C and Kappos, L and White, R and Dahlke, F and Beckmann, K and Pozzilli, C and Thompson, A and Petkau, J and Miller, D and others} } @article {polman2003neutralizing, title = {Neutralizing antibodies during treatment of secondary progressive MS with interferon β-1b}, journal = {Neurology}, volume = {60}, number = {1}, year = {2003}, pages = {37{\textendash}43}, publisher = {AAN Enterprises}, author = {Polman, C and Kappos, L and White, R and Dahlke, F and Beckmann, K and Pozzilli, C and Thompson, A and Petkau, J and Miller, D and others} } @article {polman2003neutralizing, title = {Neutralizing antibodies during treatment of secondary progressive multiple sclerosis with interferon β-1b}, journal = {Neurology}, volume = {60}, number = {1}, year = {2003}, pages = {37{\textendash}43}, publisher = {AAN Enterprises}, author = {Polman, C and Kappos, L and White, R and Dahlke, F and Beckmann, K and Pozzilli, C and Thompson, A and Petkau, J and Miller, D} } @article {doi:10.1080/0094965031000136012, title = {A new partitioning around medoids algorithm}, journal = {Journal of Statistical Computation and Simulation}, volume = {73}, number = {8}, year = {2003}, pages = {575-584}, abstract = {Kaufman and Rousseeuw (1990) proposed a clustering algorithm Partitioning Around Medoids (PAM) which maps a distance matrix into a specified number of clusters. A particularly nice property is that PAM allows clustering with respect to any specified distance metric. In addition, the medoids are robust representations of the cluster centers, which is particularly important in the common context that many elements do not belong well to any cluster. Based on our experience in clustering gene expression data, we have noticed that PAM does have problems recognizing relatively small clusters in situations where good partitions around medoids clearly exist. In this paper, we propose to partition around medoids by maximizing a criteria "Average Silhouette" defined by Kaufman and Rousseeuw (1990). We also propose a fast-to-compute approximation of "Average Silhouette". We implement these two new partitioning around medoids algorithms and illustrate their performance relative to existing partitioning methods in simulations.}, doi = {10.1080/0094965031000136012}, url = {http://dx.doi.org/10.1080/0094965031000136012}, author = {Mark Van der Laan and Katherine Pollard and Jennifer Bryan} } @article { ISI:000183261400003, title = {A new type of discrete self-decomposability and its application to continuous-time Markov processes for modeling count data time series}, journal = {Stochastic Models}, volume = {19}, number = {2}, year = {2003}, pages = {235-254}, abstract = {We propose a family of extended thinning operators, indexed by a parameter gamma in [0, 1), with the boundary case of gamma = 0 corresponding to the well-known binomial thinning operator. The extended thinning operators can be used to construct a class of continuous-time Markov processes for modeling count time series data. The class of stationary distributions of these processes is called generalized discrete self-decomposable, denoted by DSD (gamma). We obtain characterization results for the DSD (gamma) class and investigate relationships among the classes for different gamma{\textquoteright}s.}, issn = {1532-6349}, doi = {10.1081/STM-120020388}, author = {Zhu, R and Joe, H} } @article { ISI:000183556800008, title = {Numerical optimization and surface estimation with imprecise function evaluations}, journal = {Statistics and Computing}, volume = {13}, number = {3}, year = {2003}, month = {AUG}, pages = {277-286}, abstract = {This paper presents an investigation of a method for minimizing functions of several parameters where the function need not be computed precisely. Motivated by problems requiring the optimization of negative log-likelihoods, we also want to estimate the (inverse) Hessian at the point of minimum. The imprecision of the function values impedes the application of conventional optimization methods, and the goal of Hessian estimation adds a lot to the difficulty of developing an algorithm. The present class of methods is based on statistical approximation of the functional surface by a quadratic model, so is similar in motivation to many conventional techniques. The present work attempts to classify both problems and algorithmic tools in an effort to prescribe suitable techniques in a variety of situations.}, issn = {0960-3174}, doi = {10.1023/A:1024226918553}, author = {Joe, H and Nash, J C} } @inbook {petkau2003optimal, title = {Optimal group sequential designs for the Anscombe-Colton model}, booktitle = {Mathematical Statistics and Applications: Festschrift for Constance van Eeden}, volume = {42}, year = {2003}, pages = {291{\textendash}315}, publisher = {IMS Lecture Notes - Monograph Series}, organization = {IMS Lecture Notes - Monograph Series}, author = {Petkau, A.John} } @article {pmid12510037, title = {A randomized, controlled trial of the use of pulmonary-artery catheters in high-risk surgical patients}, journal = {N. Engl. J. Med.}, volume = {348}, number = {1}, year = {2003}, month = {Jan}, pages = {5{\textendash}14}, author = {Sandham, J. D. and Hull, R. D. and Brant, R. F. and Knox, L. and Pineo, G. F. and Doig, C. J. and Laporta, D. P. and Viner, S. and Passerini, L. and Devitt, H. and Kirby, A. and Jacka, M.} } @article {gustafson2003simple, title = {A simple approach to fitting Bayesian survival models}, journal = {Lifetime data analysis}, volume = {9}, number = {1}, year = {2003}, pages = {5{\textendash}19}, publisher = {Springer}, author = {Gustafson, P. and Aeschliman, D. and Levy, A.R.} } @article {chen2003single, title = {On the single item fill rate for a finite horizon}, journal = {Operations Research Letters}, volume = {31}, number = {2}, year = {2003}, pages = {119{\textendash}123}, publisher = {Elsevier}, author = {Chen, Jiahua and Lin, Dennis KJ and Thomas, Douglas J} } @article {petkau2003statistical, title = {Statistical approaches to assessing the effects of neutralizing antibodies IFNβ-1b in the pivotal trial of relapsing-remitting multiple sclerosis}, journal = {Neurology}, volume = {61:Supplement 5}, number = {9 suppl 5}, year = {2003}, pages = {S35{\textendash}S37}, publisher = {AAN Enterprises}, author = {Petkau, A.John} } @booklet {fu2003statistical, title = {A statistical characterization of a simulated Canadian annual maximum rainfall field}, journal = {TR 2003-17, Statistical and Mathematical Sciences Institute, RTP, NC}, number = {2003-5}, year = {2003}, publisher = {Statistical and Applied Mathematical Sciences Institute}, address = {North Carolina}, author = {Fu, A.Q. and Le, Nhu D. and Zidek, James V.} } @article {pmid12872055, title = {Temporal trends in antihypertensive drug prescriptions in Canada before and after introduction of the Canadian Hypertension Education Program}, journal = {J. Hypertens.}, volume = {21}, number = {8}, year = {2003}, month = {Aug}, pages = {1591{\textendash}1597}, author = {Campbell, N. R. and McAlister, F. A. and Brant, R. and Levine, M. and Drouin, D. and Feldman, R. and Herman, R. and Zarnke, K.} } @article {chen2003tests, title = {Tests for homogeneity in normal mixtures in the presence of a structural parameter}, journal = {Statistica Sinica}, volume = {13}, number = {2}, year = {2003}, pages = {351{\textendash}366}, publisher = {C/O DR HC HO, INST STATISTICAL SCIENCE, ACADEMIA SINICA, TAIPEI 115, TAIWAN}, author = {Chen, Hanfeng and Chen, Jiahua} } @article {zidek2003uncertainty, title = {Uncertainty, entropy, variance and the effect of partial information}, journal = {Lecture Notes-Monograph Series}, year = {2003}, pages = {155{\textendash}167}, author = {Zidek, James V and van Eeden, Constance} } @article {perlman_validity_2003, title = {On the validity of the likelihood ratio and maximum likelihood methods}, journal = {Journal of Statistical Planning and Inference}, volume = {117}, number = {1}, year = {2003}, month = {nov}, pages = {59{\textendash}81}, abstract = {When the null or alternative hypothesis of a statistical testing problem is a union of finitely many regions of varying dimensionality, the likelihood ratio test is statistically inappropriate. Its inappropriateness is revealed not by its performance under the Neyman{\textendash}Pearson criterion but by the fact that it yields incorrect inferences in certain regions of the sample space due to its inability to adapt to the differing dimensions in the composite hypothesis. Maximum likelihood estimators and associated model selection procedures also are inappropriate for such composite models. Tests and estimators based on the p-values associated with each of the regions that constitute the composite model are more appropriate for this geometry. Similar issues arise when the boundary of the null hypothesis is a union of finitely many regions of varying dimensionality.}, keywords = {Intersection-union test, likelihood ratio test, Model selection, Non-nested hypotheses, Union-intersection test, Varying dimensionality}, issn = {0378-3758}, doi = {10.1016/S0378-3758(02)00359-2}, url = {http://www.sciencedirect.com/science/article/pii/S0378375802003592}, author = {Perlman, Michael D. and WU, LANG} } @article {hu2003weighted, title = {The weighted likelihood}, journal = {Quality control and applied statistics}, volume = {48}, number = {5}, year = {2003}, pages = {545{\textendash}546}, publisher = {Executive Sciences Institute}, author = {Hu, F.eifang and Zidek, James V.} } @article { ISI:000177707800005, title = {Analysis of intrafamilial phenotypic variation in neurofibromatosis 1 (NF1)}, journal = {Genetic Epidemiology}, volume = {23}, number = {2}, year = {2002}, month = {AUG}, pages = {150-164}, abstract = {The relationship of genetic factors to variable expressivity in neurofibromatosis I (NF1) is poorly understood. We examined familial aggregation of NF1 features among different classes of affected relatives. Clinical information was obtained from the National NF Foundation International Database on 904 affected individuals in 373 families with 2 or more members with NF1. We used multivariate probit regression to measure the associations between various classes of relatives for each of 10 clinical features of NF1, while simultaneously adjusting for covariates including related features, age, and gender. Two distinct patterns were observed when we compared associations between first- and second-degree relatives, sibs, and parent-child pairs: Lisch nodules and cafe-au-lait spots had greater associations between first-degree relatives than between second-degree relatives, while subcutaneous neurofibromas, plexiform neurofibromas, cafe-aulait spots, and intertriginous freckling had greater associations between sibs than between parents and children. In addition, Lisch nodules, subcutaneous neurofibromas, and cutaneous neurofibromas had greater associations between affected fathers and children than between affected mothers and children. These familial patterns suggest that unlinked modifying genes and the normal NF1 allele may both be involved in the development of particular clinical features of NF1, but that the relative contributions vary for different features. Genet. Epidemiol. 23:150-164, 2002. (C) 2002 Wiley-Liss, Inc.}, issn = {0741-0395}, doi = {10.1002/gepi.01129}, author = {Szudek, J and Joe, H and Friedman, J M} } @article {gustafson2002bayesian, title = {A Bayesian approach to case{\textendash}control studies with errors in covariables}, journal = {Biostatistics}, volume = {3}, number = {2}, year = {2002}, pages = {229{\textendash}243}, publisher = {Biometrika Trust}, doi = {10.1093/biostatistics/3.2.229}, author = {Gustafson, P. and Le, N.D. and Vall{\'e}e, M.} } @article {kibria2002bayesian, title = {Bayesian spatial prediction of random space-time fields with application to mapping PM2. 5 exposure}, journal = {Journal of the American Statistical Association}, volume = {97}, number = {457}, year = {2002}, pages = {112{\textendash}124}, publisher = {Taylor and Francis}, author = {Kibria, BM Golam and Sun, Li and Zidek, James V and Le, Nhu D.} } @article {salibian2002bootstrapping, title = {Bootstrapping robust estimates of regression}, journal = {Annals of Statistics}, year = {2002}, pages = {556{\textendash}582}, publisher = {JSTOR}, author = {Salibian-Barrera, Mat{\'\i}as and Zamar, Ruben H} } @article { ISI:000175912300015, title = {Bootstrapping robust estimates of regression}, journal = {ANNALS OF STATISTICS}, volume = {30}, number = {2}, year = {2002}, month = {APR}, pages = {556-582}, publisher = {INST MATHEMATICAL STATISTICS}, type = {Article}, address = {PO BOX 22718, BEACHWOOD, OH 44122 USA}, abstract = {We introduce a new computer-intensive method to estimate the distribution of robust regression estimates. The basic idea behind Our method is to bootstrap a reweighted representation of the estimates. To obtain a bootstrap method that is asymptotically correct, we include the auxiliary scale estimate in our reweighted representation of the estimates. Our method is computationally simple because for each bootstrap sample we only have to solve a linear system of equations. The weights we use are decreasing functions of the absolute value of the residuals and hence outlying observations receive small weights. This results in a bootstrap method that is resistant to the presence of outliers in the data. The breakdown points of the quantile estimates derived with this method are higher than those obtained with the bootstrap. We illustrate our method on two datasets and we report the results of a Monte Carlo experiment on confidence intervals for the parameters of the linear model.}, keywords = {breakdown point, confidence intervals, regression}, issn = {0090-5364}, doi = {10.1214/aos/1021379865}, author = {Salibian-Barrera, M and Zamar, RH} } @article {pmid11798370, title = {Chelation therapy for ischemic heart disease: a randomized controlled trial}, journal = {JAMA}, volume = {287}, number = {4}, year = {2002}, pages = {481{\textendash}486}, author = {Knudtson, M. L. and Wyse, D. G. and Galbraith, P. D. and Brant, R. and Hildebrand, K. and Paterson, D. and Richardson, D. and Burkart, C. and Burgess, E.} } @article {pmid12402146, title = {Choroid plexus tumours}, journal = {Br. J. Cancer}, volume = {87}, number = {10}, year = {2002}, month = {Nov}, pages = {1086{\textendash}1091}, author = {Wolff, J. E. and Sajedi, M. and Brant, R. and Coppes, M. J. and Egeler, R. M.} } @article {perlman_class_2002, title = {A class of conditional tests for a multivariate one-sided alternative}, journal = {Journal of Statistical Planning and Inference}, volume = {107}, number = {1{\textendash}2}, year = {2002}, pages = {155{\textendash}171}, abstract = {Consider testing H0: μ1=...=μp=0 versus the multivariate one-sided alternative H1: μ1⩾0,{\textellipsis},μp⩾0 based on a sample from a p-dimensional normal distribution Np(μ,Σ) with Σ unknown, where μ=(μ1,{\textellipsis},μp). Perlman (Ann. Math. Statist. 40 (1969) 549) obtained the likelihood ratio test (LRT) statistic and its null distribution, while Shorack (Ann. Math. Statist. 38 (1967) 1740) and Silvapulle (J. Multivariate Anal. 55 (1995) 312) studied an alternative test statistic. Neither test is similar, however, hence both are biased, and neither dominates the other in terms of power. Tang (J. Am. Statist. Assoc. 89 (1994) 1006) proposed a test that is similar, unbiased, and everywhere more powerful than the original LRT. Here we study a new class of conditional tests based on the LRT statistic and obtain the conditional test that is most nearly similar within this class. The resulting test is more powerful than the LRT for most alternatives, is not dominated in power by Tang{\textquoteright}s test, and is more convenient to apply. Furthermore, unlike Tang{\textquoteright}s test, the conditional test always accepts H0 when μ̂=(μ̂1,{\textellipsis},μ̂p)=(0,{\textellipsis},0), where μ̂ is the MLE of μ under H1. Similar results are found for a conditional version of the Shorack{\textendash}Silvapulle test.}, keywords = {Conditional test, likelihood ratio test, Multivariate normal distribution, One-sided alternative, Tests for means}, issn = {0378-3758}, doi = {10.1016/S0378-3758(02)00250-1}, url = {http://www.sciencedirect.com/science/article/pii/S0378375802002501}, author = {Perlman, Michael D. and WU, LANG} } @article {van2002combining, title = {Combining sample information in estimating ordered normal means}, journal = {Sankhy\=a: The Indian Journal of Statistics, Series A}, year = {2002}, pages = {588{\textendash}610}, author = {van Eeden, Constance and Zidek, James V} } @article {gustafson2002biom, title = {Comparing the effects of continuous and discrete covariate measurement error, with emphasis on the dichotomization of mismeasured predictors}, journal = {Biometrics}, volume = {58}, number = {4}, year = {2002}, pages = {878-887}, doi = {10.1111/j.0006-341X.2001.00598.x}, author = {Gustafson, P. and Le, N. D.} } @article {pmid12488521, title = {Comparison of outcomes of untreated carpal tunnel syndrome and asymptomatic controls in meat packers}, journal = {Occup Med (Lond)}, volume = {52}, number = {8}, year = {2002}, month = {Dec}, pages = {491{\textendash}496}, author = {Gorsche, R. G. and Wiley, J. P. and Brant, R. and Renger, R. F. and Sasyniuk, T. M. and Burke, N.} } @booklet {eeden2002correction, title = {CORRECTION NOTE: Minimax estimation of a bounded scale parameter for scale-invariant squared-error loss}, year = {2002}, author = {Eeden, Constance van and Zidek, James V} } @article {van2002correction, title = {Correction on Estimating one of two normal means when their difference is bounded}, journal = {Statistics and Probability Letters}, volume = {57}, number = {1}, year = {2002}, pages = {111}, publisher = {North-Holland}, author = {van Eeden, Constance and Zidek, James V} } @article {perlman_defense_2002, title = {A defense of the likelihood ratio test for one-sided and order-restricted alternatives}, journal = {Journal of Statistical Planning and Inference}, volume = {107}, number = {1{\textendash}2}, year = {2002}, month = {sep}, pages = {173{\textendash}186}, abstract = {It has been asserted recently that the likelihood ratio tests (LRT) for certain multi-parameter hypothesis-testing problems with one-sided and order-restricted alternatives exhibit anomalous behaviour (Cohen and Sackrowitz (Ann. Statist. 26 (1998) 2321); Cohen et al. (J. Mult. Analysis 72 (2002) 50). For sample points x and x' such that x' apparently lies {\textquotedblleft}deeper{\textquotedblright} inside the alternative than does x, the LRT may accept the null hypothesis for x' but reject it for x. Like Silvapulle (Amer. Statist. 51 (1997) 178), we argue that this conclusion is not anomalous but correct for the usual formulation of the null hypothesis accompanying one-sided and order-restricted alternatives. This alleged anomaly of the LRT occurs only for an alternative hypothesis given by an obtuse convex cone C. In this case, the reformulated null hypothesis {\textquotedblleft}not C{\textquotedblright} both avoids the apparent anomaly and may be more appropriate scientifically.}, issn = {0378-3758}, doi = {10.1016/S0378-3758(02)00251-3}, url = {http://www.sciencedirect.com/science/article/pii/S0378375802002513}, author = {Perlman, Michael D. and WU, LANG} } @article {lim_design_2002, title = {Design and analysis of computer experiments when the output is highly correlated over the input space}, journal = {Canadian Journal of Statistics}, volume = {30}, number = {1}, year = {2002}, pages = {109{\textendash}126}, url = {http://onlinelibrary.wiley.com/doi/10.2307/3315868/abstract}, author = {Lim, Yong B. and Sacks, Jerome and Studden, W. J. and Welch, William J.} } @article {pmid12359822, title = {Differences in admission rates of children with bronchiolitis by pediatric and general emergency departments}, journal = {Pediatrics}, volume = {110}, number = {4}, year = {2002}, month = {Oct}, pages = {e49}, author = {Johnson, D. W. and Adair, C. and Brant, R. and Holmwood, J. and Mitchell, I.} } @article { ISI:000174685600010, title = {Estimating and depicting the structure of a distribution of random functions}, journal = {BIOMETRIKA}, volume = {89}, number = {1}, year = {2002}, month = {MAR}, pages = {145-158}, publisher = {BIOMETRIKA TRUST}, type = {Article}, address = {UNIV COLLEGE LONDON GOWER ST-BIOMETRIKA OFFICE, LONDON WC1E 6BT, ENGLAND}, abstract = {We suggest a nonparametric approach to making inference about the structure of distributions in a potentially infinite-dimensional space, for example a function space, and displaying information about that structure. It is suggested that the simplest way of presenting the structure is through modes and density ascent lines, the latter being the projections into the sample space of the curves of steepest ascent up the surface of a functional-data density. Modes are always points in the sample space, and ascent lines are always one-parameter structures, even when the sample space is determined by an infinite number of parameters. They are therefore relatively easily depicted. Our methodology is based on a functional form of an iterative data-sharpening algorithm.}, keywords = {bandwidth, cluster analysis, Functional data analysis, Gaussian process, generalised Fourier expansion, Karhunen-Loeve expansion, kernel methods, line of steepest ascent, mode, nonparametric density estimation, tree diagram}, issn = {0006-3444}, doi = {10.1093/biomet/89.1.145}, author = {Hall, P and Heckman, NE} } @article {hall_estimating_2002, title = {Estimating and depicting the structure of a distribution of random functions}, journal = {Biometrika}, volume = {89}, number = {1}, year = {2002}, pages = {145{\textendash}158}, url = {http://biomet.oxfordjournals.org/content/89/1/145.short}, author = {Hall, Peter and Heckman, Nancy E.} } @article {chen2002estimation, title = {Estimation of distribution function and quantiles using the model-calibrated pseudo empirical likelihood method}, journal = {Statistica Sinica}, volume = {12}, number = {4}, year = {2002}, pages = {1223{\textendash}1240}, publisher = {C/O DR HC HO, INST STATISTICAL SCIENCE, ACADEMIA SINICA, TAIPEI 115, TAIWAN}, author = {Chen, Jiahua and Wu, Changbao} } @article {BaserFriedman.ea2002, title = {Evaluation of clinical diagnostic criteria for neurofibromatosis 2}, journal = {Neurology}, volume = {59}, number = {11}, year = {2002}, pages = {1759-1765}, publisher = {Lippincott Williams \& Wilkins}, doi = {10.1212/01.WNL.0000035638.74084.F4}, author = {Baser, M E and Friedman, J M and Wallace, A J and Ramsden, R T and Joe, H and Evans, D G R} } @article {pmid12473441, title = {Evaluation of satisfaction with midwifery care}, journal = {Midwifery}, volume = {18}, number = {4}, year = {2002}, month = {Dec}, pages = {260{\textendash}267}, author = {Harvey, S. and Rach, D. and Stainton, M. C. and Jarrell, J. and Brant, R.} } @article {brauer2002exposure, title = {Exposure misclassification and threshold concentrations in time series analyses of air pollution health effects}, journal = {Risk Analysis}, volume = {22}, number = {6}, year = {2002}, pages = {1183{\textendash}1193}, publisher = {Wiley Online Library}, author = {Brauer, M and Brumm, J and Vedal, S and Petkau, AJ} } @article {wu_flexible_2002, title = {Flexible Weighted Log-Rank Tests Optimal for Detecting Early and/or Late Survival Differences}, journal = {Biometrics}, volume = {58}, number = {4}, year = {2002}, month = {dec}, pages = {997{\textendash}1004}, abstract = {Summary. At the present time, many AIDS clinical trials compare drug therapies by a time-to-event primary endpoint that measures the durability of suppression of HIV replication. For such studies, survival differences tend to occur early and/or late in the follow-up period due to drug differences in initial potency and/or durability of efficacy, and detecting these differences is of primary interest. We propose a weighted log-rank statistic that emphasizes early and/or late survival differences. We also consider some versatile tests that also emphasize these differences but are sensitive to a wider range of alternatives. The performances of the new tests are evaluated in numerical studies. For the alternatives of interest, the new tests show greater power and flexibility than commonly used weighted log-rank tests and related versatile tests. When the main interest is in detecting early and/or late survival differences, these tests may be preferable to the other versatile and weighted log-rank tests that have been studied.}, keywords = {AIDS, Asymptotics, Quadratic weight, Robust test, Versatile test}, issn = {1541-0420}, doi = {10.1111/j.0006-341X.2002.00997.x}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0006-341X.2002.00997.x/abstract}, author = {WU, LANG and Gilbert, Peter B.} } @article {chen2002analysis, title = {Genetic data analysis of affected sib pairs}, journal = {Canadian Journal of Statistics}, volume = {30}, number = {1}, year = {2002}, pages = {145{\textendash}152}, publisher = {Wiley Online Library}, author = {Chen, Jiahua and Kalbfleisch, John D and Romero-Hidalgo, Sandra} } @article {adrover2002globally, title = {Globally robust inference}, journal = {Estadistica}, volume = {54}, year = {2002}, pages = {162{\textendash}163}, author = {Adrover, Jorge and Berrendero, Jose Ramon and Salibian-Barrera, Mat{\'\i}as and Zamar, Ruben H} } @article {pmid11934533, title = {Hexachlorobenzene exposure and the proportion of male births in Turkey 1935-1990}, journal = {Reprod. Toxicol.}, volume = {16}, number = {1}, year = {2002}, pages = {65{\textendash}70}, author = {Jarrell, J. F. and Gocmen, A. and Akyol, D. and Brant, R.} } @article {wu_identification_2002, title = {Identification of significant host factors for HIV dynamics modelled by non-linear mixed-effects models}, journal = {Statistics in Medicine}, volume = {21}, number = {5}, year = {2002}, month = {mar}, pages = {753{\textendash}771}, abstract = {Non-linear mixed-effects models are powerful tools for modelling HIV viral dynamics. In AIDS clinical trials, the viral load measurements for each subject are often sparse. In such cases, linearization procedures are usually used for inferences. Under such linearization procedures, however, standard covariate selection methods based on the approximate likelihood, such as the likelihood ratio test, may not be reliable. In order to identify significant host factors for HIV dynamics, in this paper we consider two alternative approaches for covariate selection: one is based on individual non-linear least square estimates and the other is based on individual empirical Bayes estimates. Our simulation study shows that, if the within-individual data are sparse and the between-individual variation is large, the two alternative covariate selection methods are more reliable than the likelihood ratio test, and the more powerful method based on individual empirical Bayes estimates is especially preferable. We also consider the missing data in covariates. The commonly used missing data methods may lead to misleading results. We recommend a multiple imputation method to handle missing covariates. A real data set from an AIDS clinical trial is analysed based on various covariate selection methods and missing data methods. Copyright {\textcopyright} 2002 John Wiley \& Sons, Ltd.}, keywords = {AIDS, HIV, HIV dynamics, missing data, mixed-effects models, Multiple imputation}, issn = {1097-0258}, doi = {10.1002/sim.1015}, url = {http://onlinelibrary.wiley.com/doi/10.1002/sim.1015/abstract}, author = {Wu, Hulin and WU, LANG} } @conference {chuang2002ingap, title = {An InGaP/InGaAs/GaAs double channel pseudomorphic high electron mobility transistor (DC-PHEMT)}, booktitle = {Optoelectronic and Microelectronic Materials and Devices, 2002 Conference on}, year = {2002}, pages = {319{\textendash}322}, publisher = {IEEE}, organization = {IEEE}, author = {Chuang, HM and Lin, Kawuu W and Chen, CY and Chen, JY and Kao, CI and Liu, WC} } @article {young_initial_2002, title = {Initial compound selection for sequential screening}, journal = {Current Opinion in Drug Discovery and Development}, volume = {5}, number = {3}, year = {2002}, pages = {422{\textendash}427}, url = {http://genomics10.bu.edu/megonw/pdf/active_learning/sequential_screening_young.pdf}, author = {Young, S. Stanley and Lam, R. L. and Welch, William J.} } @article { ISI:000178517800007, title = {Intrafamilial correlation of clinical manifestations in neurofibromatosis 2 (NF2)}, journal = {Genetic Epidemiology}, volume = {23}, number = {3}, year = {2002}, month = {OCT}, pages = {245-259}, abstract = {Measuring correlation in clinical traits among relatives is important to our understanding of the causes of variable expressivity in Mendelian diseases. Random effects models are widely used to estimate intrafamilial correlations, but such models have limitations. We incorporated survival techniques into a random effects model so that it can be used to estimate intrafamilial correlations in continuous variables with right censoring, such as age at onset. We also describe a negative-binomial gamma mixture model to determine intrafamilial correlations of discrete (e.g., count) data. We demonstrate the utility of these methods by analyzing intrafamilial correlations among patients with neurofibromatosis 2 (NF2), an autosomal-dominant disease caused by mutations of the NF2 tumor-suppressor gene. We estimated intrafamilial correlations in age at first symptom of NF2, age at onset of hearing loss, and number of intracranial meningiomas in 390 NF2 nonprobands from 153 unrelated families. A significant intrafamilial correlation was observed for each of the three features: age at onset (0.35; 95\% confidence interval (CI) 0.23-0.47), age at onset of hearing loss (0.51; 95\% Cl, 0.35-0.64), and number of meninginomas (0.29; 95\% Cl, 0.15-0.43). Significant correlations were also observed for age at first symptom within NF2 families with truncating mutations (0.41; 95\% CI, 0.06-0.68) or splice-site mutations (0.29; 95\% CI, 0.03-0.51), for age at onset of hearing loss within families with missense mutations (0.67; 95\% CI, 0.18-0.89), and for number of meningiomas within families with splice-site mutations (0.39; 95\% CI, 0.13-0.66). Our findings are consistent with effects of both allelic and nonallelic familial factors on the clinical variability of NF2. (C) 2002 Wiley-Liss, Inc.}, issn = {0741-0395}, doi = {10.1002/gepi.10181}, author = {Zhao, Y and Kumar, R A and Baser, M E and Evans, D G R and Wallace, A and Kluwe, L and Mautner, V F and Parry, D M and Rouleau, G A and Joe, H and Friedman, J M} } @article {wu_joint_2002, title = {A Joint Model for Nonlinear Mixed-Effects Models With Censoring and Covariates Measured With Error, With Application to AIDS Studies}, journal = {Journal of the American Statistical Association}, volume = {97}, number = {460}, year = {2002}, pages = {955{\textendash}964}, issn = {0162-1459}, doi = {10.1198/016214502388618744}, url = {http://amstat.tandfonline.com/doi/abs/10.1198/016214502388618744}, author = {WU, LANG} } @booklet {wang2002mining, title = {Mining nuggets of activity in high dimensional space from high throughput screening data}, year = {2002}, publisher = {University of Waterloo URL=http://www.bisrg.uwaterloo.ca/archive/RR-02-01.pdf}, author = {Wang, Y and Chipman, HA and Welch, WJ} } @booklet {wang_mining_2002, title = {Mining nuggets of activity in high dimensional space from high throughput screening data}, year = {2002}, publisher = {Technical report, IIQP}, url = {https://www.researchgate.net/profile/William_Welch/publication/246834527_Mining_nuggets_of_activity_in_high_dimensional_space_from_high_throughput_screening_data/links/0a85e53c28a25cb5a6000000.pdf}, author = {Wang, Yuanyuan and Chipman, Hugh A. and Welch, William J.} } @article {wu_missing_2002, title = {Missing time-dependent covariates in human immunodeficiency virus dynamic models}, journal = {Journal of the Royal Statistical Society: Series C (Applied Statistics)}, volume = {51}, number = {3}, year = {2002}, month = {jul}, pages = {297{\textendash}318}, abstract = {Summary. The study of human immunodeficiency virus dynamics is one of the most important areas in research into acquired immune deficiency syndrome in recent years. Non-linear mixed effects models have been proposed for modelling viral dynamic processes. A challenging problem in the modelling is to identify repeatedly measured (time-dependent), but possibly missing, immunologic or virologic markers (covariates) for viral dynamic parameters. For missing time-dependent covariates in non-linear mixed effects models, the commonly used complete-case, mean imputation and last value carried forward methods may give misleading results. We propose a three-step hierarchical multiple-imputation method, implemented by Gibbs sampling, which imputes the missing data at the individual level but can pool information across individuals. We compare various methods by Monte Carlo simulations and find that the multiple-imputation method proposed performs the best in terms of bias and mean-squared errors in the estimates of covariate coefficients. By applying the favoured multiple-imputation method to clinical data, we conclude that there is a negative correlation between the viral decay rate (a virological response parameter) and CD4 or CD8 cell counts during the treatment; this is counter-intuitive, but biologically interpretable on the basis of findings from other clinical studies. These results may have an important influence on decisions about treatment for acquired immune deficiency syndrome patients.}, keywords = {Acquired immune deficiency syndrome, Gibbs sampler, Hierarchical model, Human immunodeficiency virus dynamics, Markov chain Monte Carlo methods, missing data, Multiple imputation, Non-linear mixed effects model}, issn = {1467-9876}, doi = {10.1111/1467-9876.00270}, url = {http://onlinelibrary.wiley.com/doi/10.1111/1467-9876.00270/abstract}, author = {WU, LANG and Wu, Hulin} } @article {pmid11809357, title = {Multiple imputation versus data enhancement for dealing with missing data in observational health care outcome analyses}, journal = {J Clin Epidemiol}, volume = {55}, number = {2}, year = {2002}, month = {Feb}, pages = {184{\textendash}191}, author = {Faris, P. D. and Ghali, W. A. and Brant, R. and Norris, C. M. and Galbraith, P. D. and Knudtson, M. L.} } @inbook {svarc2002optimal, title = {Optimal Bias Robust M{\textemdash}estimates of Regression}, booktitle = {Statistical Data Analysis Based on the L1-Norm and Related Methods}, year = {2002}, pages = {191{\textendash}200}, publisher = {Springer}, organization = {Springer}, author = {Svarc, Marcela and Yohai, V{\'\i}ctor J and Zamar, Ruben H} } @article {Bryan2002, title = {Paired and Unpaired Comparison and Clustering with Gene Expression Data}, journal = {Statistica Sinica}, volume = {12}, year = {2002}, pages = {87 - 110}, abstract = {

We have previously described a statistical framework for using gene expression data from cDNA microarrays to select meaningful subsets of genes and to place genes into clusters (van der Laan and Bryan (2001)). In this paper we extend the methodology to the setting in which expression data is collected on a common set of $p$ genes from either two observations within a subject (paired), or on subjects from two subpopulations (unpaired). We present simulation results that illustrate important issues encountered with cluster analysis in gene expression data. In particular, we see that sampling variability of the covariance structure and the presence of unrelated genes can have a strong impact on clustering algorithms and measures of cluster strength. We discuss ways to address this issue, including the application of a hybrid clustering method which incorporates both partitioning and collapsing steps. The hybrid methodology is illustrated on a cancer cell line data set with two types of cancer. We also present a method for selecting significantly differently expressed genes using a null distribution. Finally, we present theoretical results relating to sample size and consistency in this setting.

}, url = {http://www3.stat.sinica.edu.tw/statistica/j12n1/j12n15/j12n15.htm}, author = {Bryan, J. and Pollard, K. S. and Van Der Laan, M. J.} } @article { ISI:000178613800002, title = {Predictors of the risk of mortality in neurofibromatosis 2}, journal = {American Journal of Human Genetics}, volume = {71}, number = {4}, year = {2002}, note = {49th Annual Meeting of the American-Society-of-Human-Genetics, SAN FRANCISCO, CALIFORNIA, OCT 19-23, 1999}, month = {OCT}, pages = {715-723}, publisher = {Amer Soc Human Genet}, abstract = {To evaluate clinical and molecular predictors of the risk of mortality in people with neurofibromatosis 2 (NF2), we analyzed the mortality experience of 368 patients from 261 families in the United Kingdom NF2 registry, using the Cox proportional-hazards model and the jackknife method. Age at diagnosis, intracranial meningiomas, and type of treatment center were informative predictors of the risk of mortality. In Cox models, the relative risk of mortality increased 1.13-fold per year decrease in age at diagnosis (95\% confidence interval [CI] 1.08-1.18) and was 2.51-fold greater in people with meningiomas compared with those without meningiomas (95\% CI 1.38-4.57). The relative risk of mortality in patients treated at specialty centers was 0.34 compared with those treated at nonspecialty centers (95\% CI 0.12-0.98). In a separate model, the relative risk of mortality in people with constitutional NF2 missense mutations was very low compared with those with other types of mutations (nonsense or frameshift mutations, splice-site mutations, and large deletions), but the Cl could not be well quantified because there was only one death among people with missense mutations. We conclude that age at diagnosis, the strongest single predictor of the risk of mortality, is a useful index for patient counseling and clinical management (as are intracranial meningiomas). To ensure optimal care, we recommend that people with NF2 be referred to specialty treatment centers.}, issn = {0002-9297}, doi = {10.1086/342716}, author = {Baser, M E and Friedman, J M and Aeschliman, D and Joe, H and Wallace, A J and Ramsden, R T and Evans, D G R} } @article {pmid12443567, title = {Prevalence of PSA testing and effect of clinical indications on patterns of PSA testing in a population-based sample of Alberta men}, journal = {Chronic Dis Can}, volume = {23}, number = {3}, year = {2002}, pages = {111{\textendash}119}, author = {McGregor, S. E. and Bryant, H. E. and Brant, R. F. and Corbett, P. J.} } @booklet {maronna2002robust, title = {Robust multivariate estimates for high dimentional datasets}, year = {2002}, publisher = {Working paper, University of La Plata and University of British Columbia}, author = {Maronna, RA and Zamar, RH} } @article {chen30romero, title = {Romero Hidalgo*, S.(2002).{\textquotedblleft}Genetic data analysis of affected sib pairs{\textquotedblright}}, journal = {The Canadian Journal of Statistics}, volume = {30}, year = {2002}, pages = {145{\textendash}152}, author = {Chen, J and Romero Hidalgo*, S and Kalbfleisch, JD} } @conference {alqallaf2002scalable, title = {Scalable robust covariance and correlation estimates for data mining}, booktitle = {Proceedings of the eighth ACM SIGKDD international conference on Knowledge discovery and data mining}, year = {2002}, pages = {14{\textendash}23}, publisher = {ACM}, organization = {ACM}, author = {Alqallaf, Fatemah A and Konis, Kjell P and Martin, R Douglas and Zamar, Ruben H} } @article {Gustafson2002b, title = {On the simultaneous effects of model misspecification and errors in variables}, journal = {Canadian Journal of Statistics}, volume = {30}, number = {3}, year = {2002}, pages = {463{\textendash}474}, publisher = {Wiley-Blackwell}, doi = {10.2307/3316148}, author = {Gustafson, Paul} } @article {chen2002statistical, title = {Statistical inference on comparing two distribution functions with a possible crossing point}, journal = {Statistics \& probability letters}, volume = {60}, number = {3}, year = {2002}, pages = {329{\textendash}341}, publisher = {Elsevier}, author = {Chen, Guijing and Chen, Jiahua and Chen, Yuming} } @article { ISI:000177450100005, title = {Stochastic orderings in random utility models}, journal = {Mathematical Social Sciences}, volume = {43}, number = {3}, year = {2002}, note = {Conference and Workshop on Random Utility and Probabilistic Measurement Theory, DUKE UNIV, FUQUA SCH BUSINESS, DURHAM, NORTH CAROLINA, AUG 03-08, 2000}, month = {JUL}, pages = {PII S0165-4896(02)00018-5}, publisher = {Natl Sci Fdn}, abstract = {For ranking, partial ranking, top choice and subset choice probabilities, preference orderings are defined that can be used to assess whether one alternative or candidate is preferred to another in aggregate or in a population. For subset choice, the preference orderings are alternative ways of considering a social welfare ordering. When a random utility model is assumed, stochastic ordering conditions on the utility random variables are given so that the preference orderings hold. Real data are used to illustrate the various preference orderings. (C) 2002 Elsevier Science B.V. All rights reserved.}, issn = {0165-4896}, doi = {10.1016/S0165-4896(02)00018-5}, author = {Joe, H} } @article {pmid12048431, title = {Systematic error in the determination of nocturnal blood pressure dipping status by ambulatory blood pressure monitoring}, journal = {Blood Press Monit}, volume = {7}, number = {2}, year = {2002}, month = {Apr}, pages = {131{\textendash}134}, author = {Kammila, S. and Campbell, N. R. and Brant, R. and deJong, R. and Culleton, B.} } @article {10.2307/1271254, title = {Uniform Coverage Designs for Molecule Selection}, journal = {Technometrics}, volume = {44}, number = {2}, year = {2002}, pages = {99-109}, publisher = {[Taylor \& Francis, Ltd., American Statistical Association, American Society for Quality]}, abstract = {

In screening for drug discovery, chemists often select a large subset of molecules from a very large database (e. g., select 1,000 molecules from 100,000). To generate diverse leads for drug optimization, highly active compounds in several structurally different chemical classes are sought. Molecules can be characterized by numerical descriptors, and the chosen subset should cover the descriptor space or subspaces formed by several descriptors. We propose a method that concentrates on low-dimensional subspaces, a criterion for uniformity of coverage, and a fast exchange algorithm to optimize the criterion. These methods are illustrated by using a National Cancer Institute database.

}, issn = {00401706}, url = {http://www.jstor.org/stable/1271254}, author = {Lam, RLH and Welch, WJ and Young, SS} } @article {chen2002using, title = {Using empirical likelihood methods to obtain range restricted weights in regression estimators for surveys}, journal = {Biometrika}, volume = {89}, number = {1}, year = {2002}, pages = {230{\textendash}237}, publisher = {Biometrika Trust}, author = {Chen, J and Sitter, RR and Wu, C} } @article {hu2002weighted, title = {The weighted likelihood}, journal = {Canadian Journal of Statistics}, volume = {30}, number = {3}, year = {2002}, pages = {347{\textendash}371}, publisher = {Wiley Online Library}, author = {Hu, F.eifang and Zidek, James V} } @article {pmid17610772, title = {Accuracy and speed of urine pregnancy tests done in the emergency department: a prospective study}, journal = {CJEM}, volume = {3}, number = {4}, year = {2001}, month = {Oct}, pages = {292{\textendash}295}, author = {Lazarenko, G. C. and Dobson, C. and Enokson, R. and Brant, R.} } @article {gustafson2001biom, title = {Case-control analysis with partial knowledge of exposure misclassification probabilities}, journal = {Biometrics}, volume = {57}, year = {2001}, pages = {598-609}, doi = {10.1111/j.0006-341X.2001.00598.x}, author = {Gustafson, P. and Le, N. D. and Saskin, R.} } @article {pmid11572743, title = {Comparison of 2 methods for calculating adjusted survival curves from proportional hazards models}, journal = {JAMA}, volume = {286}, number = {12}, year = {2001}, month = {Sep}, pages = {1494{\textendash}1497}, author = {Ghali, W. A. and Quan, H. and Brant, R. and van Melle, G. and Norris, C. M. and Faris, P. D. and Galbraith, P. D. and Knudtson, M. L.} } @article {walker2001consolidation, title = {The consolidation/transition model in moral reasoning development.}, journal = {Developmental Psychology}, volume = {37}, number = {2}, year = {2001}, pages = {187}, publisher = {American Psychological Association}, doi = {10.1037//0012-1649.37.2.187}, author = {Walker, L.J. and Gustafson, P. and Hennig, K.H.} } @article { ISI:000173007800007, title = {CriSP: A tool for bump hunting}, journal = {JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS}, volume = {10}, number = {4}, year = {2001}, month = {DEC}, pages = {713-729}, publisher = {AMER STATISTICAL ASSOC}, type = {Article}, address = {1429 DUKE ST, ALEXANDRIA, VA 22314 USA}, abstract = {We propose a test of multimodality of regression functions and their derivatives. The test statistic is a critical smoothing parameter (CriSP), giving the minimum amount of smoothing necessary to force the regression function to satisfy the null hypothesis. The p values are computed via bootstrapping. Our idea is motivated by Silverman{\textquoteright}s test concerning the number of modes in the density function. Simulation studies indicate that the test works well, even when testing for bumps in the derivative. We apply CriSP to children{\textquoteright}s growth data, to study the number of spurts of growth.}, keywords = {bootstrap, critical smoothing parameter, growth data, multimodality testing, Smoothing}, issn = {1061-8600}, doi = {10.1198/106186001317243412}, author = {Harezlak, J and Heckman, NE} } @article {Alqallaf2001, title = {On cross-validation of Bayesian models}, journal = {Canadian Journal of Statistics}, volume = {29}, number = {2}, year = {2001}, pages = {333{\textendash}340}, publisher = {Wiley Online Library}, doi = {10.2307/3316081}, author = {Alqallaf, Fatemah and Gustafson, Paul} } @article {susko2001diagnostic, title = {A diagnostic tool for mixture models}, journal = {Journal of Statistical Computation and Simulation}, volume = {69}, number = {4}, year = {2001}, pages = {293{\textendash}313}, publisher = {Gordon and Breach Science Publishers}, author = {Susko, Edward and Chen, Jiahua and Kalbfleisch, JD} } @article { ISI:000172846900005, title = {Discussion of {\textquoteleft}{\textquoteleft}Conditionally specified distributions: An introduction", by Arnold, Castillo and Sarabia}, journal = {Statistical Science}, volume = {16}, number = {3}, year = {2001}, month = {AUG}, pages = {270-271}, issn = {0883-4237}, url = {http://projecteuclid.org/euclid.ss/1009213728}, author = {Joe, H} } @article {van2001estimating, title = {Estimating one of two normal means when their difference is bounded}, journal = {Statistics and probability letters}, volume = {51}, number = {3}, year = {2001}, pages = {277{\textendash}284}, publisher = {Elsevier}, author = {van Eeden, Constance and Zidek, James V} } @article {brauer2001exposure, title = {Exposure of chronic obstructive pulmonary disease patients to particles: Respiratory and cardiovascular health effects}, journal = {Journal of Exposure Analysis and Environmental Epidemiology}, volume = {11}, number = {6}, year = {2001}, pages = {490-500}, author = {Brauer, Michael and Ebelt, Stefanie T and Fisher, Teri V and Brumm, Jochen and Petkau, A.John and Vedal, Sverre} } @article {pmid11712876, title = {Extended out-of-hospital low-molecular-weight heparin prophylaxis against deep venous thrombosis in patients after elective hip arthroplasty: a systematic review}, journal = {Ann. Intern. Med.}, volume = {135}, number = {10}, year = {2001}, month = {Nov}, pages = {858{\textendash}869}, author = {Hull, R. D. and Pineo, G. F. and Stein, P. D. and Mah, A. F. and MacIsaac, S. M. and Dahl, O. E. and Butcher, M. and Brant, R. F. and Ghali, W. A. and Bergqvist, D. and Raskob, G. E.} } @article {pmid12933635, title = {Gene expression analysis with the parametric bootstrap}, journal = {Biostatistics}, volume = {2}, number = {4}, year = {2001}, month = {Dec}, pages = {445{\textendash}461}, abstract = {Recent developments in microarray technology make it possible to capture the gene expression profiles for thousands of genes at once. With this data researchers are tackling problems ranging from the identification of {\textquoteright}cancer genes{\textquoteright} to the formidable task of adding functional annotations to our rapidly growing gene databases. Specific research questions suggest patterns of gene expression that are interesting and informative: for instance, genes with large variance or groups of genes that are highly correlated. Cluster analysis and related techniques are proving to be very useful. However, such exploratory methods alone do not provide the opportunity to engage in statistical inference. Given the high dimensionality (thousands of genes) and small sample sizes (often <30) encountered in these datasets, an honest assessment of sampling variability is crucial and can prevent the over-interpretation of spurious results. We describe a statistical framework that encompasses many of the analytical goals in gene expression analysis; our framework is completely compatible with many of the current approaches and, in fact, can increase their utility. We propose the use of a deterministic rule, applied to the parameters of the gene expression distribution, to select a target subset of genes that are of biological interest. In addition to subset membership, the target subset can include information about relationships between genes, such as clustering. This target subset presents an interesting parameter that we can estimate by applying the rule to the sample statistics of microarray data. The parametric bootstrap, based on a multivariate normal model, is used to estimate the distribution of these estimated subsets and relevant summary measures of this sampling distribution are proposed. We focus on rules that operate on the mean and covariance. Using Bernstein{\textquoteright}s Inequality, we obtain consistency of the subset estimates, under the assumption that the sample size converges faster to infinity than the logarithm of the number of genes. We also provide a conservative sample size formula guaranteeing that the sample mean and sample covariance matrix are uniformly within a distance epsilon > 0 of the population mean and covariance. The practical performance of the method using a cluster-based subset rule is illustrated with a simulation study. The method is illustrated with an analysis of a publicly available leukemia data set.}, author = {Van Der Laan, M. J. and Bryan, J.} } @article {chen2001jackknife, title = {Jackknife variance estimation for nearest-neighbor imputation}, journal = {Journal of the American Statistical Association}, volume = {96}, number = {453}, year = {2001}, pages = {260{\textendash}269}, publisher = {Taylor \& Francis}, author = {Chen, Jiahua and Shao, Jun} } @article {chen2001large, title = {Large sample distribution of the likelihood ratio test for normal mixtures}, journal = {Statistics \& probability letters}, volume = {52}, number = {2}, year = {2001}, pages = {125{\textendash}133}, publisher = {Elsevier}, author = {Chen, Hanfeng and Chen, Jiahua} } @article {chen2001likelihood, title = {The likelihood ratio test for homogeneity in finite mixture models}, journal = {Canadian Journal of Statistics}, volume = {29}, number = {2}, year = {2001}, pages = {201{\textendash}215}, publisher = {Wiley Online Library}, author = {Chen, Hanfeng and Chen, Jiahua} } @article {berrendero2001maxbias, title = {The maxbias curve of robust regression estimates}, journal = {The Annals of Statistics}, volume = {29}, year = {2001}, pages = {224{\textendash}251}, author = {Berrendero, J.R. and Zamar, RH} } @article {Gustafson2001a, title = {On measuring sensitivity to parametric model misspecification}, journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)}, volume = {63}, number = {1}, year = {2001}, pages = {81{\textendash}94}, publisher = {Wiley Online Library}, doi = {10.1111/1467-9868.00277}, author = {Gustafson, Paul} } @article {chen2001modified, title = {A modified likelihood ratio test for homogeneity in finite mixture models}, journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)}, volume = {63}, number = {1}, year = {2001}, pages = {19{\textendash}29}, publisher = {Wiley Online Library}, author = {Chen, Hanfeng and Chen, Jiahua and Kalbfleisch, John D} } @article {wu_multiple_2001, title = {A multiple imputation method for missing covariates in non-linear mixed-effects models with application to HIV dynamics}, journal = {Statistics in Medicine}, volume = {20}, number = {12}, year = {2001}, pages = {1755{\textendash}1769}, abstract = {We propose a three-step multiple imputation method, implemented by Gibbs sampler, for estimating parameters in non-linear mixed-effects models with missing covariates. Estimates obtained by the proposed multiple imputation method are compared to those obtained by the mean-value imputation method and the complete-case method through simulations. We find that the proposed multiple imputation method offers smaller biases and smaller mean-squared errors for the estimates of covariate coefficients compared to other two methods. We apply the three missing data methods to modelling HIV viral dynamics from an AIDS clinical trial. We believe that the results from the proposed multiple imputation method are more reliable than that from the other two commonly used methods. Copyright {\textcopyright} 2001 John Wiley \& Sons, Ltd.}, issn = {1097-0258}, doi = {10.1002/sim.816}, url = {http://onlinelibrary.wiley.com/doi/10.1002/sim.816/abstract}, author = {Wu, Hulin and WU, LANG} } @article { ISI:000167262200012, title = {Multivariate extreme value distributions and coverage of ranking probabilities}, journal = {Journal of Mathematical Psychology}, volume = {45}, number = {1}, year = {2001}, month = {FEB}, pages = {180-188}, abstract = {The main result in this paper is that the class of multivariate extreme value distributions, when used as random utility models, can approximate all ranking probability distributions. This extends Theorem 1 of Dagsvik (1995). (C) 2001 Academic Press.}, issn = {0022-2496}, doi = {10.1006/jmps.1999.1294}, author = {Joe, H} } @article {fraiman2001optimal, title = {Optimal robust M-estimates of location}, journal = {Annals of statistics}, year = {2001}, pages = {194{\textendash}223}, publisher = {JSTOR}, author = {Fraiman, Ricardo and Yohai, V{\'\i}ctor J and Zamar, Ruben H} } @article {pmid11136169, title = {Poor long-term survival after coronary angiography in patients with renal insufficiency}, journal = {Am. J. Kidney Dis.}, volume = {37}, number = {1}, year = {2001}, month = {Jan}, pages = {64{\textendash}72}, author = {Hemmelgarn, B. R. and Ghali, W. A. and Quan, H. and Brant, R. and Norris, C. M. and Taub, K. J. and Knudtson, M. L.} } @article {cadigan2001properties, title = {Properties of robust m-estimators for poisson and negative binomial data*}, journal = {Journal of Statistical Computation and Simulation}, volume = {70}, number = {3}, year = {2001}, pages = {273{\textendash}288}, publisher = {Gordon and Breach Science Publishers}, author = {Cadigan, NG and Chen, J} } @article {78276, title = {The Ramp-Up Challenge in Open-Source Software Projects}, year = {2001}, author = {Davor Cubranic} } @inbook {hu2001relevance, title = {The relevance weighted likelihood with applications}, booktitle = {Empirical Bayes and Likelihood Inference}, year = {2001}, pages = {211{\textendash}235}, publisher = {Springer}, organization = {Springer}, author = {Hu, F.eifang and Zidek, James V} } @article {pmid11556927, title = {Risk adjustment using administrative data: impact of a diagnosis-type indicator}, journal = {J Gen Intern Med}, volume = {16}, number = {8}, year = {2001}, month = {Aug}, pages = {519{\textendash}524}, author = {Ghali, W. A. and Quan, H. and Brant, R.} } @conference {knorr2001robust, title = {Robust space transformations for distance-based operations}, booktitle = {Proceedings of the seventh ACM SIGKDD international conference on Knowledge discovery and data mining}, year = {2001}, pages = {126{\textendash}135}, publisher = {ACM}, organization = {ACM}, author = {Knorr, Edwin M and Ng, Raymond T and Zamar, Ruben H} } @article {le2001spatial, title = {Spatial prediction and temporal backcasting for environmental fields having monotone data patterns}, journal = {Canadian Journal of Statistics}, volume = {29}, number = {4}, year = {2001}, pages = {529{\textendash}554}, publisher = {Wiley Online Library}, author = {Le, Nhu and Sun, Li and Zidek, James V} } @article {chen_statistical_2001, title = {Statistical methods for deterministic biomathematical models}, journal = {Proceedings of the 53rd session of the international statistical institute, Seoul, Korea}, year = {2001}, url = {http://scholar.google.com/scholar?cluster=15064797966098008106\&hl=en\&oi=scholarr}, author = {Chen, Victoria CP and Welch, William J.} } @booklet {chen2001tests, title = {Tests for homogeneity in normal mixtures with presence of a structural parameter: technical details}, year = {2001}, publisher = {Working Paper 2001-06 Department of Statistics and Actuarial Science, University of Waterloo}, author = {Chen, Hanfeng and Chen, Jiahua} } @article {pmid11525697, title = {Timing of initial administration of low-molecular-weight heparin prophylaxis against deep vein thrombosis in patients following elective hip arthroplasty: a systematic review}, journal = {Arch. Intern. Med.}, volume = {161}, number = {16}, year = {2001}, month = {Sep}, pages = {1952{\textendash}1960}, author = {Hull, R. D. and Pineo, G. F. and Stein, P. D. and Mah, A. F. and MacIsaac, S. M. and Dahl, O. E. and Ghali, W. A. and Butcher, M. S. and Brant, R. F. and Bergqvist, D. and Hamulyak, K. and Francis, C. W. and Marder, V. J. and Raskob, G. E.} } @conference {265313, title = {Anchored conversations: chatting in the context of a document}, booktitle = {Computer Human Interaction}, year = {2000}, pages = {454{\textendash}461}, doi = {10.1145/332040.332475}, author = {Elizabeth F. Churchill and Jonathan Trevor and Sara A. Bly and Les Nelson and Davor Cubranic} } @article {pmid10722770, title = {Automated analysis of digital oximetry in the diagnosis of obstructive sleep apnoea}, journal = {Thorax}, volume = {55}, number = {4}, year = {2000}, month = {Apr}, pages = {302{\textendash}307}, author = {Vazquez, J. C. and Tsai, W. H. and Flemons, W. W. and Masuda, A. and Brant, R. and Hajduk, E. and Whitelaw, W. A. and Remmers, J. E.} } @article {chen2000bahadur, title = {Bahadur representations of the empirical likelihood quantile processes}, journal = {Journal of nonparametric statistics}, volume = {12}, number = {5}, year = {2000}, pages = {645{\textendash}660}, publisher = {Gordon and Breach Science Publishers}, author = {Chen, Hanfeng and Chen, Jiahua} } @booklet {kibria2000bayesian, title = {A Bayesian Approach to Backcasting and Spatially Predicting Unmeasured Multivariate Random Space-Time Fields With Application to PM 2, 5}, number = {192}, year = {2000}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancover, BC}, author = {Kibria, BM Golam and Sun, Li and Zidek, James V. and Le, Nhu D.} } @article {Gustafson2000a, title = {Bayesian regression modeling with interactions and smooth effects}, journal = {Journal of the American Statistical Association}, volume = {95}, number = {451}, year = {2000}, pages = {795{\textendash}806}, publisher = {Taylor \& Francis}, doi = {10.2307/2669463}, author = {Gustafson, Paul} } @article {chen2000biases, title = {Biases and variances of survey estimators based on nearest neighbor imputation}, journal = {Journal of Official Statistics}, volume = {16}, year = {2000}, pages = {113{\textendash}132}, author = {Chen, Jiahua and Shao, Jun} } @article {pmid10966537, title = {A Canadian comparison of data sources for coronary artery bypass surgery outcome "report cards"}, journal = {Am. Heart J.}, volume = {140}, number = {3}, year = {2000}, month = {Sep}, pages = {402{\textendash}408}, author = {Ghali, W. A. and Rothwell, D. M. and Quan, H. and Brant, R. and Tu, J. V.} } @conference {zidek2000combining, title = {Combining statistical and computer models for health risk assessment (exposure analysis)}, booktitle = {Statistical Modelling, Proceedings of the 15th International Workshop on Statistical Modelling: New Trends in Statistical Modelling. Universidad del Pais Vasco, Bilbao}, year = {2000}, pages = {95{\textendash}106}, author = {Zidek, J.V. and Meloche, J and Le, N.D. and Sun, L} } @article {heckman2000comparing, title = {Comparing the shapes of regression functions}, journal = {Biometrika}, volume = {87}, number = {1}, year = {2000}, pages = {135{\textendash}144}, publisher = {Biometrika Trust}, author = {Heckman, Nancy E and Zamar, Ruben H} } @article {heckman_comparing_2000, title = {Comparing the shapes of regression functions}, journal = {Biometrika}, volume = {87}, number = {1}, year = {2000}, pages = {135{\textendash}144}, url = {http://biomet.oxfordjournals.org/content/87/1/135.short}, author = {Heckman, Nancy E. and Zamar, Ruben H.} } @article { ISI:000086307400011, title = {Comparing the shapes of regression functions}, journal = {BIOMETRIKA}, volume = {87}, number = {1}, year = {2000}, month = {MAR}, pages = {135-144}, publisher = {BIOMETRIKA TRUST}, type = {Article}, address = {UNIV COLLEGE LONDON GOWER ST-BIOMETRIKA OFFICE, LONDON, ENGLAND WC1E 6BT}, abstract = {Does a regression function follow a specified shape? Do two regression functions have the same shape? How can regression functions be grouped, based on shape? These questions can occur when investigating monotonicity, when counting local maxima or when studying variation in families of curves. One can address these questions by considering the rank correlation coefficient between two functions. This correlation is a generalisation of the rank correlation between two finite sets of numbers and is equal to one if and only if the two functions have the same shape. A sample rank correlation based on smoothed estimates of the regression functions consistently estimates the true correlation This sample rank correlation can be used as a measure of similarity between functions in cluster analysis and as a measure of monotonicity or modality.}, keywords = {bump-hunting, monotone function, nonparametric regression, rank correlation}, issn = {0006-3444}, doi = {10.1093/biomet/87.1.135}, author = {Heckman, NE and Zamar, RH} } @article {zidek2000designing, title = {Designing and integrating composite networks for monitoring multivariate Gaussian pollution fields}, journal = {Journal of the Royal Statistical Society: Series C (Applied Statistics)}, volume = {49}, number = {1}, year = {2000}, pages = {63{\textendash}79}, publisher = {Wiley Online Library}, author = {Zidek, James V and Sun, Weimin and Le, Nhu D.} } @article {zidek2000discussion, title = {Discussion of {\textquoteleft}{\textquoteleft}The estimating function bootstrap{\textquoteright}{\textquoteright} (authors Hu, F. and Kalbfleisch, J.D.)}, journal = {Canadian Journal of Statistics}, volume = {28}, number = {3}, year = {2000}, pages = {482{\textendash}484}, publisher = {Statistical Science Association of Canada}, author = {Zidek, James V. and Wang, Steven X.} } @article {pmid11152403, title = {Effect on lipid, complete blood count and blood proteins of a standardized preparation for drawing blood: a randomized controlled trial}, journal = {Clin Invest Med}, volume = {23}, number = {6}, year = {2000}, month = {Dec}, pages = {350{\textendash}354}, author = {Campbell, N. R. and Edwards, A. L. and Brant, R. and Jones, C. and Mitchell, D.} } @article {wu_efficiency2000, title = {Efficiency of Lattice Conditional Independence Models for Missing Continuous Data}, journal = {Communication in Statistics}, volume = {29}, year = {2000}, pages = {481{\textendash}509}, author = {Wu, L and Perlman, MD} } @article {chen2000efficient, title = {Efficient random imputation for missing data in complex surveys}, journal = {Statistica Sinica}, volume = {10}, number = {4}, year = {2000}, pages = {1153{\textendash}1170}, publisher = {C/O DR HC HO, INST STATISTICAL SCIENCE, ACADEMIA SINICA, TAIPEI 115, TAIWAN}, author = {Chen, J and Rao, JNK and Sitter, RR} } @article {zhong2000empirical, title = {Empirical likelihood inference in the presence of measurement error}, journal = {Canadian Journal of Statistics}, volume = {28}, number = {4}, year = {2000}, pages = {841{\textendash}852}, publisher = {Wiley Online Library}, author = {Zhong, Bob and Chen, Jiahua and Rao, Jon NK} } @article {ebelt2000exposure, title = {Exposure of chronic obstructive pulmonary disease patients to particulate matter: Relationships between personal and ambient air concentrations}, journal = {Journal of the Air and Waste Management Association}, volume = {50}, number = {7}, year = {2000}, pages = {1081{\textendash}1094}, publisher = {Taylor \& Francis}, author = {Ebelt, Stefanie T and Petkau, A.John and Vedal, Sverre and Fisher, Teri V and Brauer, Michael} } @inbook {paszner2000impact, title = {Impact of antibodies to interferon-β during treatment of multiple sclerosis}, booktitle = {Drug Treatment of Multiple Sclerosis}, year = {2000}, pages = {89{\textendash}108}, publisher = {Adis International}, organization = {Adis International}, address = {Auckland}, author = {Paszner, B and Petkau, J and Oger, J} } @article {Joe2000, title = {Inequalities for random utility models, with applications to ranking and subset choice data}, journal = {Methodology and Computing in Applied Probability}, volume = {2}, number = {4}, year = {2000}, pages = {359{\textendash}372}, publisher = {Springer}, doi = {10.1023/A:1010058117460}, author = {Joe, H.} } @article {sun2000interpolating, title = {Interpolating Vancouver{\textquoteright}s daily ambient PM10 field}, journal = {Environmetrics}, volume = {11}, number = {6}, year = {2000}, pages = {651{\textendash}663}, publisher = {Wiley Online Library}, author = {Sun, Li and Zidek, James V and Le, Nhu D. and Ozkaynak, Haluk} } @article {wu_lattice_2000, title = {Lattice conditional independence models for seemingly unrelated regressions}, journal = {Communications in Statistics - Simulation and Computation}, volume = {29}, number = {2}, year = {2000}, month = {jan}, pages = {361{\textendash}384}, abstract = {Seemingly unrelated regressions (SUR) models appear frequently in econometrics and in the analyses of repeated measures designs and longitudinal data. It is known that iterative algorithms are generally required to obtain the MLEs of the regression parameters. Under a minimal set of lattice conditional independence (LCI) restrictions imposed on the covariance structure, however, closed-form MLEs can be obtained by standard linear regression techniques (Andersson and Perlman, 1993, 1994, 1998). In this paper, simulation is used to study the efficiency of these LCI model-based estimators. We also propose two possible improvements of the usual two-stage estimators for the regression parameters.}, issn = {0361-0918}, doi = {10.1080/03610910008813617}, url = {http://dx.doi.org/10.1080/03610910008813617}, author = {WU, LANG and Permian, Michael D.} } @inbook {Gustafson2000, title = {Local robustness in Bayesian analysis}, booktitle = {Robust Bayesian Analysis}, year = {2000}, pages = {71{\textendash}88}, publisher = {Springer}, organization = {Springer}, doi = {10.1007/978-1-4612-1306-2_4}, author = {Gustafson, Paul} } @article {pmid10904465, title = {Low-molecular-weight heparin prophylaxis using dalteparin extended out-of-hospital vs in-hospital warfarin/out-of-hospital placebo in hip arthroplasty patients: a double-blind, randomized comparison. North American Fragmin Trial Investigators}, journal = {Arch. Intern. Med.}, volume = {160}, number = {14}, year = {2000}, month = {Jul}, pages = {2208{\textendash}2215}, author = {Hull, R. D. and Pineo, G. F. and Francis, C. and Bergqvist, D. and Fellenius, C. and Soderberg, K. and Holmqvist, A. and Mant, M. and Dear, R. and Baylis, B. and Mah, A. and Brant, R.} } @article {pmid10904464, title = {Low-molecular-weight heparin prophylaxis using dalteparin in close proximity to surgery vs warfarin in hip arthroplasty patients: a double-blind, randomized comparison. The North American Fragmin Trial Investigators}, journal = {Arch. Intern. Med.}, volume = {160}, number = {14}, year = {2000}, month = {Jul}, pages = {2199{\textendash}2207}, author = {Hull, R. D. and Pineo, G. F. and Francis, C. and Bergqvist, D. and Fellenius, C. and Soderberg, K. and Holmqvist, A. and Mant, M. and Dear, R. and Baylis, B. and Mah, A. and Brant, R.} } @article {pmid10647762, title = {Low-molecular-weight heparin vs heparin in the treatment of patients with pulmonary embolism. American-Canadian Thrombosis Study Group}, journal = {Arch. Intern. Med.}, volume = {160}, number = {2}, year = {2000}, month = {Jan}, pages = {229{\textendash}236}, author = {Hull, R. D. and Raskob, G. E. and Brant, R. F. and Pineo, G. F. and Elliott, G. and Stein, P. D. and Gottschalk, A. and Valentine, K. A. and Mah, A. F.} } @article {pmid10733054, title = {Mortality and institutionalization following hip fracture}, journal = {J Am Geriatr Soc}, volume = {48}, number = {3}, year = {2000}, month = {Mar}, pages = {283{\textendash}288}, author = {Cree, M. and Soskolne, C. L. and Belseck, E. and Hornig, J. and McElhaney, J. E. and Brant, R. and Suarez-Almazor, M.} } @article { ISI:000090091900002, title = {Multivariate survival functions with a min-stable property}, journal = {Journal of Multivariate Analysis}, volume = {75}, number = {1}, year = {2000}, month = {OCT}, pages = {13-35}, abstract = {This paper introduces and studies a class of multivariate survival functions with given univariate marginal G(0), called min-stable multivariate G(0)-distributions, which includes min-stable multivariate exponential distributions as a special case. The representation of the form of Pickands (1981) is derived, and some dependence and other properties of the class are given. The functional form of the class is G(0)(A), where A is a homogeneous function on R-+(n). Conditions are obtained for G(0) and A so that a proper multivariate survival function obtains. Interesting special cases are studied including the case where G(0) is a Gamma distribution. (C) 2000 Academic Press.}, issn = {0047-259X}, doi = {10.1006/jmva.1999.1891}, author = {Joe, H and Ma, C} } @article {chen2000nearest, title = {Nearest neighbor imputation for survey data}, journal = {JOURNAL OF OFFICIAL STATISTICS-STOCKHOLM-}, volume = {16}, number = {2}, year = {2000}, pages = {113{\textendash}132}, publisher = {ALMQVIST \& WIKSELL INTERNATIONAL}, author = {Chen, Jiahua and Shao, Jun} } @article {gustafson2000parametric, title = {Parametric Bayesian analysis of case-control data with imprecise exposure measurements}, journal = {Statistics \& probability letters}, volume = {47}, number = {4}, year = {2000}, pages = {357{\textendash}363}, publisher = {Elsevier}, doi = {10.1016/s0167-7152(99)00178-9}, author = {Gustafson, P. and Le, N.D. and Vall{\'e}e, M.} } @article {heckman_penalized_2000, title = {Penalized regression with model-based penalties}, journal = {Canadian Journal of Statistics}, volume = {28}, number = {2}, year = {2000}, pages = {241{\textendash}258}, url = {http://onlinelibrary.wiley.com/doi/10.2307/3315976/abstract}, author = {Heckman, Nancy E. and Ramsay, James O.} } @article { ISI:000090039100002, title = {Penalized regression with model-based penalties}, journal = {CANADIAN JOURNAL OF STATISTICS-REVUE CANADIENNE DE STATISTIQUE}, volume = {28}, number = {2}, year = {2000}, month = {JUN}, pages = {241-258}, publisher = {CANADIAN JOURNAL STATISTICS}, type = {Article}, address = {675 DENBURY AVENUE, OTTAWA, ON K2A 2P2, CANADA}, abstract = {Nonparametric regression techniques such as spline smoothing and local fitting depend implicitly on a parametric model. For instance, the cubic smoothing spline estimate of a regression function integral mu based on observations t(i), Y-i is the minimizer of Sigma {Y-i - mu>(*) over bar * (t(i))}(2) + lambda integral>(*) over bar *(mu{\textquoteright}{\textquoteright})(2). Since integral>(*) over bar *(mu{\textquoteright}{\textquoteright})(2) is zero when mu is a line, the cubic smoothing spline estimate favors the parametric model mu>(*) over bar * (t) = alpha (0) + alpha (1)t. Here the authors consider replacing integral>(*) over bar *(mu{\textquoteright}{\textquoteright})(2) with the mon general expression integral>(*) over bar * (L mu)(2) where L is a linear differential operator with possibly nonconstant coefficients. The resulting estimate of mu performs well, particularly if L mu is small. They present an O(n) algorithm far the computation of mu. This algorithm is applicable to a wide class of L{\textquoteright}s. They also suggest a method for the estimation of L. They study their estimates via simulation and apply them to several data sets.}, keywords = {nonparametric regression, penalized least squares, splines}, issn = {0319-5724}, doi = {10.2307/3315976}, author = {Heckman, NE and Ramsay, JO} } @article {pmid11128346, title = {Prediabetes and perinatal mortality}, journal = {Diabetes Care}, volume = {23}, number = {12}, year = {2000}, month = {Dec}, pages = {1752{\textendash}1754}, author = {Wood, S. L. and Sauve, R. and Ross, S. and Brant, R. and Love, E. J.} } @article {pmid11063955, title = {Prognostic significance of diabetes as a predictor of survival after cardiac catheterization. APPROACH Investigators. Alberta Provincial Program for Outcome Assessment in Coronary Heart Disease}, journal = {Am. J. Med.}, volume = {109}, number = {7}, year = {2000}, month = {Nov}, pages = {543{\textendash}548}, author = {Ghali, W. A. and Quan, H. and Norris, C. M. and Dzavik, V. and Naylor, C. D. and Mitchell, L. B. and Brant, R. and Knudtson, M. L.} } @article {pmid10895397, title = {The relationship between COMT genotype and the clinical effectiveness of tolcapone, a COMT inhibitor, in patients with Parkinson{\textquoteright}s disease}, journal = {Clin Neuropharmacol}, volume = {23}, number = {3}, year = {2000}, pages = {143{\textendash}148}, author = {Chong, D. J. and Suchowersky, O. and Szumlanski, C. and Weinshilboum, R. M. and Brant, R. and Campbell, N. R.} } @article {hu2000relevance, title = {Relevance weighted likelihood for dependent data}, journal = {Metrika}, volume = {51}, number = {3}, year = {2000}, pages = {223{\textendash}243}, publisher = {Springer}, author = {Hu, Feifang and Rosenberger, William F and Zidek, James V} } @article {york_sloan_2000, title = {The sloan digital sky survey: Technical summary}, journal = {The Astronomical Journal}, volume = {120}, number = {3}, year = {2000}, pages = {1579}, url = {http://iopscience.iop.org/1538-3881/120/3/1579}, author = {York, Donald G. and Adelman, J. and Anderson Jr, John E. and Anderson, Scott F. and Annis, James and Bahcall, Neta A. and Bakken, J. A. and Barkhouser, Robert and Bastian, Steven and Berman, Eileen and others} } @article {wu_model-restricted_2000, title = {Some model-restricted shrinkage estimators for contingency tables with missing data}, journal = {Metrika}, volume = {50}, number = {3}, year = {2000}, month = {apr}, pages = {221{\textendash}245}, abstract = {. For contingency tables with extensive missing data, the unrestricted MLE under the saturated model, computed by the EM algorithm, is generally unsatisfactory. In this case, it may be better to fit a simpler model by imposing some restrictions on the parameter space. Perlman and Wu (1999) propose lattice conditional independence (LCI) models for contingency tables with arbitrary missing data patterns. When this LCI model fits well, the restricted MLE under the LCI model is more accurate than the unrestricted MLE under the saturated model, but not in general. Here we propose certain empirical Bayes (EB) estimators that adaptively combine the best features of the restricted and unrestricted MLEs. These EB estimators appear to be especially useful when the observed data is sparse, even in cases where the suitability of the LCI model is uncertain. We also study a restricted EM algorithm (called the ER algorithm) with similar desirable features.}, keywords = {EM algorithm, empirical Bayes estimator, Key words: Sparse data, lattice conditional independence model, restricted maximum likelihood estimator}, issn = {0026-1335, 1435-926X}, doi = {10.1007/s001840050047}, url = {http://link.springer.com/article/10.1007/s001840050047}, author = {WU, LANG and Reeves, Jaxk and Perlman, Michael D.} } @article { ISI:000088077700002, title = {Testing for monotonicity of a regression mean by calibrating for linear functions}, journal = {ANNALS OF STATISTICS}, volume = {28}, number = {1}, year = {2000}, month = {FEB}, pages = {20-39}, publisher = {INST MATHEMATICAL STATISTICS}, type = {Article}, address = {IMS BUSINESS OFFICE-SUITE 7, 3401 INVESTMENT BLVD, HAYWARD, CA 94545 USA}, abstract = {A new approach to testing. for monotonicity of a regression mean, not requiring computation of a curve estimator or a bandwidth, is suggested. It is based on the notion of {\textquoteleft}{\textquoteleft}running gradients{\textquoteright}{\textquoteright} over short, intervals, although from some viewpoints it may be regarded as an analogue for monotonicity testing of the dip/excess mass approach for testing modality hypotheses about densities. Like the latter methods, the new technique does not suffer difficulties caused by almost-Bat parts of the target function. In fact, it is calibrated so as to work well for flat response curves, and as a result it has relatively good power properties in boundary cases where the curve exhibits shoulders. Ln this respect, as well as in its construction, the {\textquoteleft}{\textquoteleft}running gradients{\textquoteright}{\textquoteright} approach differs from alternative techniques based on the notion of a critical bandwidth.}, keywords = {bootstrap, calibration, curve estimation, Monte Carlo, response curve, running gradient}, issn = {0090-5364}, author = {Hall, P and Heckman, NE} } @article {hall_testing_2000, title = {Testing for monotonicity of a regression mean by calibrating for linear functions}, journal = {Annals of Statistics}, year = {2000}, pages = {20{\textendash}39}, url = {http://www.jstor.org/stable/2673980}, author = {Hall, Peter and Heckman, Nancy E.} } @article {wu_testing_2000, title = {Testing lattice conditional independence models based on monotone missing data}, journal = {Statistics \& Probability Letters}, volume = {50}, number = {2}, year = {2000}, month = {nov}, pages = {193{\textendash}201}, abstract = {Lattice conditional independence (LCI) models (Anderson and Perlman, 1991. Statist. Probab. Lett. 12, 465{\textendash}486; 1993 Ann. Statist. 21, 1318{\textendash}1358) can be applied to the analysis of missing data problems with non-monotone missing patterns. Closed-form maximum likelihood estimates can always be obtained under the LCI models naturally determined by the observed data patterns. In practice, it is important to test the appropriateness of LCI models. In the present paper, we derive explicit likelihood ratio tests for testing LCI models based on a monotone subset of the observed data.}, keywords = {likelihood ratio test, Multivariate normal data, Restricted maximum likelihood estimates}, issn = {0167-7152}, doi = {10.1016/S0167-7152(00)00098-5}, url = {http://www.sciencedirect.com/science/article/pii/S0167715200000985}, author = {WU, LANG and Perlman, Michael D.} } @article {mcmillan_analysis_1999, title = {Analysis of protein activity data by Gaussian stochastic process models}, journal = {Journal of Biopharmaceutical Statistics}, volume = {9}, number = {1}, year = {1999}, pages = {145{\textendash}160}, url = {http://www.tandfonline.com/doi/abs/10.1081/BIP-100101005}, author = {McMillan, Nancy J. and Sacks, Jerome and Welch, William J. and Gao, Feng} } @booklet {le1999bayesian, title = {Bayesian spatial interpolation and backcasting using Gaussian-generalized inverted Wishart model}, number = {185}, year = {1999}, publisher = {Department of Statistics, University of British Columbia}, author = {Le, N.D. and Sun, L and Zidek, J.V.} } @article {pmid10551186, title = {CABG in Canada}, journal = {CMAJ}, volume = {161}, number = {8}, year = {1999}, month = {Oct}, pages = {941}, author = {Ghali, W. A. and Quan, H. and Brant, R.} } @article {shirley_a._murphy_changes_1999, title = {Changes in Parents{\textquoteright} Mental Distress After the Violent Death of an Adolescent or Young Adult Child: A Longitudinal Prospective Analysis}, journal = {Death Studies}, volume = {23}, number = {2}, year = {1999}, month = {feb}, pages = {129{\textendash}159}, abstract = {

This study examined changes in bereaved parents{\textquoteright} mental distress following the violent deaths of their 12 - to 28 - year - old children . A community - based sample of 171 bereaved mothers and 90 fathers was recruited by a review of medical examiner records . Data were collected 4 , 12 , and 24 months post - death . Repeated measures analysis of variance showed significant reductions in 8 of 10 measures of mental distress among mothers and 4 of 10 for fathers , with the most change for both genders occurring between 4 and 12 months post - death . During the 2nd year of bereavement , mothers{\textquoteright} symptoms continued to decline , whereas fathers , who started out with less distress than mothers , reported slight increases in 5 of 10 symptom domains . Nonetheless , 2 years after the deaths , mothers{\textquoteright} mental distress scores were to 5 times higher than those of {\textquotedblright}typical{\textquotedblright} U . S . women and fathers{\textquoteright} scores were to 4 times higher than {\textquotedblright}typical{\textquotedblright} U . S . men . Of the 7 intervening variables , higher scores on self - esteem and self - efficacy predicted lower distress for mothers and fathers 4 , 12 , and 24 months post - death . Repressive coping was of distress among fathers . It was concluded that violent death bereavement sustained , distressing consequences on parents of children who die as a result of , homicides , and suicide .

}, issn = {0748-1187}, doi = {10.1080/074811899201118}, url = {http://dx.doi.org/10.1080/074811899201118}, author = {Murphy, SA and Gupta, AD and Cain, KC and Johnson, LC and Wu, L and Mekwa, J} } @article {ferretti1999class, title = {A class of locally and globally robust regression estimates}, journal = {Journal of the American Statistical Association}, volume = {94}, number = {445}, year = {1999}, pages = {174{\textendash}188}, publisher = {Taylor \& Francis}, author = {Ferretti, Nelida and Kelmansky, Diana and Yohai, V{\'\i}ctor J and Zamar, Ruben H} } @article {susko1999computational, title = {Computational methods for mixture estimation}, journal = {COMPUTING SCIENCE AND STATISTICS}, year = {1999}, pages = {432{\textendash}438}, author = {Susko, E and Kalbfleisch, J and Chen, J} } @conference {671024, title = {Computer-Supported Distance Art Therapy: Beyond Computerization}, booktitle = {World Conference on the WWW and Internet}, year = {1999}, pages = {272{\textendash}276}, author = {Davor Cubranic and Kate Collie and Kellogg S. Booth} } @conference {306113, title = {Coordinating Open-Source Software Development}, booktitle = {Workshop on Enabling Technologies: Infrastructure for Collaborative Enterprises}, year = {1999}, pages = {61{\textendash}68}, doi = {10.1109/ENABL.1999.805176}, author = {Davor Cubranic and Kellogg S. Booth} } @booklet {tsai1999competition, title = {Decision theory for spatial competition}, number = {99{\textendash}22}, year = {1999}, publisher = {Department of Statistics, Purdue University}, address = {West Lafayette, Indiana}, author = {Tsai, Wen-Chi and DasGupta, Anirban and Zidek, James V.} } @article {abt_design_1999, title = {Design and analysis for modeling and predicting spatial contamination}, journal = {Mathematical Geology}, volume = {31}, number = {1}, year = {1999}, pages = {1{\textendash}22}, url = {http://link.springer.com/article/10.1023/A:1007504329298}, author = {Abt, Markus and Welch, William J. and Sacks, Jerome} } @article {cutter1999development, title = {Development of a multiple sclerosis functional composite as a clinical trials outcome measure}, journal = {Brain}, volume = {122}, number = {5}, year = {1999}, pages = {871{\textendash}882}, publisher = {Oxford Univ Press}, author = {Cutter, Gary R and Baier, Monika L and Rudick, Richard A and Cookfair, Diane L and Fischer, Jill S and Petkau, John and Syndulko, Karl and Weinshenker, Brian G and Antel, Jack P and Confavreux, Christian and Ellison, G and Lublin, F and Millar, A.E. and Rao, S.M. and Reingold, S and Thompson, A and Willoughby, E} } @article {le1999discussion, title = {Discussion of {\textquoteleft}{\textquoteleft}Bayesian spatial prediction{\textquoteright}{\textquoteright} (authors Gaudard, N., Karson, M., Linder, E. and Sinha, D.)}, journal = {Environmental and Ecological Statistics}, volume = {6}, number = {2}, year = {1999}, pages = {173{\textendash}176}, publisher = {Springer}, author = {Le, Nhu D. and Sun, Li and Zidek, James V} } @article {perlman_emperors_1999, title = {The Emperor{\textquoteright}s new tests}, journal = {Statistical Science}, volume = {14}, number = {4}, year = {1999}, month = {nov}, pages = {355{\textendash}369}, abstract = {In the past two decades, striking examples of allegedly inferior likelihood ratio tests (LRT) have appeared in the statistical literature. These examples, which arise in multiparameter hypothesis testing problems, have several common features. In each case the null hypothesis is composite, the size LRT is not similar and hence biased, and competing size tests can be constructed that are less biased, or even unbiased, and that dominate the LRT in the sense of being everywhere more powerful. It is therefore asserted that in these examples and, by implication, many other testing problems, the LR criterion produces {\textquoteleft}{\textquoteleft}inferior,{\textquoteright}{\textquoteright} {\textquoteleft}{\textquoteleft}deficient,{\textquoteright}{\textquoteright} {\textquoteleft}{\textquoteleft} undesirable,{\textquoteright}{\textquoteright} or {\textquoteleft}{\textquoteleft}flawed{\textquoteright}{\textquoteright} statistical procedures. This message, which appears to be proliferating, is wrong. In each example it is the allegedly superior test that is flawed, not the LRT. At worst, the {\textquoteleft}{\textquoteleft}superior{\textquoteright}{\textquoteright} tests provide unwarranted and inappropriate inferences and have been deemed scientifically unacceptable by applied statisticians. This reinforces the well-documented but oft-neglected fact that the Neyman-Pearson theory desideratum of a more or most powerful size test may be scientifically inappropriate; the same is true for the criteria of unbiasedness and -admissibility. Although the LR criterion is not infallible, we believe that it remains a generally reasonable first option for non-Bayesian parametric hypothesis-testing problems.}, keywords = {a-admissibility, bioequivalence problem, d-admissibility, Fisher-Neyman debate, Hypothesis test, likelihood ratio test, multiple endpoints in clinical trials, multivariate one-sided alternatives, order-restricted hypotheses, power, significance test, size test, test for qualitative interactions, unbiased test}, issn = {0883-4237, 2168-8745}, doi = {10.1214/ss/1009212517}, url = {http://projecteuclid.org/euclid.ss/1009212517}, author = {Perlman, Michael D. and WU, LANG} } @article {pmid10495458, title = {Examining the minimum important difference}, journal = {Stat Med}, volume = {18}, number = {19}, year = {1999}, month = {Oct}, pages = {2593{\textendash}2603}, author = {Brant, R. and Sutherland, L. and Hilsden, R.} } @article {berrendero1999global, title = {Global robustness of location and dispersion estimates}, journal = {Statistics \& probability letters}, volume = {44}, number = {1}, year = {1999}, pages = {63{\textendash}72}, publisher = {Elsevier}, author = {Berrendero, Jos{\'e} R and Zamar, Ruben H} } @article {perlman_lattice_1999, title = {Lattice conditional independence models for contingency tables with non-monotone missing data patterns}, journal = {Journal of Statistical Planning and Inference}, volume = {79}, number = {2}, year = {1999}, month = {jul}, pages = {259{\textendash}287}, abstract = {In the analysis of non-monotone missing data patterns in multinomial distributions for contingency tables, it is known that explicit MLEs of the unknown parameters cannot be obtained. Iterative procedures such as the EM-algorithm are therefore required to obtain the MLEs. These iterative procedures, however, may offer several potential difficulties. Andersson and Perlman [Ann. Statist. 21 (1993) 1318{\textendash}1358] introduced lattice conditional independence (LCI) models for multivariate normal distributions, which can be applied to the analysis of non-monotone missing observations in continuous data (Andersson and Perlman, Statist. Probab. Lett. 12 (1991) 465{\textendash}486). In this paper, we show that LCI models may also be applied to the analysis of categorical data with non-monotone missing data patterns. Under a parsimonious set of LCI assumptions naturally determined by the observed data pattern, the likelihood function for the observed data can be factored as in the monotone case and explicit MLEs can be obtained for the unknown parameters. Furthermore, the LCI assumptions can be tested by explicit likelihood ratio tests.}, issn = {0378-3758}, doi = {10.1016/S0378-3758(99)00003-8}, url = {http://www.sciencedirect.com/science/article/pii/S0378375899000038}, author = {Perlman, Michael D. and WU, LANG} } @article {perlman_lattice1999, title = {Lattice Conditional Independence Models for Contingency Tables with Missing Data}, journal = {Journal of Statistical Planning and Inference}, volume = {79}, year = {1999}, pages = {259{\textendash}287}, author = {Perlman, MD and Wu, L} } @article {9514, title = {Lesion load reproducibility and statistical sensitivity of clinical trials in multiple sclerosis}, journal = {Neurology}, volume = {52}, year = {1999}, pages = {433-434}, type = {Letter }, author = {Cover, K.S. and Petkau, J. and Li, D.K.B. and Paty, D.W.} } @conference {zidek1999measuring, title = {Measuring and modelling pollution for risk analysis}, booktitle = {Novartis Foundation Symposium 220-Environmental Statistics: Analysing Data for Environmental Policy}, year = {1999}, pages = {105{\textendash}121}, publisher = {Wiley Online Library}, organization = {Wiley Online Library}, author = {Zidek, James V and Le, Nhu D.} } @article {eeden1999minimax, title = {Minimax estimation of a bounded scale parameter for scale-invariant squared-error loss}, journal = {Statistics and Risk Modeling}, volume = {17}, number = {1}, year = {1999}, pages = {1{\textendash}30}, author = {Eeden, Constance van and Zidek, James V} } @article {kastrukoff1999natural, title = {Natural killer cells in relapsing-remitting MS Effect of treatment with interferon β-1B}, journal = {Neurology}, volume = {52}, number = {2}, year = {1999}, pages = {351{\textendash}351}, publisher = {AAN Enterprises}, author = {Kastrukoff, LF and Morgan, NG and Zecchini, D and White, R and Petkau, AJ and Satoh, J and Paty, DW} } @article {kastrukoff1999natural, title = {Natural killer cells in relapsing-remitting multiple sclerosis: the effect of treatment with interferon β-1B}, journal = {Neurology}, volume = {52}, number = {2}, year = {1999}, pages = {351{\textendash}359}, publisher = {AAN Enterprises}, author = {Kastrukoff, LF and Morgan, NG and Zecchini, D and White, R and Petkau, A.John and Satoh, J and Paty, DW} } @article {paszner1999neutralising, title = {Neutralising antibodies to interferon-β in the treatment of multiple sclerosis: Cause for concern?}, journal = {CNS Drugs}, volume = {11}, number = {3}, year = {1999}, pages = {225{\textendash}243}, publisher = {Springer}, author = {Paszner, Beatrix and Petkau, John and Oger, Joel} } @article {bajorski1999nonparametric, title = {Nonparametric two-sample comparisons of changes on ordinal responses}, journal = {Journal of the American Statistical Association}, volume = {94}, number = {447}, year = {1999}, pages = {970{\textendash}978}, publisher = {Taylor \& Francis}, author = {Bajorski, Peter and Petkau, A.John} } @article {pmid9927095, title = {Preoperative vs postoperative initiation of low-molecular-weight heparin prophylaxis against venous thromboembolism in patients undergoing elective hip replacement}, journal = {Arch. Intern. Med.}, volume = {159}, number = {2}, year = {1999}, month = {Jan}, pages = {137{\textendash}141}, author = {Hull, R. D. and Brant, R. F. and Pineo, G. F. and Stein, P. D. and Raskob, G. E. and Valentine, K. A.} } @article {pmid10474539, title = {Prevalence and incidence of carpal tunnel syndrome in a meat packing plant}, journal = {Occup Environ Med}, volume = {56}, number = {6}, year = {1999}, month = {Jun}, pages = {417{\textendash}422}, author = {Gorsche, R. G. and Wiley, J. P. and Renger, R. F. and Brant, R. F. and Gemer, T. Y. and Sasyniuk, T. M.} } @article {chen1999pseudo, title = {A pseudo empirical likelihood approach to the effective use of auxiliary information in complex surveys}, journal = {Statistica Sinica}, volume = {9}, number = {2}, year = {1999}, pages = {385{\textendash}406}, publisher = {C/O DR HC HO, INST STATISTICAL SCIENCE, ACADEMIA SINICA, TAIPEI 115, TAIWAN}, author = {Chen, Jiahua and Sitter, RR} } @article {perlman_rejoinder1999, title = {Rejoinder to discussion of "The Emperor{\textquoteright}s New Tests"}, journal = {Statistical Science}, volume = {14}, year = {1999}, pages = {377{\textendash}381}, author = {Perlman, MD and Wu, L} } @article {mrawira_sensitivity_1999, title = {Sensitivity analysis of computer models: World Bank HDM-III model}, journal = {Journal of Transportation Engineering}, volume = {125}, number = {5}, year = {1999}, pages = {421{\textendash}428}, url = {http://ascelibrary.org/doi/abs/10.1061/(ASCE)0733-947X(1999)125:5(421)}, author = {Mrawira, Donath and Welch, William J. and Schonlau, Matthias and Haas, Ralph} } @conference {vedal1999very, title = {Very low concentrations of PM10 and daily mortality.}, booktitle = {AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE}, volume = {159}, number = {3}, year = {1999}, pages = {A322{\textendash}A322}, publisher = {AMER LUNG ASSOC 1740 BROADWAY, NEW YORK, NY 10019 USA}, organization = {AMER LUNG ASSOC 1740 BROADWAY, NEW YORK, NY 10019 USA}, author = {Vedal, S and Brauer, M and White, R and Petkau, J} } @article {vedal1998acute, title = {Acute effects of ambient inhalable particles in asthmatic and nonasthmatic children}, journal = {American Journal of Respiratory and Critical Care Medicine}, volume = {157}, number = {4}, year = {1998}, pages = {1034{\textendash}1043}, publisher = {Am Thoracic Soc}, author = {Vedal, Sverre and Petkau, John and White, Rick and Blair, Jim} } @article {vedal1998acute, title = {Acute effects of ambient inhalable particles in asthmatic and nonasthmatic children}, journal = {American Journal of Respiratory and Critical Care Medicine}, volume = {157}, number = {4}, year = {1998}, pages = {1034{\textendash}1043}, publisher = {Am Thoracic Soc}, author = {Vedal, Sverre and Petkau, John and White, Rick and Blair, Jim} } @article {sun1998assessment, title = {Assessment of a Bayesian multivariate interpolation approach for health impact studies}, journal = {Environmetrics}, volume = {9}, number = {5}, year = {1998}, pages = {565{\textendash}586}, publisher = {Wiley Online Library}, author = {Sun, Weimin and Le, Nhu D. and Zidek, James V and Burnett, Rick} } @article {aslett_circuit_1998, title = {Circuit optimization via sequential computer experiments: design of an output buffer}, journal = {Journal of the Royal Statistical Society: Series C (Applied Statistics)}, volume = {47}, number = {1}, year = {1998}, pages = {31{\textendash}48}, url = {http://onlinelibrary.wiley.com/doi/10.1111/1467-9876.00096/abstract}, author = {Aslett, Robert and Buck, Robert J. and Duvall, Steven G. and Sacks, Jerome and Welch, William J.} } @article {pmid9489816, title = {A clinical study of the relationship between silicone breast implants and connective tissue disease}, journal = {J. Rheumatol.}, volume = {25}, number = {2}, year = {1998}, month = {Feb}, pages = {254{\textendash}260}, author = {Edworthy, S. M. and Martin, L. and Barr, S. G. and Birdsell, D. C. and Brant, R. F. and Fritzler, M. J.} } @article {pmid9720544, title = {Compliance of clinical stage I nonseminomatous germ cell tumor patients with surveillance}, journal = {J. Urol.}, volume = {160}, number = {3 Pt 1}, year = {1998}, month = {Sep}, pages = {768{\textendash}771}, author = {Hao, D. and Seidel, J. and Brant, R. and Alexander, F. and Ernst, D. S. and Summers, N. and Russell, J. A. and Stewart, D. A.} } @conference {895315, title = {Computer support for distance art therapy}, booktitle = {Computer Human Interaction}, year = {1998}, pages = {277{\textendash}278}, doi = {10.1145/286498.286758}, author = {Davor Cubranic and Kellogg S. Booth and Kate Collie} } @article {susko1998constrained, title = {Constrained nonparametric maximum-likelihood estimation for mixture models}, journal = {Canadian Journal of Statistics}, volume = {26}, number = {4}, year = {1998}, pages = {601{\textendash}617}, publisher = {Wiley Online Library}, author = {Susko, E and Kalbfleisch, JD and Chen, J} } @article {pmid9834717, title = {Coronary artery bypass grafting in Canada: hospital mortality rates, 1992-1995}, journal = {CMAJ}, volume = {159}, number = {8}, year = {1998}, month = {Oct}, pages = {926{\textendash}930}, author = {Ghali, W. A. and Quan, H. and Brant, R.} } @article {pmid9679483, title = {Coronary artery bypass grafting in Canada: national and provincial mortality trends, 1992-1995}, journal = {CMAJ}, volume = {159}, number = {1}, year = {1998}, month = {Jul}, pages = {25{\textendash}31}, author = {Ghali, W. A. and Quan, H. and Brant, R.} } @article {pmid10183336, title = {Cuing effect of "all of the above" on the reliability and validity of multiple-choice test items}, journal = {Eval Health Prof}, volume = {21}, number = {1}, year = {1998}, month = {Mar}, pages = {120{\textendash}133}, author = {Harasym, P. H. and Leong, E. J. and Violato, C. and Brant, R. and Lorscheider, F. L.} } @article {pmid9562927, title = {Different effects of heparin in males and females}, journal = {Clin Invest Med}, volume = {21}, number = {2}, year = {1998}, month = {Apr}, pages = {71{\textendash}78}, author = {Campbell, N. R. and Hull, R. D. and Brant, R. and Hogan, D. B. and Pineo, G. F. and Raskob, G. E.} } @article {jones_efficient_1998, title = {Efficient global optimization of expensive black-box functions}, journal = {Journal of Global optimization}, volume = {13}, number = {4}, year = {1998}, pages = {455{\textendash}492}, url = {http://link.springer.com/article/10.1023/A:1008306431147}, author = {Jones, Donald R. and Schonlau, Matthias and Welch, William J.} } @article {pmid9717698, title = {Evaluation of reproductive outcomes in women inadvertently exposed to hexachlorobenzene in southeastern Turkey in the 1950s}, journal = {Reprod. Toxicol.}, volume = {12}, number = {4}, year = {1998}, pages = {469{\textendash}476}, author = {Jarrell, J. and Gocmen, A. and Foster, W. and Brant, R. and Chan, S. and Sevcik, M.} } @article {berrendero1998explosion, title = {On the explosion rate of maximum-bias functions}, journal = {The Canadian Journal of Statistics/La Revue Canadienne de Statistique}, year = {1998}, pages = {333{\textendash}351}, publisher = {JSTOR}, author = {Berrendero, Jos{\'e} R and Mazzi, Sonia and Romo, Juan and Zamar, Ruben H} } @article {abt_fisher_1998, title = {Fisher information and maximum-likelihood estimation of covariance parameters in Gaussian stochastic processes}, journal = {Canadian Journal of Statistics}, volume = {26}, number = {1}, year = {1998}, pages = {127{\textendash}137}, url = {http://onlinelibrary.wiley.com/doi/10.2307/3315678/abstract}, author = {Abt, Markus and Welch, William J.} } @article {gustafson1998flexible, title = {Flexible Bayesian modelling for survival data}, journal = {Lifetime Data Analysis}, volume = {4}, number = {3}, year = {1998}, pages = {281{\textendash}299}, publisher = {Springer}, author = {Gustafson, P.} } @article {pmid9665357, title = {Fluctuations in blood lipid levels during furosemide therapy: a randomized, double-blind, placebo-controlled crossover study}, journal = {Arch. Intern. Med.}, volume = {158}, number = {13}, year = {1998}, month = {Jul}, pages = {1461{\textendash}1463}, author = {Campbell, N. and Brant, R. and Stalts, H. and Stone, J. and Mahallati, H.} } @article {chen1998geometric, title = {Geometric quality inspection}, journal = {Statistica Sinica}, volume = {8}, number = {1}, year = {1998}, pages = {135{\textendash}149}, publisher = {C/O DR HC HO, INST STATISTICAL SCIENCE, ACADEMIA SINICA, TAIPEI 115, TAIWAN}, author = {Chen, Gemai and Chen, Jiahua} } @article {schonlau_global_1998, title = {Global versus local search in constrained optimization of computer models}, journal = {Lecture Notes-Monograph Series}, year = {1998}, pages = {11{\textendash}25}, url = {http://www.jstor.org/stable/4356058}, author = {Schonlau, Matthias and Welch, William J. and Jones, Donald R.} } @article {gustafson1998guided, title = {A guided walk Metropolis algorithm}, journal = {Statistics and computing}, volume = {8}, number = {4}, year = {1998}, pages = {357{\textendash}364}, publisher = {Springer}, author = {Gustafson, P.} } @article {chen1998identifiability, title = {On the identifiability of a supersaturated design}, journal = {Journal of Statistical Planning and Inference}, volume = {72}, number = {1}, year = {1998}, pages = {99{\textendash}107}, publisher = {North-Holland}, author = {Chen, Jiahua and Lin, Dennis KJ} } @article {zidek1998imputing, title = {Imputing unmeasured explanatory variables in environmental epidemiology with application to health impact analysis of air pollution}, journal = {Environmental and Ecological Statistics}, volume = {5}, number = {2}, year = {1998}, pages = {99{\textendash}105}, publisher = {Springer}, author = {Zidek, J.V. and White, R and Sun, W and Burnett, RT and Le, N.D.} } @article {zidek1998imputing, title = {Imputing unmeasured explanatory variables in environmental epidemiology with application to health impact analysis of air pollution}, journal = {Environmental and Ecological Statistics}, volume = {5}, number = {2}, year = {1998}, pages = {99{\textendash}105}, publisher = {Springer}, author = {Zidek, JV and White, R and Sun, W and Burnett, RT and Le, ND} } @article {zidek1998including, title = {Including structural measurement errors in the nonlinear regression analysis of clustered data}, journal = {Canadian Journal of Statistics}, volume = {26}, number = {4}, year = {1998}, pages = {537{\textendash}548}, publisher = {Wiley Online Library}, author = {Zidek, J.V. and Le, N.D. and Wong, H. and Burnett, RT} } @article {chen1998intelligent, title = {Intelligent search for 2\^ 1\^ 3\^-\^ 6 and 2\^ 1\^ 4\^-\^ 7 minimum aberration designs}, journal = {Statistica Sinica}, volume = {8}, number = {4}, year = {1998}, pages = {1265{\textendash}1270}, publisher = {C/O DR HC HO, INST STATISTICAL SCIENCE, ACADEMIA SINICA, TAIPEI 115, TAIWAN}, author = {Chen, Jiahua} } @article {le1998note, title = {A note on the existence of maximum likelihood estimates for Gaussian-inverted Wishart models}, journal = {Statistics and probability letters}, volume = {40}, number = {2}, year = {1998}, pages = {133{\textendash}137}, publisher = {Elsevier}, author = {Le, N and Sun, L and Zidek, J.V.} } @article {clarke1998overall, title = {On the overall sensitivity of the posterior distribution to its inputs}, journal = {Journal of statistical planning and inference}, volume = {71}, number = {1-2}, year = {1998}, pages = {137{\textendash}150}, publisher = {Elsevier}, doi = {10.1016/s0378-3758(98)00014-7}, author = {Clarke, B. and Gustafson, P.} } @article {chen1998penalized, title = {Penalized likelihood-ratio test for finite mixture models with multinomial observations}, journal = {Canadian Journal of Statistics}, volume = {26}, number = {4}, year = {1998}, pages = {583{\textendash}599}, publisher = {Wiley-Blackwell}, author = {Chen, Jiahua} } @article {pmid9636936, title = {Prevalence and incidence of stenosing flexor tenosynovitis (trigger finger) in a meat-packing plant}, journal = {J. Occup. Environ. Med.}, volume = {40}, number = {6}, year = {1998}, month = {Jun}, pages = {556{\textendash}560}, author = {Gorsche, R. and Wiley, J. P. and Renger, R. and Brant, R. and Gemer, T. Y. and Sasyniuk, T. M.} } @article {pmid9671383, title = {The pulmonary artery catheter takes a great fall}, journal = {Crit. Care Med.}, volume = {26}, number = {7}, year = {1998}, month = {Jul}, pages = {1288{\textendash}1289}, author = {Sandham, J. D. and Hull, R. D. and Brant, R. F.} } @article { ISI:000077504300010, title = {Random utility threshold models of subset choice}, journal = {Australian Journal of Psychology}, volume = {50}, number = {3}, year = {1998}, note = {8th Australasian Mathematical Psychology Conference, UNIV WESTERN AUSTRALIA, NEDLANDS, AUSTRALIA, NOV, 1997}, month = {DEC}, pages = {175-185}, abstract = {Subset choice denotes a situation in which decision makers are offered available sets from a fixed master set of choice alternatives and each decision maker is asked to choose a subset of any size from the available set. In this paper, we study the relationships between various random utility models of subset choice. Random utility threshold models of subset choice assume that there is a (random) utility associated with each available option, and a (random) utility threshold, such that the decision maker selects those options in the available set whose utilities are greater than or equal to the threshold, ii special case of the random utility threshold model is the latent scale model, in which the threshold has a constant value and the random variables associated with the available options are independent of each other. We show that the size-independent random utility model for approval voting of Falmagne and Regenwetter (1996) is a random utility threshold model, and develop numerous results relating that model to the class of random utility threshold models in general, and to the latent scale model in particular. Among the features distinguishing some of these models is a closure property that we call stability under substructures. The size-independent model is not stable, in the sense that certain marginals of a given size-independent model for n choice alternatives may violate all size-independent models for n - 1 choice alternatives. In contrast, the general class of random utility threshold models and also the specific subclass of latent scale models are stable under substructures.}, issn = {0004-9530}, doi = {10.1080/00049539808258794}, author = {Regenwetter, M and Marley, A A J and Joe, H} } @article {kastrukoff1998role, title = {A role for natural killer cells in the immunopathogenesis of multiple sclerosis}, journal = {Journal of Neuroimmunology}, volume = {86}, number = {2}, year = {1998}, pages = {123{\textendash}133}, publisher = {Elsevier}, author = {Kastrukoff, Lorne F and Morgan, Norma G and Zecchini, Daniel and White, Richard and Petkau, A.John and Satoh, Junichi and Paty, Donald W} } @article {petkau1997statistical, title = {Statistical methods for evaluating multiple sclerosis therapies.}, journal = {Seminars in Neurology}, volume = {18}, number = {3}, year = {1998}, pages = {351{\textendash}375}, author = {Petkau, A.John} } @article {Bryan1998, title = {Temporal trends in survival after AIDS in California, 1985 - 1994}, journal = {California HIV/AIDS Update}, volume = {11}, year = {1998}, pages = {88 - 29}, author = {Bryan, J. and Sun, R.} } @article {zidek1998using, title = {Using spatial data in assessing the association between air pollution episodes and respiratory morbidity}, journal = {Statistics for the Environment}, volume = {4}, year = {1998}, pages = {117{\textendash}136}, author = {Zidek, J.V. and White, R and Le, N.D.} } @article {le1997bayesian, title = {Bayesian multivariate spatial interpolation with data missing by design}, journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)}, volume = {59}, number = {2}, year = {1997}, pages = {501{\textendash}510}, publisher = {Wiley Online Library}, author = {Le, Nhu D. and Sun, Weimin and Zidek, James V} } @article {pmid9006562, title = {Declining sex ratios in Canada}, journal = {CMAJ}, volume = {156}, number = {1}, year = {1997}, month = {Jan}, pages = {37{\textendash}41}, author = {Allan, B. B. and Brant, R. and Seidel, J. E. and Jarrell, J. F.} } @article {zidek1997discussion, title = {Discussion of {\textquoteleft}{\textquoteleft}Predicting multivariate responses in multiple linear regression{\textquoteright}{\textquoteright} (Authors. Breiman, L. and Friedman, J.)}, journal = {Journal of the Royal Statistical Society, Series B}, volume = {59}, number = {1}, year = {1997}, pages = {42{\textendash}43}, author = {Zidek, J.V.} } @conference {gough1997efficient, title = {Efficient experimental design strategy for numerical ocean modelling}, booktitle = {Canadian Meteorological and Oceanographic Society Bulletin}, volume = {25}, number = {5}, year = {1997}, pages = {95{\textendash}102}, author = {Gough, WA and Welch, WJ} } @article {sitter1997fractional, title = {Fractional Resolution and Minimum Aberration in Blocked 2 n{\textemdash}k Designs}, journal = {Technometrics}, volume = {39}, number = {4}, year = {1997}, pages = {382{\textendash}390}, publisher = {Taylor \& Francis Group}, author = {Sitter, Randy R and Chen, Jiahua and Feder, Moshe} } @article {pmid9361572, title = {The importance of initial heparin treatment on long-term clinical outcomes of antithrombotic therapy. The emerging theme of delayed recurrence}, journal = {Arch. Intern. Med.}, volume = {157}, number = {20}, year = {1997}, month = {Nov}, pages = {2317{\textendash}2321}, author = {Hull, R. D. and Raskob, G. E. and Brant, R. F. and Pineo, G. F. and Valentine, K. A.} } @article {pmid9292473, title = {Interaction of cross-sectional area, driving pressure, and airflow of passive velopharynx}, journal = {J. Appl. Physiol.}, volume = {83}, number = {3}, year = {1997}, month = {Sep}, pages = {851{\textendash}859}, author = {Isono, S. and Feroah, T. R. and Hajduk, E. A. and Brant, R. and Whitelaw, W. A. and Remmers, J. E.} } @article {zidek1997interpolating, title = {Interpolating air pollution for health impact assessment}, journal = {Barnett V, Feridun Turkman K, editors. Statistics for the environment}, volume = {3}, year = {1997}, pages = {251{\textendash}68}, author = {Zidek, J.V.} } @article {gustafson1997large, title = {Large hierarchical Bayesian analysis of multivariate survival data}, journal = {Biometrics}, year = {1997}, pages = {230{\textendash}242}, publisher = {JSTOR}, doi = {10.2307/2533110}, url = {www.jstor.org/stable/2533110}, author = {Gustafson, P.} } @article {heckman1997line, title = {Line transects of two-dimensional random fields: Estimation and design}, journal = {Canadian Journal of Statistics}, volume = {25}, number = {4}, year = {1997}, pages = {481{\textendash}501}, publisher = {Wiley Online Library}, author = {Heckman, Nancy and Rice, John} } @article {d1997longitudinal, title = {Longitudinal analyses for magnetic resonance imaging outcomes in multiple sclerosis clinical trials}, journal = {Journal of Biopharmaceutical Statistics}, volume = {7}, number = {4}, year = {1997}, pages = {501{\textendash}531}, publisher = {Taylor \& Francis}, author = {D{\textquoteright}yachkova, Yulia and Petkau, John and Whtie, Rick} } @article {justel1997multivariate, title = {A multivariate Kolmogorov-Smirnov test of goodness of fit}, journal = {Statistics \& Probability Letters}, volume = {35}, number = {3}, year = {1997}, pages = {251{\textendash}259}, publisher = {Elsevier}, author = {Justel, Ana and Pena, Daniel and Zamar, Ruben} } @book {Joe1997, title = {Multivariate Models and Dependence Concepts}, year = {1997}, publisher = {Chapman \& Hall}, organization = {Chapman \& Hall}, address = {London}, url = {http://www.crcpress.com/product/isbn/9780412073311}, author = {Joe, Harry} } @article {petkau1997neutralizing, title = {Neutralizing antibodies and the efficacy of interferon beta-1b in relapsing-remitting multiple sclerosis}, journal = {Multiple Sclerosis}, volume = {3}, number = {6}, year = {1997}, pages = {402{\textendash}402}, publisher = {SAGE Publications}, author = {Petkau, J and White, R} } @article {yohai1997optimal, title = {Optimal locally robust M-estimates of regression}, journal = {Journal of Statistical Planning and Inference}, volume = {64}, number = {2}, year = {1997}, pages = {309{\textendash}323}, publisher = {Elsevier}, author = {Yohai, V{\'\i}ctor J and Zamar, Ruben H} } @article {rudick1997recommendations, title = {Recommendations from the National Multiple Sclerosis Society clinical outcomes assessment task force}, journal = {Annals of Neurology}, volume = {42}, number = {3}, year = {1997}, pages = {379{\textendash}382}, publisher = {Wiley Online Library}, author = {Rudick, Richard and Antel, Jack and Confavreux, Christian and Cutter, Gary and Ellison, George and Fischer, Jill and Lublin, Fred and Miller, Aaron and Petkau, John and Rao, Stephen and Reingold, S and Syndulko, K and Thompson, A and Wallenberg, J and Weinshenker, B and Willoughby, E} } @article {pmid9167605, title = {Reduction in blood culture contamination rate by feedback to phlebotomists}, journal = {Arch. Pathol. Lab. Med.}, volume = {121}, number = {5}, year = {1997}, month = {May}, pages = {503{\textendash}507}, author = {Gibb, A. P. and Hill, B. and Chorel, B. and Brant, R.} } @article {pmid9531224, title = {Relation between the time to achieve the lower limit of the APTT therapeutic range and recurrent venous thromboembolism during heparin treatment for deep vein thrombosis}, journal = {Arch. Intern. Med.}, volume = {157}, number = {22}, year = {1997}, pages = {2562{\textendash}2568}, author = {Hull, R. D. and Raskob, G. E. and Brant, R. F. and Pineo, G. F. and Valentine, K. A.} } @article {liu1997segmented, title = {On segmented multivariate regression}, journal = {Statistica Sinica}, year = {1997}, pages = {497{\textendash}525}, author = {Liu, Jian and Wu, Shiying and Zidek, James V} } @article {pena1997simple, title = {A simple diagnostic tool for local prior sensitivity}, journal = {Statistics \& probability letters}, volume = {36}, number = {2}, year = {1997}, pages = {205{\textendash}212}, publisher = {Elsevier}, author = {Pena, Daniel and Zamar, Ruben} } @article {pmid9161739, title = {Sorbitol 2.5\% mannitol 0.54\% irrigation solution for hysteroscopic endometrial ablation surgery}, journal = {Can J Anaesth}, volume = {44}, number = {5 Pt 1}, year = {1997}, month = {May}, pages = {473{\textendash}478}, author = {Moir, C. L. and Mandin, H. and Brant, R.} } @article {BlockJoe1997, title = {Tail behavior of the failure rate functions of mixtures}, journal = {Lifetime Data Analysis}, volume = {3}, number = {3}, year = {1997}, pages = {269{\textendash}288}, publisher = {Springer}, doi = {10.1023/A:1009653032333}, author = {Block, H. and Joe, H.} } @article {chen1997testing, title = {On testing the number of components in finite mixture models with known relevant component distributions}, journal = {Canadian Journal of Statistics}, volume = {25}, number = {3}, year = {1997}, pages = {389{\textendash}400}, publisher = {Wiley-Blackwell}, author = {Chen, Jiahua and Cheng, Ping} } @article {pmid8774204, title = {Aging and heparin-related bleeding}, journal = {Arch. Intern. Med.}, volume = {156}, number = {8}, year = {1996}, month = {Apr}, pages = {857{\textendash}860}, author = {Campbell, N. R. and Hull, R. D. and Brant, R. and Hogan, D. B. and Pineo, G. F. and Raskob, G. E.} } @article { ISI:A1996VD98600005, title = {Analysis of trends in tropospheric ozone in the Lower Fraser Valley, British Columbia}, journal = {Atmospheric Environment}, volume = {30}, number = {20}, year = {1996}, month = {OCT}, pages = {3413-3421}, abstract = {A method of trend detection for high quantiles of a pollutant such as ozone is presented and applied to 1978-1990 data from two stations downwind of the city of Vancouver in the Lower Fraser Valley, British Columbia. Theories of order restricted inference and isotonic regression are used for the method. The new statistical methodologies in this article are (a) the use of the chi-square bar statistic from order restricted inference for estimators that are asymptotically normal and (b) a method for obtaining standard errors for estimators from (pollutant) data that are serially correlated. Our analysis uncovers opposite trends in pollution data at the two stations. We interpret these trends as due to recent changes in population distribution in the Lower Fraser Valley. Copyright (C) 1996 Elsevier Science Ltd}, issn = {1352-2310}, doi = {10.1016/1352-2310(96)00045-3}, author = {Joe, H and Steyn, D G and Susko, E} } @article {Gustafson1996e, title = {Aspects of Bayesian Robustness in Hierarchical Models [With Discussion and Rejoinder]}, journal = {Lecture Notes-Monograph Series}, year = {1996}, pages = {63{\textendash}80}, publisher = {JSTOR}, author = {Gustafson, Paul} } @book {pena1996bayesian, title = {On Bayesian robustness: an asymptotic approach}, year = {1996}, publisher = {Springer}, organization = {Springer}, author = {Pena, Daniel and Zamar, Ruben H} } @article {zidek1996causality, title = {Causality, measurement error and multicollinearity in epidemiology}, journal = {Environmetrics}, volume = {7}, number = {4}, year = {1996}, pages = {441{\textendash}451}, publisher = {London [Ont.]: Envirometrics Press, 1990-}, author = {Zidek, James V. and Wong, HUBERT and Le, N.D. and Burnett, Rick} } @article {rudick1996clinical, title = {Clinical outcomes assessment in multiple sclerosis}, journal = {Annals of Neurology}, volume = {40}, number = {3}, year = {1996}, pages = {469{\textendash}479}, publisher = {Wiley Online Library}, author = {Rudick, Richard and Fischer, Jill and Antel, Jack and Confavreux, Christian and Cutter, Gary and Ellison, George and Lublin, Fred and Miller, Aaron and Petkau, John and Rao, Stephen and Reingold, S and Syndulko, Karl and Thompson, A and Wallenberg, J and Weinshenker, B and Willoughby, E} } @article {chen1996conditional, title = {On the conditional and mixture model approaches for matched pairs}, journal = {Journal of statistical planning and inference}, volume = {55}, number = {3}, year = {1996}, pages = {319{\textendash}329}, publisher = {North-Holland}, author = {Chen, Jiahua} } @booklet {dawid1996critique, title = {Critique of ET Jaynes{\textquoteright}s "Paradoxes of probability theory"}, number = {172}, year = {1996}, publisher = {Department of Statistics, University College London}, author = {Dawid, A.P. and Stone, M. and Zidek, J.V.} } @article {pmid8959355, title = {Disease-specific quality of life: the Gallstone Impact Checklist}, journal = {Clin Invest Med}, volume = {19}, number = {6}, year = {1996}, month = {Dec}, pages = {453{\textendash}460}, author = {Russell, M. L. and Preshaw, R. M. and Brant, R. F. and Bultz, B. D. and Page, S. A.} } @article {gustafson1996effect, title = {The effect of mixing-distribution misspecification in conjugate mixture models}, journal = {Canadian Journal of Statistics}, volume = {24}, number = {3}, year = {1996}, pages = {307{\textendash}318}, publisher = {Wiley Online Library}, doi = {10.2307/3315741}, author = {Gustafson, P.} } @booklet {Joe.Xu1996, title = {The estimation method of inference functions for margins for multivariate models}, number = {166}, year = {1996}, publisher = {University of British Columbia}, url = {http://hdl.handle.net/2429/57078}, author = {Harry Joe and Xu, James J.} } @conference {Joe1996, title = {Families of $m$-variate distributions with given margins and $m(m-1)/2$ bivariate dependence parameters}, booktitle = {Distributions with Fixed Marginals and Related Topics}, volume = {28}, year = {1996}, pages = {120-141}, publisher = {Institute of Mathematical Statistics}, organization = {Institute of Mathematical Statistics}, address = {Hayward, CA}, doi = {10.1214/lnms/1215452614}, author = {Joe, H.}, editor = {L. R{\"u}schendorf and B. Schweizer and M. D. Taylor} } @booklet {brauer1996generalizedspacetime, title = {Generalized space-time models for pollution exposures of populations whose members interact with their environment}, year = {1996}, publisher = {Health Canada}, type = {Contract report}, author = {Brauer, M. and Chatfield, C. and Le, N.D. and Zhang, H. and Zidek, J.V.} } @article {pmid8868315, title = {Increased use of cardiovascular medications in seniors prescribed non-ASA non-steroidal anti-inflammatory drugs}, journal = {Clin Invest Med}, volume = {19}, number = {1}, year = {1996}, month = {Feb}, pages = {46{\textendash}54}, author = {Hogan, D. B. and Campbell, N. R. and Jennett, P. and MacLeod, N. and Brant, R.} } @article {Gustafson1996b, title = {Local sensitivity analysis}, journal = {Bayesian statistics}, volume = {5}, year = {1996}, pages = {197{\textendash}210}, publisher = {Oxford University Press}, author = {Gustafson, Paul and Srinivasan, C and Wasserman, Larry} } @article {gu1996jasa, title = {Local sensitivity of inferences to prior marginals}, journal = {Journal of the American Statistical Association}, volume = {91}, year = {1996}, pages = {774-781}, doi = {10.2307/2291672}, author = {Gustafson, P.} } @article {gu1996annstat, title = {Local sensitivity of posterior expectations}, journal = {Annals of Statistics}, volume = {24}, year = {1996}, pages = {174-195}, doi = {10.1214/aos/1033066205}, author = {Gustafson, P.} } @article {li1996m, title = {M-estimates of regression when the scale is unknown and the error distribution is possibly asymmetric: A minimax result}, journal = {The Canadian Journal of Statistics/La Revue Canadienne de Statistique}, year = {1996}, pages = {193{\textendash}206}, publisher = {JSTOR}, author = {Li, Bing and Zamar, Ruben H} } @article { ISI:A1996VX85400006, title = {A model for a multivariate binary response with covariates based on compatible conditionally specified logistic regressions}, journal = {Statistics \& Probability Letters}, volume = {31}, number = {2}, year = {1996}, month = {DEC 16}, pages = {113-120}, abstract = {A model for a multivariate binary response vector with covariates is obtained. The conditional distribution of each binary response given the other binary responses and the covariates is equivalent to a logistic regression. A simple condition on the regression parameters is necessary and sufficient for the conditional distributions to be compatible, that is, yield a multivariate distribution for the binary response vector. The multivariate model has a wide range of dependence structure for the binary response variables, so it is more generally applicable compared with previous conditional models. The model is applied to a data set from cardiac surgery.}, issn = {0167-7152}, doi = {10.1016/S0167-7152(96)00021-1}, author = {Joe, H and Liu, Y} } @article {Gustafson1996f, title = {Model influence functions based on mixtures}, journal = {Canadian Journal of Statistics}, volume = {24}, number = {4}, year = {1996}, pages = {535{\textendash}548}, publisher = {Wiley Online Library}, doi = {10.2307/3315332}, author = {Gustafson, Paul} } @article { ISI:A1996UK56800005, title = {Multivariate distributions from mixtures of max-infinitely divisible distributions}, journal = {Journal of Multivariate Analysis}, volume = {57}, number = {2}, year = {1996}, month = {MAY}, pages = {240-265}, abstract = {A class of multivariate distributions that are mixtures of the positive powers of a max-infinitely divisible distribution are studied. A subclass has the property that all weighted minima or maxima belong to a given location or scale family. By choosing appropriate parametric families for the mixing distribution and the distribution being mixed, families of multivariate copulas with a flexible dependence structure and with closed form cumulative distribution functions are obtained. Some dependence properties of the class, as well as some characterizations, are given. Conditions for max-infinite divisibility of multivariate distributions are obtained. (C) 1996 Academic Press, Inc.}, issn = {0047-259X}, doi = {10.1006/jmva.1996.0032}, author = {Joe, H and Hu, T} } @article { ISI:A1996UW54700009, title = {Nonparametric tests for bounds on the derivative of a regression function}, journal = {ANNALS OF THE INSTITUTE OF STATISTICAL MATHEMATICS}, volume = {48}, number = {2}, year = {1996}, month = {JUN}, pages = {315-336}, publisher = {KLUWER ACADEMIC PUBL}, type = {Article}, address = {SPUIBOULEVARD 50, PO BOX 17, 3300 AA DORDRECHT, NETHERLANDS}, abstract = {We consider two tests of the null hypothesis that the k-th derivative of a regression function is uniformly bounded by a specified constant. These tests can be used to study the shape of the regression function. For instance, we can test for convexity of the regression function by setting k = 2 and the constant equal to zero. Our tests are based on k-th order divided difference of the observations. The asymptotic distribution and efficacies of these tests are computed and simulation results presented.}, keywords = {convexity, derivative of a regression function, divided differences}, issn = {0020-3157}, doi = {10.1007/BF00054793}, author = {Heckman, NE and Li, B} } @article {pmid8612410, title = {Nonrespiratory predictor of mechanical ventilation dependency in intensive care unit patients}, journal = {Crit. Care Med.}, volume = {24}, number = {4}, year = {1996}, month = {Apr}, pages = {601{\textendash}607}, author = {Sapijaszko, M. J. and Brant, R. and Sandham, D. and Berthiaume, Y.} } @article {chen1996penalized, title = {Penalized minimum-distance estimates in finite mixture models}, journal = {Canadian Journal of Statistics}, volume = {24}, number = {2}, year = {1996}, pages = {167{\textendash}175}, publisher = {Wiley Online Library}, author = {Chen, Jiahua and Kalbfleisch, JD} } @article {gao_predicting_1996, title = {Predicting urban ozone levels and trends with semiparametric modeling}, journal = {Journal of Agricultural, Biological, and Environmental Statistics}, year = {1996}, pages = {404{\textendash}425}, url = {http://www.jstor.org/stable/1400436}, author = {Gao, Feng and Sacks, Jerome and Welch, William J.} } @article {pmid8620699, title = {Prevalence of gastroesophageal reflux symptoms in asthma}, journal = {Chest}, volume = {109}, number = {2}, year = {1996}, month = {Feb}, pages = {316{\textendash}322}, author = {Field, S. K. and Underwood, M. and Brant, R. and Cowie, R. L.} } @article {pmid8918269, title = {Pulmonary artery flow directed catheter: the evidence}, journal = {Lancet}, volume = {348}, number = {9038}, year = {1996}, month = {Nov}, pages = {1324}, author = {Sandham, J. D. and Hull, R. D. and Brant, R. F.} } @article {pmid8924098, title = {A randomized, controlled trial of nurse-midwifery care}, journal = {Birth}, volume = {23}, number = {3}, year = {1996}, month = {Sep}, pages = {128{\textendash}135}, author = {Harvey, S. and Jarrell, J. and Brant, R. and Stainton, C. and Rach, D.} } @article {welch_response_1996, title = {Response to James M. Lucas}, journal = {Technometrics}, volume = {38}, number = {2}, year = {1996}, pages = {199{\textendash}203}, url = {http://www.tandfonline.com/doi/pdf/10.1080/00401706.1996.10484496}, author = {Welch, William J. and Buck, Robert J. and Sacks, Jerome and Wynn, Henry P. and Morris, Max D. and Schonlau, Matthias} } @booklet {mirnazari1996robust, title = {Robust design for censored exponential data}, year = {1996}, publisher = {University of Waterloo}, url = {http://www.bisrg.uwaterloo.ca/archive/RR-96-07.pdf}, author = {Mirnazari, MT and Welch, WJ} } @article {gustafson1996robustness, title = {Robustness considerations in Bayesian analysis}, journal = {Statistical Methods in Medical Research}, volume = {5}, number = {4}, year = {1996}, pages = {357{\textendash}373}, publisher = {SAGE Publications}, doi = {10.1177/096228029600500403}, author = {Gustafson, P.} } @article {pmid8643317, title = {Smoking and middle ear disease}, journal = {Otolaryngol Head Neck Surg}, volume = {114}, number = {6}, year = {1996}, month = {Jun}, pages = {837{\textendash}840}, author = {Adair-Bischoff, C. E. and Sauve, R. S. and Kimberley, B. and Brant, R.} } @inbook {petkau1996statistical, title = {Statistical and design considerations for multiple sclerosis clinical trials}, booktitle = {Multiple Sclerosis: Advances in Clinical Trial Design, Treatment and Future Perspectives}, year = {1996}, pages = {63{\textendash}103}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, chapter = {4}, address = {London}, author = {Petkau, A.John} } @article {le1996surveillance, title = {Surveillance of clustering near point sources}, journal = {Statistics in Medicine}, volume = {15}, number = {7-9}, year = {1996}, pages = {727{\textendash}740}, publisher = {Wiley Online Library}, author = {Le, Nhu D and Petkau, A.John and Rosychuk, R} } @article { ISI:A1996VH25300007, title = {Time series models with univariate margins in the convolution-closed infinitely divisible class}, journal = {Journal of Applied Probability}, volume = {33}, number = {3}, year = {1996}, month = {SEP}, pages = {664-677}, abstract = {A unified way of obtaining stationary time series models with the univariate margins in the convolution-closed infinitely divisible class is presented. Special cases include gamma, inverse Gaussian, Poisson, negative binomial, and generalized Poisson margins. ARMA time series models obtain in the special case of normal margins, sometimes in a different stochastic representation. For the gamma and Poisson margins, some previously defined time series models are included, but for the negative binomial margin, the time series models are different and, in several ways, better than previously defined time series models. The models are related to multivariate distributions that extend a univariate distribution in the convolution-closed infinitely divisible class. Extensions to the non-stationary case and possible applications to modelling longitudinal data are mentioned.}, issn = {0021-9002}, doi = {10.2307/3215348}, author = {Joe, H} } @conference {647032, title = {V-Lynx: bringing the World Wide Web to sight impaired users}, booktitle = {ACM Conference on Assistive Technologies}, year = {1996}, pages = {23{\textendash}26}, doi = {10.1145/228347.228352}, author = {Mitchell Krell and Davor Cubranic} } @article {pmid8722550, title = {Zidovudine absorption and small intestinal function in HIV seropositive patients}, journal = {J. Antimicrob. Chemother.}, volume = {37}, number = {4}, year = {1996}, month = {Apr}, pages = {825{\textendash}829}, author = {Macnab, K. A. and Gill, M. J. and Sutherland, L. R. and Murphy, A. and Brant, R.} } @article { ISI:A1995RQ57800018, title = {Approximations to multivariate normal rectangle probabilities based on conditional expectations}, journal = {Journal of the American Statistical Association}, volume = {90}, number = {431}, year = {1995}, month = {SEP}, pages = {957-964}, abstract = {Two new approximations for multivariate normal probabilities for rectangular regions, based on conditional expectations and regression with binary variables, are proposed. One is a second-order approximation that is much more accurate but also more numerically time-consuming than the first-order approximation. A third approximation, based on the moment-generating function of a truncated multivariate normal distribution, is proposed for orthant probabilities only. Its accuracy is between the first- and second-order approximations when the dimension is less than seven and the correlations are not large. All of the approximations get worse as correlations get larger. These new approximations offer substantial improvements on previous approximations. They also compare favorably with the methods of Genz for numerical evaluation of the multivariate normal integral. The approximation methods should be especially useful within a quasi-Newton routine for parameter estimation in discrete models that involve the multivariate normal distribution.}, issn = {0162-1459}, doi = {10.2307/2291331}, author = {Joe, H} } @booklet {brauer1995hccontractreport, title = {An assessment of pNEM: a computer package for assessing population level exposures to air pollution.}, year = {1995}, publisher = {Health Canada}, type = {Contract report}, author = {Brauer, M. and Duddek, C. and Hornby, S and Le, N.D. and Stevens, J. and Sun, W. and White, R. and Zhang, H. and J.V., Zidek} } @article {gustafson1995bayesian, title = {A Bayesian analysis of bivariate survival data from a multicentre cancer clinical trial}, journal = {Statistics in medicine}, volume = {14}, number = {23}, year = {1995}, pages = {2523{\textendash}2535}, publisher = {Wiley Online Library}, doi = {10.1002/sim.4780142303}, author = {Gustafson, P.} } @booklet {sun1995bayesian, title = {Bayesian multivariate spatial interpolation: application and assessment}, number = {146}, year = {1995}, publisher = {Department of Statistics, University of British Columbia}, author = {Sun, W and Le, N.D. and Zidek, J.V. and Burnett, R} } @article {hu1995bootstrap, title = {A bootstrap based on the estimating equations of the linear model}, journal = {Biometrika}, volume = {82}, number = {2}, year = {1995}, pages = {263{\textendash}275}, publisher = {Biometrika Trust}, author = {Hu, F.eifang and Zidek, James V} } @article {pmid7634713, title = {Freezing influences the healing of rabbit medial collateral ligament autografts}, journal = {Clin. Orthop. Relat. Res.}, number = {316}, year = {1995}, month = {Jul}, pages = {244{\textendash}253}, author = {King, G. J. and Edwards, P. and Brant, R. F. and Shrive, N. G. and Frank, C. B.} } @article {pmid8591521, title = {Government, university, and community collaboration to develop a cardiac surgery database and report of morbidity and mortality while waiting for open heart surgery}, journal = {Medinfo}, volume = {8 Pt 2}, year = {1995}, pages = {1635}, author = {Kieser, T. M. and Tellett, G. and Brant, R. and Tamano, E. and Bayes, A. and Gelfand, E. T. and Wyse, D. G.} } @article {pmid8582990, title = {Human embryo implantation following in-vitro fertilization: is there a seasonal variation?}, journal = {Hum. Reprod.}, volume = {10}, number = {7}, year = {1995}, month = {Jul}, pages = {1825{\textendash}1827}, author = {Dunphy, B. C. and Anderson-Sykes, S. and Brant, R. and Pattinson, H. A. and Greene, C. A.} } @article {pmid8538849, title = {Hyperglycemia in diarrhea-associated hemolytic-uremic syndrome}, journal = {Nephron}, volume = {71}, number = {1}, year = {1995}, pages = {54{\textendash}58}, author = {Robson, W. L. and Leung, A. K. and Brant, R. and Trevenen, C. L. and Stephure, D. K.} } @booklet {hu1995incorporating, title = {Incorporating relevant sample information using the likelihood}, number = {161}, year = {1995}, publisher = {Department of Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Hu, F. and Zidek, J.V.} } @article {pmid8544029, title = {Intraoperative graft tensioning alters viscoelastic but not failure behaviours of rabbit medial collateral ligament autografts}, journal = {J. Orthop. Res.}, volume = {13}, number = {6}, year = {1995}, month = {Nov}, pages = {915{\textendash}922}, author = {King, G. J. and Edwards, P. and Brant, R. F. and Shrive, N. G. and Frank, C. B.} } @article {johnson1995likelihood, title = {A likelihood ratio test for equality of deviations from randomness}, journal = {Researches on Population Ecology}, volume = {37}, number = {2}, year = {1995}, pages = {203{\textendash}209}, publisher = {Springer}, author = {Johnson, DL and Petkau, A.John} } @article {fan_local_1995, title = {Local polynomial kernel regression for generalized linear models and quasi-likelihood functions}, journal = {Journal of the American Statistical Association}, volume = {90}, number = {429}, year = {1995}, pages = {141{\textendash}150}, url = {http://amstat.tandfonline.com/doi/abs/10.1080/01621459.1995.10476496}, author = {Fan, Jianqing and Heckman, Nancy E. and Wand, Matt P.} } @article {fan1995local, title = {Local polynomial kernel regression for generalized linear models and quasi-likelihood functions}, journal = {Journal of the American Statistical Association}, volume = {90}, number = {429}, year = {1995}, pages = {141{\textendash}150}, publisher = {Taylor \& Francis Group}, author = {Fan, Jianqing and Heckman, Nancy E and Wand, Matt P} } @article {Gustafson1995, title = {Local sensitivity diagnostics for Bayesian inference}, journal = {The Annals of Statistics}, volume = {23}, number = {6}, year = {1995}, pages = {2153{\textendash}2167}, publisher = {Institute of Mathematical Statistics}, doi = {10.1214/aos/1034713652}, author = {Gustafson, Paul and Wasserman, Larry and others} } @article {pmid7677550, title = {The low-probability lung scan. A need for change in nomenclature}, journal = {Arch. Intern. Med.}, volume = {155}, number = {17}, year = {1995}, month = {Sep}, pages = {1845{\textendash}1851}, author = {Hull, R. D. and Raskob, G. E. and Pineo, G. F. and Brant, R. F.} } @article {HuJoe1995, title = {Monotonicity of positive dependence with time for stationary reversible Markov chains}, journal = {Probability in the Engineering and Informational Sciences}, volume = {9}, number = {02}, year = {1995}, pages = {227{\textendash}237}, publisher = {Cambridge Univ Press}, doi = {10.1017/S026996480000382X}, author = {Hu, T. and Joe, H.} } @article {duddek1995multivariate, title = {Multivariate imputation in cross-sectional analysis of health effects associated with air pollution}, journal = {Environmental and ecological statistics}, volume = {2}, number = {3}, year = {1995}, pages = {191{\textendash}212}, publisher = {Springer}, author = {Duddek, C and Le, N.D. and Zidek, J.V. and Burnett, RT} } @article {chen1995optimal, title = {Optimal rate of convergence for finite mixture models}, journal = {The Annals of Statistics}, year = {1995}, pages = {221{\textendash}233}, publisher = {Institute of Mathematical Statistics}, author = {Chen, Jiahua} } @article {pmid8544030, title = {Soft-tissue "flaws" are associated with the material properties of the healing rabbit medial collateral ligament}, journal = {J. Orthop. Res.}, volume = {13}, number = {6}, year = {1995}, month = {Nov}, pages = {923{\textendash}929}, author = {Shrive, N. and Chimich, D. and Marchuk, L. and Wilson, J. and Brant, R. and Frank, C.} } @article {pmid8288669, title = {An alternative method for determination of the carpal height ratio}, journal = {J Bone Joint Surg Am}, volume = {76}, number = {1}, year = {1994}, month = {Jan}, pages = {88{\textendash}94}, author = {Nattrass, G. R. and King, G. J. and McMurtry, R. Y. and Brant, R. F.} } @article {chapman_arctic_1994, title = {Arctic sea ice variability: Model sensitivities and a multidecadal simulation}, journal = {Journal of Geophysical Research: Oceans}, volume = {99}, number = {C1}, year = {1994}, pages = {919{\textendash}935}, url = {http://onlinelibrary.wiley.com/doi/10.1029/93JC02564/full}, author = {Chapman, William L. and Welch, William J. and Bowman, Kenneth P. and Sacks, Jerome and Walsh, John E.} } @inbook {brown1994inference, title = {Aspects of uncertainty: a tribute to DV Lindley}, booktitle = {Inference for a covariance matrix}, year = {1994}, publisher = {Wiley}, organization = {Wiley}, address = {Chichester}, author = {Brown, Philip J and Le, Nhu D. and Zidek, James V} } @article {meloche1994binary, title = {Binary-image restoration}, journal = {Canadian Journal of Statistics}, volume = {22}, number = {3}, year = {1994}, pages = {335{\textendash}355}, publisher = {Wiley Online Library}, author = {Meloche, J and Zamar, RH} } @booklet {welch1994correcting, title = {Correcting for covariates in permutation tests}, year = {1994}, publisher = {University of Waterloo}, author = {Welch, WJ and Fahey, TJ} } @booklet {mirnazari1994criterion, title = {Criterion-robust optimal design}, year = {1994}, publisher = {University of Waterloo}, author = {Mirnazari, MT and Welch, WJ} } @article {FangJoe1994, title = {On the decrease in dependence with lag for stationary Markov chains}, journal = {Probability in the Engineering and Informational Sciences}, volume = {8}, number = {03}, year = {1994}, pages = {385{\textendash}401}, publisher = {Cambridge Univ Press}, doi = {10.1017/S026996480000348X}, author = {Fang, Z. and Hu, T. and Joe, H.} } @article {zamar1994estimacion, title = {Estimaci{\'o}n robusta}, journal = {Estad{\'\i}stica espa{\~n}ola}, volume = {36}, number = {137}, year = {1994}, pages = {327{\textendash}387}, publisher = {Instituto Nacional de Estad{\'\i}stica}, author = {Zamar, Ruben H} } @article {chen1994generalized, title = {Generalized likelihood-ratio test of the number of components in finite mixture models}, journal = {Canadian Journal of Statistics}, volume = {22}, number = {3}, year = {1994}, pages = {387{\textendash}399}, publisher = {Wiley Online Library}, author = {Chen, Jiahua} } @inbook {van1994groupWald, title = {Group Bayes estimation of the exponential mean: a retrospective view of the Wald theory}, booktitle = {Statistical Decision Theory and Related Topics V}, year = {1994}, pages = {35{\textendash}49}, publisher = {Springer}, organization = {Springer}, author = {van Eeden, Constance and Zidek, James V} } @article {van1994group, title = {Group-Bayes estimation of the exponential mean: A preposterior analysis}, journal = {Test}, volume = {3}, number = {1}, year = {1994}, pages = {125{\textendash}143}, publisher = {Springer}, author = {van Eeden, Constance and Zidek, James V} } @article {pmid8002520, title = {Hypoxia similarly impairs metabolic responses to cutaneous and core cold stimuli in conscious rats}, journal = {J. Appl. Physiol.}, volume = {77}, number = {2}, year = {1994}, month = {Aug}, pages = {726{\textendash}730}, author = {Giesbrecht, G. G. and Fewell, J. E. and Megirian, D. and Brant, R. and Remmers, J. E.} } @article {pmid8117785, title = {Influence of methodologic factors in a pooled analysis of 13 case-control studies of colorectal cancer and dietary fiber}, journal = {Epidemiology}, volume = {5}, number = {1}, year = {1994}, month = {Jan}, pages = {66{\textendash}79}, author = {Friedenreich, C. M. and Brant, R. F. and Riboli, E.} } @article {chen1994inverse, title = {Inverse problems in fractal construction: Hellinger distance method}, journal = {Journal of the Royal Statistical Society. Series B (Methodological)}, year = {1994}, pages = {687{\textendash}700}, publisher = {Blackwell Publishers}, author = {Chen, Jiahua and Kalbfleisch, JD} } @article {pmid7952553, title = {Likelihood ratios for a sleep apnea clinical prediction rule}, journal = {Am. J. Respir. Crit. Care Med.}, volume = {150}, number = {5 Pt 1}, year = {1994}, month = {Nov}, pages = {1279{\textendash}1285}, author = {Flemons, W. W. and Whitelaw, W. A. and Brant, R. and Remmers, J. E.} } @article { ISI:A1994NJ45600004, title = {Multivariate extreme-value distributions with applications to environmental data}, journal = {Canadian Journal of Statistics{\textendash}- Revue Canadienne de Statistique}, volume = {22}, number = {1}, year = {1994}, month = {MAR}, pages = {47-64}, abstract = {Some parametric families of multivariate extreme-value distributions have been proposed in recent years; several additional parametric families are derived here. The parametric models are fitted, using numerical maximum likelihood, to some environmental multivariate extreme data sets consisting of extreme concentrations of a pollutant at several monitoring stations in a region. Some multivariate nonnormal data analysis techniques are proposed to aid in the likelihood analysis. The new models, together with previous models, appear to be adequate for inferences in that they cover a wide range of possible dependence patterns.}, issn = {0319-5724}, doi = {10.2307/3315822}, author = {Joe, H} } @article {brown1994multivariate, title = {Multivariate spatial interpolation and exposure to air pollutants}, journal = {Canadian Journal of Statistics}, volume = {22}, number = {4}, year = {1994}, pages = {489{\textendash}509}, publisher = {Wiley Online Library}, author = {Brown, Philip J and Le, Nhu D. and Zidek, James V} } @article {le1994network, title = {Network designs for monitoring multivariate random spatial fields}, journal = {Recent advances in statistics and probability}, year = {1994}, pages = {191{\textendash}206}, publisher = {VSP Zeist}, author = {Le, N.D. and Zidek, J.V.} } @article {mcneney1994overdispersed, title = {Overdispersed Poisson regression models for studies of air pollution and human health}, journal = {Canadian Journal of Statistics}, volume = {22}, number = {4}, year = {1994}, pages = {421{\textendash}440}, publisher = {Wiley Online Library}, author = {McNeney, Brad and Petkau, A.John} } @article {pmid7851028, title = {The P1 blood group and the severity of diarrhea-associated hemolytic uremic syndrome}, journal = {Clin. Nephrol.}, volume = {42}, number = {5}, year = {1994}, month = {Nov}, pages = {288{\textendash}290}, author = {Robson, W. L. and Leung, A. K. and Bowen, T. and Brant, R. and Ching, E.} } @article {gough_parameter_1994, title = {Parameter space exploration of an ocean general circulation model using an isopycnal mixing parameterization}, journal = {Journal of Marine Research}, volume = {52}, number = {5}, year = {1994}, pages = {773{\textendash}796}, url = {http://www.ingentaconnect.com/content/jmr/jmr/1994/00000052/00000005/art00001}, author = {Gough, William A. and Welch, William J.} } @inbook {brown1993spatial, title = {Spatial association learning in hummingbirds}, booktitle = {Case Studies in Biometry}, year = {1994}, pages = {159-187}, publisher = {John Wiley \& Sons}, organization = {John Wiley \& Sons}, chapter = {9}, address = {New York}, author = {Graham, J and Petkau, A.John} } @booklet {hu1993approach, title = {An approach to bootstrapping through estimating equations}, year = {1993}, publisher = {Department of Statistics, University of British Columbia}, author = {Hu, F. and Zidek, J.V.} } @article {martin1993bias, title = {Bias robust estimation of scale}, journal = {The Annals of Statistics}, volume = {21}, number = {2}, year = {1993}, pages = {991{\textendash}1017}, publisher = {Institute of Mathematical Statistics}, author = {Martin, R Douglas and Zamar, Ruben H and others} } @article {maronna1993bias, title = {Bias-robust regression estimation: A partial survey}, journal = {New Directions in Statistical Data Analysis and Robustness, eds. S. Morgenthaler, E. Ronchetti and WA Stahel, Birkh auser, Basel}, year = {1993}, pages = {157{\textendash}176}, author = {Maronna, Ricardo A and Yohai, V{\'\i}ctor J and Zamar, Ruben J} } @article {pmid8221427, title = {Case-control study of prenatal ultrasonography exposure in children with delayed speech}, journal = {CMAJ}, volume = {149}, number = {10}, year = {1993}, month = {Nov}, pages = {1435{\textendash}1440}, author = {Campbell, J. D. and Elford, R. W. and Brant, R. F.} } @article {chen1993catalogue, title = {A catalogue of two-level and three-level fractional factorial designs with small runs}, journal = {International Statistical Review/Revue Internationale de Statistique}, year = {1993}, pages = {131{\textendash}145}, publisher = {International Statistical Institute}, author = {Chen, Jiahua and Sun, DX and Wu, CFJ} } @article {pmid8177990, title = {The clinical prediction of sleep apnea}, journal = {Sleep}, volume = {16}, number = {8 Suppl}, year = {1993}, month = {Dec}, pages = {S10}, author = {Flemons, W. W. and Remmers, J. E. and Whitelaw, W. A. and Brant, R.} } @article {pmid8441164, title = {Detecting treatment effects in patients with rheumatoid arthritis: the advantage of longitudinal data}, journal = {J. Rheumatol.}, volume = {20}, number = {1}, year = {1993}, month = {Jan}, pages = {40{\textendash}44}, author = {Edworthy, S. M. and Bloch, D. A. and Brant, R. F. and Fries, J. F.} } @article {pmid8219861, title = {Diarrhea-associated hemolytic uremic syndrome}, journal = {Can Fam Physician}, volume = {39}, year = {1993}, month = {Oct}, pages = {2139{\textendash}2145}, author = {Robson, W. L. and Leung, A. K. and Trevenen, C. L. and Brant, R.} } @article {welch_discussion_1993, title = {Discussion of the paper {\guillemotleft}The foundation of experimental design and observation{\guillemotright} by HP Wynn}, journal = {Statistical Methods \& Applications}, volume = {2}, number = {2}, year = {1993}, pages = {181{\textendash}181}, url = {http://www.springerlink.com/index/FG52588L05XQH674.pdf}, author = {Welch, William J.} } @article {chen1993edgeworth, title = {Edgeworth expansion and the bootstrap for stratified sampling without replacement from a finite population}, journal = {Canadian Journal of Statistics}, volume = {21}, number = {4}, year = {1993}, pages = {347{\textendash}357}, publisher = {Wiley-Blackwell}, author = {Chen, Jiahua and Sitter, Randy Rudolf} } @article {martin1993efficiency, title = {Efficiency-constrained bias-robust estimation of location}, journal = {The Annals of Statistics}, year = {1993}, pages = {338{\textendash}354}, publisher = {JSTOR}, author = {Martin, R Douglas and Zamar, Ruben H} } @article {chen1993empirical, title = {Empirical likelihood estimation for finite populations and the effective usage of auxiliary information}, journal = {Biometrika}, volume = {80}, number = {1}, year = {1993}, pages = {107{\textendash}116}, publisher = {Oxford University Press}, author = {Chen, Jiahua and Qin, Jing} } @article {delampady1993hierarchical, title = {Hierarchical Bayesian analysis of a discrete time series of Poisson counts}, journal = {Statistics and Computing}, volume = {3}, number = {1}, year = {1993}, pages = {7{\textendash}15}, publisher = {Springer}, author = {Delampady, M and Yee, I.M.L. and Zidek, J.V.} } @article {chen1993iterative, title = {Iterative weighted least squares estimators}, journal = {The Annals of Statistics}, year = {1993}, pages = {1071{\textendash}1092}, publisher = {JSTOR}, author = {Chen, Jiahua and Shao, Jun} } @article {paty1993magnetic, title = {Magnetic resonance imaging (MRI) as an outcome measure in multiple sclerosis}, journal = {Journal of Neurological Rehabilitation}, volume = {7}, number = {3-4}, year = {1993}, pages = {117{\textendash}129}, publisher = {SAGE Publications}, author = {Paty, Donald W and Koopmans, Robert A and Zhao, GuoJun and Li, David KB and Oger, Joel JF and Petkau, John} } @article {yohai1993minimax, title = {A minimax-bias property of the least $$\backslash$ alpha $-quantile estimates}, journal = {The Annals of Statistics}, volume = {21}, number = {4}, year = {1993}, pages = {1824{\textendash}1842}, publisher = {Institute of Mathematical Statistics}, author = {Yohai, V{\'\i}ctor J and Zamar, Ruben H and others} } @article { ISI:A1993LW65400003, title = {Multivariate dependence measures and data-analysis}, journal = {Computational Statistics \& Data Analysis}, volume = {16}, number = {3}, year = {1993}, month = {SEP}, pages = {279-297}, issn = {0167-9473}, doi = {10.1016/0167-9473(93)90130-L}, author = {Joe, H} } @article { ISI:A1993LW55600007, title = {Parametric families of multivariate distributions with given margins}, journal = {Journal of Multivariate Analysis}, volume = {46}, number = {2}, year = {1993}, month = {AUG}, pages = {262-282}, abstract = {Multivariate dependence measures based on relative entropy and concordance have previously been proposed by the author. The theory of the sample versions of these dependence measures and their standard errors is completed here for the case of mixed continuous and categorical variables; some new results for estimation of a functional of a multivariate density are needed. The measures are useful for exploratory data analysis to determine good sets of predictor variables for response variables. They are illustrated in analysis of two large data sets. The substantial contributions are unification of dependence measures for mixed types of variables, and the generality of the relative entropy measures for conditional and regression dependences.}, issn = {0047-259X}, doi = {10.1006/jmva.1993.1061}, author = {Joe, H} } @article {pmid8213930, title = {Relationship of the recovery in the glomerular filtration rate to the duration of anuria in diarrhea-associated hemolytic uremic syndrome}, journal = {Am. J. Nephrol.}, volume = {13}, number = {3}, year = {1993}, pages = {194{\textendash}197}, author = {Robson, W. L. and Leung, A. K. and Brant, R.} } @booklet {hu1993relevance, title = {A relevance weighted quantile estimator}, year = {1993}, publisher = {Department of Statistics, University of British Columbia}, author = {Hu, F. and Zidek, J.V.} } @article { ISI:A1993MR97000006, title = {A remark on algorithm-643 - FEXACT - An algorithm for performing fishers exact test in r x c contingency-tables}, journal = {ACM Transactions on Mathematical Software}, volume = {19}, number = {4}, year = {1993}, month = {DEC}, pages = {484-488}, abstract = {The network algorithm of Mehta and Patel [1986] is currently the best general algorithm for computing exact probabilities in r x c contingency tables with fixed marginals. Given here are some improvements to the network algorithm which speed its computational performance; and thus increases the size of problems which can be handled. The new code also eliminates some programming restrictions in the old code, implements the {\textquoteleft}{\textquoteright}hybrid{\textquoteright}{\textquoteright} algorithm of Mehta and Patel [1986a], and demonstrates that the exact path length bounds of Joe [1988] should always be used in place of the approximate bounds of Mehta and Patel [1986]. The new code can be much faster than the old code in some problems.}, issn = {0098-3500}, doi = {10.1145/168173.168412}, author = {Clarkson, D B and Fan, Y-A and Joe, H} } @article {price1993sexual, title = {Sexual selection when the female directly benefits}, journal = {Biological Journal of the Linnean Society}, volume = {48}, number = {3}, year = {1993}, pages = {187{\textendash}211}, publisher = {Wiley Online Library}, author = {Price, Trevor and Schluter, Dolph and Heckman, Nancy E} } @article {price_sexual_1993, title = {Sexual selection when the female directly benefits}, journal = {Biological Journal of the Linnean Society}, volume = {48}, number = {3}, year = {1993}, pages = {187{\textendash}211}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.1993.tb00887.x/full}, author = {Price, Trevor and Schluter, Dolph and Heckman, Nancy E.} } @article { ISI:A1993KM02700003, title = {Tests of uniformity for sets of lotto numbers}, journal = {Statistics \& Probability Letters}, volume = {16}, number = {3}, year = {1993}, month = {FEB 19}, pages = {181-188}, abstract = {Chi-square test statistics for tests of uniformity of margins for distributions of k-tuples, such as those arising in sets of lotto numbers, are derived. The commonly-used formula SIGMA(i)(O(i) - E(i)2 /E(i) is not appropriate in this setting. Discussion of motivation and application of the test statistics are also mentioned.}, issn = {0167-7152}, doi = {10.1016/0167-7152(93)90141-5}, author = {Joe, H} } @proceedings {guttorp1993using, title = {Using Entropy in the Redesign of an Environmental Monitoring Network}, year = {1993}, publisher = {Multivariate Environmental Statistics}, author = {Guttorp, P and Le, N.D. and Sampson, PD and Zidek, J.V.}, editor = {Patil, G.P. and Rao, C.R.} } @article {schumacher1993using, title = {Using prior information in designing intervention detection experiments}, journal = {The Annals of Statistics}, volume = {21}, number = {1}, year = {1993}, pages = {447{\textendash}463}, publisher = {Institute of Mathematical Statistics}, author = {Schumacher, Peter and Zidek, James V and others} } @conference {Joe.Verducci1992, title = {On the Babington Smith class of models for rankings}, booktitle = {Probability Models and Statistical Analyses for Ranking Data}, series = {Lecture Notes in Statistics}, year = {1992}, pages = {37-52}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, address = {New York}, doi = {10.1007/978-1-4612-2738-0_3}, author = {Joe, Harry and Verducci, J. S.}, editor = {M. A. Fligner and J. S. Verducci} } @article {zidek1992bayesian, title = {Bayesian predictive inference for samples from smooth processes}, journal = {Bayesian Statistics}, volume = {4}, year = {1992}, pages = {547{\textendash}566}, author = {Zidek, J.V. and Weerahandi, S.} } @article {zamar1992bias, title = {Bias robust estimation in orthogonal regression}, journal = {The Annals of Statistics}, volume = {20}, number = {4}, year = {1992}, pages = {1875{\textendash}1888}, publisher = {Institute of Mathematical Statistics}, author = {Zamar, Ruben H and others} } @article { ISI:A1992HB29200007, title = {Bivariate threshold methods for extremes}, journal = {Journal of the Royal Statistical Society Series B {\textendash}- Methodological}, volume = {54}, number = {1}, year = {1992}, pages = {171-183}, abstract = {An extension of the threshold method for extreme values is developed, to consider the joint distribution of extremes of two variables. The methodology is based on the point process representation of bivariate extremes. Both parametric and nonparametric models are considered. The simplest case to handle is that in which both marginal distributions are known. For the more realistic case in which the marginal distributions are unknown, a mixed parametric-nonparametric method is proposed. The techniques are illustrated with data on sulphate and nitrate levels taken from a major study of acid rain.}, issn = {0035-9246}, url = {http://www.jstor.org.ezproxy.library.ubc.ca/stable/2345953}, author = {Joe, H and Smith, R L and Weissman, I} } @article {heckman1992bump, title = {Bump hunting in regression analysis}, journal = {Statistics \& probability letters}, volume = {14}, number = {2}, year = {1992}, pages = {141{\textendash}152}, publisher = {Elsevier}, author = {Heckman, Nancy E} } @article {pmid1643678, title = {Comparison of plain with pH-adjusted bupivacaine with hyaluronidase for peribulbar block}, journal = {Can J Anaesth}, volume = {39}, number = {6}, year = {1992}, month = {Jul}, pages = {555{\textendash}558}, author = {Lewis, P. and Hamilton, R. C. and Brant, R. and Loken, R. G. and Maltby, J. R. and Strunin, L.} } @article {wu1992entropy, title = {An entropy-based analysis of data from selected NADP/NTN network sites for 1983{\textendash}1986}, journal = {Atmospheric Environment. Part A. General Topics}, volume = {26}, number = {11}, year = {1992}, pages = {2089{\textendash}2103}, publisher = {Elsevier}, author = {Wu, Shiying and Zidek, James V} } @article { ISI:A1992JU41300007, title = {Further developments on some dependence orderings for continuous bivariate distributions}, journal = {Annals of the Institute of Statistical Mathematics}, volume = {44}, number = {3}, year = {1992}, month = {SEP}, pages = {501-517}, abstract = {The dependence orderings, {\textquoteleft}{\textquoteleft}more associated{\textquoteright}{\textquoteright} and {\textquoteleft}{\textquoteleft}more regression dependent{\textquoteright}{\textquoteright}, due to Schriever (1986, Order Dependence, Centre for Mathematics and Computer Sciences, Amsterdam; 1987, Ann. Statist., 15, 1208-1214) and Yanagimoto and Okamoto (1969, Ann. Inst. Statist. Math., 21, 489-505) respectively, are studied in detail for continuous bivariate distributions. Equivalent forms of the orderings under some conditions are given so that the orderings are more easily checkable for some bivariate distributions. For several parametric bivariate families, the dependence orderings are shown to be equivalent to an ordering of the parameter. A study of functionals that are increasing with respect to the {\textquoteleft}{\textquoteleft}more associated ordering{\textquoteright}{\textquoteright} leads to inequalities, measures of dependence as well as a way of checking that this ordering does not hold for two distributions.}, issn = {0020-3157}, doi = {10.1007/BF00050701}, author = {Fang, Z and Joe, H} } @conference {joe1992generalized, title = {Generalized majorization orderings and applications}, booktitle = {Stochastic Inequalities}, volume = {22}, year = {1992}, pages = {145{\textendash}158}, publisher = {Institute of Mathematical Statistics}, organization = {Institute of Mathematical Statistics}, address = {Hayward, CA}, doi = {10.1214/lnms/1215461949}, author = {Joe, Harry}, editor = {Shaked, M. and Tong, Y.} } @article {chen1992geometric, title = {Geometric quality assurance}, journal = {Institute for Improvement in Quality and Productivity Research Report RR-92-06, University of Waterloo, Ontario}, year = {1992}, author = {Chen, Gemai and Chen, Jiahua} } @article {le1992global, title = {A global test for effects in 2k factorial design without replicates}, journal = {Journal of statistical computation and simulation}, volume = {41}, number = {1-2}, year = {1992}, pages = {41{\textendash}54}, publisher = {Taylor \& Francis}, author = {Le, Nhu D and Zamar, Ruben H} } @article {bernardo_integrated_1992, title = {Integrated circuit design optimization using a sequential strategy}, journal = {Computer-Aided Design of Integrated Circuits and Systems, IEEE Transactions on}, volume = {11}, number = {3}, year = {1992}, pages = {361{\textendash}372}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=124423}, author = {Bernardo, Maria C. and Buck, Robert and Liu, Lihsin and Nazaret, William A. and Sacks, Jerome and Welch, William J.} } @article {le1992interpolation, title = {Interpolation with uncertain spatial covariances: a Bayesian alternative to kriging}, journal = {Journal of Multivariate Analysis}, volume = {43}, number = {2}, year = {1992}, pages = {351{\textendash}374}, publisher = {Elsevier}, author = {Le, Nhu D. and Zidek, James V} } @article {pmid1351142, title = {Lower mortality in cancer patients treated with low-molecular-weight versus standard heparin}, journal = {Lancet}, volume = {339}, number = {8807}, year = {1992}, month = {Jun}, pages = {1476}, author = {Green, D. and Hull, R. D. and Brant, R. and Pineo, G. F.} } @conference {joe1992multivariate, title = {Multivariate majorization by positive combinations}, booktitle = {Stochastic Inequalities}, volume = {22}, year = {1992}, pages = {159{\textendash}181}, publisher = {Institute of Mathematical Statistics}, organization = {Institute of Mathematical Statistics}, address = {Hayward, CA}, doi = {10.1214/lnms/1215461950}, author = {Joe, Harry and Verducci, Joseph S.}, editor = {Shaked, M. and Tong, Y.} } @booklet {brown1992multivariate, title = {Multivariate spatial interpolation with Kronecker covariance structures}, year = {1992}, publisher = {Department of Statistics, University of British Columbia, Vancouver}, author = {Brown, P.J. and Le, N.D. and Zidek, J.V.} } @article {gu1992note, title = {A note on generalized cross-validation with replicates}, journal = {Statistics \& probability letters}, volume = {14}, number = {4}, year = {1992}, pages = {283{\textendash}287}, publisher = {Elsevier}, author = {Gu, Chong and Heckman, Nancy and Wahba, Grace} } @article {pmid1497392, title = {Optimal therapeutic level of heparin therapy in patients with venous thrombosis}, journal = {Arch. Intern. Med.}, volume = {152}, number = {8}, year = {1992}, month = {Aug}, pages = {1589{\textendash}1595}, author = {Hull, R. D. and Raskob, G. E. and Rosenbloom, D. and Lemaire, J. and Pineo, G. F. and Baylis, B. and Ginsberg, J. S. and Panju, A. A. and Brill-Edwards, P. and Brant, R.} } @conference {caselton1991quality, title = {Quality data network designs based on entropy}, booktitle = {Statistics in the environmental and earth sciences}, year = {1992}, pages = {10-38}, publisher = {London: Elsevier Science}, organization = {London: Elsevier Science}, author = {Caselton, W.F. and Kan, L. and Zidek, J.V.}, editor = {Walden, A.T. and Guttorp, P.} } @article {welch_screening_1992, title = {Screening, predicting, and computer experiments}, journal = {Technometrics}, volume = {34}, number = {1}, year = {1992}, pages = {15{\textendash}25}, url = {http://www.tandfonline.com/doi/abs/10.1080/00401706.1992.10485229}, author = {Welch, William J. and Buck, Robert J. and Sacks, Jerome and Wynn, Henry P. and Mitchell, Toby J. and Morris, Max D.} } @article {chen1992some, title = {Some results on 2n-k fractional factorial designs and search for minimum aberration designs}, journal = {The Annals of Statistics}, year = {1992}, pages = {2124{\textendash}2141}, publisher = {Institute of Mathematical Statistics}, author = {Chen, Jiahua} } @article {nair_taguchis_1992, title = {Taguchi{\textquoteright}s parameter design: a panel discussion}, journal = {Technometrics}, volume = {34}, number = {2}, year = {1992}, pages = {127{\textendash}161}, url = {http://amstat.tandfonline.com/doi/abs/10.1080/00401706.1992.10484904}, author = {Nair, Vijayan N. and Abraham, Bovas and MacKay, Jock and Box, George and Kacker, Raghu N. and Lorenzen, Thomas J. and Lucas, James M. and Myers, Raymond H. and Vining, G. Geoffrey and Nelder, John A. and others} } @booklet {guttorp1993using, title = {Using entropy in the redesign of an environmental monitoring network}, number = {116}, year = {1992}, publisher = {Department of Statistics. University of British Columbia}, address = {Vancouver}, author = {Guttorp, Peter and Le, Nhu D. and Sampson, Paul D and Zidek, James V} } @article {weerahandi1991generalized, title = {Generalized Nash products for bargaining games with incomplete information}, journal = {Indian Economic Journal}, volume = {38}, number = {4}, year = {1991}, pages = {98}, publisher = {University of Bombay, School of Economics and Sociology.}, author = {Weerahandi, Samaradasa and Zidek, James V.} } @article {chen1991identity, title = {On the identity relationships of 2- p designs}, journal = {Journal of statistical planning and inference}, volume = {28}, number = {1}, year = {1991}, pages = {95{\textendash}98}, publisher = {North-Holland}, author = {Chen, Jiahua and Lin, Dennis KJ} } @article {heckman1991minimax, title = {Minimax Bayes estimation in nonparametric regression}, journal = {The Annals of Statistics}, year = {1991}, pages = {2003{\textendash}2014}, publisher = {JSTOR}, author = {Heckman, Nancy E and Woodroofe, Michael} } @inbook {heckman1991minimax, title = {Minimax Bayes Estimation, Penalized Likelihood Methods, and Restricted Minimax Estimation}, booktitle = {Nonparametric Functional Estimation and Related Topics}, year = {1991}, pages = {339{\textendash}346}, publisher = {Springer}, organization = {Springer}, author = {Heckman, Nancy E} } @article {li1991min, title = {Min{\textendash}max asymptotic variance of M-estimates of location when scale is unknown}, journal = {Statistics \& Probability Letters}, volume = {11}, number = {2}, year = {1991}, pages = {139{\textendash}145}, publisher = {Elsevier}, author = {Li, Bing and Zamar, Ruben H} } @article {yu_parametric_1991, title = {Parametric yield optimization of CMOS analogue circuits by quadratic statistical circuit performance models}, journal = {International journal of circuit theory and applications}, volume = {19}, number = {6}, year = {1991}, pages = {579{\textendash}592}, url = {http://onlinelibrary.wiley.com/doi/10.1002/cta.4490190606/abstract}, author = {Yu, T. K. and Kang, S. M. and Sacks, J. and Welch, W. J.} } @inbook {yohai1991procedure, title = {A procedure for robust estimation and inference in linear regression}, booktitle = {Directions in robust statistics and diagnostics}, year = {1991}, pages = {365{\textendash}374}, publisher = {Springer}, organization = {Springer}, author = {Yohai, V{\'\i}ctor J and Stahel, Werner A and Zamar, Ruben H} } @article {pmid1941399, title = {Proteinuria and prognosis in hemolytic-uremic syndrome}, journal = {J. Pediatr.}, volume = {119}, number = {5}, year = {1991}, month = {Nov}, pages = {841{\textendash}842}, author = {Robson, W. L. and Leung, A. K. and Brant, R.} } @article { ISI:A1991FG08700011, title = {Rating systems based on paired comparison models}, journal = {Statistics \& Probability Letters}, volume = {11}, number = {4}, year = {1991}, month = {APR}, pages = {343-347}, abstract = {Assuming that a linear paired comparison model is valid for a sport (which involves pairwise competitions), an axiomatic approach is used to obtain a system for updating ratings or strengths of players in the sport. Paired competitions with or without ties are both dealt with. Existing rating systems in chess and table tennis fit within the systems derived here.}, issn = {0167-7152}, doi = {10.1016/0167-7152(91)90046-T}, author = {Joe, H} } @article {pmid1959249, title = {The relationship of the admission hemoglobin to prognosis in children with D+ hemolytic uremic syndrome}, journal = {Clin. Nephrol.}, volume = {36}, number = {4}, year = {1991}, month = {Oct}, pages = {212{\textendash}213}, author = {Robson, W. L. and Leung, A. K. and Brant, R.} } @article {chen1991some, title = {Some results on generalized regression quantiles}, journal = {Communications in Statistics-Theory and Methods}, volume = {20}, number = {3}, year = {1991}, pages = {911{\textendash}928}, publisher = {Marcel Dekker, Inc.}, author = {Chen, Jiahua and Qin, Jing} } @article {chen1991some, title = {Some results on sn-k fractional factorial designs with minimum aberration or optimal moments}, journal = {The Annals of Statistics}, year = {1991}, pages = {1028{\textendash}1041}, publisher = {Institute of Mathematical Statistics}, author = {Chen, Jiahua and Wu, CFJ} } @article {welch_system_1991, title = {A system for quality improvement via computer experiments}, journal = {Communications in Statistics-Theory and Methods}, volume = {20}, number = {2}, year = {1991}, pages = {477{\textendash}495}, url = {http://www.tandfonline.com/doi/abs/10.1080/03610929108830510}, author = {Welch, William J. and Sacks, Jerome} } @article {pmid2085632, title = {Assessing proportionality in the proportional odds model for ordinal logistic regression}, journal = {Biometrics}, volume = {46}, number = {4}, year = {1990}, month = {Dec}, pages = {1171{\textendash}1178}, author = {Brant, R.} } @conference {yohai1990bounded, title = {Bounded Influence Estimation in the Errors-in-Variables Model}, booktitle = {Statistical Analysis of Measurement Error Models and Applications: Proceedings of the AMS-IMS-SIAM Joint Summer Research Conference Held June 10-16, 1989, with Support from the National Science Foundation and the US Army Research Office}, volume = {112}, year = {1990}, pages = {243}, publisher = {American Mathematical Soc.}, organization = {American Mathematical Soc.}, author = {Yohai, V{\'\i}ctor J and Zamar, Ruben H} } @article {w._j._welch_computer_1990, title = {Computer experiments for quality control by parameter design}, journal = {Journal of Quality Technology}, volume = {22}, year = {1990}, pages = {15{\textendash}22}, url = {https://www.researchgate.net/profile/Sung-Mo_Kang/publication/239665455_Computer_Experiments_for_Quality_Control_by_Parameter_Design/links/00b7d52d5aefb98761000000.pdf}, author = {W. J. Welch and Sacks, J.} } @article {genest1990conditionalization, title = {Conditionalization and likelihood dominance in group belief formation}, journal = {Statistics and Risk Modeling}, volume = {8}, year = {1990}, pages = {183-198}, author = {Genest, C and Weerahandi, S. and Zidek, J.V.} } @article {welch_construction_1990, title = {Construction of permutation tests}, journal = {Journal of the American Statistical Association}, volume = {85}, number = {411}, year = {1990}, pages = {693{\textendash}698}, url = {http://amstat.tandfonline.com/doi/abs/10.1080/01621459.1990.10474929}, author = {Welch, William J.} } @booklet {welch1990exact, title = {Exact permutation tests based on trimmed means for matched-pairs designs}, year = {1990}, publisher = {University of Waterloo}, author = {Welch, WJ} } @article { ISI:A1990CY33400008, title = {Extended use of paired comparison models, with application to chess rankings}, journal = {Applied Statistics {\textendash}- Journal of the Royal Statistical Society Series C}, volume = {39}, number = {1}, year = {1990}, pages = {85-93}, issn = {0035-9254}, doi = {10.2307/2347814}, author = {Joe, H} } @article { ISI:A1990CG05500012, title = {Families of min-stable multivariate exponential and multivariate extreme value distributions}, journal = {Statistics \& Probability Letters}, volume = {9}, number = {1}, year = {1990}, month = {JAN}, pages = {75-81}, issn = {0167-7152}, doi = {10.1016/0167-7152(90)90098-R}, author = {Joe, H} } @article { ISI:A1990DF36400002, title = {Majorization and divergence}, journal = {Journal of Mathematical Analysis and Applications}, volume = {148}, number = {2}, year = {1990}, month = {MAY 15}, pages = {287-305}, issn = {0022-247X}, doi = {10.1016/0022-247X(90)90002-W}, author = {Joe, H} } @article { ISI:A1990ED19500002, title = {Multivariate concordance}, journal = {Journal of Multivariate Analysis}, volume = {35}, number = {1}, year = {1990}, month = {OCT}, pages = {12-30}, issn = {0047-259X}, doi = {10.1016/0047-259X(90)90013-8}, author = {Joe, H} } @article {li1990regression, title = {A regression model with random effects for beer chemistry and Canadians{\textquoteright} beer preferences}, journal = {Canadian Journal of Statistics}, volume = {18}, number = {2}, year = {1990}, pages = {108{\textendash}121}, publisher = {Wiley Online Library}, author = {Li, Bing and Petkau, A.John} } @article {zamar1990robustness, title = {Robustness against unexpected dependence in the location model}, journal = {Statistics \& probability letters}, volume = {9}, number = {4}, year = {1990}, pages = {367{\textendash}374}, publisher = {Elsevier}, author = {Zamar, Ruben H} } @article {pmid2311051, title = {Sample sizes for needles in a haystack: the case of HIV seroprevalence surveys}, journal = {Can J Public Health}, volume = {81}, number = {1}, year = {1990}, pages = {50{\textendash}52}, author = {Frank, J. W. and Coates, R. A. and Brant, R. and Garbutt, J. M.} } @article {kastrukoff1990systemic, title = {Systemic lymphoblastoid interferon therapy in chronic progressive multiple sclerosis. I. Clinical and MRI evaluation}, journal = {Neurology}, volume = {40}, number = {3 Part 1}, year = {1990}, pages = {479{\textendash}486}, publisher = {AAN Enterprises}, author = {Kastrukoff, LF and Oger, JJ and Hashimoto, SA and Sacks, SL and Li, DK and Palmer, MR and Koopmans, RA and Petkau, A.John and Berkowitz, J and Paty, DW} } @article {shi185, title = {Weak and strong representations for quantile processes from finite populations with application to simulation size in resampling inference.}, journal = {The Canadian Journal of Statistics}, volume = {18}, number = {2}, year = {1990}, pages = {141{\textendash}148}, author = {Shi, X and Wu, CFJ and Chen, J} } @article { ISI:A1990EB14300006, title = {A winning strategy for lotto games}, journal = {Canadian Journal of Statistics {\textendash}- Revue Canadienne de Statistique}, volume = {18}, number = {3}, year = {1990}, month = {SEP}, pages = {233-244}, issn = {0319-5724}, doi = {10.2307/3315454}, author = {Joe, H} } @article {martin1989asymptotically, title = {Asymptotically min{\textemdash}maX bias robust M-estimates of scale for positive random variables}, journal = {Journal of the American Statistical Association}, volume = {84}, number = {406}, year = {1989}, pages = {494{\textendash}501}, publisher = {Taylor \& Francis}, author = {Martin, R Douglas and Zamar, Ruben H} } @article {sacks_design_1989, title = {Design and analysis of computer experiments}, journal = {Statistical science}, year = {1989}, pages = {409{\textendash}423}, url = {http://www.jstor.org/stable/2245858}, author = {Sacks, Jerome and Welch, William J. and Mitchell, Toby J. and Wynn, Henry P.} } @article {sacks_designs_1989, title = {Designs for computer experiments}, journal = {Technometrics}, volume = {31}, number = {1}, year = {1989}, pages = {41{\textendash}47}, url = {http://amstat.tandfonline.com/doi/abs/10.1080/00401706.1989.10488474}, author = {Sacks, Jerome and Schiller, Susannah B. and Welch, William J.} } @article {pmid2590890, title = {Diphtheria-tetanus overimmunization in children with no records: can it be prevented?}, journal = {CMAJ}, volume = {141}, number = {12}, year = {1989}, month = {Dec}, pages = {1241{\textendash}1246}, author = {Frank, J. W. and Schabas, R. and Arshinoff, R. and Brant, R.} } @article {zidek1989get, title = {Discussion of {\textquoteleft}{\textquoteleft}How to Get Your First Research Grant{\textquoteright}{\textquoteright}}, journal = {Statistical Science}, volume = {4}, number = {2}, year = {1989}, pages = {132{\textendash}134}, author = {Zidek, James V} } @article {bather1989effect, title = {The effect of truncation on a sequential test for the drift of Brownian motion}, journal = {Sequential Analysis}, volume = {8}, number = {2}, year = {1989}, pages = {169{\textendash}190}, publisher = {Taylor \& Francis}, author = {Bather, John A and Chernoff, Herman and Petkau, A.John} } @article { ISI:A1989CH62800006, title = {Estimation of entropy and other functionals of a multivariate density}, journal = {Annals of the Institute of Statistical Mathematics}, volume = {41}, number = {4}, year = {1989}, pages = {683-697}, issn = {0020-3157}, doi = {10.1007/BF00057735}, author = {Joe, H} } @article {martin1989min, title = {Min-max bias robust regression}, journal = {The Annals of Statistics}, year = {1989}, pages = {1608{\textendash}1630}, publisher = {JSTOR}, author = {Martin, R Douglas and Yohai, V{\'\i}ctor J and Zamar, Ruben H} } @article {petkau1989models, title = {Models for quantal response experiments over time}, journal = {Biometrics}, volume = {45}, year = {1989}, pages = {1299{\textendash}1308}, publisher = {JSTOR}, author = {Petkau, A.John and Sitter, Randy R} } @article {kirkpatrick_quantitative_1989, title = {A quantitative genetic model for growth, shape, reaction norms, and other infinite-dimensional characters}, journal = {Journal of mathematical biology}, volume = {27}, number = {4}, year = {1989}, pages = {429{\textendash}450}, url = {http://link.springer.com/article/10.1007/BF00290638}, author = {Kirkpatrick, Mark and Heckman, Nancy} } @article { ISI:A1989AG84900003, title = {A QUANTITATIVE GENETIC MODEL FOR GROWTH, SHAPE, REACTION NORMS, AND OTHER INFINITE-DIMENSIONAL CHARACTERS}, journal = {JOURNAL OF MATHEMATICAL BIOLOGY}, volume = {27}, number = {4}, year = {1989}, pages = {429-450}, publisher = {SPRINGER VERLAG}, type = {Article}, address = {175 FIFTH AVE, NEW YORK, NY 10010}, issn = {0303-6812}, doi = {10.1007/BF00290638}, author = {KIRKPATRICK, M and Heckman, N} } @booklet {Wu1989sulfates, title = {Recent trends in the chemistry of precipitation in the United States: Part 2. Concentrations of sulfates}, number = {130}, year = {1989}, publisher = {Department of Statistics, University of British Columbia}, author = {Wu, Shiying and Zidek, J.V.} } @booklet {wu1989hydrogen, title = {Recent trends in the chemistry of precipitation in the United States: Part 1. Concentrations of hydrogen ions}, number = {129}, year = {1989}, publisher = {Department of Statistics, University of British Columbia}, author = {Wu, Shiying and Zidek, J.V.} } @booklet {Wu1989nitrates, title = {Recent trends in the chemistry of precipitation in the United States: Part 3. Concentrations of nitrates}, year = {1989}, publisher = {Department of Statistics, University of British Columbia}, type = {131}, address = {Vancouver, BC}, author = {Wu, Shiying and Zidek, J.V.} } @article { ISI:A1989U244700019, title = {Relative entropy measures of multivariate dependence}, journal = {Journal of the American Statistical Association}, volume = {84}, number = {405}, year = {1989}, month = {MAR}, pages = {157-164}, issn = {0162-1459}, doi = {10.2307/2289859}, author = {Joe, H} } @article {zamar1989robust, title = {Robust estimation in the errors-in-variables model}, journal = {Biometrika}, volume = {76}, number = {1}, year = {1989}, pages = {149{\textendash}160}, publisher = {Biometrika Trust}, author = {Zamar, Ruben H} } @booklet {koch1989software, title = {Software for quality-improvement experiments: An evaluation}, year = {1989}, publisher = {University of Waterloo}, url = {http://www.bisrg.uwaterloo.ca/archive/RR-89-07.pdf}, author = {Koch, DD and Welch, WJ} } @article { ISI:A1989AV96900015, title = {Statistical-inference for general-order-statistics and nonhomogeneous-Poisson-process software-reliability models}, journal = {IEEE Transactions on Software Engineering}, volume = {15}, number = {11}, year = {1989}, month = {NOV}, pages = {1485-1490}, issn = {0098-5589}, doi = {10.1109/32.41340}, author = {Joe, H} } @article {weerahandi1988bayesian, title = {Bayesian nonparametric smoothers for regular processes}, journal = {Canadian Journal of Statistics}, volume = {16}, number = {1}, year = {1988}, pages = {61{\textendash}74}, publisher = {Wiley Online Library}, author = {Weerahandi, S. and Zidek, J.V.} } @article {zidek1988golden, title = {Discussion of {\textquoteleft}{\textquoteleft}Hotelling, H. The Teaching of Statistics and The Place of Statistics in the University{\textquoteright}{\textquoteright}}, journal = {Statistical Science}, volume = {3}, year = {1988}, pages = {63{\textendash}108}, publisher = {Institute of Mathematical Statistics}, author = {Zidek, James V} } @article { ISI:A1988Q831800004, title = {Extreme probabilities for contingency-tables under row and column independence with application to Fisher{\textquoteright}s exact test}, journal = {Communications in Statistics {\textendash}- Theory and Methods}, volume = {17}, number = {11}, year = {1988}, pages = {3677-3685}, issn = {0361-0926}, doi = {10.1080/03610928808829827}, author = {Joe, H} } @article {zidek1988group, title = {Group decision analysis and its application to combining opinions}, journal = {Journal of Statistical Planning and Inference}, volume = {20}, number = {3}, year = {1988}, pages = {307{\textendash}325}, publisher = {Elsevier}, author = {Zidek, James V} } @article {yohai1988high, title = {High breakdown-point estimates of regression by means of the minimization of an efficient scale}, journal = {Journal of the American statistical association}, volume = {83}, number = {402}, year = {1988}, pages = {406{\textendash}413}, publisher = {Taylor \& Francis}, author = {Yohai, V{\'\i}ctor J and Zamar, Ruben H} } @article { ISI:A1988P078900027, title = {Majorization, entropy and paired comparisons}, journal = {Annals of Statistics}, volume = {16}, number = {2}, year = {1988}, month = {JUN}, pages = {915-925}, issn = {0090-5364}, doi = {10.1214/aos/1176350843}, author = {Joe, H} } @article { ISI:A1988R852000025, title = {MINIMAX ESTIMATES IN A SEMIPARAMETRIC MODEL}, journal = {JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION}, volume = {83}, number = {404}, year = {1988}, month = {DEC}, pages = {1090-1096}, publisher = {AMER STATISTICAL ASSOC}, type = {Article}, address = {1429 DUKE ST, ALEXANDRIA, VA 22314}, issn = {0162-1459}, doi = {10.2307/2290141}, author = {Heckman, NE} } @article {heckman_minimax_1988, title = {Minimax estimates in a semiparametric model}, journal = {Journal of the American Statistical Association}, volume = {83}, number = {404}, year = {1988}, pages = {1090{\textendash}1096}, url = {http://amstat.tandfonline.com/doi/abs/10.1080/01621459.1988.10478706}, author = {Heckman, Nancy E.} } @article {koziol1988objective, title = {Objective criteria for in-vitro responses in human tumor colony-forming assays}, journal = {Medical Decision Making}, volume = {8}, number = {4}, year = {1988}, pages = {304{\textendash}309}, publisher = {SAGE Publications}, author = {Koziol, James A and Petkau, A.John and Taetle, Raymond} } @conference {mccullagh1988regression, title = {Regression methods and performance criteria for small area population estimation}, booktitle = {Small Area Statistics{\textendash}An International Symposium. Ottowa, Canada}, year = {1988}, author = {McCullagh, P and Zidek, J.V.} } @article {welch_robust_1988, title = {Robust permutation tests for matched-pairs designs}, journal = {Journal of the American Statistical Association}, volume = {83}, number = {402}, year = {1988}, pages = {450{\textendash}455}, url = {http://amstat.tandfonline.com/doi/abs/10.1080/01621459.1988.10478616}, author = {Welch, William J. and Gutierrez, Leopoldo G.} } @article {le1988variability, title = {The variability of rainfall acidity revisited}, journal = {Canadian Journal of Statistics}, volume = {16}, year = {1988}, pages = {15{\textendash}38}, publisher = {JSTOR}, author = {Le, D.Nhu and Petkau, A.John} } @booklet {guttorp1987environmental, title = {Environmental monitoring: Models, network design, and data analysis}, year = {1987}, publisher = {Department of Statistics, University of Washington, SIMS Technical Report}, author = {Guttorp, P and Petkau, AJ and Sampson, PD and Zidek, J.V.} } @article { ISI:A1987H818800014, title = {Estimation of quantiles of the maximum of $n$ observations}, journal = {Biometrika}, volume = {74}, number = {2}, year = {1987}, month = {JUN}, pages = {347-354}, issn = {0006-3444}, doi = {10.1093/biomet/74.2.347}, author = {Joe, H} } @article { ISI:A1987J563000025, title = {Majorization, randomness and dependence for multivariate distributions}, journal = {Annals of Probability}, volume = {15}, number = {3}, year = {1987}, month = {JUL}, pages = {1217-1225}, issn = {0091-1798}, doi = {10.1214/aop/1176992093}, author = {Joe, H} } @article { ISI:A1987L837000003, title = {An ordering of dependence for distribution of k-tuples, with applications to lotto games}, journal = {Canadian Journal of Statistics {\textendash}- Revue Canadienne de Statistique}, volume = {15}, number = {3}, year = {1987}, month = {SEP}, pages = {227-238}, issn = {0319-5724}, doi = {10.2307/3314913}, author = {Joe, H} } @article {welch_rerandomizing_1987, title = {Rerandomizing the median in matched-pairs designs}, journal = {Biometrika}, volume = {74}, number = {3}, year = {1987}, pages = {609{\textendash}614}, url = {http://biomet.oxfordjournals.org/content/74/3/609.short}, author = {Welch, William J.} } @article { ISI:A1987H222100007, title = {ROBUST DESIGN IN A 2 TREATMENT COMPARISON IN THE PRESENCE OF A COVARIATE}, journal = {JOURNAL OF STATISTICAL PLANNING AND INFERENCE}, volume = {16}, number = {1}, year = {1987}, month = {MAR}, pages = {75-81}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, issn = {0378-3758}, doi = {10.1016/0378-3758(87)90057-7}, author = {Heckman, NE} } @article {petkau1987truncated, title = {Truncated sequential medical trials involving paired data}, journal = {Canadian Journal of Statistics}, volume = {15}, number = {4}, year = {1987}, pages = {363{\textendash}374}, publisher = {Wiley Online Library}, author = {Petkau, A.John} } @article {haitovsky1986approximating, title = {Approximating hierarchical normal priors using a vague component}, journal = {Journal of multivariate analysis}, volume = {19}, number = {1}, year = {1986}, pages = {48{\textendash}66}, publisher = {Elsevier}, author = {Haitovsky, Yoel and Zidek, James V} } @article {genest1986combining, title = {Combining probability distributions: A critique and an annotated bibliography}, journal = {Statistical Science}, year = {1986}, pages = {114{\textendash}135}, author = {Genest, Christian and Zidek, James V} } @article {chernoff1986numerical, title = {Numerical solutions for Bayes sequential decision problems}, journal = {SIAM Journal on Scientific and Statistical Computing}, volume = {7}, number = {1}, year = {1986}, pages = {46{\textendash}59}, publisher = {SIAM}, author = {Chernoff, Herman and Petkau, A.John} } @article { ISI:A1986E780300010, title = {REPEATED SIGNIFICANCE TESTS WITH BIASED COIN ALLOCATION SCHEMES}, journal = {PROBABILITY THEORY AND RELATED FIELDS}, volume = {73}, number = {4}, year = {1986}, pages = {627-635}, publisher = {SPRINGER VERLAG}, type = {Article}, address = {175 FIFTH AVE, NEW YORK, NY 10010}, issn = {0178-8051}, doi = {10.1007/BF00324857}, author = {Heckman, NE} } @article {heckman_spline_1986, title = {Spline smoothing in a partly linear model}, journal = {Journal of the Royal Statistical Society. Series B (Methodological)}, year = {1986}, pages = {244{\textendash}248}, url = {http://www.jstor.org/stable/2345719}, author = {Heckman, Nancy E.} } @article { ISI:A1986E462600009, title = {SPLINE SMOOTHING IN A PARTLY LINEAR-MODEL}, journal = {JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-METHODOLOGICAL}, volume = {48}, number = {2}, year = {1986}, pages = {244-248}, publisher = {BLACKWELL PUBL LTD}, type = {Article}, address = {108 COWLEY RD, OXFORD, OXON, ENGLAND OX4 1JF}, issn = {0035-9246}, author = {Heckman, NE} } @conference {zidek1986statistication, title = {Statistication: the quest for a curriculum}, booktitle = {Proceedings of the Second International Conference on Teaching Statistics (ICOTS 2), The Hague: International Statistical Institute}, year = {1986}, pages = {1{\textendash}17}, author = {Zidek, James V} } @article {welch_aced:_1985, title = {ACED: Algorithms for the construction of experimental designs}, journal = {The American Statistician}, volume = {39}, number = {2}, year = {1985}, pages = {146}, url = {http://www.jstor.org/stable/pdf/2682828.pdf}, author = {Welch, William J.} } @article { ISI:A1985AHE3000014, title = {Characterizations of life distributions from percentile residual lifetimes}, journal = {Annals of the Institute of Statistical Mathematics}, volume = {37}, number = {1}, year = {1985}, pages = {165-172}, issn = {0020-3157}, doi = {10.1007/BF02481089}, author = {Joe, H} } @article { ISI:A1985ACT4600048, title = {Estimating the number of faults in a system}, journal = {Journal of the American Statistical Association}, volume = {80}, number = {389}, year = {1985}, pages = {222-226}, issn = {0162-1459}, doi = {10.2307/2288076}, author = {Joe, H and Reid, N} } @article { ISI:A1985AKQ9500037, title = {A LOCAL LIMIT-THEOREM FOR A BIASED COIN DESIGN FOR SEQUENTIAL-TESTS}, journal = {ANNALS OF STATISTICS}, volume = {13}, number = {2}, year = {1985}, pages = {785-788}, publisher = {INST MATHEMATICAL STATISTICS}, type = {Note}, address = {IMS BUSINESS OFFICE-SUITE 6 3401 INVESTMENT BLVD, HAYWARD, CA 94545}, issn = {0090-5364}, doi = {10.1214/aos/1176349555}, author = {Heckman, NE} } @article { ISI:A1985ATJ6300008, title = {An ordering of dependence for contingency tables}, journal = {Linear Algebra and its Applications}, volume = {70}, number = {OCT}, year = {1985}, pages = {89-103}, issn = {0024-3795}, doi = {10.1016/0024-3795(85)90045-X}, author = {Joe, H} } @inbook {chernoff1983sequential, title = {Sequential medical trials with ethical cost}, booktitle = {Proceedings of the Berkeley Conference in Honor of Jerzy Neyman and Jack Kiefer}, volume = {II}, year = {1985}, pages = {521-538}, publisher = {Wadsworth}, organization = {Wadsworth}, address = {Monterey}, author = {Chernoff, Herman and Petkau, A.John} } @article { ISI:A1985AKQ9500038, title = {A SEQUENTIAL PROBABILITY RATIO TEST USING A BIASED COIN DESIGN}, journal = {ANNALS OF STATISTICS}, volume = {13}, number = {2}, year = {1985}, pages = {789-794}, publisher = {INST MATHEMATICAL STATISTICS}, type = {Note}, address = {IMS BUSINESS OFFICE-SUITE 6 3401 INVESTMENT BLVD, HAYWARD, CA 94545}, issn = {0090-5364}, doi = {10.1214/aos/1176349556}, author = {Heckman, NE} } @article {weerahandi1985smoothing, title = {Smoothing locally smooth processes by Bayesian nonparametric methods}, journal = {SIAM Institute for Mathematics and Society Technical Report}, volume = {93}, year = {1985}, author = {Weerahandi, S. and Zidek, J.V.} } @article {cote1985thiopental, title = {Thiopental requirements may be increased in children re-anesthetized at least one year after recovery from extensive thermal injury.}, journal = {Anesthesia and Analgesia}, volume = {64}, number = {12}, year = {1985}, pages = {1156{\textendash}1160}, publisher = {LWW}, author = {Cot{\'e}, Charles J and Petkau, A.John} } @article {genest1984aggregating, title = {Aggregating opinions through logarithmic pooling}, journal = {Theory and Decision}, volume = {17}, number = {1}, year = {1984}, pages = {61{\textendash}70}, publisher = {Springer}, author = {Genest, Christian and Weerahandi, S.amaradasa and Zidek, James V} } @article {JoeProschan1984, title = {Comparison of two life distributions on the basis of their percentile residual life functions}, journal = {Canadian Journal of Statistics}, volume = {12}, number = {2}, year = {1984}, pages = {91{\textendash}97}, publisher = {Wiley Online Library}, doi = {10.2307/3315173}, author = {Joe, H. and Proschan, F.} } @article {welch_computer-aided_1984, title = {Computer-aided design of experiments for response estimation}, journal = {Technometrics}, volume = {26}, number = {3}, year = {1984}, pages = {217{\textendash}224}, url = {http://amstat.tandfonline.com/doi/abs/10.1080/00401706.1984.10487958}, author = {Welch, William J.} } @booklet {zidek1984multi, title = {Multi-Bayesianity}, number = {05}, year = {1984}, publisher = {Department of Statistics, University of British columbia}, author = {Zidek, J.V.} } @article {caselton1984optimal, title = {Optimal monitoring network designs}, journal = {Statistics and Probability Letters}, volume = {2}, number = {4}, year = {1984}, pages = {223{\textendash}227}, publisher = {Elsevier}, author = {Caselton, William F and Zidek, James V} } @article { ISI:A1984TF65400019, title = {Percentile residual life functions}, journal = {Operations Research}, volume = {32}, number = {3}, year = {1984}, pages = {668-678}, issn = {0030-364X}, doi = {10.1287/opre.32.3.668}, author = {Joe, H and Proschan, F} } @article {koziol1984relative, title = {Relative efficiencies of goodness-of-fit procedures with truncated data}, journal = {Canadian Journal of Statistics}, volume = {12}, number = {2}, year = {1984}, pages = {107{\textendash}117}, publisher = {Wiley Online Library}, author = {Koziol, James A and Petkau, A.John} } @article {michelassi1983effects, title = {Effects of leukotrienes B4 and C4 on coronary circulation and myocardial contractility.}, journal = {Surgery}, volume = {94}, number = {2}, year = {1983}, pages = {267{\textendash}275}, author = {Michelassi, Fabrizio and Castorena, Guillermo and Hill, Roger D and Lowenstein, Edward and Watkins, W.David and Petkau, A.John and Zapol, Warren M} } @article {weerahandi1983elements, title = {Elements of multi-Bayesian decision theory}, journal = {The Annals of Statistics}, year = {1983}, pages = {1032{\textendash}1046}, publisher = {JSTOR}, author = {Weerahandi, S. and Zidek, J.V.} } @book {rukhin1983estimation, title = {Estimation of linear parametric functions for several exponential samples}, year = {1983}, publisher = {Department of Statistics, Purdue University}, organization = {Department of Statistics, Purdue University}, author = {Rukhin, Andrew L and Zidek, J.V.} } @article {welch_mean_1983, title = {A mean squared error criterion for the design of experiments}, journal = {Biometrika}, volume = {70}, number = {1}, year = {1983}, pages = {205{\textendash}213}, url = {http://biomet.oxfordjournals.org/content/70/1/205.short}, author = {Welch, William J.} } @booklet {de1983multi, title = {Multi-Bayesian estimation theory}, year = {1983}, publisher = {Council for Scientific and Industrial Research [CSIR], National Research Institute for Mathematical Sciences [NRIMS]}, author = {De Waal, DJ and Groenewald, PCN and van Zyl, JM and Zidek, J.V.} } @article {cote1983wasted, title = {Wasted ventilation measured in vitro with eight anesthetic circuits with and without inline humidification.}, journal = {Anesthesiology}, volume = {59}, number = {5}, year = {1983}, pages = {442{\textendash}446}, author = {Cot{\'e}, Charles J and Petkau, A.John and Ryan, John F and Welch, James P} } @article {welch_algorithmic_1982, title = {Algorithmic complexity: three NP-hard problems in computational statistics}, journal = {Journal of Statistical Computation and Simulation}, volume = {15}, number = {1}, year = {1982}, pages = {17{\textendash}25}, url = {http://www.tandfonline.com/doi/abs/10.1080/00949658208810560}, author = {Welch, William J.} } @booklet {zidek1982aspects, title = {Aspects of multi-Bayesian theory}, number = {82-11}, year = {1982}, publisher = {Institute of Applied Mathematics and Statistics, University of British Columbia}, author = {Zidek, J.V.} } @article {welch_branch-and-bound_1982, title = {Branch-and-bound search for experimental designs based on D optimality and other criteria}, journal = {Technometrics}, volume = {24}, number = {1}, year = {1982}, pages = {41{\textendash}48}, url = {http://www.tandfonline.com/doi/abs/10.1080/00401706.1982.10487707}, author = {Welch, William J.} } @article {michelassi1982leukotriene, title = {Leukotriene D4: a potent coronary artery vasoconstrictor associated with impaired ventricular contraction}, journal = {Science}, volume = {217}, number = {4562}, year = {1982}, pages = {841{\textendash}843}, publisher = {American Association for the Advancement of Science}, author = {Michelassi, F and Landa, L and Hill, RD and Lowenstein, E and Watkins, WD and Petkau, AJ and Zapol, WM} } @article {hwang1982limit, title = {Limit theorems for out-guesses with mean-guided second guessing}, journal = {Journal of Applied Probability}, year = {1982}, author = {Hwang, Jiunn Tzon and Zidek, James V} } @article {brown1982multivariate, title = {Multivariate regression shrinkage estimators with unknown covariance matrix}, journal = {Scandinavian Journal of Statistics}, year = {1982}, pages = {209{\textendash}215}, author = {Brown, P.J. and Zidek, J.V.} } @booklet {zidek1982review, title = {A review of methods for estimating the populations of local areas}, journal = {Technical Report}, number = {82{\textendash}4}, year = {1982}, publisher = {Institute of Applied Mathematics and Statistics, University of British Columbia}, address = {Vancouver, BC}, author = {Zidek, J.V.} } @article {harris1982secondary, title = {Secondary hyperparathyroidism associated with dichloromethane diphosphonate treatment of Paget{\textquoteright}s disease}, journal = {Journal of Clinical Endocrinology and Metabolism}, volume = {55}, number = {6}, year = {1982}, pages = {1100{\textendash}1107}, publisher = {The Endocrine Society}, author = {Harris, ST and Neer, RM and Segre, GV and Petkau, A.John and TULLY, GL and Daly, M and Potts, JT} } @article {olkin1981comparison, title = {A comparison of n estimators for the binomial distribution}, journal = {Journal of the American Statistical Association}, volume = {76}, number = {375}, year = {1981}, pages = {637{\textendash}642}, publisher = {Taylor and Francis}, author = {Olkin, Ingram and Petkau, A John and Zidek, James V.} } @article {olkin1981comparison, title = {A comparison of n-estimators for the binomial distribution}, journal = {Journal of the American Statistical Association}, volume = {76}, number = {375}, year = {1981}, pages = {637{\textendash}642}, publisher = {Taylor \& Francis}, author = {Olkin, Ingram and Petkau, A.John and Zidek, James V} } @article { ISI:A1981LY83000010, title = {Comparison of procedures for testing the equality of survival distributions}, journal = {Biometrics}, volume = {37}, number = {2}, year = {1981}, pages = {327-340}, issn = {0006-341X}, doi = {10.2307/2530421}, author = {Joe, H and Koziol, J A and Petkau, A J} } @article {joe1981comparison, title = {Comparison of procedures for testing the equality of two survival distributions}, journal = {Biometrics}, volume = {37}, year = {1981}, pages = {327{\textendash}340}, publisher = {JSTOR}, author = {Joe, Harry and Koziol, James A and Petkau, A.John} } @article {10.2307/2984844, title = {A Method for Constructing Valid Restricted Randomization Schemes Using the Theory of D-Optimal Design of Experiments}, journal = {Journal of the Royal Statistical Society. Series B (Methodological)}, volume = {43}, number = {2}, year = {1981}, pages = {167-172}, publisher = {[Royal Statistical Society, Wiley]}, abstract = {Complete randomization of a one-way layout design may lead to problems if the resulting choice of layout is considered unsuitable by the experimenter. Valid restricted randomization is an attempt to retain the mathematical properties of complete randomization while ensuring that the probability of selection of an unsuitable layout is zero. The problem of constructing valid restricted randomization schemes, when these exist, is shown to be equivalent to a particular problem in the theory of optimal design of experiments.}, issn = {00359246}, url = {http://www.jstor.org/stable/2984844}, author = {L. V. White, W. J. Welch} } @article {weerahandi1981multi, title = {Multi-Bayesian statistical decision theory}, journal = {Journal of the Royal Statistical Society. Series A (General)}, year = {1981}, pages = {85{\textendash}93}, publisher = {JSTOR}, author = {Weerahandi, S.amaradasa and Zidek, James V} } @article {chernoff1981sequential, title = {Sequential medical trials involving paired data}, journal = {Biometrika}, volume = {68}, number = {1}, year = {1981}, pages = {119{\textendash}132}, publisher = {Biometrika Trust}, author = {Chernoff, Herman and Petkau, A.John} } @conference {christie1981use, title = {Use of statistical response surface methodology to find operating conditions for leaching}, booktitle = {Extraction Metallurgy {\textquoteright}81}, year = {1981}, pages = {299{\textendash}307}, author = {Christie, PG and Welch, WJ} } @article {brown1980adaptive, title = {Adaptive multivariate ridge regression}, journal = {Ann. Statist.and}, year = {1980}, pages = {64{\textendash}74}, publisher = {JSTOR}, author = {Brown, Philip J and Zidek, James V} } @article {dawid1980comments, title = {Comments on Jaynes{\textquoteright}s paper {\textquoteleft}{\textquoteleft}Marginalization and prior probabilities{\textquoteright}{\textquoteright}}, journal = {Bayesian Analysis in Econometrics and Statistics}, year = {1980}, pages = {79{\textendash}82}, author = {Dawid, A PHILIP and Stone, MERVYN and Zidek, James V.} } @article {petkau1980frequentist, title = {Frequentist properties of three stopping rules for comparative clinical trials}, journal = {Biometrika}, volume = {67}, number = {3}, year = {1980}, pages = {690{\textendash}692}, publisher = {Biometrika Trust}, author = {Petkau, A.John} } @article {doi:10.1080/00949658008810389, title = {The generation of pseudo- random correlation matrices}, journal = {Journal of Statistical Computation and Simulation}, volume = {11}, number = {1}, year = {1980}, pages = {55-69}, abstract = {This paper examines a method proposed by Bendel and Afifi for generating pseudo-random correlation matrices. An alternative approach is proposed and comparisons with the method of Bendel and Afifi are made. It is shown that there are strong links between the two methods and it is suggested that the proposed method has the advantages of both simplicity and that it is possible to estimate simply the expected value of the coefficient of determination between any pair of regressors.}, doi = {10.1080/00949658008810389}, url = {http://dx.doi.org/10.1080/00949658008810389}, author = {D.G. Johnson and W.J. Welcht} } @article {tsui1980inadmissibility, title = {Inadmissibility of the best fully equivariant estimator of the generalized residual variance}, journal = {The Annals of Statistics}, year = {1980}, pages = {1156{\textendash}1159}, author = {Tsui, Kam-Wah and Weerahandi, S.amaradasa and Zidek, Jim} } @article {van1980multivariate, title = {Multivariate regression analysis and canonical variates}, journal = {Canadian Journal of Statistics}, volume = {8}, number = {1}, year = {1980}, pages = {27{\textendash}39}, publisher = {Wiley Online Library}, author = {Van Der Merwe, A and Zidek, J.V.} } @article {steele1980optimal, title = {Optimal strategies for second guessers}, journal = {Journal of the American Statistical Association}, volume = {75}, number = {371}, year = {1980}, pages = {596{\textendash}601}, publisher = {Taylor and Francis}, author = {Steele, J Michael and Zidek, James} } @article {buckland1980proposed, title = {Proposed vehicle loading of long-span bridges}, journal = {Journal of the Structural Division}, volume = {106}, number = {4}, year = {1980}, pages = {915{\textendash}932}, publisher = {ASCE}, author = {Buckland, Peter Graham and McBryde, John P. and Zidek, James V. and Navin, Frank P.D.} } @inbook {9507, title = {An application of dynamic programming in statistics}, booktitle = {Dynamic Programming and its Applications}, year = {1979}, pages = {221-232}, publisher = {Academic Press}, organization = {Academic Press}, address = {New York}, author = {Petkau, AJ} } @article {weerahandi1979characterization, title = {A characterization of the general mean}, journal = {Canadian Journal of Statistics}, volume = {7}, year = {1979}, pages = {83{\textendash}90}, publisher = {Wiley Online Library}, author = {Weerahandi, Samaradasa and Zidek, James V.} } @article {john1979exact, title = {Exact slopes for a life testing problem involving the two parameter exponential distribution}, journal = {Communications in Statistics-Theory and Methods}, volume = {A8}, number = {15}, year = {1979}, pages = {1511{\textendash}1521}, publisher = {Taylor \& Francis}, author = {Petkau, A.John} } @article {john1979life, title = {On a life testing problem involving the two parameter exponential distribution}, journal = {Communications in Statistics-Theory and Methods}, volume = {A8}, number = {15}, year = {1979}, pages = {1523{\textendash}1534}, publisher = {Taylor \& Francis}, author = {Petkau, AJ} } @inbook {chernoff1977satellite, title = {A satellite control problem.}, booktitle = {Oprimizing Methods in Statistics}, year = {1979}, pages = {89-124}, publisher = {Academic Press}, organization = {Academic Press}, address = {New York}, author = {Chernoff, Herman and Petkau, A.John} } @article {zidek1979statistics, title = {Statistics of extremes: An alternate method with application to bridge design codes}, journal = {Technometrics}, volume = {21}, number = {2}, year = {1979}, pages = {185{\textendash}191}, publisher = {Taylor and Francis}, author = {Zidek, James V and Navin, Francis PD and Lockhart, Richard} } @article {zidek1978deriving, title = {Deriving unbiased risk estimators of multinormal mean and regression coefficient estimators using zonal polynomials}, journal = {Ann. Statist.}, year = {1978}, pages = {769{\textendash}782}, publisher = {JSTOR}, author = {Zidek, J.V.} } @article {9513, title = {A fundamental question of practical statistics}, journal = {The American Statistician}, volume = {32}, year = {1978}, pages = {114}, type = {Letter}, author = {Petkau, A.John} } @booklet {weerahandi1978generalizedNash, title = {Generalized Nash solutions for bargaining with incomplete information}, number = {78-32}, year = {1978}, publisher = {Institute of Applied Mathematics and Statistics, Univ. British Columbia}, address = {Vancouver, BC}, author = {Weerahandi, S. and Zidek, J.V} } @article {chernoff1978optimal, title = {Optimal control of a Brownian motion}, journal = {SIAM Journal on Applied Mathematics}, volume = {34}, number = {4}, year = {1978}, pages = {717{\textendash}731}, publisher = {SIAM}, author = {Chernoff, Herman and Petkau, A.John} } @article {weerahandi1978pooling, title = {Pooling prior distributions}, journal = {Institute of Applied Mathematics and Statistics}, year = {1978}, pages = {78{\textendash}34}, author = {Weerahandi, S. and Zidek, J.V.} } @article {petkau1978sequential, title = {Sequential medical trials for comparing an experimental with a standard treatment}, journal = {Journal of the American Statistical Association}, volume = {73}, number = {362}, year = {1978}, pages = {328{\textendash}338}, publisher = {Taylor \& Francis Group}, author = {Petkau, AJ} } @article {koziol1978sequential, title = {Sequential testing of the equality of two survival distributions using the modified Savage statistic}, journal = {Biometrika}, volume = {65}, number = {3}, year = {1978}, pages = {615{\textendash}623}, publisher = {Biometrika Trust}, author = {Koziol, JamesA. and Petkau, A.John} } @article {buckland1978traffic, title = {Traffic loading of long span bridges}, journal = {Transportation Research Record}, number = {665}, year = {1978}, author = {Buckland, Peter G. and McBryde, John P. and Navin, Francis P.D. and Zidek, James V.} } @article {clevenson1977bayes, title = {Bayes linear estimators of the intensity function of the nonstationary Poisson process}, journal = {Journal of the American Statistical Association}, volume = {72}, number = {357}, year = {1977}, pages = {112{\textendash}120}, publisher = {Taylor and Francis}, author = {Clevenson, M Lawrence and Zidek, James V} } @article {hakstian1977best, title = {Best univocal estimates of orthogonal common factors}, journal = {Psychometrika}, volume = {42}, number = {4}, year = {1977}, pages = {627{\textendash}630}, publisher = {Springer}, author = {Hakstian, A Ralph and Zidek, James V and McDonald, Roderick P} } @booklet {samaradasa1976class, title = {A class of generalized Nash solutions for the two person bargaining problem with incomplete information}, number = {113}, year = {1976}, publisher = {Department of Statistics, Stanford University}, address = {Stanford, California}, author = {Samaradasa, W. and Zidek, James V.} } @article {navin1976design, title = {Design traffic loads on the Lion{\textquoteright}s Gate Bridge}, journal = {Transportation Research Record}, number = {607}, year = {1976}, author = {Navin, Francis P.D. and Zidek, James V. and Fisk, Caroline and Buckland, Peter G.} } @article {shorrock1976improved, title = {An improved estimator of the generalized variance}, journal = {The Annals of Statistics}, year = {1976}, pages = {629{\textendash}638}, author = {Shorrock, RW and Zidek, J.V.} } @booklet {zidek1976necessary, title = {A necessary condition for the admissibility under convex loss of equivariant estimators}, number = {113}, year = {1976}, publisher = {Department of Statistics, Stanford University}, address = {Stanford, California}, author = {Zidek, James V.} } @article {chernoff1976optimal, title = {An optimal stopping problem for sums of dichotomous random variables.}, journal = {Annals of Probability}, volume = {4}, year = {1976}, pages = {875{\textendash}889}, publisher = {JSTOR}, author = {Chernoff, H and Petkau, AJ} } @booklet {buckland1975bridge, title = {Bridge traffic loads - are we overdesigning: Lion{\textquoteright}s Gate Bridge Study}, number = {5}, year = {1975}, publisher = {Buckland and Taylor Ltd}, author = {Buckland, P.G. and Navin, F.P.D. and Zidek, J.V.} } @article {clevenson1975simultaneous, title = {Simultaneous estimation of the means of independent Poisson laws}, journal = {Journal of the American Statistical Association}, volume = {70}, year = {1975}, pages = {698{\textendash}705}, publisher = {Taylor and Francis}, author = {Clevenson, M Lawrence and Zidek, James V} } @unpublished {levy1974study, title = {A comparative study of the success rates of male and female applicants for admission to graduate studies at UBC, 1973-74: A report to the President{\textquoteright}s Committee on the Status of Women}, year = {1974}, author = {Levy, J. and Zidek, J. V.} } @article { ISI:A1973R360300023, title = {EFFECTS OF THYROID-HORMONE ON ADENINE-NUCLEOTIDE CONTENT OF RAT-LIVER}, journal = {PROCEEDINGS OF THE SOCIETY FOR EXPERIMENTAL BIOLOGY AND MEDICINE}, volume = {144}, number = {2}, year = {1973}, pages = {471-474}, publisher = {BLACKWELL SCIENCE INC}, type = {Article}, address = {350 MAIN ST, MALDEN, MA 02148}, issn = {0037-9727}, author = {ISMAILBE.F and SALIBIAN, A and KIRSTEN, E and EDELMAN, IS} } @article {zidek1973estimating, title = {Estimating the scale parameter of the exponential distribution with unknown location}, journal = {Ann Statist}, year = {1973}, pages = {264{\textendash}278}, author = {Zidek, James V} } @article {dawid1973marginalization, title = {Marginalization paradoxes in Bayesian and structural inference}, journal = {Journal of the Royal Statistical Society. Series B (Methodological)}, year = {1973}, pages = {189{\textendash}233}, author = {Dawid, A PHILIP and Stone, M.ervyn and Zidek, James V} } @article { ISI:A1973R512300218, title = {NITROGENATED EXCRETION OF CALYPTOCEPHALELLA-CAUDIVERBERA (L)}, journal = {ACTA PHYSIOLOGICA LATINOAMERICANA}, volume = {23}, number = {3}, year = {1973}, pages = {74}, publisher = {ASSN LATINOAMER CIENC FISIOL}, type = {Meeting Abstract}, address = {SERRANO 665, 1414 BUENOS AIRES, ARGENTINA}, issn = {0001-6764}, author = {ESPINA, S and ROJAS, M and SALIBIAN, A} } @article { ISI:A1972M048200010, title = {STUDY ON EFFECT OF ALDOSTERONE ON EXTRAMITOCHONDRIAL ADENINE-NUCLEOTIDE SYSTEM IN RAT-KIDNEY}, journal = {JOURNAL OF STEROID BIOCHEMISTRY}, volume = {3}, number = {2}, year = {1972}, pages = {173-\&}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, type = {Article}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, doi = {10.1016/0022-4731(72)90048-9}, author = {KIRSTEN, E and KIRSTEN, R and SALIBIAN, A} } @article {zidek1971inadmissibility, title = {Inadmissibility of a class of estimators of a normal quantile}, journal = {Ann Math Statist}, year = {1971}, pages = {1444{\textendash}1447}, author = {Zidek, James V} } @article { ISI:A1971J854300004, title = {IN-VIVO IONIC UPTAKE THROUGH SKIN OF SOUTH-AMERICAN TOAD BUFO-ARUNCO}, journal = {REVUE CANADIENNE DE BIOLOGIE}, volume = {30}, number = {2}, year = {1971}, pages = {115-\&}, publisher = {PRESSES UNIV MONTREAL}, type = {Article}, address = {PO BOX 6128, SUCCURSALE A, MONTREAL PQ H3C 3J7, CANADA}, issn = {0035-0915}, author = {SALIBIAN, A and PRELLER, A and ROBRES, L} } @article { ISI:A1970J015800294, title = {EFFECT OF NEUROHYPOPHYSEAL HORMONES IN HIDRO-MINERAL, EQUILIBRIUM OF CHILEAN FROG (CALYPTOCEPHALELLA-GAYI) .1. EFFECT OF SYNTOCINON ON NA AND CL NET FLUXES THROUGH SKIN AND ON DIURESIS}, journal = {ARCHIVOS DE BIOLOGIA Y MEDICINA EXPERIMENTALES}, volume = {7}, number = {1-3}, year = {1970}, pages = {R85-\&}, publisher = {SOCIEDAD BIOLGIA CHILE}, type = {Meeting Abstract}, address = {CASILLA 16164, SANTIAGO 9, CHILE}, issn = {0004-0533}, author = {SALIBIAN, A and ZAMORANO, B and GARCIA, F and ROBRES, L} } @article { ISI:A1970J015800227, title = {EFFECT OF NEUROHYPOPHYSEAL HORMONES ON HYDRO-MINERAL EQUILIBRIUM OF CHILEAN FROG CALYPTOCEPHALELLA-GAYI .2. EFFECT OF SYNTOCINON AND VASOTOCIN ON WATER BALANCE}, journal = {ARCHIVOS DE BIOLOGIA Y MEDICINA EXPERIMENTALES}, volume = {7}, number = {1-3}, year = {1970}, pages = {R67-\&}, publisher = {SOCIEDAD BIOLGIA CHILE}, type = {Meeting Abstract}, address = {CASILLA 16164, SANTIAGO 9, CHILE}, issn = {0004-0533}, author = {GARCIA, F and ESPINA, S and ROJAS, M and FUENTES, E and SALIBIAN, A} } @article {zidek1970estimating, title = {Estimating scale parameter of exponential distribution with unknown scale with unknown location}, journal = {Ann. Math. Statist.}, volume = {41}, number = {5}, year = {1970}, pages = {1807}, publisher = {Inst Mathematical Statistics, IMS Business Office - suite 7, 3401 INVESTMENT BLVD, HAYWARD, CA 94545}, author = {Zidek, J.V.} } @article { ISI:A1970J015800124, title = {IN-VIVO EFFECT OF ILEU-8-OXYTOCIN (MESOTOCIN) ON SODIUM AND CHLORIDE NET FLUXES THROUGH SKIN AND ON DIURESIS OF CHILEAN FROG CALYPTOCEPHALELLA-CAUDIVERBERA (DONOSO, 1970)}, journal = {ARCHIVOS DE BIOLOGIA Y MEDICINA EXPERIMENTALES}, volume = {7}, number = {1-3}, year = {1970}, pages = {R37-\&}, publisher = {SOCIEDAD BIOLGIA CHILE}, type = {Meeting Abstract}, address = {CASILLA 16164, SANTIAGO 9, CHILE}, issn = {0004-0533}, author = {SALIBIAN, A and ZAMORANO, B and CARRASCO, A} } @article { ISI:A1970J015800293, title = {IN-VIVO UPTAKE OF SODIUM AND CHLORINE THROUGH SKIN OF BUFO-SPINULOSUS}, journal = {ARCHIVOS DE BIOLOGIA Y MEDICINA EXPERIMENTALES}, volume = {7}, number = {1-3}, year = {1970}, pages = {R85-\&}, publisher = {SOCIEDAD BIOLGIA CHILE}, type = {Meeting Abstract}, address = {CASILLA 16164, SANTIAGO 9, CHILE}, issn = {0004-0533}, author = {SALIBIAN, A and PRELLER, A and ROBRES, L} } @article { ISI:A1970J015800009, title = {NA AND CL SERUM CONCENTRATION OF CHILEAN FROG CALYPTOCEPHALELLA-GAYI (DUM ET BIBR 1841) - INFLUENCE OF EXTERNAL BATH}, journal = {ARCHIVOS DE BIOLOGIA Y MEDICINA EXPERIMENTALES}, volume = {7}, number = {1-3}, year = {1970}, pages = {44-\&}, publisher = {SOCIEDAD BIOLGIA CHILE}, type = {Note}, address = {CASILLA 16164, SANTIAGO 9, CHILE}, issn = {0004-0533}, author = {SALIBIAN, A} } @article {zidek1970sufficient, title = {Sufficient conditions for the admissibility under squared errors loss of formal Bayes estimators}, journal = {Ann Math Statist}, year = {1970}, pages = {446{\textendash}456}, publisher = {JSTOR}, author = {Zidek, James V} } @article {zidek1969inadmissibility, title = {Inadmissibility of the best invariant estimator of extreme quantiles of the normal law under squared error loss}, journal = {The Annals of Mathematical Statistics}, year = {1969}, pages = {1801{\textendash}1808}, author = {Zidek, J.V.} } @article { ISI:A1969D463800007, title = {NATURE OF IN VIVO SODIUM AND CHLORIDE UPTAKE MECHANISMS THROUGH EPITHELIUM OF CHILEAN FROG CALYPTOCEPHALELLA GAYI (DUM ET BIBR, 1841) - EXCHANGES OF HYDROGEN AGAINST SODIUM AND OF BICARBONATE AGAINST CHLORIDE}, journal = {JOURNAL OF GENERAL PHYSIOLOGY}, volume = {53}, number = {6}, year = {1969}, pages = {816-\&}, publisher = {ROCKEFELLER UNIV PRESS}, type = {Article}, address = {1114 FIRST AVE, 4TH FL, NEW YORK, NY 10021}, issn = {0022-1295}, doi = {10.1085/jgp.53.6.816}, author = {ROMEU, FG and SALIBIAN, A and PEZZANIH.S} } @article { ISI:A1969G998700070, title = {NATURE OF IONIC UPTAK THROUGH IN-VIVO SKIN OF CHILEAN FROG - H+/NA AND HCO3/CL EXCHANGES AND THEIR SELECTIVE INHIBITION}, journal = {ARCHIVOS DE BIOLOGIA Y MEDICINA EXPERIMENTALES}, volume = {6}, number = {1-3}, year = {1969}, pages = {R16-\&}, publisher = {SOCIEDAD BIOLGIA CHILE}, type = {Meeting Abstract}, address = {CASILLA 16164, SANTIAGO 9, CHILE}, issn = {0004-0533}, author = {GARCIA, F and SALIBIAN, A} } @article {zidek1969representation, title = {A representation of Bayes invariant procedures in terms of Haar measure}, journal = {Annals of the Institute of Statistical Mathematics}, volume = {21}, number = {1}, year = {1969}, pages = {291{\textendash}308}, publisher = {Springer}, author = {Zidek, James V} } @article { ISI:A1968A827900028, title = {IN VIVO IONIC EXCHANGE THROUGH SKIN OF SOUTH AMERICAN FROG LEPTODACTYLUS OCELLATUS}, journal = {COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY}, volume = {25}, number = {1}, year = {1968}, pages = {311-\&}, type = {Article}, doi = {10.1016/0010-406X(68)90938-9}, author = {SALIBIAN, A and PEZZANIH.S and ROMEU, FG} } @article { ISI:A1968B035000003, title = {SODIUM UPTAKE AND AMMONIA EXCRETION THROUGH IN VIVO SKIN OF SOUTH AMERICAN FROG LEPTODACTYLUS OCELLATUS (L 1758)}, journal = {LIFE SCIENCES PART 1 PHYSIOLOGY AND PHARMACOLOGY AND PART 2 BIOCHEMISTRY GENERAL AND MOLECULAR BIOLOGY}, volume = {7}, number = {9P1}, year = {1968}, pages = {465-\&}, type = {Article}, author = {ROMEU, FG and SALIBIAN, A} } @booklet {zidek1967admissibility, title = {On the admissibility of formal Bayes estimators.}, number = {58, Nonr-225 (72)}, year = {1967}, publisher = {Department of Statistics, Stanford University}, address = {Stanford, California}, author = {Zidek, James V.} } @article { ISI:A1967A030600059, title = {ELECTROPHORESIS IN POLYACRILAMIDE GEL OF SERUM PROTEINS IN SOME TELEOST FISHES}, journal = {COMPTES RENDUS DES SEANCES DE LA SOCIETE DE BIOLOGIE ET DE SES FILIALES}, volume = {161}, number = {3}, year = {1967}, pages = {717-\&}, publisher = {MASSON EDITEUR}, type = {Meeting Abstract}, address = {120 BLVD SAINT-GERMAIN, 75280 PARIS 06, FRANCE}, issn = {0037-9026}, author = {SALIBIAN, A} } @article { ISI:A19679024900007, title = {ON HISTOCHEMICAL DEMONSTRATION OF SODIUM-ACTIVATED ADENOSINE TRIPHOSPHATASE}, journal = {JOURNAL OF HISTOCHEMISTRY \& CYTOCHEMISTRY}, volume = {15}, number = {2}, year = {1967}, pages = {114-\&}, publisher = {HISTOCHEMICAL SOC INC}, type = {Letter}, address = {UNIV WASHINGTON, DEPT BIOSTRUCTURE, BOX 357420, SEATTLE, WA 98195}, issn = {0022-1554}, author = {BOSCH, R and SALIBIAN, A and ROMEU, FG} } @article { ISI:A19668119700154, title = {ACTIVIDAD ADENOSINTRIFOS-FATASICA DEPENDIENTE DE SODIO Y DE POTASIO EN BRANQUIAS DE PIMELODUS CLARIAS}, journal = {ACTA PHYSIOLOGICA LATINOAMERICANA}, volume = {S 16}, number = {1}, year = {1966}, pages = {56-\&}, publisher = {ASSN LATINOAMER CIENC FISIOL}, type = {Meeting Abstract}, address = {SERRANO 665, 1414 BUENOS AIRES, ARGENTINA}, issn = {0001-6764}, author = {ROMEU, FG and BOSCH, R and SALIBIAN, A} } @article { ISI:A19667799100075, title = {POLYACRILAMIDE GEL ELECTROPHORESIS OF SERUM PROTEINS OF SOME TELEOST FISHES}, journal = {ACTA PHYSIOLOGICA LATINOAMERICANA}, volume = {16}, number = {1}, year = {1966}, pages = {97-\&}, publisher = {ASSN LATINOAMER CIENC FISIOL}, type = {Meeting Abstract}, address = {SERRANO 665, 1414 BUENOS AIRES, ARGENTINA}, issn = {0001-6764}, author = {SALIBIAN, A} } @booklet {rubin1965approximations, title = {Approximations to the distribution function of sums of independent chi random variables}, number = {106, Nonr-225 (52)}, year = {1965}, publisher = {Department of Statistics, Stanford University}, address = {Stanford, California}, author = {Rubin, Herman and Zidek, James V.} } @article {mcgregor1965sequence, title = {A sequence of limiting distributions of response probabilities}, journal = {Psychometrika}, volume = {30}, number = {4}, year = {1965}, pages = {491{\textendash}497}, publisher = {Springer}, author = {McGregor, JR and Zidek, J.V.} } @booklet {rubin1965waiting, title = {A waiting time distribution arising from the coupon collector{\textquoteright}s problem}, number = {107, Nonr-225(52)}, year = {1965}, publisher = {Department of Statistics, Stanford University}, address = {Stanford, California}, author = {Rubin, Herman and Zidek, James V.} } @booklet {rubin1964calculation, title = {Calculation of upper tail percentiles for the chi-square distribution(Procedure for determining upper tail percentiles of chi-square distribution with arbitrary number of degrees of freedom- numerical integration)}, number = {107, Nonr-225 (52)}, year = {1964}, publisher = {Department of Statistics, Stanford University}, address = {Stanford, California}, author = {Rubin, H. and Zidek, J.V.} } @mastersthesis {zidek1963asymptotic, title = {Asymptotic Distributions of Response Probabilities for a Stochastic Learning Model}, year = {1963}, school = {University of Alberta}, type = {phd}, author = {Zidek, James V} } @article {brewster1974improving, title = {Improving on equivariant estimators}, journal = {Ann. Statist.}, year = {197}, pages = {21{\textendash}38}, publisher = {JSTOR}, author = {Brewster, J.F. and Zidek, James V.} } @article {IsbWel2022, title = {Adaptive Partitioning Design and Analysis for Emulation of a Complex Computer Code}, journal = {Journal of Computational and Graphical Statistics}, pages = {31 pages, accepted}, author = {Sonja Isberg and William J. Welch} } @article {9211, title = {Bayesian analysis of accumulated damage models in lumber reliability}, journal = {Technometrics}, author = {Chun-Hao Yang and James V Zidek and Samuel Wong} } @article {wu1983entropy, title = {An entropy based review of selected NADP-NTN network sites for}, journal = {Atmospheric Environment}, pages = {2089{\textendash}2103}, author = {Wu, S. and Zidek, J.V.} } @article {9944, title = {A general theory for preferential sampling in environamental networks}, journal = {Annals of Applied Statistics}, month = {07/2019}, abstract = {

This paper presents a general model framework for detecting the preferential sampling of environmental monitors recording an envi- ronmental process across space and/or time. This is achieved by con- sidering the joint distribution of an environmental process with a site{\textendash}selection process that considers where and when sites are placed to measure the process. The environmental process may be spatial, temporal or spatio{\textendash}temporal in nature. By sharing random effects be- tween the two processes, the joint model is able to establish whether site placement was stochastically dependent of the environmental pro- cess under study. Furthermore, if stochastic dependence is identified between the two processes, then inferences about the probability dis- tribution of the spatio{\textendash}temporal process will change, as will predic- tions made of the process across space and time. The embedding into a spatio{\textendash}temporal framework also allows for the modelling of the dynamic site{\textemdash}selection process itself. Real{\textendash}world factors affect- ing both the size and location of the network can be easily modelled and quantified. Depending upon the choice of population of loca- tions to consider for selection across space and time under the site{\textendash} selection process, different insights about the precise nature of pref- erential sampling can be obtained. The general framework developed in the paper is designed to be easily and quickly fit using the R-INLA package. We apply this framework to a case study involving partic- ulate air pollution over the UK where a major reduction in the size of a monitoring network through time occurred. It is demonstrated that a significant response{\textendash}biased reduction in the air quality moni- toring network occurred, namely the relocation of monitoring sites to locations with the highest pollution levels, and the routine removal of sites at locations with the lowest. We also show that the network was consistently unrepresentative of the levels of particulate matter seen across much of GB throughout the operating life of the network. Finally we show that this may have led to a severe over-reporting of the population{\textendash}average exposure levels experienced across GB. This could have great impacts on estimates of the health effects of black smoke levels.

}, author = {Joe Watson and James V Zidek and Gavin Shaddick} } @article {9943, title = {A general theory for preferential sampling in environamental networks}, journal = {Annals of Applied Statistics}, month = {07/2019}, abstract = {

This paper presents a general model framework for detecting the preferential sampling of environmental monitors recording an envi- ronmental process across space and/or time. This is achieved by con- sidering the joint distribution of an environmental process with a site{\textendash}selection process that considers where and when sites are placed to measure the process. The environmental process may be spatial, temporal or spatio{\textendash}temporal in nature. By sharing random effects be- tween the two processes, the joint model is able to establish whether site placement was stochastically dependent of the environmental pro- cess under study. Furthermore, if stochastic dependence is identified between the two processes, then inferences about the probability dis- tribution of the spatio{\textendash}temporal process will change, as will predic- tions made of the process across space and time. The embedding into a spatio{\textendash}temporal framework also allows for the modelling of the dynamic site{\textemdash}selection process itself. Real{\textendash}world factors affect- ing both the size and location of the network can be easily modelled and quantified. Depending upon the choice of population of loca- tions to consider for selection across space and time under the site{\textendash} selection process, different insights about the precise nature of pref- erential sampling can be obtained. The general framework developed in the paper is designed to be easily and quickly fit using the R-INLA package. We apply this framework to a case study involving partic- ulate air pollution over the UK where a major reduction in the size of a monitoring network through time occurred. It is demonstrated that a significant response{\textendash}biased reduction in the air quality moni- toring network occurred, namely the relocation of monitoring sites to locations with the highest pollution levels, and the routine removal of sites at locations with the lowest. We also show that the network was consistently unrepresentative of the levels of particulate matter seen across much of GB throughout the operating life of the network. Finally we show that this may have led to a severe over-reporting of the population{\textendash}average exposure levels experienced across GB. This could have great impacts on estimates of the health effects of black smoke levels.

}, author = {Joe Watson and James V Zidek and Gavin Shaddick} } @article {9942, title = {A general theory for preferential sampling in environamental networks}, journal = {Annals of Applied Statistics}, month = {07/2019}, abstract = {

This paper presents a general model framework for detecting the preferential sampling of environmental monitors recording an envi- ronmental process across space and/or time. This is achieved by con- sidering the joint distribution of an environmental process with a site{\textendash}selection process that considers where and when sites are placed to measure the process. The environmental process may be spatial, temporal or spatio{\textendash}temporal in nature. By sharing random effects be- tween the two processes, the joint model is able to establish whether site placement was stochastically dependent of the environmental pro- cess under study. Furthermore, if stochastic dependence is identified between the two processes, then inferences about the probability dis- tribution of the spatio{\textendash}temporal process will change, as will predic- tions made of the process across space and time. The embedding into a spatio{\textendash}temporal framework also allows for the modelling of the dynamic site{\textemdash}selection process itself. Real{\textendash}world factors affect- ing both the size and location of the network can be easily modelled and quantified. Depending upon the choice of population of loca- tions to consider for selection across space and time under the site{\textendash} selection process, different insights about the precise nature of pref- erential sampling can be obtained. The general framework developed in the paper is designed to be easily and quickly fit using the R-INLA package. We apply this framework to a case study involving partic- ulate air pollution over the UK where a major reduction in the size of a monitoring network through time occurred. It is demonstrated that a significant response{\textendash}biased reduction in the air quality moni- toring network occurred, namely the relocation of monitoring sites to locations with the highest pollution levels, and the routine removal of sites at locations with the lowest. We also show that the network was consistently unrepresentative of the levels of particulate matter seen across much of GB throughout the operating life of the network. Finally we show that this may have led to a severe over-reporting of the population{\textendash}average exposure levels experienced across GB. This could have great impacts on estimates of the health effects of black smoke levels.

}, author = {Joe Watson and James V Zidek and Gavin Shaddick} } @article {11438, title = {Highly Multivariate Large-scale Spatial Stochastic Processes {\textendash} A Doubly Conditional Independence Approach. }, author = {Xiaoqing Chen}, editor = {Gavin Shaddick} } @article {9506, title = {A Mechanistic Nonlinear Model for Truncated and Mis-Measured Time-varying Covariates in Survival Models, with Applications in HIV/AIDS}, journal = {Journal of Royal Statistical Society, C}, month = {08/2018}, author = {Zhang, H}, editor = {Wu, L} } @article {zhu2017multi, title = {Multi-parameter One-Sided Monitoring Test}, journal = {Technometrics: arXiv preprint arXiv:1703.04799}, author = {Zhu, Guangyu and Chen, Jiahua} } @article {3972, title = {Pre-averaged kernel estimators for the drift function of a diffusion process in the presence of microstructure noise}, author = {Wooyong Lee and Priscilla E. Greenwood and Nancy Heckman and Wolfgang Wefelmeyer} } @article {9484, title = {Semiparametric inference for the dominance index under the density ratio model}, journal = {Biometrika}, author = {Zhuang, Weiwei and Hu, Boyi and Chen, Jiahua} } @article {9296, title = {Small Area Quantile Estimation}, journal = {International Statistics Review}, volume = {87}, chapter = {219-238}, url = {https://rdcu.be/7Ms3}, author = {Chen, Jiahua and Liu, Yukun} } @article {zidek2016statistics, title = {Statistics and Manufactured Forest Products: Assessing Their Engineering Properties in a Changing World}, journal = {Annual Review of Statistics and Its Applications}, volume = {3}, pages = {Submitted}, publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, California 94303-0139, USA}, author = {Zidek, James V and LUM, CONROY} }