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  4. Publications

Publications by Yongjin Park

2024

Subedi S, Sumida TS, Park YP. A highly scalable approach to topic modelling in single-cell data by approximate pseudobulk projection. bioRxiv. 2024. p. 2024.02.21.581497.

2023

Sun N, Victor MB, Park YP, Xiong X, Scannail ANi, Leary N, et al. Human microglial state dynamics in Alzheimer's disease progression. Cell. 2023; 186: 4386–4403.e29.
Hou L, Xiong X, Park Y, Boix C, James B, Sun N, et al. Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease. Nat. Genet. nature.com; 2023; 55: 1665–1676.
Xiong X, James BT, Boix CA, Park YP, Galani K, Victor MB, et al. Epigenomic dissection of Alzheimer's disease pinpoints causal variants and reveals epigenome erosion. Cell. 2023; 186: 4422–4437.e21.
Sun N, Akay LAnne, Murdock MH, Park Y, Galiana-Melendez F, Bubnys A, et al. Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer's disease. Nat. Neurosci. 2023; 26: 970–982.
Subedi S, Park YP. Single-cell pair-wise relationships untangled by composite embedding model. iScience. 2023; 26: 106025.
Ye PE, Zhang Y, Geltink RIKlein, Park YP. Tree-structured topic modelling of single-cell gene expression data uncovers hierarchical relationships between immune cell types. bioRxiv. 2023. p. 2023.11.06.565879.
Zhang Y, Khalilitousi M(sam), Park YP. Unraveling dynamically encoded latent transcriptomic patterns in pancreatic cancer cells by topic modeling. Cell Genomics. 2023; 3: 100388.

2021

Park YP, Kellis M. CoCoA-diff: counterfactual inference for single-cell gene expression analysis. Genome Biol. BioMed Central; 2021; 22: 1–23.
Xiong X, Hou L, Park YP, Molinie B, Consortium GTE, Gregory RI, et al. Genetic drivers of m6A methylation in human brain, lung, heart and muscle. Nat. Genet. 2021;.
Boix CA, James BT, Park YP, Meuleman W, Kellis M. Regulatory genomic circuitry of human disease loci by integrative epigenomics. Nature. 2021; 590: 300–307.
Park Y, Kellis M. Counterfactual inference for single-cell gene expression analysis. medRxiv. Cold Spring Harbor Laboratory Press; 2021;.
He L, Loika Y, Park Y, consortium GTissue Exp, Bennett DA, Kellis M, et al. Exome-wide age-of-onset analysis reveals exonic variants in ERN1 and SPPL2C associated with Alzheimer's disease. Transl. Psychiatry. Springer Science and Business Media LLC; 2021; 11: 146.
Park Y, He L, Davila-Velderrain J, Hou L, Mohammadi S, Mathys H, et al. Single-cell deconvolution of 3,000 post-mortem brain samples for eQTL and GWAS dissection in mental disorders. Cold Spring Harbor Laboratory. 2021. p. 2021.01.21.426000.

2019

Park Y, Sarkar A, Nguyen K, Kellis M. Causal Mediation Analysis Leveraging Multiple Types of Summary Statistics Data. 2019;.

2017

Park Y, Sarkar AK, Bhutani K, Kellis M. Multi-tissue polygenic models for transcriptome-wide association studies. bioRxiv. Cold Spring Harbor Labs Journals; 2017;: 107623.
Park Y, Bader JS. Fast and reliable inference algorithm for hierarchical stochastic block models. 2017;.
Park Y, Sarkar A, He L, Davila-Velderrain J, De Jager PL, Kellis M. A Bayesian approach to mediation analysis predicts 206 causal target genes in Alzheimer's disease. bioRxiv. bioRxiv; 2017. p. 219428.
Park Y, Kang T-H, Friedmann T, Bader J. Temporal expression divergence of network modules. bioRxiv. 2017. p. 167734.

2015

Park Y, Kellis M. Deep learning for regulatory genomics. Nat. Biotechnol. 2015; 33: 825–826.

2013

Kang THyuk, Park Y, Bader JS, Friedmann T. The housekeeping gene hypoxanthine guanine phosphoribosyltransferase (HPRT) regulates multiple developmental and metabolic pathways of murine embryonic stem cell neuronal differentiation. PLoS One. 2013; 8: e74967.

2012

Park Y, Bader JS. How networks change with time. Bioinformatics. 2012; 28: i40–8.

2011

Park Y, Bader JS. Resolving the structure of interactomes with hierarchical agglomerative clustering. BMC Bioinformatics. 2011; 12 Suppl 1: S44.

2010

Park Y, Moore C, Bader JS. Dynamic networks from hierarchical bayesian graph clustering. PLoS One. 2010; 5: e8118.