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Publications by Sara Mostafavi

2016

Mostafavi S, Yoshida H, Moodley D, LeBoité H, Rothamel K, Raj T, et al.. Parsing the Interferon Transcriptional Network and Its Disease Associations. Cell. Elsevier; 2016; 164: 564–578.

2015

Ardlie KG, DeLuca DS, Segre AV, Sullivan TJ, Young TR, Gelfand ET, et al. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. SCIENCE. 1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA: AMER ASSOC ADVANCEMENT SCIENCE; 2015; 348: 648-660. DOI: 10.1126/science.1262110
Pierson E, Koller D, Battle A, Mostafavi S, Consortium GTE. Sharing and Specificity of Co-expression Networks across 35 Human Tissues. PLOS COMPUTATIONAL BIOLOGY. 1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA: PUBLIC LIBRARY SCIENCE; 2015; 11: e1004220. DOI: 10.1371/journal.pcbi.1004220

2014

Mostafavi S, Battle A, Zhu X, Potash JB, Weissman MM, Shi J, et al. Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing. Molecular psychiatry. Nature Publishing Group; 2014; 19: 1267–1274.
Mostafavi S, Ortiz-Lopez A, Bogue MA, Hattori K, Pop C, Koller D, et al. Variation and Genetic Control of Gene Expression in Primary Immunocytes across Inbred Mouse Strains. JOURNAL OF IMMUNOLOGY. 9650 ROCKVILLE PIKE, BETHESDA, MD 20814 USA: AMER ASSOC IMMUNOLOGISTS; 2014; 193: 4485-4496. DOI: 10.4049/jimmunol.1401280
Levinson DF, Mostafavi S, Milaneschi Y, Rivera M, Ripke S, Wray NR, et al. Genetic Studies of Major Depressive Disorder: Why Are There No Genome-wide Association Study Findings and What Can We Do About It?. BIOLOGICAL PSYCHIATRY. 360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA: ELSEVIER SCIENCE INC; 2014; 76: 510-512. DOI: 10.1016/j.biopsych.2014.07.029
Raj T, Rothamel K, Mostafavi S, Ye C, Lee MN, Replogle JM, et al. Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes. SCIENCE. 1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA: AMER ASSOC ADVANCEMENT SCIENCE; 2014; 344: 519-523. DOI: 10.1126/science.1249547
Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, et al. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. GENOME RESEARCH. 1 BUNGTOWN RD, COLD SPRING HARBOR, NY 11724 USA: COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT; 2014; 24: 14-24. DOI: 10.1101/gr.155192.113

2013

Mostafavi S, Battle A, Zhu X, Urban AE, Levinson D, Montgomery SB, et al. Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge. PLOS ONE. 1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA: PUBLIC LIBRARY SCIENCE; 2013; 8: e68141. DOI: 10.1371/journal.pone.0068141
Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, Shad S, et al. The Genotype-Tissue Expression (GTEx) project. NATURE GENETICS. 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA: NATURE PUBLISHING GROUP; 2013; 45: 580-585. DOI: 10.1038/ng.2653

2012

Mostafavi S, Morris Q. Combining many interaction networks to predict gene function and analyze gene lists. PROTEOMICS. 111 RIVER ST, HOBOKEN 07030-5774, NJ USA: WILEY-BLACKWELL; 2012; 12: 1687-1696. DOI: 10.1002/pmic.201100607
Mostafavi S, Goldenberg A, Morris Q. Labeling Nodes Using Three Degrees of Propagation. PLOS ONE. 1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA: PUBLIC LIBRARY SCIENCE; 2012; 7: e51947. DOI: 10.1371/journal.pone.0051947

2011

Goldenberg A, Mostafavi S, Quon G, Boutros PC, Morris QD. Unsupervised detection of genes of influence in lung cancer using biological networks. BIOINFORMATICS. GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND: OXFORD UNIV PRESS; 2011; 27: 3166-3172. DOI: 10.1093/bioinformatics/btr533
Mostafavi S, Goldenberg A, Morris Q. Predicting node characteristics from molecular networks. Network Biology: Methods and Applications. Springer; 2011;: 399–414.

2010

Mostafavi S, Morris Q. Fast integration of heterogeneous data sources for predicting gene function with limited annotation. BIOINFORMATICS. GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND: OXFORD UNIV PRESS; 2010; 26: 1759-1765. DOI: 10.1093/bioinformatics/btq262
Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. NUCLEIC ACIDS RESEARCH. GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND: OXFORD UNIV PRESS; 2010; 38: W214-W220. DOI: 10.1093/nar/gkq537
Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, et al. The Genetic Landscape of a Cell. SCIENCE. 1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA: AMER ASSOC ADVANCEMENT SCIENCE; 2010; 327: 425-431. DOI: 10.1126/science.1180823

2009

Mostafavi S, Morris Q. Using the Gene Ontology hierarchy when predicting gene function. In Proceedings of the twenty-fifth conference on uncertainty in artificial intelligence. AUAI Press; 2009. pp. 419–427.

2008

Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q. GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. GENOME BIOLOGY. 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND: BIOMED CENTRAL LTD; 2008; 9: S4. DOI: 10.1186/gb-2008-9-s1-s4
Pena-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. GENOME BIOLOGY. 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND: BIOMED CENTRAL LTD; 2008; 9: S2. DOI: 10.1186/gb-2008-9-s1-s2