I am an Assistant Professor at UBC (Statistics and Medical Genetics). Please visit my new webpage here.

I was a postdoc in the DAGS group, at Stanford, working with Daphne Koller. I got my PhD in Computer Science from the University of Toronto in 2011, where I worked with Quaid Morris. My thesis was on integrating large-scale genomics and proteomics datasets to predict gene function. You can find my CV here.

Research Interest

My main interest lies in developing and using machine learning and statistical techniques to study and understand the genetic basis of complex diseases, with a particular interest in psychiatric disorders and cancer. I am especially interested in developing models for combining association evidence across multiple genome-wide data sources, such as gene expression and genotype data, and modeling prior biological pathways and networks for disentangling spurious from meaningful correlations.

Contact

saram[at]stat.ubc.ca; mostafavi.sara[at]gmail.com

Publications

Mostafavi S, Ortiz-Lopez A, Bogue MA, Hattori K, Pop C, Koller D, Mathis D, Benoist C and The ImmGen Consortium. Variation and Genetic Control of Gene Expression in Primary Immunocytes across Inbred Mouse Strains. Journal of Immunology (2014).(data and eQTLs)

Levinson DF, Mostafavi S, Milaneschi Y, Rivera M, Ripke S, Wray NR, Sullivan PF. Genetic Studies of Major Depressive Disorder: Why Are There No Genome-wide Association Study Findings and What Can We Do About It? Biological Psychiatry (2014).

Raj T, Rothamel K, Mostafavi S, Ye C, Lee MN, Replogle JM, Feng T, Lee M, Asinovski N, Frohlich I, Imboywa S, Von Korff A, Okada Y, Patsopoulos NA, Davis S, McCabe C, Paik HI, Srivastava GP, Raychaudhuri S, Hafler DA, Koller D, Regev A, Hacohen N, Mathis D, Benoist C, Stranger BE, De Jager PL. Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science (2014).

Mostafavi S, Battle A, Zhu X, Potash JB, Weissman MW, Shi J, Beckman K, Haudenschild C, McCormick C, Mei R, Gameroff MJ, Gindes H, Adams P, Goes FS, Mondimore FM, MacKinnon D, Notes L, Schweizer B, Furman D, Montgomery SB, Urban AE, Koller D, Levinson D. Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing. Molecular Psychiatry (2013).

Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MW, Mc-Cormick C, Haudenschild CD, Beckman K, Shi J, Mei R, Urban AE, Montgomery SB, Levinson D, Koller D. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Research (2013)

Mostafavi S, Battle A, Zhu X, Urban AE, Levinson DF, Montgomery SB, Koller D. Normalizing RNA-sequencing data by modeling hidden covariates with prior knowledge. PLoS ONE (2013)(code)

with Lonsdale and others. The Genotype-Tissue Expression (GTEx) project.Nature Genetics (2013)

Mostafavi S, Goldenberg, A, and Morris Q. Labeling nodes using three degrees of propagation. PLoS ONE (2012)(code)

Mostafavi S, and Morris Q. Combining many interaction networks to predict gene function and analyze gene lists. Proteomics (Review article) (2012)

Mostafavi S. Computational prediction of gene function from high-throughput data sources. Ph.D. dissertation (2011). [PDF]

Mostafavi S, Goldenberg A, and Morris Q. Predicting node characteristics from molecular networks. Methods in Molecular Biology (Review article) (2011)

Goldenberg A, Mostafavi S, Quon G, Boutros P, and  Morris Q. Unsupervised detection of genes of influence in lung cancer using biological networks. Bioinformatics (2011).

Mostafavi S and Morris Q. Fast integration of heterogeneous data sources for predicting gene function with limited annotation. Bioinformatics (2010). 26:1759-1765.(code and data)

with Warde-Farley D, and others. The GeneMANIA prediction server: Biological network integration for gene prioritization and predicting gene function. Nucleic Acids Research (2010). 38 Suppl: W214-220.

with Costanzo M, Baryshnikova A, and others. The genetic landscape of a cell. Science (2010). 327:425-431.

Mostafavi S and Morris Q. Using the Gene Ontology hierarchy when predicting gene function. Uncertainty in Artificial Intelligence (UAI) conference proceedings. Montreal, Canada. (2009). [PDF]

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 (2008). 9 (Suppl 1):S4, 2008.(code and data)

with Pena-Castillo L, and others. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology (2008). 9 (Suppl 1):S2.

Otaegui D, Mostafavi S, Bernard CC, de Munain AL, Mousavi P, Oksenberg JR, Baranzini SE. Increased transcriptional activity of milk-related genes following the active phase of experimental autoimmune encephalomyelitis and multiple sclerosis. Journal of Immunology. (2007) 179:4074-82.

Mostafavi S, Oksenberg J, Baranzini S, and Mousavi P. A fast and multivariate feature-selection and classification approach for prediction of therapy response in multiple sclerosis. IEEE Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) conference proceedings (2006). Toronto, Canada.

Workshop Papers

Mostafavi S, and Koller D. Using prior biological knowledge when constructing regulatory networks. ICML Workshop on Machine Learning in Genetics and Genomics (2012). Edinburgh, Scotland.[PDF]

Mostafavi S, Goldenberg A, and Morris Q. Predicting node labels in very large networks. NIPS Workshop on Networks Across Disciplines: Theory and Applications (2010). Whistler, Canada.

Mostafavi S and Morris Q. Predicting gene function in a hierarchy. NIPS workshop: Analyzing Graphs (2008). Whistler, Canada.

Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q. Predicting gene function with multiple data and annotations sources. NIPS workshop: Computational Biology (2007). Whistler, Canada.