Our Faculty

Matthew Stephens

My lab works on a wide variety of problems at the interface of Statistics and Genetics. We often tackle problems where novel statistical methods are required, or can learn something new compared with existing approaches. Thus, much of our research involves developing new statistical methodology, many of which have a non-trivial computational component. People in my lab tend to come from a quantitative background (e.g., Statistics, Computer Science), with varying levels of formal or informal Biology training.

Empirical Bayes shrinkage and false discovery rate estimation, allowing for unwanted variation.
Gerard D, Stephens M. Empirical Bayes shrinkage and false discovery rate estimation, allowing for unwanted variation. Biostatistics. 2020 01 01; 21(1):15-32.
PMID: 29985984

Creating and sharing reproducible research code the workflowr way.
Blischak JD, Carbonetto P, Stephens M. Creating and sharing reproducible research code the workflowr way. F1000Res. 2019; 8:1749.
PMID: 31723427

Bayesian multivariate reanalysis of large genetic studies identifies many new associations.
Turchin MC, Stephens M. Bayesian multivariate reanalysis of large genetic studies identifies many new associations. PLoS Genet. 2019 10; 15(10):e1008431.
PMID: 31596850

Detailed modeling of positive selection improves detection of cancer driver genes.
Zhao S, Liu J, Nanga P, Liu Y, Cicek AE, Knoblauch N, He C, Stephens M, He X. Detailed modeling of positive selection improves detection of cancer driver genes. Nat Commun. 2019 07 30; 10(1):3399.
PMID: 31363082

Regional influences on community structure across the tropical-temperate divide.
White AE, Dey KK, Mohan D, Stephens M, Price TD. Regional influences on community structure across the tropical-temperate divide. Nat Commun. 2019 06 14; 10(1):2646.
PMID: 31201312

Discovery and characterization of variance QTLs in human induced pluripotent stem cells.
Sarkar AK, Tung PY, Blischak JD, Burnett JE, Li YI, Stephens M, Gilad Y. Discovery and characterization of variance QTLs in human induced pluripotent stem cells. PLoS Genet. 2019 04; 15(4):e1008045.
PMID: 31002671

Inference and visualization of DNA damage patterns using a grade of membership model.
Al-Asadi H, Dey KK, Novembre J, Stephens M. Inference and visualization of DNA damage patterns using a grade of membership model. Bioinformatics. 2019 04 15; 35(8):1292-1298.
PMID: 30192911

Correction: A Unified Framework for Association Analysis with Multiple Related Phenotypes.
Stephens M. Correction: A Unified Framework for Association Analysis with Multiple Related Phenotypes. PLoS One. 2019; 14(3):e0213951.
PMID: 30889189

Estimating recent migration and population-size surfaces.
Al-Asadi H, Petkova D, Stephens M, Novembre J. Estimating recent migration and population-size surfaces. PLoS Genet. 2019 01; 15(1):e1007908.
PMID: 30640906

A new sequence logo plot to highlight enrichment and depletion.
Dey KK, Xie D, Stephens M. A new sequence logo plot to highlight enrichment and depletion. BMC Bioinformatics. 2018 Dec 10; 19(1):473.
PMID: 30526486

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