Research Description

My general interests include Bayesian and computational statistics, particularly when applied to problems in population genetics.  Specific interests include:

• estimating haplotypes from population genotype data (for which I distribute a software package PHASE).
• developing statistical models for patterns of linkage disequilibrium across multiple loci, and using these patterns to identify recombination hotspots.
• spatial modelling of allele frequency variation.

Selected Publications

• A Q Fu, D P Genereux, R Stoger, C D Laird, and M Stephens. Statistical inference of transmission fidelity of DNA methylation patterns over somatic cell divisions in mammals. Annals of Applied Statistics 4(2): 871-892, June 2010.
• Q Li, M MacCoss, and M Stephens. A nested mixture model for protein identification using mass spectrometry. Annals of Applied Statistics 4(2): 962-987, June 2010.
• X Wen and M Stephens. Using linear predictors to impute allele frequencies from summary or pooled genotype data. Annals of Applied Statistics 4(3): 1158-1182, September 2010.
• B E Engelhardt, and M Stephens. Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genetics 6(9): e1001117.
  Software
• J K Pickrell, J C Marioni, A A Pai, J F Degner, B E Engelhardt, E Nkadori, J B Veyrieras, M Stephens, Y Gilad, and J K Pritchard. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature, 464(7289):768-72, Mar 2010.
• M J Barber, L M Mangravite, C L Hyde, D I Chasman, J D Smith, C A McCarty, X Li, R A Wilke, M J Rieder, P T Williams, P M Ridker, A Chatterjee, J I Rotter, D A Nickerson, M Stephens, R M Krauss. Genome-wide association of lipid-lowering response to statins in combined study populations PLoS ONE, Mar 2010
  Supplementary results data page
• M Stephens and D J Balding. Bayesian statistical methods for genetic association studies. Nat Rev Genet, 10(10):681-90, Oct 2009.
• Y Guan and M Stephens. Practical issues in imputation-based association mapping. PLoS Genet, 4(12), Dec 2008.
• J Novembre, T Johnson, K Bryc, Z Kutalik, A R Boyko, A Auton, A Indap, KS King, S Bergmann, M R Nelson, M Stephens, and C D Bustamante. Genes mirror geography within Europe. Nature, 456(7218):98-101, Nov 2008.
• J B Veyrieras, S Kudaravalli, S Y Kim, E T Dermitzakis, Y Gilad, M Stephens, and J K Pritchard. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet, 4(10), Oct 2008.
• S K Wasser, W J Clark, O Drori, E S Kisamo, C Mailand, B Mutayoba, and M Stephens. Combating the illegal trade in African elephat ivory with DNA forensics. Conserv Biol, 22(4):1065-1071, Aug 2008.
• J C Marioni, C E Mason, S M Mane, M Stephens, and Y Gilad. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res, 18(9):1509-1517, Sep 2008.
• P Scheet and M Stephens. Linkage disequilibrium-based quality control for large-scale genetic studies. PLoS Genet, 4(8), 2008.
• A P Reiner, M J Barber, Y Guan, P M Ridkerm L A Lange, D I Chasman, J D Walston, G M Cooper, N S Jenny, M J Rieder, J P Durda, J D Smith, J Novembre, R P Tracy, J I Rotter, M Stephens, D A Nickerson, and R M Krauss. Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are accosicated with c-reactive protein. Am J Hum Genet., 82(5):1193-1201, May 2008.
• J Novembre and M Stephens. Interpreting principal component analyses of spatial population genetic variation. Nat Genet, 40(5):646-649, May 2008.
• B Servin and M Stephens. Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet, 3(7), Jul 2007.
• S K Wasser, C Mailand, R Booth, B Mutayoba, E Kisamo, B Clark, and M Stephens. Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban., Proc Natl Acad Sci U S A, 104(10):4228-4233, Mar 2007.