The Faculty


Bayesian and computational statistics, particularly when applied to problems in population genetics


2006 The Royal Statistical Society - Guy Medal in Bronze

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

B Howie, C Fuchsberger, M Stephens, J Marchini and Gonçalo R Abecasis. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nature Genetics, July 2012 44(8): 955-959.

X Zhou and M Stephens.  Genome-wide efficient mixed model analysis for association studies.Nature Genetics, June 2012 44(7): 821-824. 

J F Degner, A A Pai, R Pique-Regi, J-B Veyrieras, D J Gaffney, J K Pickrell, S De Leon, K Michelini, N Lewellen, G E Crawford, M Stephens, Y Gilad and J K Pritchard. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482: 390-394, February 2012. PMC 3501342

J C Maranville, F Luca, A L Richards, X Wen, D B Witonsky, S Baxter, Matthew Stephens and Anna Di Rienzo. Interactions between Glucocorticoid Treatment and Cis-Regulatory Polymorphisms Contribute to Cellular Response Phenotypes. PLoS Gentics 7(7): e1002162, July 2011. PMC3131293

Pickrell, J. K., Marioni, J. C., Pai, A. A., Jacob, F. D., Engelhardt, B. E., Nkadori, E., Veyrieras, J. B., Stephens, M., Gilad, Y. & Pritchard, J. K. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-72, 2010. PMC3089435.

Y Guan and M Stephens. Bayesian Variable Selection Regression for Genome-wide Association Studies, and other Large-Scale Problems. Annals of Applied Statistics. 5(3): 1780-1815, September 2011. PMC in Process.

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) PMC2940725

Novembre J, Stephens M. Interpreting principal component analyses of spatial population genetic variation. Nat Genet 40(5):646-9. 2008. PMID 18425127

Guan Y, Stephens M. Practical issues in imputation-based association mapping. PLoS Genet 4:e1000279, 2008.  PMC2585794

Veyrieras JB, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M, Pritchard JK. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet 4:e1000214, 2008.  PMC2556086

Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. Rna-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509-1517, 2008.  PMC2527709

R Blekhman, JC Marioni, P Zumbo, M Stephens, and Y Gilad. Sex-specific and lineage-specific alternative splicing in primates. Genome Res, 20(2):180-9, 2009. PMC2813474.

Li N, Stephens M.  Modeling linkage disequilibrium, and identifying recombination hotspots, using SNP data.  Genetics 165:2213-2233, 2003.

Scheet P, Stephens M.  A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. American Journal of Human Genetics 78:629-644, 2006.

Stephens M, Donnelly P.  A comparison of Bayesian methods for haplotype reconstruction. American Journal of Human Genetics 73:1162-1169, 2003.