Matthew Stephens, Ph.D.
Professor, Department of Human Genetics and Department of Statistics
The University of Chicago Department of Statistics Eckhart Hall Room 126 5734 S. University Avenue Chicago, IL 60637
Phone: (773) 702-8327

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

Q Li, M MacCoss, and M Stephens.

Annals of Applied Statistics 4(2): 962-987, June 2010

X Wen and M Stephens

Annals of Applied Statistics 4(3): 1158-1182, September 2010

B E Engelhardt, and M Stephens

PLoS Genetics 6(9): e1001117.

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

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

PLoS ONE, Mar 2010
Supplementary results data page


M Stephens and D J Balding

Nat Rev Genet, 10(10):681-90, Oct 2009

Y Guan and M Stephens

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

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

PLoS Genet, 4(10), Oct 2008


S K Wasser, W J Clark, O Drori, E S Kisamo, C Mailand, B Mutayoba, and M Stephens

Conserv Biol, 22(4):1065-1071, Aug 2008


J C Marioni, C E Mason, S M Mane, M Stephens, and Y Gilad

Genome Res, 18(9):1509-1517, Sep 2008


P Scheet and M Stephens

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

Am J Hum Genet., 82(5):1193-1201, May 2008


J Novembre and M Stephens

Nat Genet, 40(5):646-649, May 2008


B Servin and M Stephens

PLoS Genet, 3(7), Jul 2007


S K Wasser, C Mailand, R Booth, B Mutayoba, E Kisamo, B Clark, and M Stephens

Proc Natl Acad Sci U S A, 104(10):4228-4233, Mar 2007