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

Stephens, M., Sloan, J., Robertson, P.D., Scheet, P., and Nickerson, D.A. (2006). Automating Sequence-Based Detection and Genotyping of Single Nucleotide Polymorphisms (SNPs) from Diploid Samples. Nature Genetics, 38(3): 375-81.

Scheet, P., and Stephens, M. (2006). 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(4): 629-44.

Hellenthal, G., Pritchard J., and Stephens, M. (2006). The effects of genotype-dependent recombination, and transmission asymmetry, on linkage disequilibrium. Genetics, 172(3): 2001-5.

Crawford, D.C., Bhangale, T., Li, N., Rieder, M.J., Nickerson, D.A., and Stephens, M. (2004). Evidence for substantial fine-scale variation in recombination rates across the human genome. Nature Genetics, 36:700-706.

Wasser, S.K., Shedlock, A.M., Comstock, K., Ostrander, E.A., Mutayoba, B., and Stephens, M. (2004). Assigning Isolated African Elephant DNA to a Geographic Region of Origin: Applications to Monitoring the Ivory Trade. PNAS, 101: 14847–14852.

Li, N., and Stephens,M. (2003). Modelling Linkage Disequilibrium, and identifying recombination hotspots using SNP data. Genetics, 165:2213–2233.

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

Falush, D., Stephens, M., and Pritchard J.K. (2003). Inference of population structure from multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164 : 1567–1587.

Stephens, M., Smith N.J. and Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68 : 978–989.

Pritchard, J.K., Stephens, M. and Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155 : 945–959.

Stephens, M. and Donnelly, P. (2000). Inference in molecular population genetics. Journal of the Royal Statistical Society, Series B, 62 : 605–655.

Stephens,M. (2000). Bayesian analysis ofmixtures with an unknown number of components—an alternative to reversible jump methods. Annals of Statistics, 28 : 40–74.