My research is focussed on
population genetics methods for large scale genetic data sets. I am particularly interested in methods that make use of the correlation structure in
closely spaced genetic markers, and that are fast enough to be applied to whole
genome sequence data.
Recent work by our group investigated the contribution of archaic humans to current-day human genomes:
This work was covered by the news media, including The Washington Post,
The Los Angeles Times, and The Atlantic.
Software from my collaborations with Brian Browning, including BEAGLE, Refined IBD, IBDNe, and SPrime, can be found via Brian's website.
Browning, S. R., B. L. Browning, Y. Zhou, S. Tucci, J. M. Akey, 2018. Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture. Cell, 173:53-61 (link to article).
Browning, S. R., et al., 2018. Ancestry-specific recent effective population size in the Americas. PLOS Genetics, 14:e1007385 (link to article).
Browning, S. R. et al. 2016. Local Ancestry Inference in a large US-Based Hispanic/Latino Study: Hispanic Community Health Study / Study of Latinos (HCHS/SOL). G3, 6:1525-1534 (link to article).
Browning, B. L. and S. R. Browning, 2016. Genotype imputation with millions of reference samples. American Journal of Human Genetics, 98: 116-126 (link to article).
Browning, S. R. and B. L. Browning, 2015. Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent. American Journal of Human Genetics, 97:404-418 (link to article). IBDNe is a method for estimating recent (past 200 generations) effective population size from population samples of SNP array or sequence data.
Browning, B. L. and S. R. Browning, 2013. Improving the Accuracy and Efficiency of Identity by Descent Detection in Population Data. Genetics, 194: 459-471 (link to open access article). Beagle's Refined IBD method finds candidate IBD segments using a hashing method and evaluates their significance via a likelihood ratio. The method is accurate, powerful, and relatively fast for large data sets.
Browning, S. R. and B. L. Browning, 2012. Identity by Descent Between Distant Relatives: Detection and Applications. Annual Review of Genetics, 46: 617-633 (link with free access to article). A review article.
Browning, B. L. and S. R. Browning, 2009. A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals. American Journal of Human Genetics, 84: 210-223 (link to article).We extended our earlier haplotype phasing work to imputation of ungenotyped markers and to phasing of parent-offspring trios. Our approach is applicable
to whole genome association data, and has high computational efficiency as well as excellent accuracy.
Madsen, B. E. and S. R. Browning, 2009. A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic.
PLOS Genetics, 5: e1000384 (link to article). We provide a test for whether mutations
are more common in cases than in controls (in a gene or set of genes), which provides a useful complement to single-marker
association testing, particularly in those diseases for which de novo mutations play an important role.
Browning, S. R. and B. L. Browning, 2007. Rapid and accurate haplotype phasing and
missing data inference for whole genome association studies using localized
haplotype clustering. American Journal of Human Genetics,
to article). A method for haplotype phasing that is fast and accurate on genome wide SNP-chip data.
Browning, B. L. and S. R. Browning, 2007. Efficient multilocus association testing
for whole genome association studies using localized haplotype clustering. Genetic
Epidemiology, 31:365-375 (link
to article). Provides
efficient software implementation of the method proposed in Browning 2006, and
extensive simulation results assessing the value of the method. This paper received the
2008 Best Paper Award from the International Genetic Epidemiology Society for best paper published in
Genetic Epidemiology in 2007.
Browning, S. R., 2006. Multilocus
association mapping using variable-length Markov chains. American Journal of Human Genetics, 78:903-913
article). This is the linkage disequilibrium / haplotype frequency model that was used by BEAGLE until around 2017/2018.