We aim to understand the function and evolution of the complex molecular networks that underlie life. To do so, we integrate computational population genomics, systems biology, bioinformatics, and molecular evolution. We analyze genomic data to undercover signatures of population history and natural selection, and we build and analyze mathematical simulations of protein networks to probe their function and evolution. Our group is interdisciplinary and collaborative, with an atmosphere that promotes both hard work and creativity.


July 5, 2016
Congratulations to Brian Mannakee on his paper that just came out in PLoS Genetics. In it, we use dynamical systems biology models to predict rates of protein domain evolution. The success of these predictions suggests that natural selection is acting to preserve network dynamics in the face of perturbations from mutations. Although the models are imperfect, we think this work shows the power of systems biology models for quantitatively predicting evolutionary processes.

March 30, 2016
Congratulations to Aaron Ragsdale on his paper that was just accepted for publication in Genetics. In it, we develop a novel diffusion model for trialleic sites, which required some non-trivial applied mathematics. We then apply the model to mutually nonsynonymous codons in Drosophila, to infer the correlation between selection coefficients for mutations at the same protein site. Remarkably, our inferred correlation agrees quantitatively with direct biochemical experiments in bacteria and yeast, suggesting that the correlation we measure is a fundamental property of protein evolution.

March 25, 2016
Congratulations to Benson Hsieh on defending his Ph.D. thesis! Benson will be starting a postdoc in the laboratory of Evan Eichler in the summer.

January 29, 2016
Ryan had a wonderful time teaching at the 2016 Workshop on Population and Speciation Genomics in Cesky Krumlov, Czech Republic. Ryan lectured about demographic inference and ran tutorials on Python programming and using ∂a∂i. The slides and exercises he developed are available here.

January 21, 2016
Congratulations to Benson Hsieh on his two papers that were recently accepted for publication in Genome Research. Both result from our close collaboration with Michael Hammer, Benon's PhD co-supervisor.

In the first paper, we infer a complex demographic model for Central African Pygmies and neigboring farmers. We then use that model as the basis for whole-genome neutral simulations that account for recombination and mutation rate heterogeneity. Those simulations then act as a null model for scanning the genome for evidence of natural selection.

In the second paper, we use a similar null-model approach to test for evidence of archaic admixture into the ancestors of contemporary pygmies. We show not only that such admixture occurred, but that it likely occured several times.

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