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


October 14, 2014
Our recent work testing whether metazoan tyrosine loss was driven by selection against spurious phosphorylation has been published in Molecular Biology and Evolution. In the paper, we test an intriguing hypothesis from Rune Linding's group that the expansion of tyrosine kinases in metazoans led to proteome-wide selection against tyrosine use in proteins. We find tyrosine loss was not more dramatic in residues that are more likely to be phosphorylated or in proteins that are more likely to be phosphorylated. We also find no evidence for direction selection against tyrosine in human populations. All three results are contrary to the Linding selection hypothesis. This suggests that some other neutral or selective force is driving the evolution of tyrosine content in metazoans.

This paper was the work of multiple undergraduate and graduate students in my group, and I'm very proud of how all the analyses came together. It's great to work with wonderful students!

August 12, 2014
We are seeking a postdoc with bioinformatics skills and a strong grasp of molecular biology. They will collaborate with us, Prof. Guang Yao, and colleagues in information science on a DARPA-funded project to mine the literature and discover the Big Mechanisms behind cancer. They will also have ample time to work on other related cancer bioinformatics projects that build upon their interests and strengths. For more information and instructions on how to apply, click here.

June 23, 2014
Ryan is proud to have given an invited talk at the 2014 Kavli Indonesian-American Frontiers of Science Symposium in Medan, Indonesia. The meeting was a great opportunity to meet new colleagues in Indonesia and to learn about a very diverse range of science.

June 3, 2014
We're looking forward to SMBE 2014. Benson, Brian, and Ryan will be giving talks, and Aaron will present a poster.

May 9, 2014
Our proposal for the DARPA "Big Mechanism" Program has been chosen for funding! We are collaborating with researchers in SISTA, who will build a system for computationally inferring casual models of cancer pathways from the cancer literature. Our role, together with Guang Yao's group, is to guide the development from a biological perspective and to apply the system to generate and test hypotheses about cancer biology.

March 6, 2014
Our paper on mutation accumulation and dedifferentiation in stem-cell driven cancers is out in PLoS Computational Biology.

July 22, 2013
Ryan is proud to have been awarded the 2013 College of Science Distinguished Early-Career Award. The award particularly recognizes his efforts developing MCB 315 - Key Concepts in Quantiative Biology.

July 4, 2013
Congatulations to Sasha Jilkine who is leaving the group to become an Assistant Professor of Mathematics at the University of Notre Dame.

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