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Claus Wilke

Wilke, Claus
Professor in Integrative Biology

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Main Office: MBB 3.232 Phone: 232-2459

Mailing Address:
The University of Texas at Austin
Section of Integrative Biology, College of Natural Sciences
2500 Speedway
Austin,TX 78712


Research Summary:

I am a computational biologist. I use bioinformatical and statistical methods to analyze biological data sets, in particular whole-genome and high-throughput data sets; I also develop mathematical models and computer simulations of biological systems. While my lab does not perform any experiments, I have extensive collaborations with experimental groups and I frequently co-advise students whose research has an experimental component.

My current research covers three broad but interconnected areas: 1. biophysical mechanisms of molecular evolution; 2. microbial adaptation and experimental evolution; 3. disease dynamics. A recurring theme in my research is evolution; modern biomedical research is deeply connected to evolutionary biology.

1. One of my main research goals is to develop mechanistic, biophysical explanations for patterns of molecular evolution observable in extant genomes. Many of the patterns that we detect reflect fundamental biophysical mechanisms operating in all cellular life forms. My research in this area has led to the hypothesis that selection against protein misfolding is a major factor shaping coding-sequence evolution; we continue to test and elaborate on this hypothesis. My group has also found a universal trend of selection for efficient translation initiation in a broad survey of over 300 species, including bacteria, archaea, and eukaryotes.

2. I develop mathematical or simulation models that predict aspects of microbial adaptation, such as the expected increase in fitness over time. These models provide valuable insight to the growing number of experimentalists who carry out laboratory evolution experiments with microbes.

3. My research interests of molecular evolution and microbial adaptation have important applications for infectious diseases. My group is studying both specific disease systems, such as HIV, and broader questions, such as how viral sequence data relate to epidemiological quantities such as disease prevalence or incidence.



Publications:
2010 W. Gu, T. Zhou, and C. O. Wilke, A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes., PLoS. Comput. Biol. 6: e1000664
2009 T. P. Brennan, J. O. Woods, A. R. Sedaghat, J. D. Siliciano, R. F. Siliciano, and C. O. Wilke, Analysis of HIV-1 viremia and provirus in resting CD4+ T cells reveals a novel source of residual viremia in patients on antiretroviral therapy., J. Virol. 83: 8470-8481
2008 D. A. Drummond and C. O. Wilke, Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution., Cell 134: 341-352
2007 J.J. Bull, R. Sanjuán, and C.O. Wilke, Theory of lethal mutagenesis for viruses, J. Virol. 81: 2930-2939
2006 J. D. Bloom, D. A. Drummond, F. H. Arnold, and C. O. Wilke, Structural determinants of the rate of protein evolution in yeast, Mol. Biol. Evol. 23: 1751-1761
2006 D. A. Drummond, A. Raval, and C. O. Wilke, A single determinant dominates the rate of yeast protein evolution, Mol. Biol. Evol. 23: 327-337