User:Claus O. Wilke

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*Claus O. Wilke, PhD
*Claus O. Wilke, PhD
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*Associate Professor
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*Professor
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*Section of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute for Cell and Molecular Biology
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*Department of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology
*The University of Texas at Austin, Austin, TX 78712
*The University of Texas at Austin, Austin, TX 78712
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*[[Wilke:Lab-Home|Wilke lab]]
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*[http://wilke.openwetware.org Wilke lab page]
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*[http://serialmentor.com/blog Personal blog]
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*[http://twitter.com/ClausWilke Twitter]
*[[Special:Emailuser/Claus O. Wilke|Email me through OpenWetWare]]
*[[Special:Emailuser/Claus O. Wilke|Email me through OpenWetWare]]
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==Education==
==Education==
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# Computational evolutionary biology
# Computational evolutionary biology
# Molecular evolution
# Molecular evolution
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# Bioinformatics
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# Protein biochemistry
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# Systems biology
# Virus evolution
# Virus evolution
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==Selected Publications==
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[http://wilke.openwetware.org/Publications.html Click here for a complete list of publications.]
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# W. Gu, T. Zhou, and C. O. Wilke (2010). A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput Biol 6:e1000664. [http://dx.doi.org/10.1371/journal.pcbi.1000664 doi:10.1371/journal.pcbi.1000664] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2816680/ pmcid: PMC2816680]
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# D. A. Drummond and C. O. Wilke (2009). The evolutionary consequences of erroneous protein synthesis. Nature Reviews Genetics 10:715-724. [http://dx.doi.org/10.1038/nrg2662 doi:10.1038/nrg2662] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2764353 pmcid: PMC2764353]
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# T. P. Brennan, J. O. Woods, A. R. Sedaghat, J. D. Siliciano, R. F. Siliciano, and C. O. Wilke (2009). 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. [http://dx.doi.org/10.1128/JVI.02568-08 doi:10.1128/JVI.02568-08] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2738142 pmcid: PMC2738142]
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# T. Zhou, M. Weems, and C. O. Wilke (2009). Translationally optimal codons associate with structurally sensitive sites in proteins. Mol. Biol. Evol. 26:1571-1580. [http://dx.doi.org/10.1093/molbev/msp070 doi:10.1093/molbev/msp070]
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# D. A. Drummond and C. O. Wilke (2008). Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352. [http://dx.doi.org/10.1016/j.cell.2008.05.042 doi:10.1016/j.cell.2008.05.042] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2696314 pmcid: PMC2696314]
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# A. R. Sedaghat, J. B. Dinoso, L. Shen, C. O. Wilke, and R. F. Siliciano (2008). Decay dynamics of HIV-1 depend on the inhibited stages of the viral life cycle. Proc. Natl. Acad. Sci. USA 105:4832-4837. [http://dx.doi.org/10.1073/pnas.0711372105 doi:10.1073/pnas.0711372105] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2290747 pmcid: PMC2290747]
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# J. J. Bull, R. Sanjuán, and C. O. Wilke (2007). Theory of lethal mutagenesis for viruses. J. Virol. 81:2930-2939. [http://dx.doi.org/10.1128/JVI.01624-06 doi:10.1128/JVI.01624-06] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1865999 pmcid: PMC1865999]
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# J. D. Bloom, A. Raval, and C. O. Wilke (2007). Thermodynamics of neutral protein evolution. Genetics 175:255-266. [http://dx.doi.org/10.1534/genetics.106.061754 doi:10.1534/genetics.106.061754] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1775007 pmcid: PMC1775007]
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# J. D. Bloom, D. A. Drummond, F. H. Arnold, and C. O. Wilke (2006). Structural determinants of the rate of protein evolution in yeast. Mol. Biol. Evol. 23:1751-1761. [http://dx.doi.org/10.1093/molbev/msl040 doi:10.1093/molbev/msl040]
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# J. R. Bailey, A. R. Sedaghat, T. Kieffer, T. Brennan, P. K. Lee, M. Wind-Rotolo, C. M. Haggerty, A. R. Kamireddi, Y. Liu, J. Lee, D. Persaud, J. E. Gallant, J. Cofrancesco, Jr., T. C. Quinn, C. O. Wilke, S. C. Ray, J. D. Siliciano, R. E. Nettles, and R. F. Siliciano (2006). Residual Human Immunodeficiency Virus Type 1 viremia in some patients on antiretroviral therapy is dominated by a small number of invariant clones rarely found in circulating CD4 T cells. J. Virol. 80:6441-6457. [http://dx.doi.org/10.1128/JVI.00591-06 doi:10.1128/JVI.00591-06] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1488985 pmcid:PMC1488985]
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# D. A. Drummond, A. Raval, and C. O. Wilke (2006). A single determinant dominates the rate of yeast protein evolution. Mol. Biol. Evol. 23:327-337. [http://dx.doi.org/10.1093/molbev/msj038 doi:10.1093/molbev/msj038]
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# D. A. Drummond, J. D. Bloom, C. Adami, C. O. Wilke, and F. H. Arnold. (2005). Why highly expressed proteins evolve slowly. Proc. Natl. Acad. Sci. USA 102:14338-14343. [http://dx.doi.org/10.1073/pnas.0504070102 doi:10.1073/pnas.0504070102] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1242296 pmcid:PMC1242296]
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# C. O. Wilke (2005). Quasispecies theory in the context of population genetics. BMC Evol. Biol. 5:44. [http://dx.doi.org/10.1186/1471-2148-5-44 doi:10.1186/1471-2148-5-44] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1208876 pmcid:PMC1208876]
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# D. A. Drummond, J. J. Silberg, M. M. Meyer, C. O. Wilke, and F. H. Arnold (2005). On the conservative nature of intragenic recombination. Proc. Natl. Acad. Sci. USA 102:5380-5385. [http://dx.doi.org/10.1073/pnas.0500729102 doi:10.1073/pnas.0500729102] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC556249 pmcid:PMC556249]
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# J. D. Bloom, J. J. Silberg, C. O. Wilke, D. A. Drummond, C. Adami, and F. H. Arnold (2005). Thermodynamic prediction of protein neutrality. Proc. Natl. Acad. Sci. USA 102:606-611. [http://dx.doi.org/10.1073/pnas.0406744102 doi:10.1073/pnas.0406744102] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC545518 pmcid:PMC545518]
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# S. S. Chow*, C. O. Wilke*, C. Ofria, R. E. Lenski, and C. Adami (2004). Adaptive radiation from resource competition in digital organisms. Science 305:84-86. *Equal contribution.
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# C. O. Wilke (2004). The speed of adaptation in large asexual populations. Genetics 167:2045-2053. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1470994 pmcid:PMC1470994]
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# I. S. Novella, D. D. Reissig, and C. O. Wilke (2004). Density-dependent selection in vesicular stomatitis virus. J. Virol. 78:5799-5804.  [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC415817 pmcid:PMC415817]
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# C. O. Wilke (2003). Probability of fixation of an advantageous mutant in a viral quasispecies. Genetics 163:467-474.
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# C. O. Wilke (2001). Selection for fitness vs. selection for robustness in RNA secondary structure folding. Evolution 55:2412-2420.
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# C. O. Wilke, J. L. Wang, C. Ofria, R. E. Lenski, and C. Adami (2001). Evolution of digital organisms at high mutation rate leads to survival of the flattest. Nature 412:331-333.
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# C. O. Wilke and C. Adami (2001). Interaction between directional epistasis and average mutational effects. Proc. R. Soc. London B 268:1469-1474.
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# C. O. Wilke (2001). Adaptive evolution on neutral networks. Bull. Math. Biol. 63:715-730.
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Current revision

Contact Info

Claus O. Wilke
Claus O. Wilke

Education

  • 1999, PhD, Ruhr-University Bochum, Germany
  • 1996, Diplom, Ruhr-University Bochum, Germany

Research interests

  1. Computational evolutionary biology
  2. Molecular evolution
  3. Bioinformatics
  4. Protein biochemistry
  5. Systems biology
  6. Virus evolution

Click here for a complete list of publications.

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