User:Claus O. Wilke: Difference between revisions

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==Selected Publications==
==Selected Publications==
<biblio>
#Steinmeyer_Wilke_2009 pmid=19627995
#Brennan_et_al_2009 pmid=19535437
#Sedaghat_et_al_2009 pmid=19430101
#Zhou_et_al_2009 pmid=19349643
#Zhou_et_al_2008b pmid=19018282
#Novella_et_al_2008 pmid=18829755
#Bull_Wilke_2008 pmid=18780744
#Drummond_Wilke_2008 pmid=18662548
#Brunet_et_al_2008 pmid=18493075
#Whitehead_et_al_2008 pmid=18479505
#Zhou_et_al_2008a pmid=18379715
#Sedaghat_et_al_2008b pmid=18362342
#Dutta_et_al_2008 pmid=18287227
#Sedaghat_et_al_2008a pmid=18171475
#Rouzine_et_al_2008 pmid=18023832
<!--// leave a comment about a paper here -->
<!--#Book1 isbn=0879697164-->
</biblio>


==Useful links==
# 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]
*[[OpenWetWare:Welcome|Introductory tutorial]]
# 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]
*[[Help|OpenWetWare help pages]]
# 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]
# 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]
# 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]
# 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]
# 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]
# 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]
# 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]
# 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]
# 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]
# 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]
# 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]
# 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]
# 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]
# 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.
# 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]
# 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]
# C. O. Wilke (2003). Probability of fixation of an advantageous mutant in a viral quasispecies. Genetics 163:467-474.
# C. O. Wilke (2001). Selection for fitness vs. selection for robustness in RNA secondary structure folding. Evolution 55:2412-2420.
# 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.
# C. O. Wilke and C. Adami (2001). Interaction between directional epistasis and average mutational effects. Proc. R. Soc. London B 268:1469-1474.
# C. O. Wilke (2001). Adaptive evolution on neutral networks. Bull. Math. Biol. 63:715-730.

Revision as of 14:43, 6 May 2010

Contact Info

Claus O. Wilke
  • Claus O. Wilke
  • Section of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute for Cell and Molecular Biology
  • The University of Texas at Austin, Austin, TX 78712
  • Wilke lab
  • Email me through OpenWetWare


Education

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

Research interests

  1. Computational evolutionary biology
  2. Molecular evolution
  3. Virus evolution

Selected Publications

  1. 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. doi:10.1371/journal.pcbi.1000664 pmcid: PMC2816680
  2. D. A. Drummond and C. O. Wilke (2009). The evolutionary consequences of erroneous protein synthesis. Nature Reviews Genetics 10:715-724. doi:10.1038/nrg2662 pmcid: PMC2764353
  3. 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. doi:10.1128/JVI.02568-08 pmcid: PMC2738142
  4. 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. doi:10.1093/molbev/msp070
  5. D. A. Drummond and C. O. Wilke (2008). Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352. doi:10.1016/j.cell.2008.05.042 pmcid: PMC2696314
  6. 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. doi:10.1073/pnas.0711372105 pmcid: PMC2290747
  7. J. J. Bull, R. Sanjuán, and C. O. Wilke (2007). Theory of lethal mutagenesis for viruses. J. Virol. 81:2930-2939. doi:10.1128/JVI.01624-06 pmcid: PMC1865999
  8. J. D. Bloom, A. Raval, and C. O. Wilke (2007). Thermodynamics of neutral protein evolution. Genetics 175:255-266. doi:10.1534/genetics.106.061754 pmcid: PMC1775007
  9. 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. doi:10.1093/molbev/msl040
  10. 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. doi:10.1128/JVI.00591-06 pmcid:PMC1488985
  11. 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. doi:10.1093/molbev/msj038
  12. 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. doi:10.1073/pnas.0504070102 pmcid:PMC1242296
  13. C. O. Wilke (2005). Quasispecies theory in the context of population genetics. BMC Evol. Biol. 5:44. doi:10.1186/1471-2148-5-44 pmcid:PMC1208876
  14. 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. doi:10.1073/pnas.0500729102 pmcid:PMC556249
  15. 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. doi:10.1073/pnas.0406744102 pmcid:PMC545518
  16. 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.
  17. C. O. Wilke (2004). The speed of adaptation in large asexual populations. Genetics 167:2045-2053. pmcid:PMC1470994
  18. I. S. Novella, D. D. Reissig, and C. O. Wilke (2004). Density-dependent selection in vesicular stomatitis virus. J. Virol. 78:5799-5804. pmcid:PMC415817
  19. C. O. Wilke (2003). Probability of fixation of an advantageous mutant in a viral quasispecies. Genetics 163:467-474.
  20. C. O. Wilke (2001). Selection for fitness vs. selection for robustness in RNA secondary structure folding. Evolution 55:2412-2420.
  21. 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.
  22. C. O. Wilke and C. Adami (2001). Interaction between directional epistasis and average mutational effects. Proc. R. Soc. London B 268:1469-1474.
  23. C. O. Wilke (2001). Adaptive evolution on neutral networks. Bull. Math. Biol. 63:715-730.
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