Wilke:Publications

Notice: The Wilke Lab page has moved to http://wilkelab.org.
The page you are looking at is kept for archival purposes and will not be further updated.

THE WILKE LAB

Home        Contact        People        Research        Publications        Materials

Peer-Reviewed Articles and Book Chapters

2010

1. S. H. Steinmeyer, C. O. Wilke, and K. M. Pepin. Methods of modeling viral disease dynamics across the within- and between-host scales: The impact of virus dose on host population immunity. Phil. Trans. R. Soc. B, in press.
2. T. Zhou, W. Gu, and C. O. Wilke. Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol. Biol. Evol., in press
3. S. D. Smith-Tsurkan, C. O. Wilke, and I. S. Novella. Incongruent fitness landscapes, not tradeoffs, dominate the adaptation of VSV to novel host types. J. Gen. Virol., in press.
4. I. S. Novella, J. B. Presloid, T. Zhou, S. D. Smith-Tsurkan, B. E. Ebendick-Corpus, R. N. Dutta, K. L. Lust, and C. O. Wilke. Genomic evolution of vesicular stomatitis virus strains with differences in adaptability. J. Virol., in press.
5. C. O. Wilke and D. A. Drummond. Signatures of protein biophysics in coding sequence evolution. Cur. Opin. Struct. Biol., in press. DOI:10.1016/j.sbi.2010.03.004
6. 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

2009

1. 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
2. A. R. Sedaghat, D. A. Rastegar, K. A. O'Connell, J. B. Dionso, C. O. Wilke, and J. N. Blankson (2009). T cell dynamics and the response to HAART in a cohort of HIV-1 infected elite suppressors. Clin. Inf. Diseases 49:1763-1766. DOI:10.1086/648081
3. S. H. Steinmeyer and C. O. Wilke (2009). Lethal mutagenesis in a structured environment. J. Theor. Biol. 261:67-73.
4. 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.

   Featured in Science Daily.

5. 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.
6. A. R. Sedaghat, R. F. Siliciano, and C. O. Wilke (2009). Constraints on the dominant mechanism for HIV viral dynamics in patients on raltegravir. Antiviral Therapy 14:263-271.

2008

1. T. Zhou, P. J. Enyeart, and C. O. Wilke (2008). Detecting Clusters of Mutations. PLoS ONE 3:e3765.
2. I. S. Novella, R. N. Dutta, and C. O. Wilke (2008). A linear relationship between fitness and log critical bottleneck size in vesicular stomatitis virus. J. Virol. 82:12589-12590.
3. J. J. Bull and C. O. Wilke (2008). Lethal mutagenesis of bacteria. Genetics 180:1061-1070.
4. D. A. Drummond and C. O. Wilke (2008). Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352.
5. D. J. Whitehead*, C. O. Wilke*, D. Vernazobres, and E. Bornberg-Bauer (2008). The look-ahead effect of phenotypic mutations. Biology Direct 3:18. *Equal contribution.
6. É. Brunet, I. M. Rouzine, and C. O. Wilke (2008). The stochastic edge in adaptive evolution. Genetics 179:603-620.
7. T. Zhou, D. A. Drummond, and C. O. Wilke (2008) Contact density affects protein evolutionary rate from bacteria to animals. J. Mol. Evol. 66:395-404.
8. R. N. Dutta, I. M. Rouzine, S. D. Smith, C. O. Wilke, and I. S. Novella (2008). Rapid adaptive amplification of preexisting variation in an RNA virus. J. Virol. 82:4354-4362.
9. 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.
10. J. J. Bull, R. Sanjuán, and C. O. Wilke (2008). Lethal mutagenesis. In E. Domingo, C. R. Parrish, and J. J. Holland, eds., Origin and Evolution of Viruses, 2nd ed., pp. 207--218. Elsevier.
11. I. M. Rouzine, É. Brunet, and C. O. Wilke (2008). The traveling-wave approach to asexual evolution: Muller's ratchet and speed of adaptation. Theor. Popul. Biol. 73:24-46.
12. A. R. Sedaghat, R. F. Siliciano, and C. O. Wilke (2008). Low-level HIV-1 replication and the dynamics of the resting CD4+ T cell reservoir for HIV-1 in the setting of HAART. BMC Inf. Dis. 8:2.

2007

1. Forster R and Wilke CO. Frequency-Dependent Selection in a Periodic Environment. Physica A. 2007 Jul 15;381:255-264. DOI:10.1016/j.physa.2007.03.017 |
2. Sedaghat AR, Siliciano JD, Brennan TP, Wilke CO, and Siliciano RF. Limits on replenishment of the resting CD4+ T cell reservoir for HIV in patients on HAART. PLoS Pathog. 2007 Aug 31;3(8):e122. DOI:10.1371/journal.ppat.0030122 |
3. Elena SF, Wilke CO, Ofria C, and Lenski RE. Effects of population size and mutation rate on the evolution of mutational robustness. Evolution. 2007 Mar;61(3):666-74. DOI:10.1111/j.1558-5646.2007.00064.x |
4. Bull JJ, Sanjuán R, and Wilke CO. Theory of lethal mutagenesis for viruses. J Virol. 2007 Mar;81(6):2930-9. DOI:10.1128/JVI.01624-06 |
5. Bloom JD, Raval A, and Wilke CO. Thermodynamics of neutral protein evolution. Genetics. 2007 Jan;175(1):255-66. DOI:10.1534/genetics.106.061754 |

2006

6. Forster R, Adami C, and Wilke CO. Selection for mutational robustness in finite populations. J Theor Biol. 2006 Nov 21;243(2):181-90. DOI:10.1016/j.jtbi.2006.06.020 |
7. Bloom JD, Drummond DA, Arnold FH, and Wilke CO. Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol. 2006 Sep;23(9):1751-61. DOI:10.1093/molbev/msl040 |
8. Bailey JR, Sedaghat AR, Kieffer T, Brennan T, Lee PK, Wind-Rotolo M, Haggerty CM, Kamireddi AR, Liu Y, Lee J, Persaud D, Gallant JE, Cofrancesco J Jr, Quinn TC, Wilke CO, Ray SC, Siliciano JD, Nettles RE, and Siliciano RF. 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. 2006 Jul;80(13):6441-57. DOI:10.1128/JVI.00591-06 |
9. Wilke CO, Forster R, and Novella IS. Quasispecies in time-dependent environments. Curr Top Microbiol Immunol. 2006;299:33-50. DOI:10.1007/3-540-26397-7_2 |
10. Wilke CO and Drummond DA. Population genetics of translational robustness. Genetics. 2006 May;173(1):473-81. DOI:10.1534/genetics.105.051300 |
11. Drummond DA, Raval A, and Wilke CO. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol. 2006 Feb;23(2):327-37. DOI:10.1093/molbev/msj038 |

2005

12. Forster R and Wilke CO. Tradeoff between short-term and long-term adaptation in a changing environment. Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Oct;72(4 Pt 1):041922. DOI:10.1103/PhysRevE.72.041922 |
13. Drummond DA, Bloom JD, Adami C, Wilke CO, and Arnold FH. Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A. 2005 Oct 4;102(40):14338-43. DOI:10.1073/pnas.0504070102 |
14. Wilke CO, Bloom JD, Drummond DA, and Raval A. Predicting the tolerance of proteins to random amino acid substitution. Biophys J. 2005 Dec;89(6):3714-20. DOI:10.1529/biophysj.105.062125 |
15. Wilke CO. Quasispecies theory in the context of population genetics. BMC Evol Biol. 2005 Aug 17;5:44. DOI:10.1186/1471-2148-5-44 |
16. Drummond DA, Silberg JJ, Meyer MM, Wilke CO, and Arnold FH. On the conservative nature of intragenic recombination. Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5380-5. DOI:10.1073/pnas.0500729102 |
17. Bloom JD, Silberg JJ, Wilke CO, Drummond DA, Adami C, and Arnold FH. Thermodynamic prediction of protein neutrality. Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):606-11. DOI:10.1073/pnas.0406744102 |

18. Ofria C and Wilke CO. Avida: Evolution experiments with self-replicating computer programs. In Adamatzky A and Komosinski M, eds. Artificial Life Models in Software. 2005; Springer pp. 3-36.

19. Wilke CO and Chow SS. Exploring the evolution of ecosystems with digital organisms. In Pascual M and Dunne J, eds. Ecological Networks. Linking Structure to Dynamics in Food Webs. 2005; Oxford University Press.

Editorial materials

20. Bloom JD, Arnold FH, and Wilke CO. Breaking proteins with mutations: threads and thresholds in evolution. Mol Syst Biol. 2007;3:76. DOI:10.1038/msb4100119 |

21. Wilke CO. Biology through the robustness lens. BioScience 2006; 56 695-6.

22. Wilke CO. Molecular clocks: the heavy, the cold, and the slow. Heredity (Edinb). 2005 Aug;95(2):115. DOI:10.1038/sj.hdy.6800681 |