Wilke:Publications

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THE WILKE LAB

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Peer-Reviewed Articles and Book Chapters

2010

1. E. B. O'Dea, T. E. Keller, and C. O. Wilke. Does mutational robustness inhibit extinction by lethal mutagenesis in viral populations? PLoS Comp. Biol., in press.
2. 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.
3. 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
4. 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.
5. 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.
6. 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
7. 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.

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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. doi:10.1371/journal.pone.0003765
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. doi:10.1128/JVI.01394-08
3. J. J. Bull and C. O. Wilke (2008). Lethal mutagenesis of bacteria. Genetics 180:1061-1070. doi:10.1534/genetics.108.091413
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. doi:10.1016/j.cell.2008.05.042
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. doi:10.1186/1745-6150-3-18 *Equal contribution.
6. É. Brunet, I. M. Rouzine, and C. O. Wilke (2008). The stochastic edge in adaptive evolution. Genetics 179:603-620. doi:10.1534/genetics.107.079319
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. doi:10.1007/s00239-008-9094-4
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. doi:10.1128/JVI.02446-07
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. doi:10.1073/pnas.0711372105
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. doi:10.1016/j.tpb.2007.10.004
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. doi:10.1186/1471-2334-8-2

2007

1. A. R. Sedaghat, J. D. Siliciano, T. P. Brennan, C. O. Wilke, and R. F. Siliciano (2007). Limits on replenishment of the resting CD4+ T cell reservoir for HIV in patients on HAART. PLoS Pathogens 3:e122. doi:10.1371/journal.ppat.0030122
2. R. Forster and C. O. Wilke (2007). Frequency-dependent selection in a periodic environment. Physica A 381:255-264. doi:10.1016/j.physa.2007.03.017
3. 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
4. S. F. Elena, C. O. Wilke, C. Ofria, and R. E. Lenski (2007). Effects of population size and mutation rate on the evolution of mutational robustness. Evolution 61:666-674. doi:10.1111/j.1558-5646.2007.00064.x
5. 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

2006

1. R. Forster, C. Adami, and C. O. Wilke (2006). Selection for mutational robustness in finite populations. J. Theor. Biol. 243:181-190. doi:10.1016/j.jtbi.2006.06.020
2. 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
3. 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
4. C. O. Wilke and D. A. Drummond (2006). Population genetics of translational robustness. Genetics 173:473-481. doi:10.1534/genetics.105.051300
5. 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
6. C. O. Wilke, R. Forster, and I. S. Novella (2006). Quasispecies in time-dependent environments. Curr. Topics Microbiol. Immun. 299:33-50.

2005

1. R. Forster and C. O. Wilke (2005). Tradeoff between short-term and long-term adaptation in a changing environment. Phys. Rev. E 72:041922.
2. C. O. Wilke, J. D. Bloom, D. A. Drummond, and A. Raval (2005). Predicting the tolerance of proteins to random amino acid substitution. Biophys. J. 89:3714-3720. doi:10.1529/biophysj.105.062125
3. 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
4. C. O. Wilke (2005). Quasispecies theory in the context of population genetics. BMC Evol. Biol. 5:44. doi:10.1186/1471-2148-5-44
5. 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
6. 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
7. C. Ofria and C. O. Wilke (2005). Avida: Evolution experiments with self-replicating computer programs. In A. Adamatzky and M. Komosinski, eds. Artificial Life Models in Software. Springer, pp. 3-36.
8. C. O. Wilke and S. S. Chow (2005). Exploring the evolution of ecosystems with digital organisms. In M. Pascual and J. Dunne, eds. Ecological Networks. Linking Structure to Dynamics in Food Webs. Oxford University Press.

Editorial materials

1. J. D. Bloom, F. H. Arnold, and C. O. Wilke (2007). Breaking proteins with mutations: threads and thresholds in evolution. Mol. Syst. Biol. 3:76.
2. C. O. Wilke (2006). Biology through the robustness lens. BioScience 56:695-696.
3. C. O. Wilke (2005). Molecular clocks: the heavy, the cold, and the slow. Heredity 95:115. doi:10.1038/sj.hdy.6800681