Wilke:Publications

= Peer-Reviewed Articles =

In press

 * 1) D. C. Ramsey, M. P. Scherrer, T. Zhou, and C. O. Wilke (2011). The Relationship Between Relative Solvent Accessibility and Evolutionary Rate in Protein Evolution. Genetics. doi:10.1534/genetics.111.128025
 * 2) A. Spivak, A. Rabi, M. A. McMahon, L. Shan, A. R. Sedaghat, C. O. Wilke, R. Siliciano (2011). Dynamic Constraints on the Second Phase Compartment of HIV-infected Cells. AIDS Res. Hum. Retroviruses. doi:10.1089/AID.2010.0199

2011

 * 1) T. Zhou and C. O. Wilke (2011). Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses. BMC Evol. Biol. 11:59. doi:10.1186/1471-2148-11-59 pmcid: PMC3072339
 * 2) A. T. Ciota, E. M. Koch, G. G. Willsey, L. J. Davis, G. V. S. Jerzak, D. J. Ehrbar, C. O. Wilke, and L. D. Kramer (2011). Temporal and spatial alterations in mutant swarm size of St. Louis encephalitis virus in mosquito hosts. Infection, Genetics and Evolution 11:460-468. doi:10.1016/j.meegid.2010.12.007
 * 3) E. B. O'Dea and C. O. Wilke (2011). Contact heterogeneity and phylodynamics: How contact networks shape parasite evolutionary trees. Interdiscip. Persp. Inf. Dis. 2011:238743. doi:10.1155/2011/238743 pmcid: PMC2995904

2010

 * 1) Y. Lee, T. Zhou, G. G. Tartaglia, M. Vendruscolo, and C. O. Wilke (2010). Translationally optimal codons associate with aggregation-prone sites in proteins. Proteomics 10:4163-4171. doi:10.1002/pmic.201000229 pmcid: PMC3037288
 * 2) K. Pepin, I. Volkov, J. R. Banavar, C. O. Wilke, and B. T. Grenfell (2010). Phenotypic differences in viral immune-escape explained by linking within-host dynamics to host-population immunity. J. Theor. Biol. 265:501-510. doi:10.1016/j.jtbi.2010.05.036
 * 3) T. Zhou, W. Gu, and C. O. Wilke (2010). Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol. Biol. Evol. 27:1912-1922. doi:10.1093/molbev/msq077
 * 4) E. B. O'Dea, T. E. Keller, and C. O. Wilke (2010). Does mutational robustness inhibit extinction by lethal mutagenesis in viral populations? PLoS Comp. Biol. 6:e1000811. doi:10.1371/journal.pcbi.1000811
 * 5) S. D. Smith-Tsurkan, C. O. Wilke, and I. S. Novella (2010). Incongruent fitness landscapes, not tradeoffs, dominate the adaptation of VSV to novel host types. J. Gen. Virol. 91:1484-1493. doi:10.1099/vir.0.017855-0
 * 6) A. R. Sedaghat, D. A. Rastegar, K. A. O’Connell, J. B. Dinoso, C. O. Wilke, and J. N. Blankson (2010). Is it time to treat HIV elite controllers with combined antiretroviral therapy? - Reply. Clinical Infectious Diseases 50:1425-1426. doi:10.1086/652285
 * 7) S. H. Steinmeyer, C. O. Wilke, and K. M. Pepin (2010). 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 365:1931-1941.doi:10.1098/rstb.2010.0065  pmcid: PMC2880116
 * 8) 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 (2010). Genomic evolution of vesicular stomatitis virus strains with differences in adaptability. J. Virol. 84:4960-4968. doi:10.1128/JVI.00710-09 pmcid: PMC2863795
 * 9) C. O. Wilke and D. A. Drummond (2010). Signatures of protein biophysics in coding sequence evolution. Cur. Opin. Struct. Biol. 20:385-389. doi:10.1016/j.sbi.2010.03.004 pmcid: PMC2905607
 * 10) 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
 * Featured in genomeweb, Feb. 8, 2010.

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. doi:10.1016/j.jtbi.2009.07.014
 * 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. doi:10.1128/JVI.02568-08 pmcid: PMC2738142
 * Featured in Science Daily.
 * 1) 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 pmcid: PMC2980788
 * 2) 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. pmcid:PMC2980788

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 pmcid: PMC2582452
 * 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 pmcid: PMC2593322
 * 3) J. J. Bull and C. O. Wilke (2008). Lethal mutagenesis of bacteria. Genetics 180:1061-1070. doi:10.1534/genetics.108.091413 pmcid: PMC2567356
 * 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 pmcid: PMC2696314
 * Featured in Cell Preview.
 * 1) 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 pmcid: PMC2423361 *Equal contribution.
 * 2) 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 pmcid: PMC2390637
 * 3) 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
 * 4) 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 pmcid: PMC2293023
 * 5) 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
 * 6) 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.
 * 7) 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 pmcid: PMC2246079
 * 8) 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 pmcid: PMC2254415

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 pmcid: PMC1959378
 * 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 pmcid: PMC2031831
 * 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 pmcid: PMC1865999
 * 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 pmcid: PMC1775007

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 pmcid:PMC1488985
 * 4) C. O. Wilke and D. A. Drummond (2006). Population genetics of translational robustness. Genetics 173:473-481. doi:10.1534/genetics.105.051300 pmcid:PMC1461446
 * 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.
 * 7) C. Ofria and C. O. Wilke (2006). 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 (2006). 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.

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.  doi:10.1103/PhysRevE.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  pmcid:PMC1366941
 * 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 pmcid:PMC1242296
 * 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 pmcid:PMC1208876
 * 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 pmcid:PMC556249
 * 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 pmcid:PMC545518

2004

 * 1) C. O. Wilke (2004). Molecular clock in neutral protein evolution. BMC Genetics 5:25. pmcid:PMC517495
 * 2) 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.
 * 3) R. Froissart, C. O. Wilke, R. Montville, S. K. Remold, L. Chao, and P. E. Turner (2004) Co-infection weakens selection against epistatic mutations in RNA viruses. Genetics 168:9-19. pmcid:PMC1448111
 * 4) C. O. Wilke (2004). The speed of adaptation in large asexual populations. Genetics 167:2045-2053. pmcid:PMC1470994
 * 5) J. D. Bloom, C. O. Wilke, F. H. Arnold, and C. Adami (2004). Stability and the evolvability of function in a model protein. Biophys. J. 86:2758-2764.  pmcid:PMC1304146
 * 6) 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
 * 7) C. O. Wilke, D. D. Reissig, and I. S. Novella (2004). Replication at periodically changing multiplicity of infection promotes stable coexistence of competing viral populations. Evolution 58:900-905.
 * 8) C. Adami and C. O. Wilke (2004). Experiments in Evolution. Artificial Life 10:117-122.
 * 9) Y. Li and C. O. Wilke (2004). Digital Evolution in Time-Dependent Fitness Landscapes. Artificial Life 10:123-134.
 * 10) T. J. Johnson and C. O. Wilke (2004). Evolution of Resource Competition Between Mutually Dependent Digital Organisms. Artificial Life 10:145-156.
 * 11) C. Ofria and C. O. Wilke (2004). Avida: A Software Platform for Research in Computational Evolutionary Biology. Artificial Life 10:191-229.
 * 12) P. R. A. Campos, C. Adami, and C. O. Wilke (2004). Modelling Stochastic Clonal Interference. In G. Ciobanu and G. Rozenberg, eds., Modelling in Molecular Biology. Springer Series in Natural Computing, pp. 21-39.

2003

 * 1) C. O. Wilke, I. S. Novella (2003). Phenotypic mixing and hiding may contribute to memory in viral quasispecies. BMC Microbiology 3:11.
 * 2) C. O. Wilke (2003). Does the Red Queen reign in the kingdom of digital organisms? Lect. Notes. Artif. Int. 2801:405-414.
 * 3) C. O. Wilke (2003). Probability of fixation of an advantageous mutant in a viral quasispecies. Genetics 163:467-474.
 * 4) C. O. Wilke, R. E. Lenski, and C. Adami (2003). Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding. BMC Evolutionary Biology 3:3.
 * 5) C. O. Wilke, C. Adami (2003). Evolution of mutational robustness. Mut. Res. 522:3-11.

2002

 * 1) C. Kamp, C. O. Wilke, C. Adami and S. Bornholdt (2002). Viral evolution under the pressure of an adaptive immune system - optimal mutation rates for viral escape. Complexity 8:28-33.
 * Featured in Nature News and Views, Vol. 420:367-369 (2002).
 * 1) C. O. Wilke, C. Adami (2002). The biology of digital organisms. Trends. Ecol. Evol. 17:528-532.
 * 2) C. O. Wilke, P. R. A. Campos, and J. F. Fontanari (2002). The genealogical process in a correlated fitness landscape. J. Exp. Zool. (Mol. Dev. Evol.) 294:274-284.
 * 3) C. O. Wilke (2002). Maternal effects in molecular evolution. Phys. Rev. Lett. 88:078101.
 * 4) P. R. A. Campos, C. Adami, and C. O. Wilke (2002). Optimal adaptive performance and delocalization in NK fitness landscapes. Physica A 304:495-506.

2001

 * 1) C. O. Wilke (2001). Selection for fitness vs. selection for robustness in RNA secondary structure folding. Evolution 55:2412-2420.
 * 2) 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.
 * Featured in Nature highlights, July 19, 2001.
 * 1) C. Ronnewinkel, C. O. Wilke and T. Martinetz (2001). Genetic algorithms in time-dependent environments. In L. Kallel, B. Naudts and A. Rogers, editors, Theoretical Aspects of Evolutionary Computing, pp. 261-285. Natural Computing, Springer Verlag.
 * 2) C. O. Wilke (2001). Adaptive evolution on neutral networks. Bull. Math. Biol. 63:715-730.
 * 3) C. O. Wilke and C. Adami (2001). Interaction between directional epistasis and average mutational effects. Proc. R. Soc. London B 268:1469-1474.
 * Featured in National Georaphic News 07/2001.
 * 1) C. O. Wilke, C. Ronnewinkel and T. Martinetz (2001). Dynamic fitness landscapes in molecular evolution. Phys. Rep. 349:395-446.
 * 2) C. O. Wilke and C. Ronnewinkel (2001). Dynamic fitness landscapes: Expansions for small mutation rates. Physica A 290:475-490.

2000

 * 1) C. O. Wilke (2000). Dynamische Fitnesslandschaften. KI 14:20-25 (in german).

1999

 * 1) C. O. Wilke and T. Martinetz (1999). Adaptive walks on time-dependent fitness landscapes. Phys. Rev. E 60:2154-2159.
 * 2) C. O. Wilke and T. Martinetz (1999). Lifetimes of agents under external stress  Phys. Rev. E Rapid Communications 59:R2512-R2515.
 * 3) C. O. Wilke, C. Ronnewinkel, and T. Martinetz (1999). Molecular Evolution in Time Dependent Environments. Lect. Notes. Artif. Int. 1674:417-421.

1998

 * 1) C. Wilke and T. Martinetz (1998). Hierarchical noise in large systems of independent agents. Phys. Rev. E 58:7101-7108.
 * 2) C. Wilke, S. Altmeyer, and T. Martinetz (1998). Aftershocks in Coherent-Noise Models. Physica D, 120:401-417.
 * 3) S. Altmeyer, C. Wilke, and T. Martinetz (1998). How fast do structures emerge in hypercycle systems? In C. Wilke, S. Altmeyer, and T. Martinetz, editors, Third German Workshop on Artificial Life. Verlag Harri Deutsch.
 * 4) C. Wilke, S. Altmeyer, and T. Martinetz (1998). Large-scale evolution and extinction in a hierarchically structured environment. In C. Adami, R. Belew, H. Kitano, and C. Taylor, editors, Proc. of Artificial Life VI, Los Angeles, June 26-29, 1998. MIT Press.

1997

 * 1) C. Wilke and T. Martinetz (1997). Simple model of evolution with variable system size. Phys. Rev. E 56:7128-7131.
 * 2) M. Kachelrieß, C. Wilke, and G. Wunner (1997). Axion cyclotron emissivity of magnetized white dwarfs and neutron stars. Phys. Rev. D 56:1313-1319.
 * 3) C. Wilke and G. Wunner (1997). Photon splitting in strong magnetic fields: asymptotic approximation formulae vs. accurate numerical results. Phys. Rev. D 55:997-1000.

= 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. doi:10.1038/msb4100119 pmcid: PMC1800353
 * 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
 * 4) C. O. Wilke (2004). Supplementary materials need the right format. Nature 430:291.