Wilke:Publications: Difference between revisions

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= Peer-Reviewed Articles =
<font size="5"><b> Peer-Reviewed Publications</b> </font>


== In press ==
''' In press '''
# 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.
# S. J. Spielman, E. T. Dawson, C. O. Wilke. Limited utility of residue masking for positive-selection inference. Mol. Biol. Evol., in press. [http://dx.doi.org/10.1093/molbev/msu183 doi:10.1093/molbev/msu183]
# 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. [http://dx.doi.org/10.1089/AID.2010.0199 doi:10.1089/AID.2010.0199]
# A. R. Sedaghat, C. O. Wilke, M. J. Cunningham, S. L. Ishman. Socioeconomic disparities in the presentation of acute bacterial sinusitis complications in children. The Laryngoscope, in press. [http://dx.doi.org/10.1002/lary.24492 doi:10.1002/lary.24492]


== 2011 ==
''' 2014 '''
# 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. [http://dx.doi.org/10.1186/1471-2148-11-59 doi:10.1186/1471-2148-11-59] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072339 pmcid: PMC3072339]
# E. B. O’Dea, K. M. Pepin, B. A. Lopman, C. O. Wilke (2014). Fitting outbreak models to data from many small norovirus outbreaks. Epidemics 6:18-29. [http://dx.doi.org/10.1016/j.epidem.2013.12.002 doi:10.1016/j.epidem.2013.12.002]
# 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. [http://dx.doi.org/10.1016/j.meegid.2010.12.007 doi:10.1016/j.meegid.2010.12.007]
# A. G. Meyer​, S. L. Sawyer, A. D. Ellington, C. O. Wilke (2014). Analyzing Machupo virus-receptor binding by molecular dynamics simulations. PeerJ 2:e266. [http://dx.doi.org/10.7717/peerj.266 doi:10.7717/peerj.266]
# 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. [http://dx.doi.org/10.1155/2011/238743 doi:10.1155/2011/238743] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995904 pmcid: PMC2995904]


''' 2013 '''
# M. Z. Tien, A. G. Meyer, D. K. Sydykova, S. J. Spielman, C. O. Wilke (2013). Maximum allowed solvent accessibilites of residues in proteins. PLOS ONE 8:e80635. [http://dx.doi.org/10.1371/journal.pone.0080635 doi:10.1371/journal.pone.0080635]
# E. L. Jackson, N. Ollikainen, A. W. Covert III, T. Kortemme, C. O. Wilke (2013). Amino-acid site variability among natural and designed proteins. PeerJ 1:e211. [http://dx.doi.org/10.7717/peerj.211 doi:10.7717/peerj.211]
# A. R. Sedaghat, S. T. Gray, K. J. Chambers, C. O. Wilke, and D. S. Caradonna (2013). Sinonasal anatomic variants and asthma are associated with faster development of chronic rhinosinusitis in patients with allergic rhinitis. Int. Forum Allergy Rhinol. 3:755-761. [http://dx.doi.org/10.1002/alr.21163 doi:10.1002/alr.21163]
# A. W. Covert, R. E. Lenski, C. O. Wilke, and C. Ofria (2013). Experiments on the role of deleterious mutations as stepping stones in adaptive evolution. Proc. Natl. Acad. Sci. USA 110:E3171-E3178. [http://dx.doi.org/10.1073/pnas.1313424110 doi:10.1073/pnas.1313424110] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3752215 pmcid:PMC3752215]
# S. D. Smith-Tsurkan, R. A. Herr, S. Khuder, C. O. Wilke, and I. S. Novella (2013). The role of environmental factors on the evolution of phenotypic diversity in vesicular stomatitis virus populations. J. Gen. Virol. 94:860-868. [http://dx.doi.org/10.1099/vir.0.048082-0 doi:10.1099/vir.0.048082-0]
# I. S. Novella, J. B. Presloid, C. Beech, C. O. Wilke (2013). Congruent evolution of fitness and genetic robustness in VSV. J. Virol. 87:4923-4928. [http://dx.doi.org/10.1128/JVI.02796-12 doi:10.1128/JVI.02796-12] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3624304 pmcid:PMC3624304]
# C. Lee, R. A. Harris, J. K. Wall, R. D. Mayfield, C. O Wilke (2013). RNaseIII and T4 Polynucleotide Kinase sequence biases and solutions during RNA-seq library construction. Biology Direct 8:16. [http://dx.doi.org/10.1186/1745-6150-8-16 doi:10.1186/1745-6150-8-16] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710281 pmcid:PMC3710281]
# M. Z. Tien, D. K. Sydykova, A. G. Meyer, C. O. Wilke (2013). PeptideBuilder: A simple Python library to generate model peptides. PeerJ 1:e80. [http://dx.doi.org/10.7717/peerj.80 doi:10.7717/peerj.80] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3661355 pmcid:PMC3661355]
# S. J. Spielman and C. O. Wilke (2013). Membrane environment imposes unique selection pressures on transmembrane domains of G protein-coupled receptors. J. Mol. Evol. 76:172-182. [http://dx.doi.org/10.1007/s00239-012-9538-8 doi:10.1007/s00239-012-9538-8] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712645/ pmcid:PMC3712645]
# A. G. Meyer, E. T. Dawson, and C. O. Wilke (2013). Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin. Phil. Trans. R. Soc. B. 368:20120334. [http://dx.doi.org/10.1098/rstb.2012.0334 doi:10.1098/rstb.2012.0334] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3678335 pmcid:PMC3678335]
# A. G. Meyer and C. O. Wilke (2013). Integrating sequence variation and protein structure to identify sites under selection. Mol. Biol. Evol. 30:36-44 [http://dx.doi.org/10.1093/molbev/mss217 doi:10.1093/molbev/mss217] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3525147/ pmcid:PMC3525147]


== 2010 ==
''' 2012 '''
# 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. [http://dx.doi.org/10.1002/pmic.201000229 doi:10.1002/pmic.201000229]
# M. P. Scherrer, A. G. Meyer, and C. O. Wilke (2012). Modeling coding-sequence evolution within the context of residue solvent accessibility. BMC Evol. Biol. 12:179. [http://dx.doi.org/10.1186/1471-2148-12-179 doi:10.1186/1471-2148-12-179] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527230 pmcid:PMC3527230] 
# J. J. Bull, I. J. Molineux, and C. O. Wilke (2012). Slow fitness recovery in a codon-modified viral genome. Mol. Biol. Evol. 29:2997-3004. [http://dx.doi.org/10.1093/molbev/mss119 doi:10.1093/molbev/mss119] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457771/ pmcid:PMC3457771]
# A. R. Sedaghat, S. T. Gray, C. O. Wilke, and D. S. Caradonna (2012). Risk factors for development of chronic rhinosinusitis in patients with allergic rhinitis. Int. Forum Allergy Rhinol. 2:370-375. [http://dx.doi.org/10.1002/alr.21055 doi:10.1002/alr.21055]
# T. E. Keller, C. O. Wilke and J. J. Bull (2012). Interactions between evolutionary processes at high mutation rates. Evolution 66:2303-2314. [http://dx.doi.org/10.1111/j.1558-5646.2012.01596.x doi:10.1111/j.1558-5646.2012.01596.x] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389706/ pmcid:PMC3389706]
# C. O. Wilke (2012). Bringing molecules back into molecular evolution. PLoS Comp. Biol. 8:e1002572. [http://dx.doi.org/10.1371/journal.pcbi.1002572 doi:10.1371/journal.pcbi.1002572] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386153/ pmcid:PMC3386153]
# A. W. Covert III, J. Carlson-Stevermer, D. Z. Derryberry, and C. O. Wilke (2012). The role of deleterious mutations in the adaptation to a novel envrionment. In Proceedings of the Thirteenth International Conference on the Simulation and Synthesis of Living Systems, C. Adami, D. M. Bryson, C. Ofria and R. T. Pennock, eds., pp. 27-31. MIT Press. [http://dx.doi.org/10.7551/978-0-262-31050-5-ch004 doi:10.7551/978-0-262-31050-5-ch004]
# A. W. Covert III, L. Smith, D. Z. Derryberry, and C. O. Wilke (2012). What does sex have to do with it: tracking the fate of deleterious mutations in sexual populations. In Proceedings of the Thirteenth International Conference on the Simulation and Synthesis of Living Systems, C. Adami, D. M. Bryson, C. Ofria and R. T. Pennock, eds., pp. 32-36. MIT Press. [http://dx.doi.org/10.7551/978-0-262-31050-5-ch005 doi:10.7551/978-0-262-31050-5-ch005]
# T. E. Keller, S. D. Mis, K. E. Jia, and C. O. Wilke (2012). Reduced mRNA secondary-structure stability near the start codon indicates functional genes in prokaryotes. Genome Biol. Evol. 4:80-88. [http://dx.doi.org/10.1093/gbe/evr129 doi:10.1093/gbe/evr129] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3269970 pmcid:PMC3269970]
# D. Wang, M. K. Markey, C. O. Wilke, and A. Arapostathis (2012). Eigen-genomic System Dynamic-pattern Analysis (ESDA): Modeling mRNA degradation and self-regulation. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9:430-437.
# D. Wang, A. Arapostathis, C. O. Wilke, and M. K. Markey (2012). Principal-oscillation-pattern analysis of gene expression. PLoS ONE 7:e28805. [http://dx.doi.org/10.1371/journal.pone.0028805 doi:10.1371/journal.pone.0028805] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3254616 pmcid:PMC3254616]
 
''' 2011 '''
# I. S. Novella, J. B. Presloid, S. D. Smith, and C. O. Wilke (2011). Specific and nonspecific host adaptation during arboviral experimental evolution. J. Mol. Microbiol. Biotech. 21:71-81. [http://dx.doi.org/10.1159/000332752 doi:10.1159/000332752]
# J. J. Bull, R. H. Heineman, and C. O. Wilke (2011). The phenotype-fitness map in experimental evolution of phages. PLoS ONE 6:e27796. [http://dx.doi.org/10.1371/journal.pone.0027796 doi:10.1371/journal.pone.0027796] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222649 pmcid:PMC3222649]
# A. R. Sedaghat and C. O. Wilke (2011). Kinetics of the viral cycle influence pharmacodynamics of antiretroviral therapy. Biology Direct 6:42. [http://dx.doi.org/10.1186/1745-6150-6-42 doi:10.1186/1745-6150-6-42]
# 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 188:479-488. [http://dx.doi.org/10.1534/genetics.111.128025 doi:10.1534/genetics.111.128025] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3122320 pmcid:PMC3122320]
# 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 27:759-761. [http://dx.doi.org/10.1089/AID.2010.0199 doi:10.1089/AID.2010.0199]
# 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. [http://dx.doi.org/10.1186/1471-2148-11-59 doi:10.1186/1471-2148-11-59] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072339 pmcid:PMC3072339]
# 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. [http://dx.doi.org/10.1016/j.meegid.2010.12.007 doi:10.1016/j.meegid.2010.12.007] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251332 pmcid:PMC3251332]
# 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. [http://dx.doi.org/10.1155/2011/238743 doi:10.1155/2011/238743] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995904 pmcid:PMC2995904]
 
''' 2010 '''
# 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. [http://dx.doi.org/10.1002/pmic.201000229 doi:10.1002/pmic.201000229] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037288 pmcid:PMC3037288]
# 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. [http://dx.doi.org/10.1016/j.jtbi.2010.05.036 doi:10.1016/j.jtbi.2010.05.036]
# 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. [http://dx.doi.org/10.1016/j.jtbi.2010.05.036 doi:10.1016/j.jtbi.2010.05.036]
# 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. [http://dx.doi.org/10.1093/molbev/msq077 doi:10.1093/molbev/msq077]
# 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. [http://dx.doi.org/10.1093/molbev/msq077 doi:10.1093/molbev/msq077]
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# 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. [http://dx.doi.org/10.1099/vir.0.017855-0 doi:10.1099/vir.0.017855-0]
# 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. [http://dx.doi.org/10.1099/vir.0.017855-0 doi:10.1099/vir.0.017855-0]
# 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. [http://dx.doi.org/10.1086/652285 doi:10.1086/652285]
# 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. [http://dx.doi.org/10.1086/652285 doi:10.1086/652285]
# 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.[http://dx.doi.org/10.1098/rstb.2010.0065 doi:10.1098/rstb.2010.0065]
# 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.[http://dx.doi.org/10.1098/rstb.2010.0065 doi:10.1098/rstb.2010.0065]  [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880116 pmcid:PMC2880116]
# 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. [http://dx.doi.org/10.1128/JVI.00710-09 doi:10.1128/JVI.00710-09] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2863795 pmcid: PMC2863795]
# 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. [http://dx.doi.org/10.1128/JVI.00710-09 doi:10.1128/JVI.00710-09] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2863795 pmcid:PMC2863795]
# C. O. Wilke and D. A. Drummond (2010). Signatures of protein biophysics in coding sequence evolution. Cur. Opin. Struct. Biol. 20:385-389. [http://dx.doi.org/10.1016/j.sbi.2010.03.004 doi:10.1016/j.sbi.2010.03.004] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905607/ pmcid: PMC2905607]
# C. O. Wilke and D. A. Drummond (2010). Signatures of protein biophysics in coding sequence evolution. Cur. Opin. Struct. Biol. 20:385-389. [http://dx.doi.org/10.1016/j.sbi.2010.03.004 doi:10.1016/j.sbi.2010.03.004] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905607/ pmcid:PMC2905607]
# 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]
# 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]
#:'''Featured in [http://www.genomeweb.com/node/933145 genomeweb, Feb. 8, 2010.]'''
#:'''Featured in [http://www.genomeweb.com/node/933145 genomeweb, Feb. 8, 2010.]'''


== 2009 ==
''' 2009 '''


# 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]
# 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]
# 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. [http://dx.doi.org/10.1086/648081 doi:10.1086/648081]
# 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. [http://dx.doi.org/10.1086/648081 doi:10.1086/648081] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783537 pmcid:PMC2783537]
# S. H. Steinmeyer and C. O. Wilke (2009). Lethal mutagenesis in a structured environment. J. Theor. Biol. 261:67-73. [http://dx.doi.org/10.1016/j.jtbi.2009.07.014 doi:10.1016/j.jtbi.2009.07.014]
# S. H. Steinmeyer and C. O. Wilke (2009). Lethal mutagenesis in a structured environment. J. Theor. Biol. 261:67-73. [http://dx.doi.org/10.1016/j.jtbi.2009.07.014 doi:10.1016/j.jtbi.2009.07.014]
# 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. 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]
#:'''Featured in [http://www.sciencedaily.com/releases/2009/08/090825082656.htm Science Daily.]'''
#:'''Featured in [http://www.sciencedaily.com/releases/2009/08/090825082656.htm Science Daily.]'''
# 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]
# 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] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734146/ pmcid:PMC2980788]
# 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.
# 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. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2980788/ pmcid:PMC2980788]


== 2008 ==
''' 2008 '''


# T. Zhou, P. J. Enyeart, and C. O. Wilke (2008). Detecting Clusters of Mutations. PLoS ONE 3:e3765. [http://dx.doi.org/10.1371/journal.pone.0003765 doi:10.1371/journal.pone.0003765] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2582452 pmcid: PMC2582452]
# T. Zhou, P. J. Enyeart, and C. O. Wilke (2008). Detecting Clusters of Mutations. PLoS ONE 3:e3765. [http://dx.doi.org/10.1371/journal.pone.0003765 doi:10.1371/journal.pone.0003765] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2582452 pmcid:PMC2582452]
# 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. [http://dx.doi.org/10.1128/JVI.01394-08 doi:10.1128/JVI.01394-08] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593322 pmcid: PMC2593322]
# 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. [http://dx.doi.org/10.1128/JVI.01394-08 doi:10.1128/JVI.01394-08] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593322 pmcid:PMC2593322]
# J. J. Bull and C. O. Wilke (2008). Lethal mutagenesis of bacteria. Genetics 180:1061-1070. [http://dx.doi.org/10.1534/genetics.108.091413 doi:10.1534/genetics.108.091413] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567356 pmcid: PMC2567356]
# J. J. Bull and C. O. Wilke (2008). Lethal mutagenesis of bacteria. Genetics 180:1061-1070. [http://dx.doi.org/10.1534/genetics.108.091413 doi:10.1534/genetics.108.091413] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567356 pmcid:PMC2567356]
# 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]
# 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]
#:'''Featured in [http://dx.doi.org/10.1016/j.cell.2008.07.005 Cell Preview.]'''
#:'''Featured in [http://dx.doi.org/10.1016/j.cell.2008.07.005 Cell Preview.]'''
# D. J. Whitehead*, C. O. Wilke*, D. Vernazobres, and E. Bornberg-Bauer (2008). The look-ahead effect of phenotypic mutations. Biology Direct 3:18. [http://dx.doi.org/10.1186/1745-6150-3-18 doi:10.1186/1745-6150-3-18] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2423361 pmcid: PMC2423361] *Equal contribution.
# D. J. Whitehead*, C. O. Wilke*, D. Vernazobres, and E. Bornberg-Bauer (2008). The look-ahead effect of phenotypic mutations. Biology Direct 3:18. [http://dx.doi.org/10.1186/1745-6150-3-18 doi:10.1186/1745-6150-3-18] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2423361 pmcid:PMC2423361] *Equal contribution.
# É. Brunet, I. M. Rouzine, and C. O. Wilke (2008). The stochastic edge in adaptive evolution. Genetics 179:603-620. [http://dx.doi.org/10.1534/genetics.107.079319 doi:10.1534/genetics.107.079319] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390637 pmcid: PMC2390637]
# É. Brunet, I. M. Rouzine, and C. O. Wilke (2008). The stochastic edge in adaptive evolution. Genetics 179:603-620. [http://dx.doi.org/10.1534/genetics.107.079319 doi:10.1534/genetics.107.079319] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390637 pmcid:PMC2390637]
# 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. [http://dx.doi.org/10.1007/s00239-008-9094-4 doi:10.1007/s00239-008-9094-4]
# 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. [http://dx.doi.org/10.1007/s00239-008-9094-4 doi:10.1007/s00239-008-9094-4]
# 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. [http://dx.doi.org/10.1128/JVI.02446-07 doi:10.1128/JVI.02446-07] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2293023 pmcid: PMC2293023]
# 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. [http://dx.doi.org/10.1128/JVI.02446-07 doi:10.1128/JVI.02446-07] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2293023 pmcid:PMC2293023]
# 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]
# 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 (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.  
# 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.  
# 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. [http://dx.doi.org/10.1016/j.tpb.2007.10.004 doi:10.1016/j.tpb.2007.10.004] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246079 pmcid: PMC2246079]
# 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. [http://dx.doi.org/10.1016/j.tpb.2007.10.004 doi:10.1016/j.tpb.2007.10.004] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246079 pmcid:PMC2246079]
# 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. [http://dx.doi.org/10.1186/1471-2334-8-2 doi:10.1186/1471-2334-8-2] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2254415 pmcid: PMC2254415]
# 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. [http://dx.doi.org/10.1186/1471-2334-8-2 doi:10.1186/1471-2334-8-2] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2254415 pmcid:PMC2254415]


== 2007 ==
''' 2007 '''


# 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.  [http://dx.doi.org/10.1371/journal.ppat.0030122 doi:10.1371/journal.ppat.0030122] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1959378 pmcid: PMC1959378]
# 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.  [http://dx.doi.org/10.1371/journal.ppat.0030122 doi:10.1371/journal.ppat.0030122] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1959378 pmcid:PMC1959378]
# R. Forster and C. O. Wilke (2007). Frequency-dependent selection in a periodic environment. Physica A 381:255-264.  [http://dx.doi.org/10.1016/j.physa.2007.03.017 doi:10.1016/j.physa.2007.03.017] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2031831 pmcid: PMC2031831]
# R. Forster and C. O. Wilke (2007). Frequency-dependent selection in a periodic environment. Physica A 381:255-264.  [http://dx.doi.org/10.1016/j.physa.2007.03.017 doi:10.1016/j.physa.2007.03.017] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2031831 pmcid:PMC2031831]
# 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. 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]
# 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. [http://dx.doi.org/10.1111/j.1558-5646.2007.00064.x doi:10.1111/j.1558-5646.2007.00064.x]  
# 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. [http://dx.doi.org/10.1111/j.1558-5646.2007.00064.x doi:10.1111/j.1558-5646.2007.00064.x]  
# 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, 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]


== 2006 ==
''' 2006 '''


# R. Forster, C. Adami, and C. O. Wilke (2006). Selection for mutational robustness in finite populations. J. Theor. Biol. 243:181-190. [http://dx.doi.org/10.1016/j.jtbi.2006.06.020 doi:10.1016/j.jtbi.2006.06.020]
# R. Forster, C. Adami, and C. O. Wilke (2006). Selection for mutational robustness in finite populations. J. Theor. Biol. 243:181-190. [http://dx.doi.org/10.1016/j.jtbi.2006.06.020 doi:10.1016/j.jtbi.2006.06.020]
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# 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.
# 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 ==
''' 2005 '''


# R. Forster and C. O. Wilke (2005). Tradeoff between short-term and long-term adaptation in a changing environment. Phys. Rev. E 72:041922.  [http://dx.doi.org/10.1103/PhysRevE.72.041922  doi:10.1103/PhysRevE.72.041922]
# R. Forster and C. O. Wilke (2005). Tradeoff between short-term and long-term adaptation in a changing environment. Phys. Rev. E 72:041922.  [http://dx.doi.org/10.1103/PhysRevE.72.041922  doi:10.1103/PhysRevE.72.041922]
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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]
# 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]


== 2004 ==
''' 2004 '''


# C. O. Wilke (2004). Molecular clock in neutral protein evolution. BMC Genetics 5:25. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC517495 pmcid:PMC517495]
# C. O. Wilke (2004). Molecular clock in neutral protein evolution. BMC Genetics 5:25. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC517495 pmcid:PMC517495]
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# 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.
# 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 ==
''' 2003 '''


# C. O. Wilke, I. S. Novella (2003). Phenotypic mixing and hiding may contribute to memory in viral quasispecies. BMC Microbiology 3:11.  
# C. O. Wilke, I. S. Novella (2003). Phenotypic mixing and hiding may contribute to memory in viral quasispecies. BMC Microbiology 3:11.  
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# C. O. Wilke, C. Adami (2003). Evolution of mutational robustness. Mut. Res. 522:3-11.
# C. O. Wilke, C. Adami (2003). Evolution of mutational robustness. Mut. Res. 522:3-11.


== 2002 ==
''' 2002 '''
# 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.  
# 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 [http://dx.doi.org/10.1038/420367a Nature News and Views, Vol. 420:367-369 (2002).]'''
#:'''Featured in [http://dx.doi.org/10.1038/420367a Nature News and Views, Vol. 420:367-369 (2002).]'''
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# 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.
# 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 ==
''' 2001 '''


# C. O. Wilke (2001). Selection for fitness vs. selection for robustness in RNA secondary structure folding. Evolution 55:2412-2420.  
# 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 and C. Ronnewinkel (2001). Dynamic fitness landscapes: Expansions for small mutation rates. Physica A 290:475-490.
# C. O. Wilke and C. Ronnewinkel (2001). Dynamic fitness landscapes: Expansions for small mutation rates. Physica A 290:475-490.


== 2000 ==
''' 2000 '''
# C. O. Wilke (2000). Dynamische Fitnesslandschaften. KI 14:20-25 (in german).  
# C. O. Wilke (2000). Dynamische Fitnesslandschaften. KI 14:20-25 (in german).  


== 1999 ==
''' 1999 '''
# C. O. Wilke and T. Martinetz (1999). Adaptive walks on time-dependent fitness landscapes. Phys. Rev. E 60:2154-2159.
# C. O. Wilke and T. Martinetz (1999). Adaptive walks on time-dependent fitness landscapes. Phys. Rev. E 60:2154-2159.
# C. O. Wilke and T. Martinetz (1999). Lifetimes of agents under external stress  Phys. Rev. E Rapid Communications 59:R2512-R2515.
# C. O. Wilke and T. Martinetz (1999). Lifetimes of agents under external stress  Phys. Rev. E Rapid Communications 59:R2512-R2515.
# C. O. Wilke, C. Ronnewinkel, and T. Martinetz (1999). Molecular Evolution in Time Dependent Environments. Lect. Notes. Artif. Int. 1674:417-421.
# C. O. Wilke, C. Ronnewinkel, and T. Martinetz (1999). Molecular Evolution in Time Dependent Environments. Lect. Notes. Artif. Int. 1674:417-421.


== 1998 ==
''' 1998 '''
# C. Wilke and T. Martinetz (1998). Hierarchical noise in large systems of independent agents. Phys. Rev. E 58:7101-7108.
# C. Wilke and T. Martinetz (1998). Hierarchical noise in large systems of independent agents. Phys. Rev. E 58:7101-7108.
# C. Wilke, S. Altmeyer, and T. Martinetz (1998). Aftershocks in Coherent-Noise Models. Physica D, 120:401-417.
# C. Wilke, S. Altmeyer, and T. Martinetz (1998). Aftershocks in Coherent-Noise Models. Physica D, 120:401-417.
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== 1997 ==
''' 1997 '''
# C. Wilke and T. Martinetz (1997). Simple model of evolution with variable system size. Phys. Rev. E 56:7128-7131.
# C. Wilke and T. Martinetz (1997). Simple model of evolution with variable system size. Phys. Rev. E 56:7128-7131.
# M. Kachelrieß, C. Wilke, and G. Wunner (1997). Axion cyclotron emissivity of magnetized white dwarfs and neutron stars. Phys. Rev. D 56:1313-1319.
# M. Kachelrieß, C. Wilke, and G. Wunner (1997). Axion cyclotron emissivity of magnetized white dwarfs and neutron stars. Phys. Rev. D 56:1313-1319.
# 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.
# 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 =
== Editorial materials ==
# 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. [http://dx.doi.org/10.1038/msb4100119 doi:10.1038/msb4100119] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800353 pmcid: PMC1800353]
# C. O. Wilke (2011). Transcriptional robustness complements nonsense-mediated decay in humans. PLoS Genet. 7:e1002296. [http://dx.doi.org/10.1371/journal.pgen.1002296 doi:10.1371/journal.pgen.1002296]  [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192817 pmcid:PMC3192817]
# 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. [http://dx.doi.org/10.1038/msb4100119 doi:10.1038/msb4100119] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800353 pmcid:PMC1800353]
# C. O. Wilke (2006). Biology through the robustness lens. BioScience 56:695-696.
# C. O. Wilke (2006). Biology through the robustness lens. BioScience 56:695-696.
# C. O. Wilke (2005). Molecular clocks: the heavy, the cold, and the slow. Heredity 95:115. [http://dx.doi.org/10.1038/sj.hdy.6800681 doi:10.1038/sj.hdy.6800681]
# C. O. Wilke (2005). Molecular clocks: the heavy, the cold, and the slow. Heredity 95:115. [http://dx.doi.org/10.1038/sj.hdy.6800681 doi:10.1038/sj.hdy.6800681]
# C. O. Wilke (2004). Supplementary materials need the right format. Nature 430:291.
# C. O. Wilke (2004). Supplementary materials need the right format. Nature 430:291.

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Peer-Reviewed Publications

In press

  1. S. J. Spielman, E. T. Dawson, C. O. Wilke. Limited utility of residue masking for positive-selection inference. Mol. Biol. Evol., in press. doi:10.1093/molbev/msu183
  2. A. R. Sedaghat, C. O. Wilke, M. J. Cunningham, S. L. Ishman. Socioeconomic disparities in the presentation of acute bacterial sinusitis complications in children. The Laryngoscope, in press. doi:10.1002/lary.24492

2014

  1. E. B. O’Dea, K. M. Pepin, B. A. Lopman, C. O. Wilke (2014). Fitting outbreak models to data from many small norovirus outbreaks. Epidemics 6:18-29. doi:10.1016/j.epidem.2013.12.002
  2. A. G. Meyer​, S. L. Sawyer, A. D. Ellington, C. O. Wilke (2014). Analyzing Machupo virus-receptor binding by molecular dynamics simulations. PeerJ 2:e266. doi:10.7717/peerj.266

2013

  1. M. Z. Tien, A. G. Meyer, D. K. Sydykova, S. J. Spielman, C. O. Wilke (2013). Maximum allowed solvent accessibilites of residues in proteins. PLOS ONE 8:e80635. doi:10.1371/journal.pone.0080635
  2. E. L. Jackson, N. Ollikainen, A. W. Covert III, T. Kortemme, C. O. Wilke (2013). Amino-acid site variability among natural and designed proteins. PeerJ 1:e211. doi:10.7717/peerj.211
  3. A. R. Sedaghat, S. T. Gray, K. J. Chambers, C. O. Wilke, and D. S. Caradonna (2013). Sinonasal anatomic variants and asthma are associated with faster development of chronic rhinosinusitis in patients with allergic rhinitis. Int. Forum Allergy Rhinol. 3:755-761. doi:10.1002/alr.21163
  4. A. W. Covert, R. E. Lenski, C. O. Wilke, and C. Ofria (2013). Experiments on the role of deleterious mutations as stepping stones in adaptive evolution. Proc. Natl. Acad. Sci. USA 110:E3171-E3178. doi:10.1073/pnas.1313424110 pmcid:PMC3752215
  5. S. D. Smith-Tsurkan, R. A. Herr, S. Khuder, C. O. Wilke, and I. S. Novella (2013). The role of environmental factors on the evolution of phenotypic diversity in vesicular stomatitis virus populations. J. Gen. Virol. 94:860-868. doi:10.1099/vir.0.048082-0
  6. I. S. Novella, J. B. Presloid, C. Beech, C. O. Wilke (2013). Congruent evolution of fitness and genetic robustness in VSV. J. Virol. 87:4923-4928. doi:10.1128/JVI.02796-12 pmcid:PMC3624304
  7. C. Lee, R. A. Harris, J. K. Wall, R. D. Mayfield, C. O Wilke (2013). RNaseIII and T4 Polynucleotide Kinase sequence biases and solutions during RNA-seq library construction. Biology Direct 8:16. doi:10.1186/1745-6150-8-16 pmcid:PMC3710281
  8. M. Z. Tien, D. K. Sydykova, A. G. Meyer, C. O. Wilke (2013). PeptideBuilder: A simple Python library to generate model peptides. PeerJ 1:e80. doi:10.7717/peerj.80 pmcid:PMC3661355
  9. S. J. Spielman and C. O. Wilke (2013). Membrane environment imposes unique selection pressures on transmembrane domains of G protein-coupled receptors. J. Mol. Evol. 76:172-182. doi:10.1007/s00239-012-9538-8 pmcid:PMC3712645
  10. A. G. Meyer, E. T. Dawson, and C. O. Wilke (2013). Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin. Phil. Trans. R. Soc. B. 368:20120334. doi:10.1098/rstb.2012.0334 pmcid:PMC3678335
  11. A. G. Meyer and C. O. Wilke (2013). Integrating sequence variation and protein structure to identify sites under selection. Mol. Biol. Evol. 30:36-44 doi:10.1093/molbev/mss217 pmcid:PMC3525147

2012

  1. M. P. Scherrer, A. G. Meyer, and C. O. Wilke (2012). Modeling coding-sequence evolution within the context of residue solvent accessibility. BMC Evol. Biol. 12:179. doi:10.1186/1471-2148-12-179 pmcid:PMC3527230
  2. J. J. Bull, I. J. Molineux, and C. O. Wilke (2012). Slow fitness recovery in a codon-modified viral genome. Mol. Biol. Evol. 29:2997-3004. doi:10.1093/molbev/mss119 pmcid:PMC3457771
  3. A. R. Sedaghat, S. T. Gray, C. O. Wilke, and D. S. Caradonna (2012). Risk factors for development of chronic rhinosinusitis in patients with allergic rhinitis. Int. Forum Allergy Rhinol. 2:370-375. doi:10.1002/alr.21055
  4. T. E. Keller, C. O. Wilke and J. J. Bull (2012). Interactions between evolutionary processes at high mutation rates. Evolution 66:2303-2314. doi:10.1111/j.1558-5646.2012.01596.x pmcid:PMC3389706
  5. C. O. Wilke (2012). Bringing molecules back into molecular evolution. PLoS Comp. Biol. 8:e1002572. doi:10.1371/journal.pcbi.1002572 pmcid:PMC3386153
  6. A. W. Covert III, J. Carlson-Stevermer, D. Z. Derryberry, and C. O. Wilke (2012). The role of deleterious mutations in the adaptation to a novel envrionment. In Proceedings of the Thirteenth International Conference on the Simulation and Synthesis of Living Systems, C. Adami, D. M. Bryson, C. Ofria and R. T. Pennock, eds., pp. 27-31. MIT Press. doi:10.7551/978-0-262-31050-5-ch004
  7. A. W. Covert III, L. Smith, D. Z. Derryberry, and C. O. Wilke (2012). What does sex have to do with it: tracking the fate of deleterious mutations in sexual populations. In Proceedings of the Thirteenth International Conference on the Simulation and Synthesis of Living Systems, C. Adami, D. M. Bryson, C. Ofria and R. T. Pennock, eds., pp. 32-36. MIT Press. doi:10.7551/978-0-262-31050-5-ch005
  8. T. E. Keller, S. D. Mis, K. E. Jia, and C. O. Wilke (2012). Reduced mRNA secondary-structure stability near the start codon indicates functional genes in prokaryotes. Genome Biol. Evol. 4:80-88. doi:10.1093/gbe/evr129 pmcid:PMC3269970
  9. D. Wang, M. K. Markey, C. O. Wilke, and A. Arapostathis (2012). Eigen-genomic System Dynamic-pattern Analysis (ESDA): Modeling mRNA degradation and self-regulation. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9:430-437.
  10. D. Wang, A. Arapostathis, C. O. Wilke, and M. K. Markey (2012). Principal-oscillation-pattern analysis of gene expression. PLoS ONE 7:e28805. doi:10.1371/journal.pone.0028805 pmcid:PMC3254616

2011

  1. I. S. Novella, J. B. Presloid, S. D. Smith, and C. O. Wilke (2011). Specific and nonspecific host adaptation during arboviral experimental evolution. J. Mol. Microbiol. Biotech. 21:71-81. doi:10.1159/000332752
  2. J. J. Bull, R. H. Heineman, and C. O. Wilke (2011). The phenotype-fitness map in experimental evolution of phages. PLoS ONE 6:e27796. doi:10.1371/journal.pone.0027796 pmcid:PMC3222649
  3. A. R. Sedaghat and C. O. Wilke (2011). Kinetics of the viral cycle influence pharmacodynamics of antiretroviral therapy. Biology Direct 6:42. doi:10.1186/1745-6150-6-42
  4. 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 188:479-488. doi:10.1534/genetics.111.128025 pmcid:PMC3122320
  5. 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 27:759-761. doi:10.1089/AID.2010.0199
  6. 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
  7. 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 pmcid:PMC3251332
  8. 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 pmcid:PMC2783537
  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.
  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. doi:10.1093/molbev/msp070 pmcid:PMC2980788
  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. 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.
  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 pmcid:PMC2423361 *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 pmcid:PMC2390637
  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 pmcid:PMC2293023
  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 pmcid:PMC2290747
  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 pmcid:PMC2246079
  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 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).
  2. C. O. Wilke, C. Adami (2002). The biology of digital organisms. Trends. Ecol. Evol. 17:528-532.
  3. 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.
  4. C. O. Wilke (2002). Maternal effects in molecular evolution. Phys. Rev. Lett. 88:078101.
  5. 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.
  3. 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.
  4. C. O. Wilke (2001). Adaptive evolution on neutral networks. Bull. Math. Biol. 63:715-730.
  5. 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.
  6. C. O. Wilke, C. Ronnewinkel and T. Martinetz (2001). Dynamic fitness landscapes in molecular evolution. Phys. Rep. 349:395-446.
  7. 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. C. O. Wilke (2011). Transcriptional robustness complements nonsense-mediated decay in humans. PLoS Genet. 7:e1002296. doi:10.1371/journal.pgen.1002296 pmcid:PMC3192817
  2. 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
  3. C. O. Wilke (2006). Biology through the robustness lens. BioScience 56:695-696.
  4. C. O. Wilke (2005). Molecular clocks: the heavy, the cold, and the slow. Heredity 95:115. doi:10.1038/sj.hdy.6800681
  5. C. O. Wilke (2004). Supplementary materials need the right format. Nature 430:291.
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