Publications

2014    2012    2010    2008    2006    2004    2002    2000    1998   

    Preprint
  • Preprint
  • 161. M. Umut Caglar​, Ashley I. Teufel, Claus O Wilke (preprint). Sicegar: R package for sigmoidal and double-sigmoidal curve fitting. PeerJ Preprints 5:e3116v1.
    doi: 10.7287/peerj.preprints.3116v1  
  • 2017
  • 2017
  • 160. B. L. Smith, C. O. Wilke (2017). Virus Evolution: A new twist in measuring mutation rates. eLife 6:e29586.
    doi: 10.7554/eLife.29586  
  • 159. B. R. Jack, D. R. Boutz, M. L. Paff, B. L. Smith, J. J. Bull, C. O. Wilke (2017). Reduced protein expression in a virus attenuated by codon deoptimization. G3: GENES, GENOMES, GENETICS, in press.
    doi: 10.1534/g3.117.041020  
  • 158. D. K. Sydykova, C. O. Wilke (2017). Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates. PeerJ 5:e3391.
    doi: 10.7717/peerj.3391  
  • 157. J. Echave, C. O. Wilke (2017). Biophysical models of protein evolution: Understanding the patterns of evolutionary sequence divergence. Ann. Rev. Biophys. 46:85–103.
    doi: 10.1146/annurev-biophys-070816-033819  
  • 156. M. U. Caglar, J. R. Houser, C. S. Barnhart, D. R. Boutz, S. M. Carroll, A. Dasgupta, W. F. Lenoir, B. L. Smith, V. Sridhara, D. K. Sydykova, D. Vander Wood, C. J. Marx, E. M. Marcotte, J. E. Barrick, C. O. Wilke (2017). The E. coli molecular phenotype under different growth conditions. Scientific Reports 7:45303.
    doi: 10.1038/srep45303  
  • 155. S. D. Chapman, C. Adami, C. O. Wilke, D. B. KC (2017). The evolution of logic circuits for the purpose of protein contact map prediction. PeerJ 5:e3139.
    doi: 10.7717/peerj.3139  
  • 154. C. W. Brown, V. Sridhara, D. R. Boutz, M. D. Person, E. M. Marcotte, J. E. Barrick, C. O. Wilke (2017). Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions. BMC Genomics 18:301.
    doi: 10.1186/s12864-017-3676-8  
  • 153. E. L. Jackson, S. J. Spielman, C. O. Wilke (2017). Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein. PLoS ONE 12:e0164905.
    doi: 10.1371/journal.pone.0164905  
  • 152. A. I. Teufel, C. O. Wilke (2017). Accelerated simulation of evolutionary trajectories in origin-fixation models. J. R. Soc. Interface 14:20160906.
    doi: 10.1098/rsif.2016.0906  
  • 2016
  • 2016
  • 151. M. Lipsitch, W. Barclay, R. Raman, C. J. Russell, J. A. Belser, S. Cobey, P. M. Kasson, J. O. Lloyd-Smith, S. Maurer-Stroh, S. Riley, C. A. A. Beauchemin, T. Bedford, T. C. Friedrich, A. Handel, S. Herfst, P. R. Murcia, B. Roche, C. O. Wilke, C. A. Russell (2016). Viral factors in influenza pandemic risk assessment. eLife 5:e18491.
    doi: 10.7554/eLife.18491   pmcid: PMC5156527  
  • 150. C. D. McWhite, A. G. Meyer, C. O. Wilke (2016). Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza virus H3N2 hemagglutinin. Virus Evol. 2:vew026.
    doi: 10.1093/ve/vew026   pmcid: PMC5049878  
  • 149. S. J. Spielman, C. O. Wilke (2016). Extensively parameterized mutation–selection models reliably capture site-specific selective constraint. Mol. Biol. Evol. 33:2990–3002.
    doi: 10.1093/molbev/msw171   pmcid: PMC5062325  
  • 148. S. J. Spielman, S. Wan, C. O. Wilke (2016). A comparison of one-rate and two-rate inference frameworks for site-specific dN/dS estimation. Genetics 204:499–511.
    doi: 10.1534/genetics.115.185264   pmcid: PMC5068842  
  • 147. C. O. Wilke, S. L. Sawyer (2016). Adaptive evolution: At the mercy of viruses. eLife 5:e16758.
    doi: 10.7554/eLife.16758   pmcid: PMC4869909  
  • 146. B. R. Jack, A. G. Meyer, J. Echave, C. O. Wilke (2016). Functional sites induce long-range evolutionary constraints in enzymes. PLOS Biol 14:e1002452.
    doi: 10.1371/journal.pbio.1002452   pmcid: PMC4854464  
  • 145. C. O. Wilke, J. D. Bloom (2016). Protein Biophysics and Evolution. Kliman, R.M. (ed.), Encyclopedia of Evolutionary Biology. vol. 3, pp. 339–343. Oxford: Academic Press.
    doi: 10.1016/B978-0-12-800049-6.00180-3  
  • 144. A. Shahmoradi, C. O. Wilke (2016). Dissecting the roles of local packing density and longer-range effects in protein sequence evolution. Proteins 84:841–854.
    doi: 10.1002/prot.25034  
  • 143. E. L. Jackson, A. Shahmoradi, S. J. Spielman, B. R. Jack, C. O. Wilke (2016). Intermediate divergence levels maximize the strength of structure–sequence correlations in enzymes and viral proteins. Protein Science 25:1341–1353.
    doi: 10.1002/pro.2920   pmcid: PMC4918415  
  • 142. J. Echave, S. J. Spielman, C. O. Wilke (2016). Causes of evolutionary rate variation among protein sites. Nature Rev. Genet. 17:109–121.
    doi: 10.1038/nrg.2015.18   pmcid: PMC4724262  
  • 141. D. Z. Derryberry, M. C. Cowperthwaite, C. O. Wilke (2016). Reproducibility of SNV-calling in multiple sequencing runs from single tumors. PeerJ 4:e1508.
    doi: 10.7717/peerj.1508   pmcid: PMC4741064  
  • 2015
  • 2015
  • 140. C. O. Wilke (2015). Evolutionary paths of least resistance. Proc. Natl. Acad. Sci. USA 112:12553–12554.
    doi: 10.1073/pnas.1517390112   pmcid: PMC4611625  
  • 139. S. A. Kerr, E. L. Jackson, O. I. Lungu, A. G. Meyer, A. Demogines, A. D. Ellington, G. Georgiou, C. O. Wilke, S. L. Sawyer (2015). Computational and functional analysis of the virus-receptor interface reveals host range trade-offs in New World arenaviruses. J. Virol. 89:11643–11653.
    doi: 10.1128/JVI.01408-15   pmcid: PMC4645654  
  • 138. A. G. Meyer, C. O. Wilke (2015). The utility of protein structure as a predictor of site-wise dN/dS varies widely among HIV-1 proteins. J. R. Soc. Interface 12:20150579.
    doi: 10.1098/rsif.2015.0579   pmcid: PMC4614493  
  • 137. S. J. Spielman, C. O. Wilke (2015). Pyvolve: A flexible flexible Python module for simulating sequences along phylogenies. PLOS ONE 10:e0139047.
    doi: 10.1371/journal.pone.0139047   pmcid: PMC4580465  
  • 136. A. G. Meyer, S. J. Spielman, T. Bedford, C. O. Wilke (2015). On the time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak. Virus Evolution 1:vev006.
    doi: 10.1093/ve/vev006   pmcid: PMC4710376  
  • 135. J. R. Houser, C. Barnhart, D. R. Boutz, S. M. Carroll, A. Dasgupta, J. K. Michener, B. D. Needham, O. Papoulas, V. Sridhara, D. K. Sydykova, C. J. Marx, M. S. Trent, J. E. Barrick, E. M. Marcotte, C. O. Wilke (2015). Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation. PLOS Comput. Biol. 11:e1004400.
    doi: 10.1371/journal.pcbi.1004400   pmcid: PMC4537216  
  • 134. A. G. Meyer, C. O. Wilke (2015). Geometric constraints dominate the antigenic evolution of influenza H3N2 hemagglutinin. PLOS Pathogens 11:e1004940.
    doi: 10.1371/journal.ppat.1004940   pmcid: PMC4447415  
  • 133. A. H. Kachroo, J. M. Laurent, C. M. Yellman, A. G. Meyer, C. O. Wilke, E. M. Marcotte (2015). Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Science 348:921–925.
    doi: 10.1126/science.aaa0769   pmcid: PMC4718922  
  • 132. S. J. Spielman, K. Kumar, C. O. Wilke (2015). Comprehensive, structurally-curated alignment and phylogeny of vertebrate biogenic amine receptors. PeerJ 3:e773.
    doi: 10.7717/peerj.773   pmcid: PMC4338800  
  • 131. J. Echave, E. L. Jackson, C. O. Wilke (2015). Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites. Phys. Biol. 12:025002.
    doi: 10.1088/1478-3975/12/2/025002   pmcid: PMC4391963  
  • 130. S. J. Spielman, C. O. Wilke (2015). The relationship between dN/dS and scaled selection coefficients. Mol. Biol. Evol. 32:1097–1108.
    doi: 10.1093/molbev/msv003   pmcid: PMC4379412  
  • 2014
  • 2014
  • 129. V. Sridhara, A. G. Meyer, P. Rai, J. E. Barrick, P. Ravikumar, D. Segrè, C. O. Wilke (2014). Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli. PLOS ONE 9:e114608.
    doi: 10.1371/journal.pone.0114608   pmcid: PMC4264753  
  • 128. A. Shahmoradi, D. K. Sydykova, S. J. Spielman, E. L. Jackson, E. T. Dawson, A. G. Meyer, C. O. Wilke (2014). Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design. J. Mol. Evol. 79:130–142.
    doi: 10.1007/s00239-014-9644-x   pmcid: PMC4216736  
  • 127. R. W. Buckheit III, S. B. Sexauer, A. R. Sedaghat, C. O. Wilke, O. Laeyendecker, C. R. Basseth, J. N. Blankson (2014). Long-term control of viral replication in a Group O, Human Immunodeficiency Virus Type 1-infected individual. AIDS Research and Human Retroviruses 30:511–513.
    doi: 10.1089/aid.2014.0054   pmcid: PMC4046214  
  • 126. S. J. Spielman, E. T. Dawson, C. O. Wilke (2014). Limited utility of residue masking for positive-selection inference. Mol. Biol. Evol. 31:2496–2500.
    doi: 10.1093/molbev/msu183   pmcid: PMC4137709  
  • 125. A. R. Sedaghat, C. O. Wilke, M. J. Cunningham, S. L. Ishman (2014). Socioeconomic disparities in the presentation of acute bacterial sinusitis complications in children. The Laryngoscope 124:1700–1706.
    doi: 10.1002/lary.24492  
  • 124. 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   pmcid: PMC4218779  
  • 123. 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   pmcid: PMC3940602  
  • 2013
  • 2013
  • 122. 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   pmcid: PMC3836772  
  • 121. 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   pmcid: PMC3828621  
  • 120. A. R. Sedaghat, S. T. Gray, K. J. Chambers, C. O. Wilke, 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  
  • 119. A. W. Covert, R. E. Lenski, C. O. Wilke, 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  
  • 118. S. D. Smith-Tsurkan, R. A. Herr, S. Khuder, C. O. Wilke, 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   pmcid: PMC3709682  
  • 117. 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  
  • 116. 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  
  • 115. 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  
  • 114. S. J. Spielman, 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  
  • 113. A. G. Meyer, E. T. Dawson, 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  
  • 112. A. G. Meyer, 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
  • 2012
  • 111. M. P. Scherrer, A. G. Meyer, 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  
  • 110. J. J. Bull, I. J. Molineux, 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  
  • 109. A. R. Sedaghat, S. T. Gray, C. O. Wilke, 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  
  • 108. T. E. Keller, C. O. Wilke, 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  
  • 107. C. O. Wilke (2012). Bringing molecules back into molecular evolution. PLoS Comp. Biol. 8:e1002572.
    doi: 10.1371/journal.pcbi.1002572   pmcid: PMC3386153  
  • 106. A. W. Covert III, J. Carlson-Stevermer, D. Z. Derryberry, 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  
  • 105. A. W. Covert III, L. Smith, D. Z. Derryberry, 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  
  • 104. T. E. Keller, S. D. Mis, K. E. Jia, 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  
  • 103. D. Wang, M. K. Markey, C. O. Wilke, 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.
    doi: 10.1109/TCBB.2011.150  
  • 102. D. Wang, A. Arapostathis, C. O. Wilke, M. K. Markey (2012). Principal-oscillation-pattern analysis of gene expression. PLOS ONE 7:e28805.
    doi: 10.1371/journal.pone.0028805   pmcid: PMC3254616  
  • 2011
  • 2011
  • 101. I. S. Novella, J. B. Presloid, S. D. Smith, C. O. Wilke (2011). Specific and nonspecific host adaptation during arboviral experimental evolution. J. Mol. Microbiol. Biotech. 21:71–81.
    doi: 10.1159/000332752   pmcid: PMC3697271  
  • 100. J. J. Bull, R. H. Heineman, 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  
  • 99. A. R. Sedaghat, 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   pmcid: PMC3203257  
  • 98. C. O. Wilke (2011). Transcriptional robustness complements nonsense-mediated decay in humans. PLoS Genet. 7:e1002296.
    doi: 10.1371/journal.pgen.1002296   pmcid: PMC3192817  
  • 97. D. C. Ramsey, M. P. Scherrer, T. Zhou, 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  
  • 96. 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   pmcid: PMC3123527  
  • 95. T. Zhou, 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  
  • 94. A. T. Ciota, E. M. Koch, G. G. Willsey, L. J. Davis, G. V. S. Jerzak, D. J. Ehrbar, C. O. Wilke, 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  
  • 93. E. B. O'Dea, 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
  • 2010
  • 92. Y. Lee, T. Zhou, G. G. Tartaglia, M. Vendruscolo, 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  
  • 91. K. Pepin, I. Volkov, J. R. Banavar, C. O. Wilke, 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   pmcid: PMC4537168  
  • 90. T. Zhou, W. Gu, 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   pmcid: PMC2915641  
  • 89. E. B. O'Dea, T. E. Keller, 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   pmcid: PMC2883602  
  • 88. S. D. Smith-Tsurkan, C. O. Wilke, 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   pmcid: PMC2888165  
  • 87. A. R. Sedaghat, D. A. Rastegar, K. A. O’Connell, J. B. Dinoso, C. O. Wilke, 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  
  • 86. S. H. Steinmeyer, C. O. Wilke, 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  
  • 85. I. S. Novella, J. B. Presloid, T. Zhou, S. D. Smith-Tsurkan, B. E. Ebendick-Corpus, R. N. Dutta, K. L. Lust, 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  
  • 84. C. O. Wilke, 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  
  • 83. W. Gu, T. Zhou, 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
  • 2009
  • 82. D. A. Drummond, C. O. Wilke (2009). The evolutionary consequences of erroneous protein synthesis. Nature Reviews Genetics 10:715–724.
    doi: 10.1038/nrg2662   pmcid: PMC2764353  
  • 81. A. R. Sedaghat, D. A. Rastegar, K. A. O'Connell, J. B. Dionso, C. O. Wilke, 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  
  • 80. S. H. Steinmeyer, C. O. Wilke (2009). Lethal mutagenesis in a structured environment. J. Theor. Biol. 261:67–73.
    doi: 10.1016/j.jtbi.2009.07.014   pmcid: PMC2867491  
  • 79. T. P. Brennan, J. O. Woods, A. R. Sedaghat, J. D. Siliciano, R. F. Siliciano, 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  
  • 78. C. Ofria, D. M. Bryson, C. O. Wilke (2009). Avida: Evolution experiments with self-replicating computer programs. In A. Adamatzky and M. Komosinski, eds. Artificial Life Models in Software, 2nd ed. Springer, pp. 3–35.
    doi: 10.1007/978-1-84882-285-6_1  
  • 77. T. Zhou, M. Weems, 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: PMC2734146  
  • 76. A. R. Sedaghat, R. F. Siliciano, 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
  • 2008
  • 75. T. Zhou, P. J. Enyeart, C. O. Wilke (2008). Detecting clusters of mutations. PLoS ONE 3:e3765.
    doi: 10.1371/journal.pone.0003765   pmcid: PMC2582452  
  • 74. I. S. Novella, R. N. Dutta, 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  
  • 73. J. J. Bull, C. O. Wilke (2008). Lethal mutagenesis of bacteria. Genetics 180:1061–1070.
    doi: 10.1534/genetics.108.091413   pmcid: PMC2567356  
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  • 55. 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, 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.
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