Claus Wilke - Publications

Affiliations: 
University of Texas, Austin, Texas 

159 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Teufel AI, Liu W, Draghi JA, Cameron CE, Wilke CO. Modeling poliovirus replication dynamics from live time-lapse single-cell imaging data. Scientific Reports. 11: 9622. PMID 33953215 DOI: 10.1038/s41598-021-87694-x  0.88
2020 Johnson MM, Wilke CO. Site-Specific Amino Acid Distributions Follow a Universal Shape. Journal of Molecular Evolution. PMID 33230664 DOI: 10.1007/s00239-020-09976-8  0.32
2020 Zhang Y, Moy AJ, Feng X, Nguyen HTM, Sebastian KR, Reichenberg JS, Wilke CO, Markey MK, Tunnell JW. Assessment of Raman Spectroscopy for Reducing Unnecessary Biopsies for Melanoma Screening. Molecules (Basel, Switzerland). 25. PMID 32575717 DOI: 10.3390/Molecules25122852  0.4
2020 Laurent JM, Garge RK, Teufel AI, Wilke CO, Kachroo AH, Marcotte EM. Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs. Plos Biology. 18: e3000627. PMID 32421706 DOI: 10.1371/Journal.Pbio.3000627  0.88
2020 Sydykova DK, LaBar T, Adami C, Wilke CO. Moderate Amounts of Epistasis are Not Evolutionarily Stable in Small Populations. Journal of Molecular Evolution. PMID 32350572 DOI: 10.1007/S00239-020-09942-4  0.92
2019 Jack BR, Boutz DR, Paff ML, Smith BL, Wilke CO. Transcript degradation and codon usage regulate gene expression in a lytic phage. Virus Evolution. 5: vez055. PMID 31908847 DOI: 10.1093/Ve/Vez055  0.52
2019 Liu W, Caglar MU, Mao Z, Woodman A, Arnold JJ, Wilke CO, Cameron CE. More than efficacy revealed by single-cell analysis of antiviral therapeutics. Science Advances. 5: eaax4761. PMID 31692968 DOI: 10.1126/Sciadv.Aax4761  0.68
2019 DuPai CD, McWhite CD, Smith CB, Garten R, Maurer-Stroh S, Wilke CO. Influenza passaging annotations: what they tell us and why we should listen. Virus Evolution. 5: vez016. PMID 31275610 DOI: 10.1093/Ve/Vez016  0.48
2019 Jack BR, Wilke CO. Pinetree: a step-wise gene expression simulator with codon-specific translation rates. Bioinformatics (Oxford, England). PMID 30923831 DOI: 10.1093/bioinformatics/btz203  0.52
2018 Teufel AI, Johnson MM, Laurent JM, Kachroo AH, Marcotte EM, Wilke CO. The many nuanced evolutionary consequences of duplicated genes. Molecular Biology and Evolution. PMID 30445614 DOI: 10.1093/Molbev/Msy216  0.88
2018 Teufel AI, Johnson MM, Laurent JM, Kachroo AH, Marcotte EM, Wilke CO. The many nuanced evolutionary consequences of duplicated genes. Molecular Biology and Evolution. PMID 30428072 DOI: 10.1093/Molbev/Msy210  0.88
2018 Caglar MU, Hockenberry AJ, Wilke CO. Predicting bacterial growth conditions from mRNA and protein abundances. Plos One. 13: e0206634. PMID 30388153 DOI: 10.1371/journal.pone.0206634  0.68
2018 Teufel AI, Ritchie AM, Wilke CO, Liberles DA. Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences. Genes. 9. PMID 30104502 DOI: 10.3390/Genes9080409  0.88
2018 Paff ML, Jack BR, Smith BL, Bull JJ, Wilke CO. Combinatorial Approaches to Viral Attenuation. Msystems. 3. PMID 30073203 DOI: 10.1128/mSystems.00046-18  0.52
2018 Jiang Q, Teufel AI, Jackson EL, Wilke CO. Beyond Thermodynamic Constraints: Evolutionary Sampling Generates Realistic Protein Sequence Variation. Genetics. PMID 29382650 DOI: 10.1534/genetics.118.300699  0.88
2018 Caglar MU, Teufel AI, Wilke CO. Sicegar: R package for sigmoidal and double-sigmoidal curve fitting. Peerj. 6: e4251. PMID 29362694 DOI: 10.7717/peerj.4251  0.88
2017 Sydykova DK, Jack BR, Spielman SJ, Wilke CO. Measuring evolutionary rates of proteins in a structural context. F1000research. 6: 1845. PMID 29167739 DOI: 10.12688/f1000research.12874.1  0.92
2017 Guo F, Li S, Caglar MU, Mao Z, Liu W, Woodman A, Arnold JJ, Wilke CO, Huang TJ, Cameron CE. Single-Cell Virology: On-Chip Investigation of Viral Infection Dynamics. Cell Reports. 21: 1692-1704. PMID 29117571 DOI: 10.1016/J.Celrep.2017.10.051  0.68
2017 Jack BR, Boutz DR, Paff ML, Smith BL, Bull JJ, Wilke CO. Reduced Protein Expression in a Virus Attenuated by Codon Deoptimization. G3 (Bethesda, Md.). PMID 28698233 DOI: 10.1534/G3.117.041020  0.52
2017 Sydykova DK, Wilke CO. Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates. Peerj. 5: e3391. PMID 28584717 DOI: 10.7717/peerj.3391  0.92
2017 Chapman SD, Adami C, Wilke CO, B Kc D. The evolution of logic circuits for the purpose of protein contact map prediction. Peerj. 5: e3139. PMID 28439455 DOI: 10.7717/Peerj.3139  0.6
2017 Caglar MU, Houser JR, Barnhart CS, Boutz DR, Carroll SM, Dasgupta A, Lenoir WF, Smith BL, Sridhara V, Sydykova DK, Vander Wood D, Marx CJ, Marcotte EM, Barrick JE, Wilke CO. The E. coli molecular phenotype under different growth conditions. Scientific Reports. 7: 45303. PMID 28417974 DOI: 10.1038/Srep45303  0.92
2017 Brown CW, Sridhara V, Boutz DR, Person MD, Marcotte EM, Barrick JE, Wilke CO. Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions. Bmc Genomics. 18: 301. PMID 28412930 DOI: 10.1186/S12864-017-3676-8  0.32
2017 Jackson EL, Spielman SJ, Wilke CO. Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein. Plos One. 12: e0164905. PMID 28369116 DOI: 10.1371/journal.pone.0164905  0.68
2017 Echave J, Wilke CO. Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence. Annual Review of Biophysics. PMID 28301766 DOI: 10.1146/annurev-biophys-070816-033819  0.52
2017 Teufel AI, Wilke CO. Accelerated simulation of evolutionary trajectories in origin-fixation models. Journal of the Royal Society, Interface. 14. PMID 28228542 DOI: 10.1098/rsif.2016.0906  0.88
2016 Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, ... ... Wilke CO, et al. Viral factors in influenza pandemic risk assessment. Elife. 5. PMID 27834632 DOI: 10.7554/Elife.18491  0.44
2016 McWhite CD, Meyer AG, Wilke CO. Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza virus H3N2 hemagglutinin. Virus Evolution. 2. PMID 27713835 DOI: 10.1093/Ve/Vew026  0.92
2016 Spielman SJ, Wan S, Wilke CO. A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specific dN/dS Estimation. Genetics. PMID 27535929 DOI: 10.1534/genetics.115.185264  0.68
2016 Spielman SJ, Wilke CO. Extensively parameterized mutation-selection models reliably capture site-specific selective constraint. Molecular Biology and Evolution. PMID 27512115 DOI: 10.1093/molbev/msw171  0.68
2016 Wilke CO, Sawyer SL. At the mercy of viruses. Elife. 5. PMID 27187565 DOI: 10.7554/Elife.16758  1
2016 Jack BR, Meyer AG, Echave J, Wilke CO. Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes. Plos Biology. 14: e1002452. PMID 27138088 DOI: 10.1371/Journal.Pbio.1002452  0.92
2016 Shahmoradi A, Wilke CO. Dissecting the roles of local packing density and longer-range effects in protein sequence evolution. Proteins. PMID 26990194 DOI: 10.1002/Prot.25034  1
2016 Jackson EL, Shahmoradi A, Spielman SJ, Jack BR, Wilke CO. Intermediate divergence levels maximize the strength of structure -sequence correlations in enzymes and viral proteins. Protein Science : a Publication of the Protein Society. PMID 26971720 DOI: 10.1002/Pro.2920  1
2016 Echave J, Spielman SJ, Wilke CO. Causes of evolutionary rate variation among protein sites. Nature Reviews. Genetics. PMID 26781812 DOI: 10.1038/nrg.2015.18  0.68
2015 Meyer AG, Spielman SJ, Bedford T, Wilke CO. Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak. Virus Evolution. 1. PMID 26770819 DOI: 10.1093/Ve/Vev006  0.92
2015 Meyer AG, Wilke CO. The utility of protein structure as a predictor of site-wise dN/dS varies widely among HIV-1 proteins. Journal of the Royal Society, Interface / the Royal Society. 12. PMID 26468068 DOI: 10.1098/Rsif.2015.0579  1
2015 Wilke CO. Evolutionary paths of least resistance. Proceedings of the National Academy of Sciences of the United States of America. 112: 12553-4. PMID 26430238 DOI: 10.1073/pnas.1517390112  1
2015 Spielman SJ, Wilke CO. Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies. Plos One. 10: e0139047. PMID 26397960 DOI: 10.1371/journal.pone.0139047  1
2015 Kerr SA, Jackson EL, Lungu OI, Meyer AG, Demogines A, Ellington AD, Georgiou G, Wilke CO, Sawyer SL. Computational and Functional Analysis of the Virus-Receptor Interface Reveals Host Range Trade-Offs in New World Arenaviruses. Journal of Virology. 89: 11643-53. PMID 26355089 DOI: 10.1128/Jvi.01408-15  1
2015 Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO. Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation. Plos Computational Biology. 11: e1004400. PMID 26275208 DOI: 10.1371/Journal.Pcbi.1004400  0.92
2015 Meyer AG, Wilke CO. Geometric Constraints Dominate the Antigenic Evolution of Influenza H3N2 Hemagglutinin. Plos Pathogens. 11: e1004940. PMID 26020774 DOI: 10.1371/Journal.Ppat.1004940  1
2015 Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM. Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Science (New York, N.Y.). 348: 921-5. PMID 25999509 DOI: 10.1126/Science.Aaa0769  1
2015 Echave J, Jackson EL, Wilke CO. Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites. Physical Biology. 12: 025002. PMID 25787027 DOI: 10.1088/1478-3975/12/2/025002  1
2015 Spielman SJ, Kumar K, Wilke CO. Comprehensive, structurally-informed alignment and phylogeny of vertebrate biogenic amine receptors. Peerj. 3: e773. PMID 25737813 DOI: 10.7717/peerj.773  1
2015 Spielman SJ, Wilke CO. The relationship between dN/dS and scaled selection coefficients. Molecular Biology and Evolution. 32: 1097-108. PMID 25576365 DOI: 10.1093/molbev/msv003  1
2015 Shahmoradi A, Wilke C. Dissecting the relationship between protein structure and sequence variation Bulletin of the American Physical Society. 2015. DOI: 10.15781/T2Zs3T  1
2015 Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO. Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation Plos Computational Biology. 11. DOI: 10.1371/journal.pcbi.1004400  1
2014 Sridhara V, Meyer AG, Rai P, Barrick JE, Ravikumar P, Segrè D, Wilke CO. Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli. Plos One. 9: e114608. PMID 25502413 DOI: 10.1371/Journal.Pone.0114608  1
2014 Shahmoradi A, Sydykova DK, Spielman SJ, Jackson EL, Dawson ET, Meyer AG, Wilke CO. Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design. Journal of Molecular Evolution. 79: 130-42. PMID 25217382 DOI: 10.1007/S00239-014-9644-X  1
2014 Spielman SJ, Dawson ET, Wilke CO. Limited utility of residue masking for positive-selection inference. Molecular Biology and Evolution. 31: 2496-500. PMID 24899665 DOI: 10.1093/molbev/msu183  1
2014 Buckheit RW, Sexauer SB, Sedaghat AR, Wilke CO, Laeyendecker O, Basseth CR, Blankson JN. Long-term control of viral replication in a Group O, human immunodeficiency virus type 1-infected individual. Aids Research and Human Retroviruses. 30: 511-3. PMID 24798496 DOI: 10.1089/Aid.2014.0054  1
2014 Meyer AG, Sawyer SL, Ellington AD, Wilke CO. Analyzing machupo virus-receptor binding by molecular dynamics simulations. Peerj. 2: e266. PMID 24624315 DOI: 10.7717/Peerj.266  1
2014 O'Dea EB, Pepin KM, Lopman BA, Wilke CO. Fitting outbreak models to data from many small norovirus outbreaks. Epidemics. 6: 18-29. PMID 24593918 DOI: 10.1016/J.Epidem.2013.12.002  1
2014 Sedaghat AR, Wilke CO, Cunningham MJ, Ishman SL. Socioeconomic disparities in the presentation of acute bacterial sinusitis complications in children. The Laryngoscope. 124: 1700-6. PMID 24338779 DOI: 10.1002/Lary.24492  1
2014 Paff ML, Stolte SP, Bull JJ. Lethal mutagenesis failure may augment viral adaptation. Molecular Biology and Evolution. 31: 96-105. PMID 24092771 DOI: 10.1093/molbev/mst173  0.48
2013 Tien MZ, Meyer AG, Sydykova DK, Spielman SJ, Wilke CO. Maximum allowed solvent accessibilites of residues in proteins. Plos One. 8: e80635. PMID 24278298 DOI: 10.1371/Journal.Pone.0080635  1
2013 Jackson EL, Ollikainen N, Covert AW, Kortemme T, Wilke CO. Amino-acid site variability among natural and designed proteins. Peerj. 1: e211. PMID 24255821 DOI: 10.7717/Peerj.211  1
2013 Covert AW, Lenski RE, Wilke CO, Ofria C. Experiments on the role of deleterious mutations as stepping stones in adaptive evolution. Proceedings of the National Academy of Sciences of the United States of America. 110: E3171-8. PMID 23918358 DOI: 10.1073/Pnas.1313424110  1
2013 Lee C, Harris RA, Wall JK, Mayfield RD, Wilke CO. RNaseIII and T4 polynucleotide Kinase sequence biases and solutions during RNA-seq library construction. Biology Direct. 8: 16. PMID 23826734 DOI: 10.1186/1745-6150-8-16  1
2013 Tien MZ, Sydykova DK, Meyer AG, Wilke CO. PeptideBuilder: A simple Python library to generate model peptides. Peerj. 1: e80. PMID 23717802 DOI: 10.7717/Peerj.80  1
2013 Sedaghat AR, Gray ST, Chambers KJ, Wilke CO, Caradonna DS. Sinonasal anatomic variants and asthma are associated with faster development of chronic rhinosinusitis in patients with allergic rhinitis. International Forum of Allergy & Rhinology. 3: 755-61. PMID 23504927 DOI: 10.1002/alr.21163  1
2013 Novella IS, Presloid JB, Beech C, Wilke CO. Congruent evolution of fitness and genetic robustness in vesicular stomatitis virus. Journal of Virology. 87: 4923-8. PMID 23408631 DOI: 10.1128/JVI.02796-12  1
2013 Meyer AG, Dawson ET, Wilke CO. Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 368: 20120334. PMID 23382434 DOI: 10.1098/Rstb.2012.0334  1
2013 Spielman SJ, Wilke CO. Membrane environment imposes unique selection pressures on transmembrane domains of G protein-coupled receptors. Journal of Molecular Evolution. 76: 172-82. PMID 23355009 DOI: 10.1007/s00239-012-9538-8  1
2013 Smith-Tsurkan SD, Herr RA, Khuder S, Wilke CO, Novella IS. The role of environmental factors on the evolution of phenotypic diversity in vesicular stomatitis virus populations. The Journal of General Virology. 94: 860-8. PMID 23239575 DOI: 10.1099/vir.0.048082-0  1
2013 Meyer AG, Wilke CO. Integrating sequence variation and protein structure to identify sites under selection. Molecular Biology and Evolution. 30: 36-44. PMID 22977116 DOI: 10.1093/Molbev/Mss217  1
2012 Scherrer MP, Meyer AG, Wilke CO. Modeling coding-sequence evolution within the context of residue solvent accessibility. Bmc Evolutionary Biology. 12: 179. PMID 22967129 DOI: 10.1186/1471-2148-12-179  1
2012 Wilke CO. Bringing molecules back into molecular evolution. Plos Computational Biology. 8: e1002572. PMID 22761562 DOI: 10.1371/journal.pcbi.1002572  1
2012 Keller TE, Wilke CO, Bull JJ. Interactions between evolutionary processes at high mutation rates. Evolution; International Journal of Organic Evolution. 66: 2303-14. PMID 22759303 DOI: 10.1111/J.1558-5646.2012.01596.X  1
2012 Sedaghat AR, Gray ST, Wilke CO, Caradonna DS. Risk factors for development of chronic rhinosinusitis in patients with allergic rhinitis. International Forum of Allergy & Rhinology. 2: 370-5. PMID 22648994 DOI: 10.1002/alr.21055  1
2012 Bull JJ, Molineux IJ, Wilke CO. Slow fitness recovery in a codon-modified viral genome. Molecular Biology and Evolution. 29: 2997-3004. PMID 22532576 DOI: 10.1093/Molbev/Mss119  1
2012 Wang D, Arapostathis A, Wilke CO, Markey MK. Principal-oscillation-pattern analysis of gene expression. Plos One. 7: e28805. PMID 22253697 DOI: 10.1371/Journal.Pone.0028805  1
2012 Keller TE, Mis SD, Jia KE, Wilke CO. Reduced mRNA secondary-structure stability near the start codon indicates functional genes in prokaryotes. Genome Biology and Evolution. 4: 80-8. PMID 22138151 DOI: 10.1093/Gbe/Evr129  1
2012 Wang D, Markey MK, Wilke CO, Arapostathis A. Eigen-genomic system dynamic-pattern analysis (ESDA): modeling mRNA degradation and self-regulation. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 9: 430-7. PMID 22084146 DOI: 10.1109/Tcbb.2011.150  1
2012 Covert AW, Carlson-Stevermer J, Derrberry DZ, Wilke CO. The role of deleterious mutations in the adaptation to a novel environment Artificial Life 13: Proceedings of the 13th International Conference On the Simulation and Synthesis of Living Systems, Alife 2012. 27-31.  1
2012 Covert AW, Smith L, Derrberry DZ, Wilke CO. What does sex have to do with it: Tracking the fate of deleterious mutations in sexual populations Artificial Life 13: Proceedings of the 13th International Conference On the Simulation and Synthesis of Living Systems, Alife 2012. 32-36.  1
2011 Novella IS, Presloid JB, Smith SD, Wilke CO. Specific and nonspecific host adaptation during arboviral experimental evolution. Journal of Molecular Microbiology and Biotechnology. 21: 71-81. PMID 22248544 DOI: 10.1159/000332752  1
2011 Bull JJ, Heineman RH, Wilke CO. The phenotype-fitness map in experimental evolution of phages. Plos One. 6: e27796. PMID 22132144 DOI: 10.1371/Journal.Pone.0027796  1
2011 Wilke CO. Transcriptional robustness complements nonsense-mediated decay in humans. Plos Genetics. 7: e1002296. PMID 22022274 DOI: 10.1371/journal.pgen.1002296  1
2011 Sedaghat AR, Wilke CO. Kinetics of the viral cycle influence pharmacodynamics of antiretroviral therapy. Biology Direct. 6: 42. PMID 21910865 DOI: 10.1186/1745-6150-6-42  1
2011 Ramsey DC, Scherrer MP, Zhou T, Wilke CO. The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Genetics. 188: 479-88. PMID 21467571 DOI: 10.1534/Genetics.111.128025  1
2011 Zhou T, Wilke CO. Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses. Bmc Evolutionary Biology. 11: 59. PMID 21385374 DOI: 10.1186/1471-2148-11-59  1
2011 Ciota AT, Koch EM, Willsey GG, Davis LJ, Jerzak GV, Ehrbar DJ, Wilke CO, Kramer LD. Temporal and spatial alterations in mutant swarm size of St. Louis encephalitis virus in mosquito hosts. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 11: 460-8. PMID 21215334 DOI: 10.1016/J.Meegid.2010.12.007  1
2011 O'Dea EB, Wilke CO. Contact heterogeneity and phylodynamics: how contact networks shape parasite evolutionary trees. Interdisciplinary Perspectives On Infectious Diseases. 2011: 238743. PMID 21151699 DOI: 10.1155/2011/238743  1
2011 Spivak AM, Rabi SA, McMahon MA, Shan L, Sedaghat AR, Wilke CO, Siliciano RF. Short communication: dynamic constraints on the second phase compartment of HIV-infected cells. Aids Research and Human Retroviruses. 27: 759-61. PMID 21105850 DOI: 10.1089/Aid.2010.0199  1
2010 Lee Y, Zhou T, Tartaglia GG, Vendruscolo M, Wilke CO. Translationally optimal codons associate with aggregation-prone sites in proteins. Proteomics. 10: 4163-71. PMID 21046618 DOI: 10.1002/Pmic.201000229  1
2010 Pepin KM, Volkov I, Banavar JR, Wilke CO, Grenfell BT. Phenotypic differences in viral immune escape explained by linking within-host dynamics to host-population immunity. Journal of Theoretical Biology. 265: 501-10. PMID 20570681 DOI: 10.1016/J.Jtbi.2010.05.036  1
2010 O'Dea EB, Keller TE, Wilke CO. Does mutational robustness inhibit extinction by lethal mutagenesis in viral populations? Plos Computational Biology. 6: e1000811. PMID 20548958 DOI: 10.1371/Journal.Pcbi.1000811  1
2010 Steinmeyer SH, Wilke CO, Pepin KM. Methods of modelling viral disease dynamics across the within- and between-host scales: the impact of virus dose on host population immunity. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365: 1931-41. PMID 20478888 DOI: 10.1098/Rstb.2010.0065  1
2010 Wilke CO, Drummond DA. Signatures of protein biophysics in coding sequence evolution. Current Opinion in Structural Biology. 20: 385-9. PMID 20395125 DOI: 10.1016/J.Sbi.2010.03.004  1
2010 Zhou T, Gu W, Wilke CO. Detecting positive and purifying selection at synonymous sites in yeast and worm. Molecular Biology and Evolution. 27: 1912-22. PMID 20231333 DOI: 10.1093/molbev/msq077  1
2010 Novella IS, Presloid JB, Zhou T, Smith-Tsurkan SD, Ebendick-Corpus BE, Dutta RN, Lust KL, Wilke CO. Genomic evolution of vesicular stomatitis virus strains with differences in adaptability. Journal of Virology. 84: 4960-8. PMID 20181701 DOI: 10.1128/JVI.00710-09  1
2010 Gu W, Zhou T, Wilke CO. A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. Plos Computational Biology. 6: e1000664. PMID 20140241 DOI: 10.1371/journal.pcbi.1000664  1
2010 Smith-Tsurkan SD, Wilke CO, Novella IS. Incongruent fitness landscapes, not tradeoffs, dominate the adaptation of vesicular stomatitis virus to novel host types. The Journal of General Virology. 91: 1484-93. PMID 20107014 DOI: 10.1099/vir.0.017855-0  1
2010 Sedaghat AR, Rastegar DA, O'Connell KA, Dinoso JB, Wilke CO, Blankson JN. Reply to torre Clinical Infectious Diseases. 50: 1425-1426. DOI: 10.1086/652285  1
2009 Sedaghat AR, Rastegar DA, O'Connell KA, Dinoso JB, Wilke CO, Blankson JN. T cell dynamics and the response to HAART in a cohort of HIV-1-infected elite suppressors. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 49: 1763-6. PMID 19857162 DOI: 10.1086/648081  1
2009 Drummond DA, Wilke CO. The evolutionary consequences of erroneous protein synthesis. Nature Reviews. Genetics. 10: 715-24. PMID 19763154 DOI: 10.1038/Nrg2662  1
2009 Steinmeyer SH, Wilke CO. Lethal mutagenesis in a structured environment. Journal of Theoretical Biology. 261: 67-73. PMID 19627995 DOI: 10.1016/j.jtbi.2009.07.014  1
2009 Brennan TP, Woods JO, Sedaghat AR, Siliciano JD, Siliciano RF, Wilke CO. Analysis of human immunodeficiency virus type 1 viremia and provirus in resting CD4+ T cells reveals a novel source of residual viremia in patients on antiretroviral therapy. Journal of Virology. 83: 8470-81. PMID 19535437 DOI: 10.1128/Jvi.02568-08  1
2009 Sedaghat AR, Siliciano RF, Wilke CO. Constraints on the dominant mechanism for HIV viral dynamics in patients on raltegravir. Antiviral Therapy. 14: 263-71. PMID 19430101  1
2009 Zhou T, Weems M, Wilke CO. Translationally optimal codons associate with structurally sensitive sites in proteins. Molecular Biology and Evolution. 26: 1571-80. PMID 19349643 DOI: 10.1093/molbev/msp070  1
2009 Ofria C, Bryson DM, Wilke CO. Avida: A software platform for research in computational evolutionary biology Artificial Life Models in Software (Second Edition). 3-35. DOI: 10.1007/978-1-84882-285-6_1  1
2008 Zhou T, Enyeart PJ, Wilke CO. Detecting clusters of mutations. Plos One. 3: e3765. PMID 19018282 DOI: 10.1371/journal.pone.0003765  1
2008 Novella IS, Dutta RN, Wilke CO. A linear relationship between fitness and the logarithm of the critical bottleneck size in vesicular stomatitis virus populations. Journal of Virology. 82: 12589-90. PMID 18829755 DOI: 10.1128/JVI.01394-08  1
2008 Bull JJ, Wilke CO. Lethal mutagenesis of bacteria. Genetics. 180: 1061-70. PMID 18780744 DOI: 10.1534/genetics.108.091413  1
2008 Drummond DA, Wilke CO. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell. 134: 341-52. PMID 18662548 DOI: 10.1016/J.Cell.2008.05.042  1
2008 Brunet E, Rouzine IM, Wilke CO. The stochastic edge in adaptive evolution. Genetics. 179: 603-20. PMID 18493075 DOI: 10.1534/genetics.107.079319  1
2008 Whitehead DJ, Wilke CO, Vernazobres D, Bornberg-Bauer E. The look-ahead effect of phenotypic mutations. Biology Direct. 3: 18. PMID 18479505 DOI: 10.1186/1745-6150-3-18  1
2008 Zhou T, Drummond DA, Wilke CO. Contact density affects protein evolutionary rate from bacteria to animals. Journal of Molecular Evolution. 66: 395-404. PMID 18379715 DOI: 10.1007/S00239-008-9094-4  1
2008 Sedaghat AR, Dinoso JB, Shen L, Wilke CO, Siliciano RF. Decay dynamics of HIV-1 depend on the inhibited stages of the viral life cycle. Proceedings of the National Academy of Sciences of the United States of America. 105: 4832-7. PMID 18362342 DOI: 10.1073/Pnas.0711372105  1
2008 Dutta RN, Rouzine IM, Smith SD, Wilke CO, Novella IS. Rapid adaptive amplification of preexisting variation in an RNA virus. Journal of Virology. 82: 4354-62. PMID 18287227 DOI: 10.1128/JVI.02446-07  1
2008 Sedaghat AR, Siliciano RF, Wilke CO. Low-level HIV-1 replication and the dynamics of the resting CD4+ T cell reservoir for HIV-1 in the setting of HAART. Bmc Infectious Diseases. 8: 2. PMID 18171475 DOI: 10.1186/1471-2334-8-2  1
2008 Rouzine IM, Brunet E, Wilke CO. The traveling-wave approach to asexual evolution: Muller's ratchet and speed of adaptation. Theoretical Population Biology. 73: 24-46. PMID 18023832 DOI: 10.1016/j.tpb.2007.10.004  1
2007 Forster R, Wilke CO. Frequency-Dependent Selection in a Periodic Environment. Physica A. 381: 255-264. PMID 17940581 DOI: 10.1016/J.Physa.2007.03.017  1
2007 Sedaghat AR, Siliciano JD, Brennan TP, Wilke CO, Siliciano RF. Limits on replenishment of the resting CD4+ T cell reservoir for HIV in patients on HAART. Plos Pathogens. 3: e122. PMID 17784786 DOI: 10.1371/Journal.Ppat.0030122  1
2007 Elena SF, Wilke CO, Ofria C, Lenski RE. Effects of population size and mutation rate on the evolution of mutational robustness. Evolution; International Journal of Organic Evolution. 61: 666-74. PMID 17348929 DOI: 10.1111/J.1558-5646.2007.00064.X  1
2007 Takeuchi N, Hogeweg P. Error-threshold exists in fitness landscapes with lethal mutants. Bmc Evolutionary Biology. 7: 15; author reply 15. PMID 17286853 DOI: 10.1186/1471-2148-7-15  1
2007 Bloom JD, Arnold FH, Wilke CO. Breaking proteins with mutations: threads and thresholds in evolution. Molecular Systems Biology. 3: 76. PMID 17262035 DOI: 10.1038/Msb4100119  1
2007 Bull JJ, Sanjuán R, Wilke CO. Theory of lethal mutagenesis for viruses Journal of Virology. 81: 2930-2939. PMID 17202214 DOI: 10.1128/JVI.01624-06  1
2007 Bloom JD, Raval A, Wilke CO. Thermodynamics of neutral protein evolution. Genetics. 175: 255-66. PMID 17110496 DOI: 10.1534/genetics.106.061754  1
2006 Forster R, Adami C, Wilke CO. Selection for mutational robustness in finite populations. Journal of Theoretical Biology. 243: 181-90. PMID 16901510 DOI: 10.1016/J.Jtbi.2006.06.020  1
2006 Bloom JD, Drummond DA, Arnold FH, Wilke CO. Structural determinants of the rate of protein evolution in yeast. Molecular Biology and Evolution. 23: 1751-61. PMID 16782762 DOI: 10.1093/Molbev/Msl040  1
2006 Bailey JR, Sedaghat AR, Kieffer T, Brennan T, Lee PK, Wind-Rotolo M, Haggerty CM, Kamireddi AR, Liu Y, Lee J, Persaud D, Gallant JE, Cofrancesco J, Quinn TC, Wilke CO, et al. 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. Journal of Virology. 80: 6441-57. PMID 16775332 DOI: 10.1128/Jvi.00591-06  1
2006 Wilke CO, Forster R, Novella IS. Quasispecies in time-dependent environments Current Topics in Microbiology and Immunology. 299: 33-50. PMID 16568895 DOI: 10.1007/3-540-26397-7_2  1
2006 Wilke CO, Drummond DA. Population genetics of translational robustness. Genetics. 173: 473-81. PMID 16489231 DOI: 10.1534/Genetics.105.051300  1
2006 Drummond DA, Raval A, Wilke CO. A single determinant dominates the rate of yeast protein evolution. Molecular Biology and Evolution. 23: 327-37. PMID 16237209 DOI: 10.1093/Molbev/Msj038  1
2005 Forster R, Wilke CO. Tradeoff between short-term and long-term adaptation in a changing environment. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 041922. PMID 16383435 DOI: 10.1103/Physreve.72.041922  1
2005 Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. Why highly expressed proteins evolve slowly. Proceedings of the National Academy of Sciences of the United States of America. 102: 14338-43. PMID 16176987 DOI: 10.1073/Pnas.0504070102  1
2005 Wilke CO, Bloom JD, Drummond DA, Raval A. Predicting the tolerance of proteins to random amino acid substitution. Biophysical Journal. 89: 3714-20. PMID 16150971 DOI: 10.1529/Biophysj.105.062125  1
2005 Wilke CO. Quasispecies theory in the context of population genetics. Bmc Evolutionary Biology. 5: 44. PMID 16107214 DOI: 10.1186/1471-2148-5-44  1
2005 Wilke CO. Molecular clocks: The heavy, the cold, and the slow Heredity. 95: 115. PMID 15931251 DOI: 10.1038/sj.hdy.6800681  1
2005 Bloom JD, Silberg JJ, Wilke CO, Drummond DA, Adami C, Arnold FH. Thermodynamic prediction of protein neutrality. Proceedings of the National Academy of Sciences of the United States of America. 102: 606-11. PMID 15644440 DOI: 10.1073/Pnas.0406744102  0.6
2005 Ofria C, Wilke CO. Avida: Evolution experiments with self-replicating computer programs Artificial Life Models in Software. 3-35. DOI: 10.1007/1-84628-214-4_1  1
2004 Froissart R, Wilke CO, Montville R, Remold SK, Chao L, Turner PE. Co-infection weakens selection against epistatic mutations in RNA viruses. Genetics. 168: 9-19. PMID 15454523 DOI: 10.1534/Genetics.104.030205  1
2004 Wilke CO. The speed of adaptation in large asexual populations. Genetics. 167: 2045-53. PMID 15342539 DOI: 10.1534/genetics.104.027136  1
2004 Wilke CO. Molecular clock in neutral protein evolution. Bmc Genetics. 5: 25. PMID 15333142 DOI: 10.1186/1471-2156-5-25  1
2004 Wilke CO. Supplementary materials need the right format. Nature. 430: 291. PMID 15254513 DOI: 10.1038/430291c  1
2004 Chow SS, Wilke CO, Ofria C, Lenski RE, Adami C. Adaptive radiation from resource competition in digital organisms. Science (New York, N.Y.). 305: 84-6. PMID 15232105 DOI: 10.1126/Science.1096307  1
2004 Bloom JD, Wilke CO, Arnold FH, Adami C. Stability and the evolvability of function in a model protein. Biophysical Journal. 86: 2758-64. PMID 15111394 DOI: 10.1016/S0006-3495(04)74329-5  1
2004 Ofria C, Wilke CO. Avida: a software platform for research in computational evolutionary biology. Artificial Life. 10: 191-229. PMID 15107231 DOI: 10.1162/106454604773563612  1
2004 Johnson TJ, Wilke CO. Evolution of resource competition between mutually dependent digital organisms. Artificial Life. 10: 145-56. PMID 15107227 DOI: 10.1162/106454604773563577  1
2004 Li Y, Wilke CO. Digital evolution in time-dependent fitness landscapes. Artificial Life. 10: 123-34. PMID 15107225 DOI: 10.1162/106454604773563559  1
2004 Adami C, Wilke CO. Experiments in digital evolution (Editors' introduction to the special issue) Artificial Life. 10: 117-122. DOI: 10.1162/106454604773563540  1
2003 Wilke CO. Probability of fixation of an advantageous mutant in a viral quasispecies. Genetics. 163: 467-74. PMID 12618386  1
2003 Wilke CO, Lenski RE, Adami C. Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding. Bmc Evolutionary Biology. 3: 3. PMID 12590655 DOI: 10.1186/1471-2148-3-3  1
2003 Wilke CO, Adami C. Evolution of mutational robustness. Mutation Research. 522: 3-11. PMID 12517406 DOI: 10.1016/S0027-5107(02)00307-X  1
2002 Wilke CO. Maternal effects in molecular evolution. Physical Review Letters. 88: 078101. PMID 11863942 DOI: 10.1103/PhysRevLett.88.078101  1
2002 Campos PRA, Adami C, Wilke CO. Optimal adaptive performance and delocalization in NK fitness landscapes Physica a: Statistical Mechanics and Its Applications. 304: 495-506. DOI: 10.1016/S0378-4371(01)00572-6  1
2002 Wilke CO, Adami C. The biology of digital organisms Trends in Ecology and Evolution. 17: 528-532. DOI: 10.1016/S0169-5347(02)02612-5  1
2001 Wilke CO. Selection for fitness versus selection for robustness in RNA secondary structure folding Evolution. 55: 2412-2420. PMID 11831657 DOI: 10.1111/j.0014-3820.2001.tb00756.x  1
2001 Wilke CO. Adaptive evolution on neutral networks Bulletin of Mathematical Biology. 63: 715-730. PMID 11497165 DOI: 10.1006/bulm.2001.0244  1
2001 Wilke CO, Wang JL, Ofria C, Lenski RE, Adami C. Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature. 412: 331-3. PMID 11460163 DOI: 10.1038/35085569  1
2001 Wilke CO, Adami C. Interaction between directional epistasis and average mutational effects Proceedings of the Royal Society B: Biological Sciences. 268: 1469-1474. PMID 11454290 DOI: 10.1098/Rspb.2001.1690  1
2001 Wilke CO, Ronnewinkel C. Dynamic fitness landscapes: Expansions for small mutation rates Physica a: Statistical Mechanics and Its Applications. 290: 475-490. DOI: 10.1016/S0378-4371(00)00585-9  1
1999 Wilke CO, Martinetz T. Adaptive walks on time-dependent fitness landscapes. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 60: 2154-9. PMID 11970008 DOI: 10.1103/Physreve.60.2154  1
1999 Wilke CO, Ronnewinkel C, Martinetz T. Molecular evolution in time-dependent environments Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1674: 417-421. DOI: 10.1007/3-540-48304-7_57  1
1998 Wilke C, Altmeyer S, Martinetz T. Aftershocks in coherent-noise models Physica D: Nonlinear Phenomena. 120: 401-417. DOI: 10.1016/S0167-2789(98)00092-X  1
1997 Wilke C, Martinetz T. Simple model of evolution with variable system size Physical Review E. 56: 7128-7131. DOI: 10.1103/Physreve.56.7128  1
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