C. W. Kosonocky, C. O. Wilke, E. M. Marcotte, A. D. Ellington (preprint). Mining patents with large language models demonstrates congruence of functional labels and chemical structures. arXiv:2309.08765.
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J. R. Randall, L. C. Vieira, C. O. Wilke, B. W. Davies (preprint). Deep mutational scanning and machine learning uncover antimicrobial peptide features driving membrane selectivity. bioRxiv 551017.
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C. W. Kosonocky, A. L. Feller, C. O. Wilke, A. D. Ellington (preprint). Prompt engineering for transformer-based chemical similarity search identifies structurally distinct functional analogues. arXiv:2305.16330.
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M. M. Johnson, C. O. Wilke (preprint). Recombination rate inference via deep learning is limited by sequence diversity. bioRxiv 498489.
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A. J. Hockenberry, D. C. Weaver, C. O. Wilke (preprint). Virulent but not temperate bacteriophages display hallmarks of rapid translation initiation. bioRxiv 440840.
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D. K. Sydykova, C. O. Wilke (preprint). Theory of measurement for site-specific evolutionary rates in amino-acid sequences. bioRxiv 411025.
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A. V. Kulikova, D. J. Diaz, T. Chen, T. J. Cole, A. D. Ellington, C. O. Wilke (2023). Two sequence-and two structure-based ML models have learned different aspects of protein biochemistry. Sci. Rep. 13:13280.
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M. M. Johnson, A. J. Hockenberry, M. J. McGuffie, L. C. Vieira, C. O. Wilke (2023). Growth-dependent gene expression variation influences the strength of codon usage biases. Mol. Biol. Evol. 40:msad189.
pmcid: PMC10482319
D. J. Diaz, A. V. Kulikova, A. D. Ellington, C. O. Wilke (2023). Using machine learning to predict the effects and consequences of mutations in proteins. Curr. Opin. Struct. Biol. 78, 102518.
J. R. Randall, C. D. DuPai, T. J. Cole, G. Davidson, K. E. Groover, S. L. Slater, D. A. Mavridou, C. O. Wilke, B. W. Davies (2023). Designing and identifying β-hairpin peptide macrocycles with antibiotic potential. Science Advances 9:eade0008.
doi: 10.1126/sciadv.ade0008


T. J. Cole, J. K. Parker, A. L. Feller, C. O. Wilke, B. W. Davies (2022). Evidence for widespread class II microcins in Enterobacterales genomes. Applied and Environmental Microbiology 88:e01486-22.
S. B. Shah, A. M. Hill, C. O. Wilke, A. J. Hockenberry (2022). Generating dynamic gene expression patterns without the need for regulatory circuits. PLoS One 17:e0268883.
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J. R. Rybarski, K. Hu, A. M. Hill, C. O. Wilke, I. J. Finkelstein (2021). Metagenomic Discovery of CRISPR-Associated Transposons. Proc. Natl. Acad. Sci. USA 118:e2112279118.
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A. V. Kulikova, D. J. Diaz, J. M. Loy, A. D. Ellington, C. O. Wilke (2021). Learning the local landscape of protein structures with convolutional neural networks. J. Biol. Phys. 47:435-454.
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pmcid: PMC8603988
A. M. Hill, J. R. Rybarski, K. Hu, I. J. Finkelstein, C. O. Wilke (2021). Opfi: A Python package for identifying gene clusters in large genomics and metagenomics data sets. Journal of Open Source Software 6:3678.
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A. J. Hockenberry, C. O. Wilke (2021). BACPHLIP: Predicting bacteriophage lifestyle from conserved protein domains. PeerJ 9:e11396.
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A. I. Teufel, W. Liu, J. A. Draghi, C. E. Cameron, C. O. Wilke (2021). Modeling poliovirus replication dynamics from live time-lapse single-cell imaging data. Scientific Reports 11:9622.
doi: 10.1038/s41598-021-87694-x
pmcid: PMC8100109
C. D. DuPai, B. W. Davies, C. O. Wilke (2021). A systematic analysis of the beta hairpin motif in the Protein Data Bank. Protein Science 30:613-623.
doi: 10.1002/pro.4020
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C. D. DuPai, A. L. Cunningham, A. R. Conrado, C. O. Wilke, B. W. Davies (2020). TsrA Regulates Virulence and Intestinal Colonization in Vibrio cholerae. mSphere 5:e01014-20.
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A. Zeileis, J. C. Fisher, K. Hornik, R. Ihaka, C. D. McWhite, P. Murrell, R. Stauffer, C. O. Wilke (2020). colorspace: A Toolbox for Manipulating and Assessing Colors and Palettes. J. Stat. Soft. 96(1):1–49.
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M. M. Johnson, C. O. Wilke (2020). Site-specific amino acid distributions follow a universal shape. J. Mol. Evol. 88:731–741.
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pmcid: PMC7717668
C. O. Wilke, C. T. Bergstrom (2020). Predicting an epidemic trajectory is difficult. Proc. Natl. Acad. Sci. USA 117:28549–28551.
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C. D. DuPai, C. O. Wilke, B. W. Davies (2020). A comprehensive co-expression network analysis in Vibrio cholerae. mSystems 5:e00550-20.
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pmcid: PMC7343309
Y. Zhang, A. J. Moy, X. Feng, H. T. M. Nguyen, K. R. Sebastian, J. S. Reichenberg, C. O. Wilke, M. K. Markey, J. W. Tunnell (2020). Assessment of Raman spectroscopy for reducing unnecessary biopsies for melanoma screening. Molecules 25:2852.
doi: 10.3390/molecules25122852
pmcid: PMC7355922
J. M. Laurent, R. K. Garge, A. I. Teufel, C. O. Wilke, A. H. Kachroo, E. M. Marcotte (2020). Humanization of yeast genes with multiple human orthologs reveals principles of functional divergence between paralogs. PLOS Biol. 18:e3000627.
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pmcid: PMC7259792
D. K. Sydykova, T. O. LaBar, C. Adami, C. O. Wilke (2020). Moderate amounts of epistasis are not evolutionarily stable in small populations. J. Mol. Evol. 88:435–444.
doi: 10.1007/s00239-020-09942-4


B. R. Jack, D. R. Boutz, M. L. Paff, B. L. Smith, C. O. Wilke (2019). Transcript degradation and codon usage regulate gene expression in a lytic phage. Virus Evol. 5:vez055.
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H. Wickham, M. Averick, J. Bryan, W. Chang, L. D'Agostino McGowan, R. François, G. Grolemund, A. Hayes, L. Henry, J. Hester, M. Kuhn, T. Lin Pedersen, E. Miller, S. Milton Bache, K. Müller, J. Ooms, D. Robinson, D. Paige Seidel, V. Spinu, K. Takahashi, D. Vaughan, C. Wilke, K. Woo, H. Yutani (2019). Welcome to the Tidyverse. JOSS 4:1686.
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W. Liu, M. U. Caglar, Z. Mao, A. Woodman, J. J. Arnold, C. O. Wilke, C. E. Cameron (2019). More than efficacy revealed by single-cell analysis of antiviral therapeutics. Science Advances 5:eaax4761.
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A. J. Hockenberry, C. O. Wilke (2019). Phylogenetic weighting does little to improve the accuracy of evolutionary coupling analyses. Entropy 21:1000.
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A. J. Hockenberry, C. O. Wilke (2019). Evolutionary couplings detect side-chain interactions. PeerJ 7:e7280.
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C. D. DuPai, C. D. McWhite, C. B. Smith, R. Garten, S. Maurer-Stroh, and C. O. Wilke (2019). Influenza passaging annotations: what they tell us and why we should listen. Virus Evol. 5:vez016.
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pmcid: PMC6599686
B. R. Jack, C. O. Wilke (2019). Pinetree: a step-wise gene expression simulator with codon-specific translation rates. Bioinformatics 35:4176–4178.
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pmcid: PMC6792109
A. I. Teufel, M. M. Johnson, J. M. Laurent, A. H. Kachroo, E. M. Marcotte, C. O. Wilke (2019). The many nuanced evolutionary consequences of duplicated genes. Mol. Biol. Evol. 36:304–314.
doi: 10.1093/molbev/msy210
pmcid: PMC6409435


M. U. Caglar, A. J. Hockenberry, C. O. Wilke (2018). Predicting bacterial growth conditions from mRNA and protein abundances. PLoS ONE 13:e0206634.
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pmcid: PMC6214550
A. J. Hockenberry, M. C. Jewett, L. A. N. Amaral, C. O. Wilke (2018). Within-gene Shine-Dalgarno sequences are not selected for function. Mol. Biol. Evol. 35:2487–2498.
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A. I. Teufel, A. M. Ritchie, C. O. Wilke, D. A. Liberles (2018). Using the mutation–selection framework to characterize selection on protein sequences. Genes 9:409.
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M. L. Paff, B. R. Jack, B. L. Smith, J. J. Bull, C. O. Wilke (2018). Combinatorial approaches to viral attenuation. mSystems 3:e00046.
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B. L. Smith, G. Chen, C. O. Wilke, R. M. Krug (2018). Avian influenza virus PB1 gene in H3N2 viruses evolved in humans to reduce interferon inhibition by skewing codon usage toward interferon-altered tRNA pools. mBio 9:e01222-18.
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D. C. Wu, J. Yao, K. S. Ho, A. M. Lambowitz, C. O. Wilke (2018). Limitations of alignment-free tools in total RNA-seq quantification. BMC Genomics 19:510.
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Q. Jiang, A. I. Teufel, E. L. Jackson, C. O. Wilke (2018). Beyond thermodynamic constraints: Evolutionary history shapes protein sequence variation. Genetics 208:1387–1395.
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D. K. Sydykova, B. R. Jack, S. J. Spielman, C. O. Wilke (2018). Measuring evolutionary rates of proteins in a structural context [version 2; referees: 4 approved]. F1000Research 2018, 6:1845.
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M. U. Caglar, A. I. Teufel, C. O. Wilke (2018). Sicegar: R package for sigmoidal and double-sigmoidal curve fitting. PeerJ 6:e4251.
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A. T. Tucker, S. P. Leonard, C. D. DuBois, G. A. Knauf, A. L. Cunningham, C. O. Wilke, S. Trent, B. W. Davies (2018). Discovery of next-generation antimicrobials through bacterial self-screening of surface-displayed peptide libraries. Cell 172:618–628.e13.
doi: 10.1016/j.cell.2017.12.009
pmcid: PMC5786472


F. Guo, S. Li, M. U. Caglar, Z. Mao, W. Liu, A. Woodman, J. J. Arnold, C. O. Wilke, T. J. Huang, C. E. Cameron (2017). Single-cell virology: On-chip investigation of viral infection dynamics. Cell Reports 21:1692–1704.
doi: 10.1016/j.celrep.2017.10.051
pmcid: PMC5689460
B. L. Smith, C. O. Wilke (2017). Virus Evolution: A new twist in measuring mutation rates. eLife 6:e29586.
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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 7:2957–2968.
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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.
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J. Echave, C. O. Wilke (2017). Biophysical models of protein evolution: Understanding the patterns of evolutionary sequence divergence. Ann. Rev. Biophys. 46:85–103.
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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.
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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.
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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
pmcid: PMC5392934
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
pmcid: PMC5378326
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
pmcid: PMC5332577


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.
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pmcid: PMC5156527
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.
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pmcid: PMC5049878
S. J. Spielman, C. O. Wilke (2016). Extensively parameterized mutation–selection models reliably capture site-specific selective constraint. Mol. Biol. Evol. 33:2990–3002.
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pmcid: PMC5062325
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.
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pmcid: PMC5068842
C. O. Wilke, S. L. Sawyer (2016). Adaptive evolution: At the mercy of viruses. eLife 5:e16758.
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pmcid: PMC4869909
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.
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pmcid: PMC4854464
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.
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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.
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pmcid: PMC5292938
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.
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pmcid: PMC4918415
J. Echave, S. J. Spielman, C. O. Wilke (2016). Causes of evolutionary rate variation among protein sites. Nature Rev. Genet. 17:109–121.
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pmcid: PMC4724262
D. Z. Derryberry, M. C. Cowperthwaite, C. O. Wilke (2016). Reproducibility of SNV-calling in multiple sequencing runs from single tumors. PeerJ 4:e1508.
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pmcid: PMC4741064


C. O. Wilke (2015). Evolutionary paths of least resistance. Proc. Natl. Acad. Sci. USA 112:12553–12554.
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pmcid: PMC4611625
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.
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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.
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pmcid: PMC4614493
S. J. Spielman, C. O. Wilke (2015). Pyvolve: A flexible flexible Python module for simulating sequences along phylogenies. PLOS ONE 10:e0139047.
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pmcid: PMC4580465
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 Evol. 1:vev006.
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pmcid: PMC4710376
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
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
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
S. J. Spielman, K. Kumar, C. O. Wilke (2015). Comprehensive, structurally-curated alignment and phylogeny of vertebrate biogenic amine receptors. PeerJ 3:e773.
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pmcid: PMC4338800
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
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


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
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.
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pmcid: PMC4216736
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.
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pmcid: PMC4046214
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
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
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
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


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.
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pmcid: PMC3836772
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.
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pmcid: PMC3828621
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.
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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.
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pmcid: PMC3752215
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.
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pmcid: PMC3709682
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.
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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.
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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.
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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.
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pmcid: PMC3712645
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.
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A. G. Meyer, C. O. Wilke (2013). Integrating sequence variation and protein structure to identify sites under selection. Mol. Biol. Evol. 30:36–44.
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pmcid: PMC3525147


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.
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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.
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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.
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T. E. Keller, C. O. Wilke, J. J. Bull (2012). Interactions between evolutionary processes at high mutation rates. Evolution 66:2303–2314.
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C. O. Wilke (2012). Bringing molecules back into molecular evolution. PLoS Comp. Biol. 8:e1002572.
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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.
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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.
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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.
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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.
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D. Wang, A. Arapostathis, C. O. Wilke, M. K. Markey (2012). Principal-oscillation-pattern analysis of gene expression. PLOS ONE 7:e28805.
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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.
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J. J. Bull, R. H. Heineman, C. O. Wilke (2011). The phenotype-fitness map in experimental evolution of phages. PLoS ONE 6:e27796.
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A. R. Sedaghat, C. O. Wilke (2011). Kinetics of the viral cycle influence pharmacodynamics of antiretroviral therapy. Biology Direct 6:42.
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C. O. Wilke (2011). Transcriptional robustness complements nonsense-mediated decay in humans. PLoS Genet. 7:e1002296.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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C. O. Wilke, D. A. Drummond (2010). Signatures of protein biophysics in coding sequence evolution. Cur. Opin. Struct. Biol. 20:385–389.
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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.
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D. A. Drummond, C. O. Wilke (2009). The evolutionary consequences of erroneous protein synthesis. Nature Reviews Genetics 10:715–724.
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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.
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S. H. Steinmeyer, C. O. Wilke (2009). Lethal mutagenesis in a structured environment. J. Theor. Biol. 261:67–73.
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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.
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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.
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T. Zhou, M. Weems, C. O. Wilke (2009). Translationally optimal codons associate with structurally sensitive sites in proteins. Mol. Biol. Evol. 26:1571–1580.
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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.
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T. Zhou, P. J. Enyeart, C. O. Wilke (2008). Detecting clusters of mutations. PLoS ONE 3:e3765.
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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.
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J. J. Bull, C. O. Wilke (2008). Lethal mutagenesis of bacteria. Genetics 180:1061–1070.
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D. A. Drummond, C. O. Wilke (2008). Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341–352.
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D. J. Whitehead, C. O. Wilke, D. Vernazobres, E. Bornberg-Bauer (2008). The look-ahead effect of phenotypic mutations. Biology Direct 3:18.
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É. Brunet, I. M. Rouzine, C. O. Wilke (2008). The stochastic edge in adaptive evolution. Genetics 179:603–620.
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T. Zhou, D. A. Drummond, C. O. Wilke (2008). Contact density affects protein evolutionary rate from bacteria to animals. J. Mol. Evol. 66:395–404.
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R. N. Dutta, I. M. Rouzine, S. D. Smith, C. O. Wilke, I. S. Novella (2008). Rapid adaptive amplification of preexisting variation in an RNA virus. J. Virol. 82:4354–4362.
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A. R. Sedaghat, J. B. Dinoso, L. Shen, C. O. Wilke, 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.
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J. J. Bull, R. Sanjuán, 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.
I. M. Rouzine, É. Brunet, C. O. Wilke (2008). The traveling-wave approach to asexual evolution: Muller's ratchet and speed of adaptation. Theor. Popul. Biol. 73:24–46.
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A. R. Sedaghat, R. F. Siliciano, 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.
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A. R. Sedaghat, J. D. Siliciano, T. P. Brennan, C. O. Wilke, R. F. Siliciano (2007). Limits on replenishment of the resting CD4+ T cell reservoir for HIV in patients on HAART. PLoS Pathogens 3:e122.
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R. Forster, C. O. Wilke (2007). Frequency-dependent selection in a periodic environment. Physica A 381:255–264.
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J. J. Bull, R. Sanjuán, C. O. Wilke (2007). Theory of lethal mutagenesis for viruses. J. Virol. 81:2930–2939.
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J. D. Bloom, F. H. Arnold, C. O. Wilke (2007). Breaking proteins with mutations: threads and thresholds in evolution. Mol. Syst. Biol. 3:76.
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S. F. Elena, C. O. Wilke, C. Ofria, R. E. Lenski (2007). Effects of population size and mutation rate on the evolution of mutational robustness. Evolution 61:666–674.
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J. D. Bloom, A. Raval, C. O. Wilke (2007). Thermodynamics of neutral protein evolution. Genetics 175:255–266.
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R. Forster, C. Adami, C. O. Wilke (2006). Selection for mutational robustness in finite populations. J. Theor. Biol. 243:181–190.
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J. D. Bloom, D. A. Drummond, F. H. Arnold, C. O. Wilke (2006). Structural determinants of the rate of protein evolution in yeast. Mol. Biol. Evol. 23:1751–1761.
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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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C. O. Wilke, D. A. Drummond (2006). Population genetics of translational robustness. Genetics 173:473–481.
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D. A. Drummond, A. Raval, C. O. Wilke (2006). A single determinant dominates the rate of yeast protein evolution. Mol. Biol. Evol. 23:327–337.
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C. O. Wilke (2006). Biology through the robustness lens. BioScience 56:695–696.
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C. O. Wilke, R. Forster, I. S. Novella (2006). Quasispecies in time-dependent environments. Curr. Topics Microbiol. Immun. 299:33–50.
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C. Ofria, 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.
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C. O. Wilke, 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.


R. Forster, C. O. Wilke (2005). Tradeoff between short-term and long-term adaptation in a changing environment. Phys. Rev. E 72:041922.
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C. O. Wilke, J. D. Bloom, D. A. Drummond, A. Raval (2005). Predicting the tolerance of proteins to random amino acid substitution. Biophys. J. 89:3714–3720.
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C. O. Wilke (2005). Molecular clocks: the heavy, the cold, and the slow. Heredity 95:115.
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D. A. Drummond, J. D. Bloom, C. Adami, C. O. Wilke, F. H. Arnold (2005). Why highly expressed proteins evolve slowly. Proc. Natl. Acad. Sci. USA 102:14338–14343.
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C. O. Wilke (2005). Quasispecies theory in the context of population genetics. BMC Evol. Biol. 5:44.
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D. A. Drummond, J. J. Silberg, M. M. Meyer, C. O. Wilke, F. H. Arnold (2005). On the conservative nature of intragenic recombination. Proc. Natl. Acad. Sci. USA 102:5380–5385.
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J. D. Bloom, J. J. Silberg, C. O. Wilke, D. A. Drummond, C. Adami, F. H. Arnold (2005). Thermodynamic prediction of protein neutrality. Proc. Natl. Acad. Sci. USA 102:606–611.
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C. O. Wilke (2004). Molecular clock in neutral protein evolution. BMC Genetics 5:25.
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S. S. Chow, C. O. Wilke, C. Ofria, R. E. Lenski, C. Adami (2004). Adaptive radiation from resource competition in digital organisms. Science 305:84–86.
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R. Froissart, C. O. Wilke, R. Montville, S. K. Remold, L. Chao, P. E. Turner (2004). Co-infection weakens selection against epistatic mutations in RNA viruses. Genetics 168:9–19.
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C. O. Wilke (2004). Supplementary materials need the right format. Nature 430:291.
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C. O. Wilke (2004). The speed of adaptation in large asexual populations. Genetics 167:2045–2053.
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J. D. Bloom, C. O. Wilke, F. H. Arnold, C. Adami (2004). Stability and the evolvability of function in a model protein. Biophys. J. 86:2758–2764.
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I. S. Novella, D. D. Reissig, C. O. Wilke (2004). Density-dependent selection in vesicular stomatitis virus. J. Virol. 78:5799–5804.
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C. O. Wilke, D. D. Reissig, I. S. Novella (2004). Replication at periodically changing multiplicity of infection promotes stable coexistence of competing viral populations. Evolution 58:900–905.
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C. Adami, C. O. Wilke (2004). Experiments in digital evolution. Artificial Life 10:117–122.
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Y. Li, C. O. Wilke (2004). Digital evolution in time-dependent fitness landscapes. Artificial Life 10:123–134.
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T. J. Johnson, C. O. Wilke (2004). Evolution of resource competition between mutually dependent digital organisms. Artificial Life 10:145–156.
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C. Ofria, C. O. Wilke (2004). Avida: A software platform for research in computational evolutionary biology. Artificial Life 10:191–229.
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P. R. A. Campos, C. Adami, 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.
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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 (2003). Does the Red Queen reign in the kingdom of digital organisms? Lect. Notes. Artif. Int. 2801:405–414.
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C. O. Wilke (2003). Probability of fixation of an advantageous mutant in a viral quasispecies. Genetics 163:467–474.
C. O. Wilke, R. E. Lenski, C. Adami (2003). Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding. BMC Evolutionary Biology 3:3.
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C. O. Wilke, C. Adami (2003). Evolution of mutational robustness. Mut. Res. 522:3–11.
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C. Kamp, C. O. Wilke, C. Adami, S. Bornholdt (2002). Viral evolution under the pressure of an adaptive immune system – optimal mutation rates for viral escape. Complexity 8:28–33.
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C. O. Wilke, C. Adami (2002). The biology of digital organisms. Trends. Ecol. Evol. 17:528–532.
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C. O. Wilke, P. R. A. Campos, J. F. Fontanari (2002). Genealogical process on a correlated fitness landscape. J. Exp. Zool. 294:274–284.
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C. O. Wilke (2002). Maternal effects in molecular evolution. Phys. Rev. Lett. 88:078101.
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P. R. A. Campos, C. Adami, C. O. Wilke (2002). Optimal adaptive performance and delocalization in NK fitness landscapes. Physica A 304:495–506.
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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, J. L. Wang, C. Ofria, R. E. Lenski, C. Adami (2001). Evolution of digital organisms at high mutation rate leads to survival of the flattest. Nature 412:331–333.
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C. Ronnewinkel, C. O. Wilke, 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.
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C. O. Wilke (2001). Adaptive evolution on neutral networks. Bull. Math. Biol. 63:715–730.
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C. O. Wilke, C. Adami (2001). Interaction between directional epistasis and average mutational effects. Proc. R. Soc. London B 268:1469–1474.
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C. O. Wilke, C. Ronnewinkel, T. Martinetz (2001). Dynamic fitness landscapes in molecular evolution. Phys. Rep. 349:395–446.
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C. O. Wilke, C. Ronnewinkel (2001). Dynamic fitness landscapes: Expansions for small mutation rates. Physica A 290:475–490.
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C. O. Wilke (2000). Dynamische Fitnesslandschaften. KI 14:20–25 (in german).


C. O. Wilke, T. Martinetz (1999). Adaptive walks on time-dependent fitness landscapes. Phys. Rev. E 60:2154–2159.
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C. O. Wilke, T. Martinetz (1999). Lifetimes of agents under external stress. Phys. Rev. E Rapid Communications 59:R2512–R2515.
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C. O. Wilke, C. Ronnewinkel, T. Martinetz (1999). Molecular evolution in time dependent environments. Lect. Notes. Artif. Int. 1674:417–421.
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C. Wilke, T. Martinetz (1998). Hierarchical noise in large systems of independent agents. Phys. Rev. E 58:7101–7108.
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C. Wilke, S. Altmeyer, T. Martinetz (1998). Aftershocks in coherent-noise models. Physica D 120:401–417.
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S. Altmeyer, C. Wilke, 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.
C. Wilke, S. Altmeyer, 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.


C. Wilke, T. Martinetz (1997). Simple model of evolution with variable system size. Phys. Rev. E 56:7128–7131.
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M. Kachelrieß, C. Wilke, G. Wunner (1997). Axion cyclotron emissivity of magnetized white dwarfs and neutron stars. Phys. Rev. D 56:1313–1319.
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