Publications

preprint

205.
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.
doi: 10.48550/arXiv.2309.08765
204.
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.
doi: 10.1101/2023.07.28.551017
203.
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.
doi: 10.48550/arXiv.2305.16330
202.
M. M. Johnson, C. O. Wilke (preprint). Recombination rate inference via deep learning is limited by sequence diversity. bioRxiv 498489.
doi: 10.1101/2022.07.01.498489
201.
A. J. Hockenberry, D. C. Weaver, C. O. Wilke (preprint). Virulent but not temperate bacteriophages display hallmarks of rapid translation initiation. bioRxiv 440840.
doi: 10.1101/2021.04.21.440840
200.
D. K. Sydykova, C. O. Wilke (preprint). Theory of measurement for site-specific evolutionary rates in amino-acid sequences. bioRxiv 411025.
doi: 10.1101/411025

2023

199.
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.
doi: 10.1038/s41598-023-40247-w
198.
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
197.
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.
doi: https://doi.org/10.1016/j.sbi.2022.102518
196.
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

2022

195.
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.
doi: https://doi.org/10.1128/aem.01486-22
194.
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.
doi: 10.1371/journal.pone.0268883
pmcid: PMC9135205

2021

193.
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.
doi: 10.1073/pnas.2112279118
pmcid: PMC8670466
192.
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.
doi: 10.1007/s10867-021-09593-6
pmcid: PMC8603988
191.
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.
doi: 10.21105/joss.03678
pmcid: PMC9017871
190.
A. J. Hockenberry, C. O. Wilke (2021). BACPHLIP: Predicting bacteriophage lifestyle from conserved protein domains. PeerJ 9:e11396.
doi: 10.7717/peerj.11396
pmcid: PMC8106911
189.
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
188.
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
pmcid: PMC7888580

2020

187.
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.
doi: 10.1128/mSphere.01014-20
pmcid: PMC7729259
186.
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.
doi: 10.18637/jss.v096.i01
185.
M. M. Johnson, C. O. Wilke (2020). Site-specific amino acid distributions follow a universal shape. J. Mol. Evol. 88:731–741.
doi: 10.1007/s00239-020-09976-8
pmcid: PMC7717668
184.
C. O. Wilke, C. T. Bergstrom (2020). Predicting an epidemic trajectory is difficult. Proc. Natl. Acad. Sci. USA 117:28549–28551.
doi: 10.1073/pnas.2020200117
pmcid: PMC7682412
183.
C. D. DuPai, C. O. Wilke, B. W. Davies (2020). A comprehensive co-expression network analysis in Vibrio cholerae. mSystems 5:e00550-20.
doi: 10.1128/mSystems.00550-20
pmcid: PMC7343309
182.
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
181.
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.
doi: 10.1371/journal.pbio.3000627
pmcid: PMC7259792
180.
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

2019

179.
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.
doi: 10.1093/ve/vez055
pmcid: PMC6938266
178.
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.
doi: 10.21105/joss.01686
177.
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.
doi: 10.1126/sciadv.aax4761
pmcid: PMC6821460
176.
A. J. Hockenberry, C. O. Wilke (2019). Phylogenetic weighting does little to improve the accuracy of evolutionary coupling analyses. Entropy 21:1000.
doi: 10.3390/e21101000
pmcid: PMC6818970
175.
A. J. Hockenberry, C. O. Wilke (2019). Evolutionary couplings detect side-chain interactions. PeerJ 7:e7280.
doi: 10.7717/peerj.7280
pmcid: PMC6622159
174.
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.
doi: 10.1093/ve/vez016
pmcid: PMC6599686
173.
B. R. Jack, C. O. Wilke (2019). Pinetree: a step-wise gene expression simulator with codon-specific translation rates. Bioinformatics 35:4176–4178.
doi: 10.1093/bioinformatics/btz203
pmcid: PMC6792109
172.
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

2018

171.
M. U. Caglar, A. J. Hockenberry, C. O. Wilke (2018). Predicting bacterial growth conditions from mRNA and protein abundances. PLoS ONE 13:e0206634.
doi: 10.1371/journal.pone.0206634
pmcid: PMC6214550
170.
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.
doi: 10.1093/molbev/msy150
pmcid: PMC6188533
169.
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.
doi: 10.3390/genes9080409
pmcid: PMC6115872
168.
M. L. Paff, B. R. Jack, B. L. Smith, J. J. Bull, C. O. Wilke (2018). Combinatorial approaches to viral attenuation. mSystems 3:e00046.
doi: 10.1128/mSystems.00046-18
pmcid: PMC6068830
167.
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.
doi: 10.1128/mBio.01222-18
pmcid: PMC6030557
166.
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.
doi: 10.1186/s12864-018-4869-5
pmcid: PMC6042521
165.
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.
doi: 10.1534/genetics.118.300699
pmcid: PMC5887137
164.
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.
doi: 10.12688/f1000research.12874.2
pmcid: PMC5676193
163.
M. U. Caglar, A. I. Teufel, C. O. Wilke (2018). Sicegar: R package for sigmoidal and double-sigmoidal curve fitting. PeerJ 6:e4251.
doi: 10.7717/peerj.4251
pmcid: PMC5774301
162.
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

2017

161.
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
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
pmcid: PMC5511007
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 7:2957–2968.
doi: 10.1534/g3.117.041020
pmcid: PMC5592923
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
pmcid: PMC5452972
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
pmcid: PMC5800964
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
pmcid: PMC5394689
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
pmcid: PMC5398280
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
pmcid: PMC5392934
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
pmcid: PMC5378326
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
pmcid: PMC5332577

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
pmcid: PMC5292938
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

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 Evol. 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

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

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.
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C. O. Wilke (2001). Adaptive evolution on neutral networks. Bull. Math. Biol. 63:715–730.
doi: 10.1006/bulm.2001.0244
14.
C. O. Wilke, C. Adami (2001). Interaction between directional epistasis and average mutational effects. Proc. R. Soc. London B 268:1469–1474.
doi: 10.1098/rspb.2001.1690
13.
C. O. Wilke, C. Ronnewinkel, T. Martinetz (2001). Dynamic fitness landscapes in molecular evolution. Phys. Rep. 349:395–446.
doi: 10.1016/S0370-1573(00)00118-6
12.
C. O. Wilke, C. Ronnewinkel (2001). Dynamic fitness landscapes: Expansions for small mutation rates. Physica A 290:475–490.
doi: 10.1016/S0378-4371(00)00585-9

2000

11.
C. O. Wilke (2000). Dynamische Fitnesslandschaften. KI 14:20–25 (in german).

1999

10.
C. O. Wilke, T. Martinetz (1999). Adaptive walks on time-dependent fitness landscapes. Phys. Rev. E 60:2154–2159.
doi: 10.1103/PhysRevE.60.2154
9.
C. O. Wilke, T. Martinetz (1999). Lifetimes of agents under external stress. Phys. Rev. E Rapid Communications 59:R2512–R2515.
doi: 10.1103/PhysRevE.59.R2512
8.
C. O. Wilke, C. Ronnewinkel, T. Martinetz (1999). Molecular evolution in time dependent environments. Lect. Notes. Artif. Int. 1674:417–421.
doi: 10.1007/3-540-48304-7_57

1998

7.
C. Wilke, T. Martinetz (1998). Hierarchical noise in large systems of independent agents. Phys. Rev. E 58:7101–7108.
doi: 10.1103/PhysRevE.58.7101
6.
C. Wilke, S. Altmeyer, T. Martinetz (1998). Aftershocks in coherent-noise models. Physica D 120:401–417.
doi: 10.1016/S0167-2789(98)00092-X
5.
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.
4.
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.

1997

3.
C. Wilke, T. Martinetz (1997). Simple model of evolution with variable system size. Phys. Rev. E 56:7128–7131.
doi: 10.1103/PhysRevE.56.7128
2.
M. Kachelrieß, C. Wilke, G. Wunner (1997). Axion cyclotron emissivity of magnetized white dwarfs and neutron stars. Phys. Rev. D 56:1313–1319.
doi: 10.1103/PhysRevD.56.1313
1.
C. Wilke, G. Wunner (1997). Photon splitting in strong magnetic fields: asymptotic approximation formulae vs. accurate numerical results. Phys. Rev. D 55:997–1000.
doi: 10.1103/PhysRevD.55.997