The Wilke Lab
Publications People Software

Publications

preprint

212.
B. Allman, L. Vieira, D. J. Diaz, C. O. Wilke (preprint). A systematic evaluation of the language-of-viral-escape model using multiple machine learning frameworks. bioRxiv 611278.
doi: 10.1101/2024.09.04.611278
211.
A. L. Feller, C. O. Wilke (preprint). Peptide-specific chemical language model successfully predicts membrane diffusion of cyclic peptides. bioRxiv 607221.
doi: 10.1101/2024.08.09.607221
210.
A. M. Hill, T. A. Ingle, C. O. Wilke (preprint). A computational model for bacteriophage ϕX174 gene expression. bioRxiv 586356.
doi: 10.1101/2024.03.22.586356
209.
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
208.
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
207.
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

2024

206.
A. V. Kulikova, J. K. Parker, B. W. Davies, C. O. Wilke (2024). Semantic search using protein large language models detects class II microcins in bacterial genomes. mSystems, in press.
doi: 10.1101/2023.11.15.567263
205.
K. Hu, C.-W. Chou, C. O. Wilke, I. J. Finkelstein (2024). Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons. Nature Commun. 15:6653.
doi: 10.1038/s41467-024-50816-w
pmcid: PMC11300857
204.
J. R. Randall, L. C. Vieira, C. O. Wilke, B. W. Davies (2024). Deep mutational scanning and machine learning for the analysis of antimicrobial-peptide features driving membrane selectivity. Nature Biomed. Eng. 8:842–853.
doi: 10.1038/s41551-024-01243-1
203.
C. O. Wilke (2024). The biophysical landscape of viral evolution. PNAS 121:e2409667121.
doi: 10.1073/pnas.2409667121
pmcid: PMC11228502
202.
M. M. Reimert, J. D. Parry, M. Denwood, M. K. Gussmann, C. O. Wilke, I. Kosenkov, M. Milton, A. Thomason (2024). extendr: Frictionless bindings for R and Rust. Journal of Open Source Software 9:6394.
doi: 10.21105/joss.06394
201.
C. W. Kosonocky, C. O. Wilke, E. M. Marcotte, A. D. Ellington (2024). Mining patents with large language models elucidates the chemical function landscape. Digital Discovery 3:1150–1159.
doi: 10.1039/D4DD00011K
pmcid: PMC11167698

2023

200.
C. W. Kosonocky, A. L. Feller, C. O. Wilke, A. D. Ellington (2023). Using alternative SMILES representations to identify novel functional analogues in chemical similarity vector searches. Patterns 4:100865.
doi: 10.1016/j.patter.2023.100865
pmcid: PMC10724362
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
pmcid: PMC10432456
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
pmcid: PMC9908841
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
pmcid: PMC9833666

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
pmcid: PMC9746304
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.
C. Lee, R. A. Harris, J. K. Wall, R. D. Mayfield, C. O Wilke (2013). RNaseIII and T4 Polynucleotide Kinase sequence biases and solutions during RNA-seq library construction. Biology Direct 8:16.
doi: 10.1186/1745-6150-8-16
pmcid: PMC3710281
115.
M. Z. Tien, D. K. Sydykova, A. G. Meyer, C. O. Wilke (2013). PeptideBuilder: A simple Python library to generate model peptides. PeerJ 1:e80.
doi: 10.7717/peerj.80
pmcid: PMC3661355
114.
S. J. Spielman, C. O. Wilke (2013). Membrane environment imposes unique selection pressures on transmembrane domains of G protein-coupled receptors. J. Mol. Evol. 76:172–182.
doi: 10.1007/s00239-012-9538-8
pmcid: PMC3712645
113.
A. G. Meyer, E. T. Dawson, C. O. Wilke (2013). Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin. Phil. Trans. R. Soc. B. 368:20120334.
doi: 10.1098/rstb.2012.0334
pmcid: PMC3678335
112.
A. G. Meyer, C. O. Wilke (2013). Integrating sequence variation and protein structure to identify sites under selection. Mol. Biol. Evol. 30:36–44.
doi: 10.1093/molbev/mss217
pmcid: PMC3525147

2012

111.
M. P. Scherrer, A. G. Meyer, C. O. Wilke (2012). Modeling coding-sequence evolution within the context of residue solvent accessibility. BMC Evol. Biol. 12:179.
doi: 10.1186/1471-2148-12-179
pmcid: PMC3527230
110.
J. J. Bull, I. J. Molineux, C. O. Wilke (2012). Slow fitness recovery in a codon-modified viral genome. Mol. Biol. Evol. 29:2997–3004.
doi: 10.1093/molbev/mss119
pmcid: PMC3457771
109.
A. R. Sedaghat, S. T. Gray, C. O. Wilke, D. S. Caradonna (2012). Risk factors for development of chronic rhinosinusitis in patients with allergic rhinitis. Int. Forum Allergy Rhinol. 2:370–375.
doi: 10.1002/alr.21055
108.
T. E. Keller, C. O. Wilke, J. J. Bull (2012). Interactions between evolutionary processes at high mutation rates. Evolution 66:2303–2314.
doi: 10.1111/j.1558-5646.2012.01596.x
pmcid: PMC3389706
107.
C. O. Wilke (2012). Bringing molecules back into molecular evolution. PLoS Comp. Biol. 8:e1002572.
doi: 10.1371/journal.pcbi.1002572
pmcid: PMC3386153
106.
A. W. Covert III, J. Carlson-Stevermer, D. Z. Derryberry, C. O. Wilke (2012). The role of deleterious mutations in the adaptation to a novel envrionment. In Proceedings of the Thirteenth International Conference on the Simulation and Synthesis of Living Systems, C. Adami, D. M. Bryson, C. Ofria and R. T. Pennock, eds., pp. 27–31. MIT Press.
doi: 10.7551/978-0-262-31050-5-ch004
105.
A. W. Covert III, L. Smith, D. Z. Derryberry, C. O. Wilke (2012). What does sex have to do with it: tracking the fate of deleterious mutations in sexual populations. In Proceedings of the Thirteenth International Conference on the Simulation and Synthesis of Living Systems, C. Adami, D. M. Bryson, C. Ofria and R. T. Pennock, eds., pp. 32–36. MIT Press.
doi: 10.7551/978-0-262-31050-5-ch005
104.
T. E. Keller, S. D. Mis, K. E. Jia, C. O. Wilke (2012). Reduced mRNA secondary-structure stability near the start codon indicates functional genes in prokaryotes. Genome Biol. Evol. 4:80–88.
doi: 10.1093/gbe/evr129
pmcid: PMC3269970
103.
D. Wang, M. K. Markey, C. O. Wilke, A. Arapostathis (2012). Eigen-genomic System Dynamic-pattern Analysis (ESDA): Modeling mRNA degradation and self-regulation. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9:430–437.
doi: 10.1109/TCBB.2011.150
102.
D. Wang, A. Arapostathis, C. O. Wilke, M. K. Markey (2012). Principal-oscillation-pattern analysis of gene expression. PLOS ONE 7:e28805.
doi: 10.1371/journal.pone.0028805
pmcid: PMC3254616

2011

101.
I. S. Novella, J. B. Presloid, S. D. Smith, C. O. Wilke (2011). Specific and nonspecific host adaptation during arboviral experimental evolution. J. Mol. Microbiol. Biotech. 21:71–81.
doi: 10.1159/000332752
pmcid: PMC3697271
100.
J. J. Bull, R. H. Heineman, C. O. Wilke (2011). The phenotype-fitness map in experimental evolution of phages. PLoS ONE 6:e27796.
doi: 10.1371/journal.pone.0027796
pmcid: PMC3222649
99.
A. R. Sedaghat, C. O. Wilke (2011). Kinetics of the viral cycle influence pharmacodynamics of antiretroviral therapy. Biology Direct 6:42.
doi: 10.1186/1745-6150-6-42
pmcid: PMC3203257
98.
C. O. Wilke (2011). Transcriptional robustness complements nonsense-mediated decay in humans. PLoS Genet. 7:e1002296.
doi: 10.1371/journal.pgen.1002296
pmcid: PMC3192817
97.
D. C. Ramsey, M. P. Scherrer, T. Zhou, C. O. Wilke (2011). The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Genetics 188:479–488.
doi: 10.1534/genetics.111.128025
pmcid: PMC3122320
96.
A. Spivak, A. Rabi, M. A. McMahon, L. Shan, A. R. Sedaghat, C. O. Wilke, R. Siliciano (2011). Dynamic constraints on the second phase compartment of HIV-infected cells. AIDS Res. Hum. Retroviruses 27:759–761.
doi: 10.1089/AID.2010.0199
pmcid: PMC3123527
95.
T. Zhou, C. O. Wilke (2011). Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses. BMC Evol. Biol. 11:59.
doi: 10.1186/1471-2148-11-59
pmcid: PMC3072339
94.
A. T. Ciota, E. M. Koch, G. G. Willsey, L. J. Davis, G. V. S. Jerzak, D. J. Ehrbar, C. O. Wilke, L. D. Kramer (2011). Temporal and spatial alterations in mutant swarm size of St. Louis encephalitis virus in mosquito hosts. Infection, Genetics and Evolution 11:460–468.
doi: 10.1016/j.meegid.2010.12.007
pmcid: PMC3251332
93.
E. B. O'Dea, C. O. Wilke (2011). Contact heterogeneity and phylodynamics: How contact networks shape parasite evolutionary trees. Interdiscip. Persp. Inf. Dis. 2011:238743.
doi: 10.1155/2011/238743
pmcid: PMC2995904

2010

92.
Y. Lee, T. Zhou, G. G. Tartaglia, M. Vendruscolo, C. O. Wilke (2010). Translationally optimal codons associate with aggregation-prone sites in proteins. Proteomics 10:4163–4171.
doi: 10.1002/pmic.201000229
pmcid: PMC3037288
91.
K. Pepin, I. Volkov, J. R. Banavar, C. O. Wilke, B. T. Grenfell (2010). Phenotypic differences in viral immune-escape explained by linking within-host dynamics to host-population immunity. J. Theor. Biol. 265:501–510.
doi: 10.1016/j.jtbi.2010.05.036
pmcid: PMC4537168
90.
T. Zhou, W. Gu, C. O. Wilke (2010). Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol. Biol. Evol. 27:1912–1922.
doi: 10.1093/molbev/msq077
pmcid: PMC2915641
89.
E. B. O'Dea, T. E. Keller, C. O. Wilke (2010). Does mutational robustness inhibit extinction by lethal mutagenesis in viral populations? PLoS Comp. Biol. 6:e1000811.
doi: 10.1371/journal.pcbi.1000811
pmcid: PMC2883602
88.
S. D. Smith-Tsurkan, C. O. Wilke, I. S. Novella (2010). Incongruent fitness landscapes, not tradeoffs, dominate the adaptation of VSV to novel host types. J. Gen. Virol. 91:1484–1493.
doi: 10.1099/vir.0.017855-0
pmcid: PMC2888165
87.
A. R. Sedaghat, D. A. Rastegar, K. A. O’Connell, J. B. Dinoso, C. O. Wilke, J. N. Blankson (2010). Is it time to treat HIV elite controllers with combined antiretroviral therapy? - Reply. Clinical Infectious Diseases 50:1425–1426.
doi: 10.1086/652285
86.
S. H. Steinmeyer, C. O. Wilke, K. M. Pepin (2010). Methods of modeling viral disease dynamics across the within- and between-host scales: The impact of virus dose on host population immunity. Phil. Trans. R. Soc. B 365:1931–1941.
doi: 10.1098/rstb.2010.0065
pmcid: PMC2880116
85.
I. S. Novella, J. B. Presloid, T. Zhou, S. D. Smith-Tsurkan, B. E. Ebendick-Corpus, R. N. Dutta, K. L. Lust, C. O. Wilke (2010). Genomic evolution of vesicular stomatitis virus strains with differences in adaptability. J. Virol. 84:4960–4968.
doi: 10.1128/JVI.00710-09
pmcid: PMC2863795
84.
C. O. Wilke, D. A. Drummond (2010). Signatures of protein biophysics in coding sequence evolution. Cur. Opin. Struct. Biol. 20:385–389.
doi: 10.1016/j.sbi.2010.03.004
pmcid: PMC2905607
83.
W. Gu, T. Zhou, C. O. Wilke (2010). A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput. Biol. 6:e1000664.
doi: 10.1371/journal.pcbi.1000664
pmcid: PMC2816680

2009

82.
D. A. Drummond, C. O. Wilke (2009). The evolutionary consequences of erroneous protein synthesis. Nature Reviews Genetics 10:715–724.
doi: 10.1038/nrg2662
pmcid: PMC2764353
81.
A. R. Sedaghat, D. A. Rastegar, K. A. O'Connell, J. B. Dionso, C. O. Wilke, J. N. Blankson (2009). T cell dynamics and the response to HAART in a cohort of HIV-1 infected elite suppressors. Clin. Inf. Diseases 49:1763–1766.
doi: 10.1086/648081
pmcid: PMC2783537
80.
S. H. Steinmeyer, C. O. Wilke (2009). Lethal mutagenesis in a structured environment. J. Theor. Biol. 261:67–73.
doi: 10.1016/j.jtbi.2009.07.014
pmcid: PMC2867491
79.
T. P. Brennan, J. O. Woods, A. R. Sedaghat, J. D. Siliciano, R. F. Siliciano, C. O. Wilke (2009). Analysis of HIV-1 viremia and provirus in resting CD4+ T cells reveals a novel source of residual viremia in patients on antiretroviral therapy. J. Virol. 83:8470–8481.
doi: 10.1128/JVI.02568-08
pmcid: PMC2738142
78.
C. Ofria, D. M. Bryson, C. O. Wilke (2009). Avida: Evolution experiments with self-replicating computer programs. In A. Adamatzky and M. Komosinski, eds. Artificial Life Models in Software, 2nd ed. Springer, pp. 3–35.
doi: 10.1007/978-1-84882-285-6_1
77.
T. Zhou, M. Weems, C. O. Wilke (2009). Translationally optimal codons associate with structurally sensitive sites in proteins. Mol. Biol. Evol. 26:1571–1580.
doi: 10.1093/molbev/msp070
pmcid: PMC2734146
76.
A. R. Sedaghat, R. F. Siliciano, C. O. Wilke (2009). Constraints on the dominant mechanism for HIV viral dynamics in patients on raltegravir. Antiviral Therapy 14:263–271.
pmcid: PMC2980788

2008

75.
T. Zhou, P. J. Enyeart, C. O. Wilke (2008). Detecting clusters of mutations. PLoS ONE 3:e3765.
doi: 10.1371/journal.pone.0003765
pmcid: PMC2582452
74.
I. S. Novella, R. N. Dutta, C. O. Wilke (2008). A linear relationship between fitness and log critical bottleneck size in vesicular stomatitis virus. J. Virol. 82:12589–12590.
doi: 10.1128/JVI.01394-08
pmcid: PMC2593322
73.
J. J. Bull, C. O. Wilke (2008). Lethal mutagenesis of bacteria. Genetics 180:1061–1070.
doi: 10.1534/genetics.108.091413
pmcid: PMC2567356
72.
D. A. Drummond, C. O. Wilke (2008). Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341–352.
doi: 10.1016/j.cell.2008.05.042
pmcid: PMC2696314
71.
D. J. Whitehead, C. O. Wilke, D. Vernazobres, E. Bornberg-Bauer (2008). The look-ahead effect of phenotypic mutations. Biology Direct 3:18.
doi: 10.1186/1745-6150-3-18
pmcid: PMC2423361
70.
É. Brunet, I. M. Rouzine, C. O. Wilke (2008). The stochastic edge in adaptive evolution. Genetics 179:603–620.
doi: 10.1534/genetics.107.079319
pmcid: PMC2390637
69.
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.
doi: 10.1007/s00239-008-9094-4
68.
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.
doi: 10.1128/JVI.02446-07
pmcid: PMC2293023
67.
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.
doi: 10.1073/pnas.0711372105
pmcid: PMC2290747
66.
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.
65.
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.
doi: 10.1016/j.tpb.2007.10.004
pmcid: PMC2246079
64.
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.
doi: 10.1186/1471-2334-8-2
pmcid: PMC2254415

2007

63.
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.
doi: 10.1371/journal.ppat.0030122
pmcid: PMC1959378
62.
R. Forster, C. O. Wilke (2007). Frequency-dependent selection in a periodic environment. Physica A 381:255–264.
doi: 10.1016/j.physa.2007.03.017
pmcid: PMC2031831
61.
J. J. Bull, R. Sanjuán, C. O. Wilke (2007). Theory of lethal mutagenesis for viruses. J. Virol. 81:2930–2939.
doi: 10.1128/JVI.01624-06
pmcid: PMC1865999
60.
J. D. Bloom, F. H. Arnold, C. O. Wilke (2007). Breaking proteins with mutations: threads and thresholds in evolution. Mol. Syst. Biol. 3:76.
doi: 10.1038/msb4100119
pmcid: PMC1800353
59.
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.
doi: 10.1111/j.1558-5646.2007.00064.x
58.
J. D. Bloom, A. Raval, C. O. Wilke (2007). Thermodynamics of neutral protein evolution. Genetics 175:255–266.
doi: 10.1534/genetics.106.061754
pmcid: PMC1775007

2006

57.
R. Forster, C. Adami, C. O. Wilke (2006). Selection for mutational robustness in finite populations. J. Theor. Biol. 243:181–190.
doi: 10.1016/j.jtbi.2006.06.020
56.
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.
doi: 10.1093/molbev/msl040
55.
J. R. Bailey, A. R. Sedaghat, T. Kieffer, T. Brennan, P. K. Lee, M. Wind-Rotolo, C. M. Haggerty, A. R. Kamireddi, Y. Liu, J. Lee, D. Persaud, J. E. Gallant, J. Cofrancesco, Jr., T. C. Quinn, C. O. Wilke, S. C. Ray, J. D. Siliciano, R. E. Nettles, R. F. Siliciano (2006). Residual Human Immunodeficiency Virus Type 1 viremia in some patients on antiretroviral therapy is dominated by a small number of invariant clones rarely found in circulating CD4 T cells. J. Virol. 80:6441–6457.
doi: 10.1128/JVI.00591-06
pmcid: PMC1488985
54.
C. O. Wilke, D. A. Drummond (2006). Population genetics of translational robustness. Genetics 173:473–481.
doi: 10.1534/genetics.105.051300
pmcid: PMC1461446
53.
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.
doi: 10.1093/molbev/msj038
52.
C. O. Wilke (2006). Biology through the robustness lens. BioScience 56:695–696.
doi: 10.1641/0006-3568(2006)56[695:RAEILS]2.0.CO;2
51.
C. O. Wilke, R. Forster, I. S. Novella (2006). Quasispecies in time-dependent environments. Curr. Topics Microbiol. Immun. 299:33–50.
doi: 10.1007/3-540-26397-7_2
50.
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.
doi: 10.1007/1-84628-214-4_1
49.
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.

2005

48.
R. Forster, C. O. Wilke (2005). Tradeoff between short-term and long-term adaptation in a changing environment. Phys. Rev. E 72:041922.
doi: 10.1103/PhysRevE.72.041922
47.
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.
doi: 10.1529/biophysj.105.062125
pmcid: PMC1366941
46.
C. O. Wilke (2005). Molecular clocks: the heavy, the cold, and the slow. Heredity 95:115.
doi: 10.1038/sj.hdy.6800681
45.
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.
doi: 10.1073/pnas.0504070102
pmcid: PMC1242296
44.
C. O. Wilke (2005). Quasispecies theory in the context of population genetics. BMC Evol. Biol. 5:44.
doi: 10.1186/1471-2148-5-44
pmcid: PMC1208876
43.
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.
doi: 10.1073/pnas.0500729102
pmcid: PMC556249
42.
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.
doi: 10.1073/pnas.0406744102
pmcid: PMC545518

2004

41.
C. O. Wilke (2004). Molecular clock in neutral protein evolution. BMC Genetics 5:25.
doi: 10.1186/1471-2156-5-25
pmcid: PMC517495
40.
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.
doi: 10.1126/science.1096307
39.
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.
doi: 10.1534/genetics.104.030205
pmcid: PMC1448111
38.
C. O. Wilke (2004). Supplementary materials need the right format. Nature 430:291.
doi: 10.1038/430291c
37.
C. O. Wilke (2004). The speed of adaptation in large asexual populations. Genetics 167:2045–2053.
doi: 10.1534/genetics.104.027136
pmcid: PMC1470994
36.
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.
doi: 10.1016/S0006-3495(04)74329-5
pmcid: PMC1304146
35.
I. S. Novella, D. D. Reissig, C. O. Wilke (2004). Density-dependent selection in vesicular stomatitis virus. J. Virol. 78:5799–5804.
doi: 10.1128/JVI.78.11.5799-5804.2004
pmcid: PMC415817
34.
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.
doi: 10.1111/j.0014-3820.2004.tb00422.x
33.
C. Adami, C. O. Wilke (2004). Experiments in digital evolution. Artificial Life 10:117–122.
doi: 10.1162/106454604773563540
32.
Y. Li, C. O. Wilke (2004). Digital evolution in time-dependent fitness landscapes. Artificial Life 10:123–134.
doi: 10.1162/106454604773563559
31.
T. J. Johnson, C. O. Wilke (2004). Evolution of resource competition between mutually dependent digital organisms. Artificial Life 10:145–156.
doi: 10.1162/106454604773563577
30.
C. Ofria, C. O. Wilke (2004). Avida: A software platform for research in computational evolutionary biology. Artificial Life 10:191–229.
doi: 10.1162/106454604773563612
29.
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.
doi: 10.1007/978-3-642-18734-6_2

2003

28.
C. O. Wilke, I. S. Novella (2003). Phenotypic mixing and hiding may contribute to memory in viral quasispecies. BMC Microbiology 3:11.
doi: 10.1186/1471-2180-3-11
27.
C. O. Wilke (2003). Does the Red Queen reign in the kingdom of digital organisms? Lect. Notes. Artif. Int. 2801:405–414.
doi: 10.1007/978-3-540-39432-7_43
26.
C. O. Wilke (2003). Probability of fixation of an advantageous mutant in a viral quasispecies. Genetics 163:467–474.
25.
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.
doi: 10.1186/1471-2148-3-3
24.
C. O. Wilke, C. Adami (2003). Evolution of mutational robustness. Mut. Res. 522:3–11.
doi: 10.1016/S0027-5107(02)00307-X

2002

23.
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.
doi: 10.1002/cplx.10067
22.
C. O. Wilke, C. Adami (2002). The biology of digital organisms. Trends. Ecol. Evol. 17:528–532.
doi: 10.1016/S0169-5347(02)02612-5
21.
C. O. Wilke, P. R. A. Campos, J. F. Fontanari (2002). Genealogical process on a correlated fitness landscape. J. Exp. Zool. 294:274–284.
doi: 10.1002/jez.10146
20.
C. O. Wilke (2002). Maternal effects in molecular evolution. Phys. Rev. Lett. 88:078101.
doi: 10.1103/PhysRevLett.88.078101
19.
P. R. A. Campos, C. Adami, C. O. Wilke (2002). Optimal adaptive performance and delocalization in NK fitness landscapes. Physica A 304:495–506.
doi: 10.1016/S0378-4371(01)00572-6

2001

18.
C. O. Wilke (2001). Selection for fitness vs. selection for robustness in RNA secondary structure folding. Evolution 55:2412–2420.
doi: 10.1111/j.0014-3820.2001.tb00756.x
17.
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.
doi: 10.1038/35085569
16.
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.
doi: 10.1007/978-3-662-04448-3_13
15.
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