| Year |
Citation |
Score |
| 2021 |
Teufel AI, Liu W, Draghi JA, Cameron CE, Wilke CO. Modeling poliovirus replication dynamics from live time-lapse single-cell imaging data. Scientific Reports. 11: 9622. PMID 33953215 DOI: 10.1038/s41598-021-87694-x |
0.728 |
|
| 2020 |
Zhang Y, Moy AJ, Feng X, Nguyen HTM, Sebastian KR, Reichenberg JS, Wilke CO, Markey MK, Tunnell JW. Assessment of Raman Spectroscopy for Reducing Unnecessary Biopsies for Melanoma Screening. Molecules (Basel, Switzerland). 25. PMID 32575717 DOI: 10.3390/Molecules25122852 |
0.427 |
|
| 2020 |
Laurent JM, Garge RK, Teufel AI, Wilke CO, Kachroo AH, Marcotte EM. Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs. Plos Biology. 18: e3000627. PMID 32421706 DOI: 10.1371/Journal.Pbio.3000627 |
0.718 |
|
| 2020 |
Sydykova DK, LaBar T, Adami C, Wilke CO. Moderate Amounts of Epistasis are Not Evolutionarily Stable in Small Populations. Journal of Molecular Evolution. PMID 32350572 DOI: 10.1007/S00239-020-09942-4 |
0.79 |
|
| 2018 |
Teufel AI, Johnson MM, Laurent JM, Kachroo AH, Marcotte EM, Wilke CO. The many nuanced evolutionary consequences of duplicated genes. Molecular Biology and Evolution. PMID 30445614 DOI: 10.1093/Molbev/Msy216 |
0.744 |
|
| 2018 |
Teufel AI, Johnson MM, Laurent JM, Kachroo AH, Marcotte EM, Wilke CO. The many nuanced evolutionary consequences of duplicated genes. Molecular Biology and Evolution. PMID 30428072 DOI: 10.1093/Molbev/Msy210 |
0.744 |
|
| 2018 |
Teufel AI, Ritchie AM, Wilke CO, Liberles DA. Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences. Genes. 9. PMID 30104502 DOI: 10.3390/Genes9080409 |
0.803 |
|
| 2018 |
Jiang Q, Teufel AI, Jackson EL, Wilke CO. Beyond Thermodynamic Constraints: Evolutionary Sampling Generates Realistic Protein Sequence Variation. Genetics. PMID 29382650 DOI: 10.1534/genetics.118.300699 |
0.752 |
|
| 2018 |
Caglar MU, Teufel AI, Wilke CO. Sicegar: R package for sigmoidal and double-sigmoidal curve fitting. Peerj. 6: e4251. PMID 29362694 DOI: 10.7717/peerj.4251 |
0.713 |
|
| 2017 |
Chapman SD, Adami C, Wilke CO, B Kc D. The evolution of logic circuits for the purpose of protein contact map prediction. Peerj. 5: e3139. PMID 28439455 DOI: 10.7717/Peerj.3139 |
0.469 |
|
| 2017 |
Jackson EL, Spielman SJ, Wilke CO. Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein. Plos One. 12: e0164905. PMID 28369116 DOI: 10.1371/journal.pone.0164905 |
0.301 |
|
| 2017 |
Echave J, Wilke CO. Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence. Annual Review of Biophysics. PMID 28301766 DOI: 10.1146/annurev-biophys-070816-033819 |
0.32 |
|
| 2017 |
Teufel AI, Wilke CO. Accelerated simulation of evolutionary trajectories in origin-fixation models. Journal of the Royal Society, Interface. 14. PMID 28228542 DOI: 10.1098/rsif.2016.0906 |
0.722 |
|
| 2016 |
McWhite CD, Meyer AG, Wilke CO. Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza virus H3N2 hemagglutinin. Virus Evolution. 2. PMID 27713835 DOI: 10.1093/Ve/Vew026 |
0.633 |
|
| 2016 |
Jack BR, Meyer AG, Echave J, Wilke CO. Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes. Plos Biology. 14: e1002452. PMID 27138088 DOI: 10.1371/Journal.Pbio.1002452 |
0.652 |
|
| 2016 |
Shahmoradi A, Wilke CO. Dissecting the roles of local packing density and longer-range effects in protein sequence evolution. Proteins. PMID 26990194 DOI: 10.1002/Prot.25034 |
0.661 |
|
| 2016 |
Jackson EL, Shahmoradi A, Spielman SJ, Jack BR, Wilke CO. Intermediate divergence levels maximize the strength of structure -sequence correlations in enzymes and viral proteins. Protein Science : a Publication of the Protein Society. PMID 26971720 DOI: 10.1002/Pro.2920 |
0.682 |
|
| 2015 |
Meyer AG, Spielman SJ, Bedford T, Wilke CO. Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak. Virus Evolution. 1. PMID 26770819 DOI: 10.1093/Ve/Vev006 |
0.666 |
|
| 2015 |
Meyer AG, Wilke CO. The utility of protein structure as a predictor of site-wise dN/dS varies widely among HIV-1 proteins. Journal of the Royal Society, Interface / the Royal Society. 12. PMID 26468068 DOI: 10.1098/Rsif.2015.0579 |
0.66 |
|
| 2015 |
Kerr SA, Jackson EL, Lungu OI, Meyer AG, Demogines A, Ellington AD, Georgiou G, Wilke CO, Sawyer SL. Computational and Functional Analysis of the Virus-Receptor Interface Reveals Host Range Trade-Offs in New World Arenaviruses. Journal of Virology. 89: 11643-53. PMID 26355089 DOI: 10.1128/Jvi.01408-15 |
0.637 |
|
| 2015 |
Meyer AG, Wilke CO. Geometric Constraints Dominate the Antigenic Evolution of Influenza H3N2 Hemagglutinin. Plos Pathogens. 11: e1004940. PMID 26020774 DOI: 10.1371/Journal.Ppat.1004940 |
0.651 |
|
| 2015 |
Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM. Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Science (New York, N.Y.). 348: 921-5. PMID 25999509 DOI: 10.1126/Science.Aaa0769 |
0.651 |
|
| 2015 |
Echave J, Jackson EL, Wilke CO. Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites. Physical Biology. 12: 025002. PMID 25787027 DOI: 10.1088/1478-3975/12/2/025002 |
0.328 |
|
| 2015 |
Shahmoradi A, Wilke C. Dissecting the relationship between protein structure and sequence variation Bulletin of the American Physical Society. 2015. DOI: 10.15781/T2Zs3T |
0.685 |
|
| 2014 |
Sridhara V, Meyer AG, Rai P, Barrick JE, Ravikumar P, Segrè D, Wilke CO. Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli. Plos One. 9: e114608. PMID 25502413 DOI: 10.1371/Journal.Pone.0114608 |
0.615 |
|
| 2014 |
Shahmoradi A, Sydykova DK, Spielman SJ, Jackson EL, Dawson ET, Meyer AG, Wilke CO. Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design. Journal of Molecular Evolution. 79: 130-42. PMID 25217382 DOI: 10.1007/S00239-014-9644-X |
0.771 |
|
| 2014 |
Meyer AG, Sawyer SL, Ellington AD, Wilke CO. Analyzing machupo virus-receptor binding by molecular dynamics simulations. Peerj. 2: e266. PMID 24624315 DOI: 10.7717/Peerj.266 |
0.678 |
|
| 2014 |
O'Dea EB, Pepin KM, Lopman BA, Wilke CO. Fitting outbreak models to data from many small norovirus outbreaks. Epidemics. 6: 18-29. PMID 24593918 DOI: 10.1016/J.Epidem.2013.12.002 |
0.746 |
|
| 2013 |
Tien MZ, Meyer AG, Sydykova DK, Spielman SJ, Wilke CO. Maximum allowed solvent accessibilites of residues in proteins. Plos One. 8: e80635. PMID 24278298 DOI: 10.1371/Journal.Pone.0080635 |
0.637 |
|
| 2013 |
Covert AW, Lenski RE, Wilke CO, Ofria C. Experiments on the role of deleterious mutations as stepping stones in adaptive evolution. Proceedings of the National Academy of Sciences of the United States of America. 110: E3171-8. PMID 23918358 DOI: 10.1073/Pnas.1313424110 |
0.7 |
|
| 2013 |
Tien MZ, Sydykova DK, Meyer AG, Wilke CO. PeptideBuilder: A simple Python library to generate model peptides. Peerj. 1: e80. PMID 23717802 DOI: 10.7717/Peerj.80 |
0.614 |
|
| 2013 |
Meyer AG, Dawson ET, Wilke CO. Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 368: 20120334. PMID 23382434 DOI: 10.1098/Rstb.2012.0334 |
0.654 |
|
| 2013 |
Meyer AG, Wilke CO. Integrating sequence variation and protein structure to identify sites under selection. Molecular Biology and Evolution. 30: 36-44. PMID 22977116 DOI: 10.1093/Molbev/Mss217 |
0.692 |
|
| 2012 |
Scherrer MP, Meyer AG, Wilke CO. Modeling coding-sequence evolution within the context of residue solvent accessibility. Bmc Evolutionary Biology. 12: 179. PMID 22967129 DOI: 10.1186/1471-2148-12-179 |
0.781 |
|
| 2012 |
Keller TE, Wilke CO, Bull JJ. Interactions between evolutionary processes at high mutation rates. Evolution; International Journal of Organic Evolution. 66: 2303-14. PMID 22759303 DOI: 10.1111/J.1558-5646.2012.01596.X |
0.559 |
|
| 2012 |
Wang D, Arapostathis A, Wilke CO, Markey MK. Principal-oscillation-pattern analysis of gene expression. Plos One. 7: e28805. PMID 22253697 DOI: 10.1371/Journal.Pone.0028805 |
0.488 |
|
| 2012 |
Keller TE, Mis SD, Jia KE, Wilke CO. Reduced mRNA secondary-structure stability near the start codon indicates functional genes in prokaryotes. Genome Biology and Evolution. 4: 80-8. PMID 22138151 DOI: 10.1093/Gbe/Evr129 |
0.49 |
|
| 2012 |
Wang D, Markey MK, Wilke CO, Arapostathis A. Eigen-genomic system dynamic-pattern analysis (ESDA): modeling mRNA degradation and self-regulation. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 9: 430-7. PMID 22084146 DOI: 10.1109/Tcbb.2011.150 |
0.499 |
|
| 2011 |
Ramsey DC, Scherrer MP, Zhou T, Wilke CO. The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Genetics. 188: 479-88. PMID 21467571 DOI: 10.1534/Genetics.111.128025 |
0.776 |
|
| 2011 |
O'Dea EB, Wilke CO. Contact heterogeneity and phylodynamics: how contact networks shape parasite evolutionary trees. Interdisciplinary Perspectives On Infectious Diseases. 2011: 238743. PMID 21151699 DOI: 10.1155/2011/238743 |
0.751 |
|
| 2010 |
O'Dea EB, Keller TE, Wilke CO. Does mutational robustness inhibit extinction by lethal mutagenesis in viral populations? Plos Computational Biology. 6: e1000811. PMID 20548958 DOI: 10.1371/Journal.Pcbi.1000811 |
0.8 |
|
| 2010 |
Wilke CO, Drummond DA. Signatures of protein biophysics in coding sequence evolution. Current Opinion in Structural Biology. 20: 385-9. PMID 20395125 DOI: 10.1016/J.Sbi.2010.03.004 |
0.576 |
|
| 2009 |
Drummond DA, Wilke CO. The evolutionary consequences of erroneous protein synthesis. Nature Reviews. Genetics. 10: 715-24. PMID 19763154 DOI: 10.1038/Nrg2662 |
0.506 |
|
| 2009 |
Ofria C, Bryson DM, Wilke CO. Avida: A software platform for research in computational evolutionary biology Artificial Life Models in Software (Second Edition). 3-35. DOI: 10.1007/978-1-84882-285-6_1 |
0.531 |
|
| 2008 |
Drummond DA, Wilke CO. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell. 134: 341-52. PMID 18662548 DOI: 10.1016/J.Cell.2008.05.042 |
0.592 |
|
| 2008 |
Zhou T, Drummond DA, Wilke CO. Contact density affects protein evolutionary rate from bacteria to animals. Journal of Molecular Evolution. 66: 395-404. PMID 18379715 DOI: 10.1007/S00239-008-9094-4 |
0.545 |
|
| 2007 |
Forster R, Wilke CO. Frequency-Dependent Selection in a Periodic Environment. Physica A. 381: 255-264. PMID 17940581 DOI: 10.1016/J.Physa.2007.03.017 |
0.59 |
|
| 2007 |
Elena SF, Wilke CO, Ofria C, Lenski RE. Effects of population size and mutation rate on the evolution of mutational robustness. Evolution; International Journal of Organic Evolution. 61: 666-74. PMID 17348929 DOI: 10.1111/J.1558-5646.2007.00064.X |
0.705 |
|
| 2007 |
Bloom JD, Arnold FH, Wilke CO. Breaking proteins with mutations: threads and thresholds in evolution. Molecular Systems Biology. 3: 76. PMID 17262035 DOI: 10.1038/Msb4100119 |
0.509 |
|
| 2007 |
Bloom JD, Raval A, Wilke CO. Thermodynamics of neutral protein evolution. Genetics. 175: 255-66. PMID 17110496 DOI: 10.1534/genetics.106.061754 |
0.601 |
|
| 2006 |
Forster R, Adami C, Wilke CO. Selection for mutational robustness in finite populations. Journal of Theoretical Biology. 243: 181-90. PMID 16901510 DOI: 10.1016/J.Jtbi.2006.06.020 |
0.714 |
|
| 2006 |
Bloom JD, Drummond DA, Arnold FH, Wilke CO. Structural determinants of the rate of protein evolution in yeast. Molecular Biology and Evolution. 23: 1751-61. PMID 16782762 DOI: 10.1093/Molbev/Msl040 |
0.695 |
|
| 2006 |
Wilke CO, Forster R, Novella IS. Quasispecies in time-dependent environments Current Topics in Microbiology and Immunology. 299: 33-50. PMID 16568895 DOI: 10.1007/3-540-26397-7_2 |
0.603 |
|
| 2006 |
Wilke CO, Drummond DA. Population genetics of translational robustness. Genetics. 173: 473-81. PMID 16489231 DOI: 10.1534/Genetics.105.051300 |
0.565 |
|
| 2006 |
Drummond DA, Raval A, Wilke CO. A single determinant dominates the rate of yeast protein evolution. Molecular Biology and Evolution. 23: 327-37. PMID 16237209 DOI: 10.1093/Molbev/Msj038 |
0.589 |
|
| 2005 |
Forster R, Wilke CO. Tradeoff between short-term and long-term adaptation in a changing environment. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 041922. PMID 16383435 DOI: 10.1103/Physreve.72.041922 |
0.582 |
|
| 2005 |
Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. Why highly expressed proteins evolve slowly. Proceedings of the National Academy of Sciences of the United States of America. 102: 14338-43. PMID 16176987 DOI: 10.1073/Pnas.0504070102 |
0.744 |
|
| 2005 |
Wilke CO, Bloom JD, Drummond DA, Raval A. Predicting the tolerance of proteins to random amino acid substitution. Biophysical Journal. 89: 3714-20. PMID 16150971 DOI: 10.1529/Biophysj.105.062125 |
0.663 |
|
| 2005 |
Drummond DA, Silberg JJ, Meyer MM, Wilke CO, Arnold FH. On the conservative nature of intragenic recombination. Proceedings of the National Academy of Sciences of the United States of America. 102: 5380-5. PMID 15809422 DOI: 10.1073/Pnas.0500729102 |
0.6 |
|
| 2005 |
Bloom JD, Silberg JJ, Wilke CO, Drummond DA, Adami C, Arnold FH. Thermodynamic prediction of protein neutrality. Proceedings of the National Academy of Sciences of the United States of America. 102: 606-11. PMID 15644440 DOI: 10.1073/Pnas.0406744102 |
0.731 |
|
| 2005 |
Ofria C, Wilke CO. Avida: Evolution experiments with self-replicating computer programs Artificial Life Models in Software. 3-35. DOI: 10.1007/1-84628-214-4_1 |
0.526 |
|
| 2004 |
Chow SS, Wilke CO, Ofria C, Lenski RE, Adami C. Adaptive radiation from resource competition in digital organisms. Science (New York, N.Y.). 305: 84-6. PMID 15232105 DOI: 10.1126/Science.1096307 |
0.758 |
|
| 2004 |
Bloom JD, Wilke CO, Arnold FH, Adami C. Stability and the evolvability of function in a model protein. Biophysical Journal. 86: 2758-64. PMID 15111394 DOI: 10.1016/S0006-3495(04)74329-5 |
0.639 |
|
| 2004 |
Ofria C, Wilke CO. Avida: a software platform for research in computational evolutionary biology. Artificial Life. 10: 191-229. PMID 15107231 DOI: 10.1162/106454604773563612 |
0.556 |
|
| 2004 |
Adami C, Wilke CO. Experiments in digital evolution (Editors' introduction to the special issue) Artificial Life. 10: 117-122. DOI: 10.1162/106454604773563540 |
0.44 |
|
| 2003 |
Wilke CO, Lenski RE, Adami C. Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding. Bmc Evolutionary Biology. 3: 3. PMID 12590655 DOI: 10.1186/1471-2148-3-3 |
0.654 |
|
| 2003 |
Wilke CO, Adami C. Evolution of mutational robustness. Mutation Research. 522: 3-11. PMID 12517406 DOI: 10.1016/S0027-5107(02)00307-X |
0.522 |
|
| 2003 |
Campos P, Adami C, Wilke C. Erratum to “Optimal adaptive performance and delocalization in NK fitness landscapes” Physica a: Statistical Mechanics and Its Applications. 318: 637. DOI: 10.1016/S0378-4371(02)01554-6 |
0.426 |
|
| 2002 |
Campos PRA, Adami C, Wilke CO. Optimal adaptive performance and delocalization in NK fitness landscapes Physica a: Statistical Mechanics and Its Applications. 304: 495-506. DOI: 10.1016/S0378-4371(01)00572-6 |
0.524 |
|
| 2002 |
Wilke CO, Adami C. The biology of digital organisms Trends in Ecology and Evolution. 17: 528-532. DOI: 10.1016/S0169-5347(02)02612-5 |
0.479 |
|
| 2002 |
Kamp C, Wilke CO, Adami C, Bornholdt S. 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 |
0.511 |
|
| 2001 |
Wilke CO, Wang JL, Ofria C, Lenski RE, Adami C. Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature. 412: 331-3. PMID 11460163 DOI: 10.1038/35085569 |
0.752 |
|
| 2001 |
Wilke CO, Adami C. Interaction between directional epistasis and average mutational effects Proceedings of the Royal Society B: Biological Sciences. 268: 1469-1474. PMID 11454290 DOI: 10.1098/Rspb.2001.1690 |
0.536 |
|
| 1999 |
Wilke CO, Martinetz T. Adaptive walks on time-dependent fitness landscapes. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 60: 2154-9. PMID 11970008 DOI: 10.1103/Physreve.60.2154 |
0.549 |
|
| 1999 |
Wilke CO, Martinetz T. Lifetimes of agents under external stress Physical Review E. 59: R2512-R2515. DOI: 10.1103/Physreve.59.R2512 |
0.5 |
|
| 1999 |
Wilke CO, Ronnewinkel C, Martinetz T. Molecular evolution in time-dependent environments Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1674: 417-421. DOI: 10.1007/3-540-48304-7_57 |
0.513 |
|
| 1998 |
Wilke C, Martinetz T. Hierarchical noise in large systems of independent agents Physical Review E. 58: 7101-7108. DOI: 10.1103/PhysRevE.58.7101 |
0.467 |
|
| 1998 |
Wilke C, Altmeyer S, Martinetz T. Aftershocks in coherent-noise models Physica D: Nonlinear Phenomena. 120: 401-417. DOI: 10.1016/S0167-2789(98)00092-X |
0.567 |
|
| 1997 |
Wilke C, Martinetz T. Simple model of evolution with variable system size Physical Review E. 56: 7128-7131. DOI: 10.1103/Physreve.56.7128 |
0.585 |
|
| Show low-probability matches. |