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Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences.

Teufel AI, Ritchie AM, Wilke CO, Liberles DA.

Genes (Basel). 2018 Aug 13;9(8). pii: E409. doi: 10.3390/genes9080409. Review.


Within-Gene Shine-Dalgarno Sequences Are Not Selected for Function.

Hockenberry AJ, Jewett MC, Amaral LAN, Wilke CO.

Mol Biol Evol. 2018 Oct 1;35(10):2487-2498. doi: 10.1093/molbev/msy150.


Combinatorial Approaches to Viral Attenuation.

Paff ML, Jack BR, Smith BL, Bull JJ, Wilke CO.

mSystems. 2018 Jul 31;3(4). pii: e00046-18. doi: 10.1128/mSystems.00046-18. eCollection 2018 Jul-Aug.


Limitations of alignment-free tools in total RNA-seq quantification.

Wu DC, Yao J, Ho KS, Lambowitz AM, Wilke CO.

BMC Genomics. 2018 Jul 3;19(1):510. doi: 10.1186/s12864-018-4869-5.


Measuring evolutionary rates of proteins in a structural context.

Sydykova DK, Jack BR, Spielman SJ, Wilke CO.

Version 2. F1000Res. 2017 Oct 16 [revised 2018 Jan 1];6:1845. doi: 10.12688/f1000research.12874.2. eCollection 2017.


Beyond Thermodynamic Constraints: Evolutionary Sampling Generates Realistic Protein Sequence Variation.

Jiang Q, Teufel AI, Jackson EL, Wilke CO.

Genetics. 2018 Apr;208(4):1387-1395. doi: 10.1534/genetics.118.300699. Epub 2018 Jan 30.


Sicegar: R package for sigmoidal and double-sigmoidal curve fitting.

Caglar MU, Teufel AI, Wilke CO.

PeerJ. 2018 Jan 16;6:e4251. doi: 10.7717/peerj.4251. eCollection 2018.


Discovery of Next-Generation Antimicrobials through Bacterial Self-Screening of Surface-Displayed Peptide Libraries.

Tucker AT, Leonard SP, DuBois CD, Knauf GA, Cunningham AL, Wilke CO, Trent MS, Davies BW.

Cell. 2018 Jan 25;172(3):618-628.e13. doi: 10.1016/j.cell.2017.12.009. Epub 2018 Jan 4.


Single-Cell Virology: On-Chip Investigation of Viral Infection Dynamics.

Guo F, Li S, Caglar MU, Mao Z, Liu W, Woodman A, Arnold JJ, Wilke CO, Huang TJ, Cameron CE.

Cell Rep. 2017 Nov 7;21(6):1692-1704. doi: 10.1016/j.celrep.2017.10.051.


A new twist in measuring mutation rates.

Smith BL, Wilke CO.

Elife. 2017 Jul 14;6. pii: e29586. doi: 10.7554/eLife.29586.


Reduced Protein Expression in a Virus Attenuated by Codon Deoptimization.

Jack BR, Boutz DR, Paff ML, Smith BL, Bull JJ, Wilke CO.

G3 (Bethesda). 2017 Sep 7;7(9):2957-2968. doi: 10.1534/g3.117.041020.


Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates.

Sydykova DK, Wilke CO.

PeerJ. 2017 May 30;5:e3391. doi: 10.7717/peerj.3391. eCollection 2017.


The evolution of logic circuits for the purpose of protein contact map prediction.

Chapman SD, Adami C, Wilke CO, B Kc D.

PeerJ. 2017 Apr 18;5:e3139. doi: 10.7717/peerj.3139. eCollection 2017.


The E. coli molecular phenotype under different growth conditions.

Caglar MU, Houser JR, Barnhart CS, Boutz DR, Carroll SM, Dasgupta A, Lenoir WF, Smith BL, Sridhara V, Sydykova DK, Vander Wood D, Marx CJ, Marcotte EM, Barrick JE, Wilke CO.

Sci Rep. 2017 Apr 18;7:45303. doi: 10.1038/srep45303.


Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions.

Brown CW, Sridhara V, Boutz DR, Person MD, Marcotte EM, Barrick JE, Wilke CO.

BMC Genomics. 2017 Apr 17;18(1):301. doi: 10.1186/s12864-017-3676-8.


Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein.

Jackson EL, Spielman SJ, Wilke CO.

PLoS One. 2017 Apr 3;12(4):e0164905. doi: 10.1371/journal.pone.0164905. eCollection 2017.


Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence.

Echave J, Wilke CO.

Annu Rev Biophys. 2017 May 22;46:85-103. doi: 10.1146/annurev-biophys-070816-033819. Epub 2017 Mar 15. Review.


Accelerated simulation of evolutionary trajectories in origin-fixation models.

Teufel AI, Wilke CO.

J R Soc Interface. 2017 Feb;14(127). pii: 20160906. doi: 10.1098/rsif.2016.0906.


Viral factors in influenza pandemic risk assessment.

Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CA.

Elife. 2016 Nov 11;5. pii: e18491. doi: 10.7554/eLife.18491.


A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specific dN/dS Estimation.

Spielman SJ, Wan S, Wilke CO.

Genetics. 2016 Oct;204(2):499-511. Epub 2016 Aug 17.


Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint.

Spielman SJ, Wilke CO.

Mol Biol Evol. 2016 Nov;33(11):2990-3002. Epub 2016 Aug 10.


At the mercy of viruses.

Wilke CO, Sawyer SL.

Elife. 2016 May 17;5. pii: e16758. doi: 10.7554/eLife.16758.


Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes.

Jack BR, Meyer AG, Echave J, Wilke CO.

PLoS Biol. 2016 May 3;14(5):e1002452. doi: 10.1371/journal.pbio.1002452. eCollection 2016 May.


Dissecting the roles of local packing density and longer-range effects in protein sequence evolution.

Shahmoradi A, Wilke CO.

Proteins. 2016 Jun;84(6):841-54. doi: 10.1002/prot.25034. Epub 2016 Apr 9.


Intermediate divergence levels maximize the strength of structure-sequence correlations in enzymes and viral proteins.

Jackson EL, Shahmoradi A, Spielman SJ, Jack BR, Wilke CO.

Protein Sci. 2016 Jul;25(7):1341-53. doi: 10.1002/pro.2920. Epub 2016 Mar 24.


Reproducibility of SNV-calling in multiple sequencing runs from single tumors.

Derryberry DZ, Cowperthwaite MC, Wilke CO.

PeerJ. 2016 Jan 4;4:e1508. doi: 10.7717/peerj.1508. eCollection 2016.


Causes of evolutionary rate variation among protein sites.

Echave J, Spielman SJ, Wilke CO.

Nat Rev Genet. 2016 Feb;17(2):109-21. doi: 10.1038/nrg.2015.18. Epub 2016 Jan 19. Review.


Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak.

Meyer AG, Spielman SJ, Bedford T, Wilke CO.

Virus Evol. 2015 Jan;1(1). pii: vev006. Epub 2015 Jan 1.


The utility of protein structure as a predictor of site-wise dN/dS varies widely among HIV-1 proteins.

Meyer AG, Wilke CO.

J R Soc Interface. 2015 Oct 6;12(111):20150579. doi: 10.1098/rsif.2015.0579.


Evolutionary paths of least resistance.

Wilke CO.

Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):12553-4. doi: 10.1073/pnas.1517390112. Epub 2015 Oct 1. No abstract available.


Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies.

Spielman SJ, Wilke CO.

PLoS One. 2015 Sep 23;10(9):e0139047. doi: 10.1371/journal.pone.0139047. eCollection 2015.


Computational and Functional Analysis of the Virus-Receptor Interface Reveals Host Range Trade-Offs in New World Arenaviruses.

Kerr SA, Jackson EL, Lungu OI, Meyer AG, Demogines A, Ellington AD, Georgiou G, Wilke CO, Sawyer SL.

J Virol. 2015 Nov;89(22):11643-53. doi: 10.1128/JVI.01408-15. Epub 2015 Sep 9.


Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation.

Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO.

PLoS Comput Biol. 2015 Aug 14;11(8):e1004400. doi: 10.1371/journal.pcbi.1004400. eCollection 2015 Aug.


Geometric Constraints Dominate the Antigenic Evolution of Influenza H3N2 Hemagglutinin.

Meyer AG, Wilke CO.

PLoS Pathog. 2015 May 28;11(5):e1004940. doi: 10.1371/journal.ppat.1004940. eCollection 2015 May.


Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity.

Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM.

Science. 2015 May 22;348(6237):921-5. doi: 10.1126/science.aaa0769.


Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites.

Echave J, Jackson EL, Wilke CO.

Phys Biol. 2015 Mar 19;12(2):025002. doi: 10.1088/1478-3975/12/2/025002.


Comprehensive, structurally-informed alignment and phylogeny of vertebrate biogenic amine receptors.

Spielman SJ, Kumar K, Wilke CO.

PeerJ. 2015 Feb 17;3:e773. doi: 10.7717/peerj.773. eCollection 2015.


The relationship between dN/dS and scaled selection coefficients.

Spielman SJ, Wilke CO.

Mol Biol Evol. 2015 Apr;32(4):1097-108. doi: 10.1093/molbev/msv003. Epub 2015 Jan 8.


Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli.

Sridhara V, Meyer AG, Rai P, Barrick JE, Ravikumar P, Segrè D, Wilke CO.

PLoS One. 2014 Dec 12;9(12):e114608. doi: 10.1371/journal.pone.0114608. eCollection 2014.


Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design.

Shahmoradi A, Sydykova DK, Spielman SJ, Jackson EL, Dawson ET, Meyer AG, Wilke CO.

J Mol Evol. 2014 Oct;79(3-4):130-42. doi: 10.1007/s00239-014-9644-x. Epub 2014 Sep 13.


Limited utility of residue masking for positive-selection inference.

Spielman SJ, Dawson ET, Wilke CO.

Mol Biol Evol. 2014 Sep;31(9):2496-500. doi: 10.1093/molbev/msu183. Epub 2014 Jun 3.


Long-term control of viral replication in a Group O, human immunodeficiency virus type 1-infected individual.

Buckheit RW 3rd, Sexauer SB, Sedaghat AR, Wilke CO, Laeyendecker O, Basseth CR, Blankson JN.

AIDS Res Hum Retroviruses. 2014 Jun;30(6):511-3. doi: 10.1089/AID.2014.0054. No abstract available.


Analyzing machupo virus-receptor binding by molecular dynamics simulations.

Meyer AG, Sawyer SL, Ellington AD, Wilke CO.

PeerJ. 2014 Feb 27;2:e266. doi: 10.7717/peerj.266. eCollection 2014.


Fitting outbreak models to data from many small norovirus outbreaks.

O'Dea EB, Pepin KM, Lopman BA, Wilke CO.

Epidemics. 2014 Mar;6:18-29. doi: 10.1016/j.epidem.2013.12.002. Epub 2014 Jan 8.


Socioeconomic disparities in the presentation of acute bacterial sinusitis complications in children.

Sedaghat AR, Wilke CO, Cunningham MJ, Ishman SL.

Laryngoscope. 2014 Jul;124(7):1700-6. doi: 10.1002/lary.24492. Epub 2013 Dec 11.


Maximum allowed solvent accessibilites of residues in proteins.

Tien MZ, Meyer AG, Sydykova DK, Spielman SJ, Wilke CO.

PLoS One. 2013 Nov 21;8(11):e80635. doi: 10.1371/journal.pone.0080635. eCollection 2013.


Amino-acid site variability among natural and designed proteins.

Jackson EL, Ollikainen N, Covert AW 3rd, Kortemme T, Wilke CO.

PeerJ. 2013 Nov 12;1:e211. doi: 10.7717/peerj.211. eCollection 2013.


Experiments on the role of deleterious mutations as stepping stones in adaptive evolution.

Covert AW 3rd, Lenski RE, Wilke CO, Ofria C.

Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):E3171-8. doi: 10.1073/pnas.1313424110. Epub 2013 Aug 5.

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