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Items: 1 to 20 of 123


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. [Epub ahead of print]


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.


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.


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.


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.


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.


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. 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.


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. 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.


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.


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.


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.


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.

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