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Items: 20

1.

Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces.

Spielman SJ, Weaver S, Shank SD, Magalis BR, Li M, Kosakovsky Pond SL.

Methods Mol Biol. 2019;1910:427-468. doi: 10.1007/978-1-4939-9074-0_14.

PMID:
31278673
2.

Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature.

Maddamsetti R, Johnson DT, Spielman SJ, Petrie KL, Marks DS, Meyer JR.

Evolution. 2018 Oct;72(10):2234-2243. doi: 10.1111/evo.13586. Epub 2018 Sep 11.

3.

Relative evolutionary rates in proteins are largely insensitive to the substitution model.

Spielman SJ, Kosakovsky Pond SL.

Mol Biol Evol. 2018 Jun 19. doi: 10.1093/molbev/msy127. [Epub ahead of print]

4.

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.

5.

Relative evolutionary rate inference in HyPhy with LEISR.

Spielman SJ, Kosakovsky Pond SL.

PeerJ. 2018 Feb 5;6:e4339. doi: 10.7717/peerj.4339. eCollection 2018.

6.

Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes.

Weaver S, Shank SD, Spielman SJ, Li M, Muse SV, Kosakovsky Pond SL.

Mol Biol Evol. 2018 Jan 2. doi: 10.1093/molbev/msx335. [Epub ahead of print]

7.

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.

8.

Regulation of clathrin-mediated endocytosis by hierarchical allosteric activation of AP2.

Kadlecova Z, Spielman SJ, Loerke D, Mohanakrishnan A, Reed DK, Schmid SL.

J Cell Biol. 2017 Jan 2;216(1):167-179. doi: 10.1083/jcb.201608071. Epub 2016 Dec 21.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

Membrane environment imposes unique selection pressures on transmembrane domains of G protein-coupled receptors.

Spielman SJ, Wilke CO.

J Mol Evol. 2013 Mar;76(3):172-82. doi: 10.1007/s00239-012-9538-8. Epub 2013 Jan 26. Erratum in: J Mol Evol. 2013 Mar;76(3):183.

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