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Causes of evolutionary rate variation among protein sites.

Echave J, Spielman SJ, Wilke CO. Echave J, et al. Among authors: spielman sj. Nat Rev Genet. 2016 Feb;17(2):109-21. doi: 10.1038/nrg.2015.18. Epub 2016 Jan 19. Nat Rev Genet. 2016. PMID: 26781812 Free PMC article. Review.

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HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies.

Kosakovsky Pond SL, Poon AFY, Velazquez R, Weaver S, Hepler NL, Murrell B, Shank SD, Magalis BR, Bouvier D, Nekrutenko A, Wisotsky S, Spielman SJ, Frost SDW, Muse SV. Kosakovsky Pond SL, et al. Among authors: spielman sj. Mol Biol Evol. 2020 Jan 1;37(1):295-299. doi: 10.1093/molbev/msz197. Mol Biol Evol. 2020. PMID: 31504749 Free PMC article.

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Relative model selection of evolutionary substitution models can be sensitive to multiple sequence alignment uncertainty.

Spielman SJ, Miraglia ML. Spielman SJ, et al. BMC Ecol Evol. 2021 Nov 29;21(1):214. doi: 10.1186/s12862-021-01931-5. BMC Ecol Evol. 2021. PMID: 34844571 Free PMC article.

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Relative evolutionary rate inference in HyPhy with LEISR.

Spielman SJ, Kosakovsky Pond SL. Spielman SJ, et al. PeerJ. 2018 Feb 5;6:e4339. doi: 10.7717/peerj.4339. eCollection 2018. PeerJ. 2018. PMID: 29423346 Free PMC article.

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The evolving redox chemistry and bioavailability of vanadium in deep time.

Moore EK, Hao J, Spielman SJ, Yee N. Moore EK, et al. Among authors: spielman sj. Geobiology. 2020 Mar;18(2):127-138. doi: 10.1111/gbi.12375. Epub 2020 Feb 12. Geobiology. 2020. PMID: 32048807

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Measuring evolutionary rates of proteins in a structural context.

Sydykova DK, Jack BR, Spielman SJ, Wilke CO. Sydykova DK, et al. Among authors: spielman sj. F1000Res. 2017 Oct 16;6:1845. doi: 10.12688/f1000research.12874.2. eCollection 2017. F1000Res. 2017. PMID: 29167739 Free PMC article.

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Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics.

Spielman SJ. Spielman SJ. Mol Biol Evol. 2020 Jul 1;37(7):2110-2123. doi: 10.1093/molbev/msaa075. Mol Biol Evol. 2020. PMID: 32191313 Free PMC article.

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

Spielman SJ, Weaver S, Shank SD, Magalis BR, Li M, Kosakovsky Pond SL. Spielman SJ, et al. Methods Mol Biol. 2019;1910:427-468. doi: 10.1007/978-1-4939-9074-0_14. Methods Mol Biol. 2019. PMID: 31278673

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

Kadlecova Z, Spielman SJ, Loerke D, Mohanakrishnan A, Reed DK, Schmid SL. Kadlecova Z, et al. Among authors: spielman sj. J Cell Biol. 2017 Jan 2;216(1):167-179. doi: 10.1083/jcb.201608071. Epub 2016 Dec 21. J Cell Biol. 2017. PMID: 28003333 Free PMC article.

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

Spielman SJ, Wilke CO. Spielman SJ, et al. Mol Biol Evol. 2016 Nov;33(11):2990-3002. doi: 10.1093/molbev/msw171. Epub 2016 Aug 10. Mol Biol Evol. 2016. PMID: 27512115 Free PMC article.

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