Kosakovsky Pond SL - Search Results

1

Viral CpG Deficiency Provides No Evidence That Dogs Were Intermediate Hosts for SARS-CoV-2.

Pollock DD, Castoe TA, Perry BW, Lytras S, Wade KJ, Robertson DL, Holmes EC, Boni MF, Kosakovsky Pond SL, Parry R, Carlton EJ, Wood JLN, Pennings PS, Goldstein RA. Pollock DD, et al. Among authors: kosakovsky pond sl. Mol Biol Evol. 2020 Sep 1;37(9):2706-2710. doi: 10.1093/molbev/msaa178. Mol Biol Evol. 2020. PMID: 32658964 Free PMC article.

2

HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens.

Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, Wertheim JO. Kosakovsky Pond SL, et al. Mol Biol Evol. 2018 Jul 1;35(7):1812-1819. doi: 10.1093/molbev/msy016. Mol Biol Evol. 2018. PMID: 29401317 Free PMC article.

3

Neutral Theory and Rapidly Evolving Viral Pathogens.

Frost SDW, Magalis BR, Kosakovsky Pond SL. Frost SDW, et al. Among authors: kosakovsky pond sl. Mol Biol Evol. 2018 Jun 1;35(6):1348-1354. doi: 10.1093/molbev/msy088. Mol Biol Evol. 2018. PMID: 29688481 Free PMC article.

4

Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution Model.

Spielman SJ, Kosakovsky Pond SL. Spielman SJ, et al. Among authors: kosakovsky pond sl. Mol Biol Evol. 2018 Sep 1;35(9):2307-2317. doi: 10.1093/molbev/msy127. Mol Biol Evol. 2018. PMID: 29924340 Free PMC article.

5

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. Among authors: kosakovsky pond sl. Methods Mol Biol. 2019;1910:427-468. doi: 10.1007/978-1-4939-9074-0_14. Methods Mol Biol. 2019. PMID: 31278673

6

Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril.

Wisotsky SR, Kosakovsky Pond SL, Shank SD, Muse SV. Wisotsky SR, et al. Among authors: kosakovsky pond sl. Mol Biol Evol. 2020 Aug 1;37(8):2430-2439. doi: 10.1093/molbev/msaa037. Mol Biol Evol. 2020. PMID: 32068869 Free PMC article.

7

Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen.

MacLean OA, Lytras S, Weaver S, Singer JB, Boni MF, Lemey P, Kosakovsky Pond SL, Robertson DL. MacLean OA, et al. Among authors: kosakovsky pond sl. bioRxiv [Preprint]. 2020 Jul 30:2020.05.28.122366. doi: 10.1101/2020.05.28.122366. bioRxiv. 2020. PMID: 32577659 Free PMC article. Updated. Preprint.

8

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.

MacLean OA, Lytras S, Weaver S, Singer JB, Boni MF, Lemey P, Kosakovsky Pond SL, Robertson DL. MacLean OA, et al. Among authors: kosakovsky pond sl. PLoS Biol. 2021 Mar 12;19(3):e3001115. doi: 10.1371/journal.pbio.3001115. eCollection 2021 Mar. PLoS Biol. 2021. PMID: 33711012 Free PMC article.

9

Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses.

Mei H, Kosakovsky Pond S, Nekrutenko A. Mei H, et al. Mol Biol Evol. 2021 Dec 9;38(12):5678-5684. doi: 10.1093/molbev/msab265. Mol Biol Evol. 2021. PMID: 34505896 Free PMC article.

10

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.

Martin DP, Weaver S, Tegally H, San JE, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ; NGS-SA; COVID-19 Genomics UK (COG-UK); Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL. Martin DP, et al. Among authors: kosakovsky pond sl. Cell. 2021 Sep 30;184(20):5189-5200.e7. doi: 10.1016/j.cell.2021.09.003. Epub 2021 Sep 7. Cell. 2021. PMID: 34537136 Free PMC article.

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