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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: nekrutenko a. Mol Biol Evol. 2020 Jan 1;37(1):295-299. doi: 10.1093/molbev/msz197. Mol Biol Evol. 2020. PMID: 31504749 Free PMC article.
Windshield splatter analysis with the Galaxy metagenomic pipeline.
Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A; Galaxy Team. Kosakovsky Pond S, et al. Among authors: nekrutenko a. Genome Res. 2009 Nov;19(11):2144-53. doi: 10.1101/gr.094508.109. Epub 2009 Oct 9. Genome Res. 2009. PMID: 19819906 Free PMC article.
No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics.
Baker D, van den Beek M, Blankenberg D, Bouvier D, Chilton J, Coraor N, Coppens F, Eguinoa I, Gladman S, Grüning B, Keener N, Larivière D, Lonie A, Kosakovsky Pond S, Maier W, Nekrutenko A, Taylor J, Weaver S. Baker D, et al. Among authors: nekrutenko a. PLoS Pathog. 2020 Aug 13;16(8):e1008643. doi: 10.1371/journal.ppat.1008643. eCollection 2020 Aug. PLoS Pathog. 2020. PMID: 32790776 Free PMC article.
Using Galaxy to Perform Large-Scale Interactive Data Analyses-An Update.
Ostrovsky A, Hillman-Jackson J, Bouvier D, Clements D, Afgan E, Blankenberg D, Schatz MC, Nekrutenko A, Taylor J, Team TG, Lariviere D. Ostrovsky A, et al. Among authors: nekrutenko a. Curr Protoc. 2021 Feb;1(2):e31. doi: 10.1002/cpz1.31. Curr Protoc. 2021. PMID: 33583104
Ready-to-use public infrastructure for global SARS-CoV-2 monitoring.
Maier W, Bray S, van den Beek M, Bouvier D, Coraor N, Miladi M, Singh B, De Argila JR, Baker D, Roach N, Gladman S, Coppens F, Martin DP, Lonie A, Grüning B, Kosakovsky Pond SL, Nekrutenko A. Maier W, et al. Among authors: nekrutenko a. Nat Biotechnol. 2021 Oct;39(10):1178-1179. doi: 10.1038/s41587-021-01069-1. Nat Biotechnol. 2021. PMID: 34588690 Free PMC article. No abstract available.
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function.
Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins GW, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A; NGS-SA; Williamson C, Hsiao NY, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL. Martin DP, et al. Among authors: nekrutenko a. Mol Biol Evol. 2022 Apr 11;39(4):msac061. doi: 10.1093/molbev/msac061. Mol Biol Evol. 2022. PMID: 35325204 Free PMC article.
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.
Wertheim JO, Wang JC, Leelawong M, Martin DP, Havens JL, Chowdhury MA, Pekar JE, Amin H, Arroyo A, Awandare GA, Chow HY, Gonzalez E, Luoma E, Morang'a CM, Nekrutenko A, Shank SD, Silver S, Quashie PK, Rakeman JL, Ruiz V, Torian LV, Vasylyeva TI, Kosakovsky Pond SL, Hughes S. Wertheim JO, et al. Among authors: nekrutenko a. Nat Commun. 2022 Jun 25;13(1):3645. doi: 10.1038/s41467-022-31247-x. Nat Commun. 2022. PMID: 35752633 Free PMC article.
101 results