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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: kosakovsky pond sl. Mol Biol Evol. 2022 Apr 11;39(4):msac061. doi: 10.1093/molbev/msac061. Mol Biol Evol. 2022. PMID: 35325204 Free PMC article.
Modeling HIV-1 drug resistance as episodic directional selection.
Murrell B, de Oliveira T, Seebregts C, Kosakovsky Pond SL, Scheffler K; Southern African Treatment and Resistance Network-SATuRN Consortium. Murrell B, et al. Among authors: kosakovsky pond sl. PLoS Comput Biol. 2012;8(5):e1002507. doi: 10.1371/journal.pcbi.1002507. Epub 2012 May 10. PLoS Comput Biol. 2012. PMID: 22589711 Free PMC article.
Detecting individual sites subject to episodic diversifying selection.
Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL. Murrell B, et al. Among authors: kosakovsky pond sl. PLoS Genet. 2012;8(7):e1002764. doi: 10.1371/journal.pgen.1002764. Epub 2012 Jul 12. PLoS Genet. 2012. PMID: 22807683 Free PMC article.
FUBAR: a fast, unconstrained bayesian approximation for inferring selection.
Murrell B, Moola S, Mabona A, Weighill T, Sheward D, Kosakovsky Pond SL, Scheffler K. Murrell B, et al. Among authors: kosakovsky pond sl. Mol Biol Evol. 2013 May;30(5):1196-205. doi: 10.1093/molbev/mst030. Epub 2013 Feb 18. Mol Biol Evol. 2013. PMID: 23420840 Free PMC article.
IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform.
Hepler NL, Scheffler K, Weaver S, Murrell B, Richman DD, Burton DR, Poignard P, Smith DM, Kosakovsky Pond SL. Hepler NL, et al. Among authors: kosakovsky pond sl. PLoS Comput Biol. 2014 Sep 25;10(9):e1003842. doi: 10.1371/journal.pcbi.1003842. eCollection 2014 Sep. PLoS Comput Biol. 2014. PMID: 25254639 Free PMC article.
155 results