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Scalable Bayesian phylogenetics.
Fisher AA, Hassler GW, Ji X, Baele G, Suchard MA, Lemey P. Fisher AA, et al. Philos Trans R Soc Lond B Biol Sci. 2022 Oct 10;377(1861):20210242. doi: 10.1098/rstb.2021.0242. Epub 2022 Aug 22. Philos Trans R Soc Lond B Biol Sci. 2022. PMID: 35989603 Free PMC article. Review.
Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer.
McBride DS, Garushyants SK, Franks J, Magee AF, Overend SH, Huey D, Williams AM, Faith SA, Kandeil A, Trifkovic S, Miller L, Jeevan T, Patel A, Nolting JM, Tonkovich MJ, Genders JT, Montoney AJ, Kasnyik K, Linder TJ, Bevins SN, Lenoch JB, Chandler JC, DeLiberto TJ, Koonin EV, Suchard MA, Lemey P, Webby RJ, Nelson MI, Bowman AS. McBride DS, et al. Nat Commun. 2023 Aug 28;14(1):5105. doi: 10.1038/s41467-023-40706-y. Nat Commun. 2023. PMID: 37640694 Free PMC article.
Genomic epidemiology uncovers the timing and origin of the emergence of mpox in humans.
Parker E, Omah IF, Varilly P, Magee A, Ayinla AO, Sijuwola AE, Ahmed MI, Ope-Ewe OO, Ogunsanya OA, Olono A, Eromon P, Tomkins-Tinch CH, Otieno JR, Akanbi O, Egwuenu A, Ehiakhamen O, Chukwu C, Suleiman K, Akinpelu A, Ahmad A, Imam KI, Ojedele R, Oripenaye V, Ikeata K, Adelakun S, Olajumoke B, Djuicy DD, Essengue LLM, Yifomnjou MHM, Zeller M, Gangavarapu K, O'Toole Á, Park DJ, Mboowa G, Tessema SK, Tebeje YK, Folarin O, Happi A, Lemey P, Suchard MA, Andersen KG, Sabeti P, Rambaut A, Njoum R, Ihekweazu C, Jide I, Adetifa I, Happi CT. Parker E, et al. medRxiv [Preprint]. 2024 Jun 19:2024.06.18.24309104. doi: 10.1101/2024.06.18.24309104. medRxiv. 2024. PMID: 38947052 Free PMC article. Preprint.
Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1.
Tsui JL, McCrone JT, Lambert B, Bajaj S, Inward RPD, Bosetti P, Pena RE, Tegally H, Hill V, Zarebski AE, Peacock TP, Liu L, Wu N, Davis M, Bogoch II, Khan K, Kall M, Abdul Aziz NIB, Colquhoun R, O'Toole Á, Jackson B, Dasgupta A, Wilkinson E, de Oliveira T; COVID-19 Genomics UK (COG-UK) consortium¶; Connor TR, Loman NJ, Colizza V, Fraser C, Volz E, Ji X, Gutierrez B, Chand M, Dellicour S, Cauchemez S, Raghwani J, Suchard MA, Lemey P, Rambaut A, Pybus OG, Kraemer MUG. Tsui JL, et al. Science. 2023 Jul 21;381(6655):336-343. doi: 10.1126/science.adg6605. Epub 2023 Jul 20. Science. 2023. PMID: 37471538 Free PMC article.
Data integration in Bayesian phylogenetics.
Hassler GW, Magee A, Zhang Z, Baele G, Lemey P, Ji X, Fourment M, Suchard MA. Hassler GW, et al. Annu Rev Stat Appl. 2023;10:353-377. doi: 10.1146/annurev-statistics-033021-112532. Epub 2022 Sep 28. Annu Rev Stat Appl. 2023. PMID: 38774036 Free PMC article.
Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer.
McBride D, Garushyants S, Franks J, Magee A, Overend S, Huey D, Williams A, Faith S, Kandeil A, Trifkovic S, Miller L, Jeevan T, Patel A, Nolting J, Tonkovich M, Genders JT, Montoney A, Kasnyik K, Linder T, Bevins S, Lenoch J, Chandler J, DeLiberto T, Koonin E, Suchard M, Lemey P, Webby R, Nelson M, Bowman A. McBride D, et al. Res Sq [Preprint]. 2023 Feb 16:rs.3.rs-2574993. doi: 10.21203/rs.3.rs-2574993/v1. Res Sq. 2023. Update in: Nat Commun. 2023 Aug 28;14(1):5105. doi: 10.1038/s41467-023-40706-y PMID: 36824718 Free PMC article. Updated. Preprint.
Variational Supertrees for Bayesian Phylogenetics.
Karcher MD, Zhang C, Matsen FA 4th. Karcher MD, et al. Bull Math Biol. 2024 Aug 5;86(9):114. doi: 10.1007/s11538-024-01338-5. Bull Math Biol. 2024. PMID: 39101994 Free PMC article.
32 results