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Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M. Mavian C, et al. Among authors: lam tt. Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12522-12523. doi: 10.1073/pnas.2007295117. Epub 2020 May 7. Proc Natl Acad Sci U S A. 2020. PMID: 32381734 Free PMC article. No abstract available.
Spatial dynamics of human-origin H1 influenza A virus in North American swine.
Nelson MI, Lemey P, Tan Y, Vincent A, Lam TT, Detmer S, Viboud C, Suchard MA, Rambaut A, Holmes EC, Gramer M. Nelson MI, et al. Among authors: lam tt. PLoS Pathog. 2011 Jun;7(6):e1002077. doi: 10.1371/journal.ppat.1002077. Epub 2011 Jun 9. PLoS Pathog. 2011. PMID: 21695237 Free PMC article.
Phylodynamics of H5N1 avian influenza virus in Indonesia.
Lam TT, Hon CC, Lemey P, Pybus OG, Shi M, Tun HM, Li J, Jiang J, Holmes EC, Leung FC. Lam TT, et al. Mol Ecol. 2012 Jun;21(12):3062-77. doi: 10.1111/j.1365-294X.2012.05577.x. Epub 2012 May 11. Mol Ecol. 2012. PMID: 22574738
Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region.
Dellicour S, Lemey P, Artois J, Lam TT, Fusaro A, Monne I, Cattoli G, Kuznetsov D, Xenarios I, Dauphin G, Kalpravidh W, Von Dobschuetz S, Claes F, Newman SH, Suchard MA, Baele G, Gilbert M. Dellicour S, et al. Among authors: lam tt. Bioinformatics. 2020 Apr 1;36(7):2098-2104. doi: 10.1093/bioinformatics/btz882. Bioinformatics. 2020. PMID: 31790143 Free PMC article.
Unlocking capacities of genomics for the COVID-19 response and future pandemics.
Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TT, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. Knyazev S, et al. Among authors: lam tt. Nat Methods. 2022 Apr;19(4):374-380. doi: 10.1038/s41592-022-01444-z. Nat Methods. 2022. PMID: 35396471 Free PMC article.
424 results