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SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method.
de Bernardi Schneider A, Su M, Hinrichs AS, Wang J, Amin H, Bell J, Wadford DA, O'Toole Á, Scher E, Perry MD, Turakhia Y, De Maio N, Hughes S, Corbett-Detig R. de Bernardi Schneider A, et al. Among authors: turakhia y. Virus Evol. 2024 Jan 11;10(1):vead085. doi: 10.1093/ve/vead085. eCollection 2024. Virus Evol. 2024. PMID: 38361813 Free PMC article.
DecentTree: scalable Neighbour-Joining for the genomic era.
Wang W, Barbetti J, Wong T, Thornlow B, Corbett-Detig R, Turakhia Y, Lanfear R, Minh BQ. Wang W, et al. Among authors: turakhia y. Bioinformatics. 2023 Sep 2;39(9):btad536. doi: 10.1093/bioinformatics/btad536. Bioinformatics. 2023. PMID: 37651445 Free PMC article.
Maximum likelihood pandemic-scale phylogenetics.
De Maio N, Kalaghatgi P, Turakhia Y, Corbett-Detig R, Minh BQ, Goldman N. De Maio N, et al. Among authors: turakhia y. Nat Genet. 2023 May;55(5):746-752. doi: 10.1038/s41588-023-01368-0. Epub 2023 Apr 10. Nat Genet. 2023. PMID: 37038003 Free PMC article.
30 results