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Page 1
Maximum likelihood pandemic-scale phylogenetics.
De Maio N, Kalaghatgi P, Turakhia Y, Corbett-Detig R, Minh BQ, Goldman N. De Maio N, et al. 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.
Stability of SARS-CoV-2 phylogenies.
Turakhia Y, De Maio N, Thornlow B, Gozashti L, Lanfear R, Walker CR, Hinrichs AS, Fernandes JD, Borges R, Slodkowicz G, Weilguny L, Haussler D, Goldman N, Corbett-Detig R. Turakhia Y, et al. PLoS Genet. 2020 Nov 18;16(11):e1009175. doi: 10.1371/journal.pgen.1009175. eCollection 2020 Nov. PLoS Genet. 2020. PMID: 33206635 Free PMC article.
Inferring multi-locus selection in admixed populations.
Ayala NM, Genetti M, Corbett-Detig R. Ayala NM, et al. PLoS Genet. 2023 Nov 28;19(11):e1011062. doi: 10.1371/journal.pgen.1011062. eCollection 2023 Nov. PLoS Genet. 2023. PMID: 38015992 Free PMC article.
Mixed Wolbachia infections resolve rapidly during in vitro evolution.
Mirchandani C, Wang P, Jacobs J, Genetti M, Pepper-Tunick E, Sullivan WT, Corbett-Detig R, Russell SL. Mirchandani C, et al. PLoS Pathog. 2024 Jul 25;20(7):e1012149. doi: 10.1371/journal.ppat.1012149. eCollection 2024 Jul. PLoS Pathog. 2024. PMID: 39052691 Free PMC article.
The UCSC SARS-CoV-2 Genome Browser.
Fernandes JD, Hinrichs AS, Clawson H, Gonzalez JN, Lee BT, Nassar LR, Raney BJ, Rosenbloom KR, Nerli S, Rao AA, Schmelter D, Fyfe A, Maulding N, Zweig AS, Lowe TM, Ares M Jr, Corbet-Detig R, Kent WJ, Haussler D, Haeussler M. Fernandes JD, et al. Nat Genet. 2020 Oct;52(10):991-998. doi: 10.1038/s41588-020-0700-8. Nat Genet. 2020. PMID: 32908258 Free PMC article.
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.
Hunt M, Hinrichs AS, Anderson D, Karim L, Dearlove BL, Knaggs J, Constantinides B, Fowler PW, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, Kotzen B, de Maio N, Amenga-Etego LN, Amuzu DSY, Avaro M, Awandare GA, Ayivor-Djanie R, Barkham T, Bashton M, Batty EM, Bediako Y, De Belder D, Benedetti E, Bergthaler A, Boers SA, Campos J, Carr RAA, Chen YYC, Cuba F, Dattero ME, Dejnirattisai W, Dilthey A, Duedu KO, Endler L, Engelmann I, Francisco NM, Fuchs J, Gnimpieba EZ, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao NY, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki KKK, Kurkela S, Lappalainen M, Lataretu M, Lemieux J, Liu C, Malavige GN, Mashe T, Mongkolsapaya J, Montes B, Mora JAM, Morang'a CM, Mvula B, Nagarajan N, Nelson A, Ngoi JM, da Paixão JP, Panning M, Poklepovich T, Quashie PK, Ranasinghe D, Russo M, San JE, Sanderson ND, Scaria V, Screaton G, Sessions OM, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson RJ, Williamson C, Zair X; IMSSC2 Laboratory Network Consortium; de Oliveira T, Peto TE, Crook D, Corbett-Detig R, Iqbal Z. Hunt M, et al. bioRxiv [Preprint]. 2024 Nov 5:2024.04.29.591666. doi: 10.1101/2024.04.29.591666. bioRxiv. 2024. PMID: 38746185 Free PMC article. Preprint.
VGsim: Scalable viral genealogy simulator for global pandemic.
Shchur V, Spirin V, Sirotkin D, Burovski E, De Maio N, Corbett-Detig R. Shchur V, et al. PLoS Comput Biol. 2022 Aug 24;18(8):e1010409. doi: 10.1371/journal.pcbi.1010409. eCollection 2022 Aug. PLoS Comput Biol. 2022. PMID: 36001646 Free PMC article.
Inferring Adaptive Introgression Using Hidden Markov Models.
Svedberg J, Shchur V, Reinman S, Nielsen R, Corbett-Detig R. Svedberg J, et al. Mol Biol Evol. 2021 May 4;38(5):2152-2165. doi: 10.1093/molbev/msab014. Mol Biol Evol. 2021. PMID: 33502512 Free PMC article.
41 results