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Page 1
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. Among authors: hinrichs as. bioRxiv [Preprint]. 2024 Nov 5:2024.04.29.591666. doi: 10.1101/2024.04.29.591666. bioRxiv. 2024. PMID: 38746185 Free PMC article. Preprint.
A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control.
Thornlow B, Hinrichs AS, Jain M, Dhillon N, La S, Kapp JD, Anigbogu I, Cassatt-Johnstone M, McBroome J, Haeussler M, Turakhia Y, Chang T, Olsen HE, Sanford J, Stone M, Vaske O, Bjork I, Akeson M, Shapiro B, Haussler D, Kilpatrick AM, Corbett-Detig R. Thornlow B, et al. Among authors: hinrichs as. bioRxiv [Preprint]. 2021 Apr 6:2021.04.05.438352. doi: 10.1101/2021.04.05.438352. bioRxiv. 2021. PMID: 33851162 Free PMC article. Preprint.
Pandemic-scale phylogenetics.
Ye C, Thornlow B, Kramer A, McBroome J, Hinrichs A, Corbett-Detig R, Turakhia Y. Ye C, et al. bioRxiv [Preprint]. 2021 Dec 6:2021.12.03.470766. doi: 10.1101/2021.12.03.470766. bioRxiv. 2021. PMID: 34927180 Free PMC article. Preprint.
Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches.
Thornlow B, Kramer A, Ye C, De Maio N, McBroome J, Hinrichs AS, Lanfear R, Turakhia Y, Corbett-Detig R. Thornlow B, et al. Among authors: hinrichs as. bioRxiv [Preprint]. 2022 May 18:2021.12.02.471004. doi: 10.1101/2021.12.02.471004. bioRxiv. 2022. Update in: Syst Biol. 2023 Nov 1;72(5):1039-1051. doi: 10.1093/sysbio/syad031 PMID: 35611334 Free PMC article. Updated. Preprint.
Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus below the Subgroup Level.
Goya S, Ruis C, Neher RA, Meijer A, Aziz A, Hinrichs AS, von Gottberg A, Roemer C, Amoako DG, Acuña D, McBroome J, Otieno JR, Bhiman JN, Everatt J, Muñoz-Escalante JC, Ramaekers K, Duggan K, Presser LD, Urbanska L, Venter M, Wolter N, Peret TCT, Salimi V, Potdar V, Borges V, Viegas M. Goya S, et al. Among authors: hinrichs as. Emerg Infect Dis. 2024 Aug;30(8):1631-1641. doi: 10.3201/eid3008.240209. Emerg Infect Dis. 2024. PMID: 39043393 Free PMC article.
The UCSC Genome Browser database: 2025 update.
Perez G, Barber GP, Benet-Pages A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Nassar LR, Raney BJ, Speir ML, van Baren MJ, Vaske CJ, Haussler D, Kent WJ, Haeussler M. Perez G, et al. Among authors: hinrichs as. Nucleic Acids Res. 2024 Oct 26:gkae974. doi: 10.1093/nar/gkae974. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39460617
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: hinrichs as. Virus Evol. 2024 Jan 11;10(1):vead085. doi: 10.1093/ve/vead085. eCollection 2024. Virus Evol. 2024. PMID: 38361813 Free PMC article.
67 results