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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. Among authors: hinrichs a. 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.
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, de Maio N, Amenga-Etego LN, Amuzu DSY, Avaro M, Awandare GA, Ayivor-Djanie R, Bashton M, Batty EM, Bediako Y, De Belder D, Benedetti E, Bergthaler A, Boers SA, Campos J, Carr RAA, 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, Liu C, Malavige GN, Mashe T, Mongkolsapaya J, Montes B, Molina Mora JA, 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, 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; 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 Apr 30:2024.04.29.591666. doi: 10.1101/2024.04.29.591666. bioRxiv. 2024. PMID: 38746185 Free PMC article. Preprint.
The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group. Danecek P, et al. Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7. Bioinformatics. 2011. PMID: 21653522 Free PMC article.
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.
221 results