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RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis.
Lucaci AG, Zehr JD, Shank SD, Bouvier D, Mei H, Nekrutenko A, Martin DP, Kosakovsky Pond SL. Lucaci AG, et al. Among authors: kosakovsky pond sl. bioRxiv [Preprint]. 2022 Jan 18:2022.01.15.476448. doi: 10.1101/2022.01.15.476448. bioRxiv. 2022. PMID: 35075458 Free PMC article. Updated. Preprint.
Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring.
Maier W, Bray S, van den Beek M, Bouvier D, Coraor N, Miladi M, Singh B, De Argila JR, Baker D, Roach N, Gladman S, Coppens F, Martin DP, Lonie A, Grüning B, Kosakovsky Pond SL, Nekrutenko A. Maier W, et al. Among authors: kosakovsky pond sl. bioRxiv [Preprint]. 2021 Mar 25:2021.03.25.437046. doi: 10.1101/2021.03.25.437046. bioRxiv. 2021. PMID: 33791701 Free PMC article. Updated. Preprint.
Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function.
Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins G, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A; NGS-SA; Williamson C, Hsiao NY, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL. Martin DP, et al. Among authors: kosakovsky pond sl. bioRxiv [Preprint]. 2022 Jan 18:2022.01.14.476382. doi: 10.1101/2022.01.14.476382. bioRxiv. 2022. PMID: 35075456 Free PMC article. Updated. Preprint.
Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models.
Sianga-Mete R, Hartnady P, Mandikumba WC, Rutherford K, Currin CB, Phelanyane F, Stefan S, Kosakovsky Pond SL, Martin DP. Sianga-Mete R, et al. Among authors: kosakovsky pond sl. Res Sq [Preprint]. 2022 Dec 29:rs.3.rs-2407778. doi: 10.21203/rs.3.rs-2407778/v1. Res Sq. 2022. PMID: 36597548 Free PMC article. Preprint.
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.
Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bomberg E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJC, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PGS, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Kosakovsky Pond SL, LaPolice TM, Lee C, Lewis AP, Loh YE, Masterson P, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O'Neill RJ, Eichler E, Phillippy AM. Makova KD, et al. Among authors: kosakovsky pond sl. bioRxiv [Preprint]. 2023 Dec 1:2023.11.30.569198. doi: 10.1101/2023.11.30.569198. bioRxiv. 2023. PMID: 38077089 Free PMC article. Preprint.
The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus.
Langedijk AC, Vrancken B, Lebbink RJ, Wilkins D, Kelly EJ, Baraldi E, Mascareñas de Los Santos AH, Danilenko DM, Choi EH, Palomino MA, Chi H, Keller C, Cohen R, Papenburg J, Pernica J, Greenough A, Richmond P, Martinón-Torres F, Heikkinen T, Stein RT, Hosoya M, Nunes MC, Verwey C, Evers A, Kragten-Tabatabaie L, Suchard MA, Kosakovsky Pond SL, Poletto C, Colizza V, Lemey P, Bont LJ; INFORM-RSV Study Group. Langedijk AC, et al. Among authors: kosakovsky pond sl. Nat Commun. 2024 Apr 10;15(1):3083. doi: 10.1038/s41467-024-47118-6. Nat Commun. 2024. PMID: 38600104 Free PMC article.
Anti-COVID drug accelerates viral evolution.
Kosakovsky Pond SL, Martin D. Kosakovsky Pond SL, et al. Nature. 2023 Nov;623(7987):486-487. doi: 10.1038/d41586-023-03248-3. Nature. 2023. PMID: 37875683 No abstract available.
Recommendations on data sharing in HIV drug resistance research.
Inzaule SC, Siedner MJ, Little SJ, Avila-Rios S, Ayitewala A, Bosch RJ, Calvez V, Ceccherini-Silberstein F, Charpentier C, Descamps D, Eshleman SH, Fokam J, Frenkel LM, Gupta RK, Ioannidis JPA, Kaleebu P, Kantor R, Kassaye SG, Kosakovsky Pond SL, Kouamou V, Kouyos RD, Kuritzkes DR, Lessells R, Marcelin AG, Mbuagbaw L, Minalga B, Ndembi N, Neher RA, Paredes R, Pillay D, Raizes EG, Rhee SY, Richman DD, Ruxrungtham K, Sabeti PC, Schapiro JM, Sirivichayakul S, Steegen K, Sugiura W, van Zyl GU, Vandamme AM, Wensing AMJ, Wertheim JO, Gunthard HF, Jordan MR, Shafer RW. Inzaule SC, et al. Among authors: kosakovsky pond sl. PLoS Med. 2023 Sep 22;20(9):e1004293. doi: 10.1371/journal.pmed.1004293. eCollection 2023 Sep. PLoS Med. 2023. PMID: 37738247 Free PMC article.
145 results