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Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data.
Mayne R, Secret S, Geoghegan C, Trebes A, Kean K, Reid K, Lin GL, Ansari MA, de Cesare M, Bonsall D, Elliott I, Piazza P, Brown A, Bray J, Knight JC, Harvala H, Breuer J, Simmonds P, Bowden RJ, Golubchik T. Mayne R, et al. Among authors: golubchik t. Bioinformatics. 2024 Oct 1;40(10):btae591. doi: 10.1093/bioinformatics/btae591. Bioinformatics. 2024. PMID: 39360992 Free PMC article.
Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses.
Buddle S, Forrest L, Akinsuyi N, Martin Bernal LM, Brooks T, Venturini C, Miller C, Brown JR, Storey N, Atkinson L, Best T, Roy S, Goldsworthy S, Castellano S, Simmonds P, Harvala H, Golubchik T, Williams R, Breuer J, Morfopoulou S, Torres Montaguth OE. Buddle S, et al. Among authors: golubchik t. Genome Med. 2024 Sep 9;16(1):111. doi: 10.1186/s13073-024-01380-x. Genome Med. 2024. PMID: 39252069 Free PMC article.
Improving the representativeness of UK's national COVID-19 Infection Survey through spatio-temporal regression and post-stratification.
Pouwels KB, Eyre DW, House T, Aspey B, Matthews PC, Stoesser N, Newton JN, Diamond I, Studley R, Taylor NGH, Bell JI, Farrar J, Kolenchery J, Marsden BD, Hoosdally S, Jones EY, Stuart DI, Crook DW, Peto TEA, Walker AS; COVID−19 Infection Survey Team. Pouwels KB, et al. Nat Commun. 2024 Jun 24;15(1):5340. doi: 10.1038/s41467-024-49201-4. Nat Commun. 2024. PMID: 38914564 Free PMC article.
Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus.
Lin GL, Drysdale SB, Snape MD, O'Connor D, Brown A, MacIntyre-Cockett G, Mellado-Gomez E, de Cesare M, Ansari MA, Bonsall D, Bray JE, Jolley KA, Bowden R, Aerssens J, Bont L, Openshaw PJM, Martinon-Torres F, Nair H, Golubchik T, Pollard AJ; RESCEU Consortium. Lin GL, et al. Among authors: golubchik t. Nat Commun. 2024 Mar 16;15(1):2379. doi: 10.1038/s41467-024-46648-3. Nat Commun. 2024. PMID: 38493135 Free PMC article.
Prevalence of persistent SARS-CoV-2 in a large community surveillance study.
Ghafari M, Hall M, Golubchik T, Ayoubkhani D, House T, MacIntyre-Cockett G, Fryer HR, Thomson L, Nurtay A, Kemp SA, Ferretti L, Buck D, Green A, Trebes A, Piazza P, Lonie LJ, Studley R, Rourke E, Smith DL, Bashton M, Nelson A, Crown M, McCann C, Young GR, Santos RAND, Richards Z, Tariq MA, Cahuantzi R; Wellcome Sanger Institute COVID-19 Surveillance Team; COVID-19 Infection Survey Group; COVID-19 Genomics UK (COG-UK) Consortium; Barrett J, Fraser C, Bonsall D, Walker AS, Lythgoe K. Ghafari M, et al. Among authors: golubchik t. Nature. 2024 Feb;626(8001):1094-1101. doi: 10.1038/s41586-024-07029-4. Epub 2024 Feb 21. Nature. 2024. PMID: 38383783 Free PMC article.
Advancing pathogen genomics in resource-limited settings.
Pronyk PM, de Alwis R, Rockett R, Basile K, Boucher YF, Pang V, Sessions O, Getchell M, Golubchik T, Lam C, Lin R, Mak TM, Marais B, Twee-Hee Ong R, Clapham HE, Wang L, Cahyorini Y, Polotan FGM, Rukminiati Y, Sim E, Suster C, Smith GJD, Sintchenko V. Pronyk PM, et al. Among authors: golubchik t. Cell Genom. 2023 Nov 17;3(12):100443. doi: 10.1016/j.xgen.2023.100443. eCollection 2023 Dec 13. Cell Genom. 2023. PMID: 38116115 Free PMC article. Review.
112 results