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Page 1
Twelve years of SAMtools and BCFtools.
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Danecek P, et al. Among authors: bonfield jk. Gigascience. 2021 Feb 16;10(2):giab008. doi: 10.1093/gigascience/giab008. Gigascience. 2021. PMID: 33590861 Free PMC article.
Gap5--editing the billion fragment sequence assembly.
Bonfield JK, Whitwham A. Bonfield JK, et al. Bioinformatics. 2010 Jul 15;26(14):1699-703. doi: 10.1093/bioinformatics/btq268. Epub 2010 May 30. Bioinformatics. 2010. PMID: 20513662 Free PMC article.
De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms.
Giordano F, Aigrain L, Quail MA, Coupland P, Bonfield JK, Davies RM, Tischler G, Jackson DK, Keane TM, Li J, Yue JX, Liti G, Durbin R, Ning Z. Giordano F, et al. Among authors: bonfield jk. Sci Rep. 2017 Jun 21;7(1):3935. doi: 10.1038/s41598-017-03996-z. Sci Rep. 2017. PMID: 28638050 Free PMC article.
Genomic reconstruction of the SARS-CoV-2 epidemic in England.
Vöhringer HS, Sanderson T, Sinnott M, De Maio N, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani CV, Gonçalves S, Jackson DK, Johnston I, Jung AW, Saint C, Sillitoe J, Suciu M, Goldman N, Panovska-Griffiths J; Wellcome Sanger Institute COVID-19 Surveillance Team; COVID-19 Genomics UK (COG-UK) Consortium*; Birney E, Volz E, Funk S, Kwiatkowski D, Chand M, Martincorena I, Barrett JC, Gerstung M. Vöhringer HS, et al. Nature. 2021 Dec;600(7889):506-511. doi: 10.1038/s41586-021-04069-y. Epub 2021 Oct 14. Nature. 2021. PMID: 34649268 Free PMC article.
SARS-CoV-2 evolution during treatment of chronic infection.
Kemp SA, Collier DA, Datir RP, Ferreira IATM, Gayed S, Jahun A, Hosmillo M, Rees-Spear C, Mlcochova P, Lumb IU, Roberts DJ, Chandra A, Temperton N; CITIID-NIHR BioResource COVID-19 Collaboration; COVID-19 Genomics UK (COG-UK) Consortium; Sharrocks K, Blane E, Modis Y, Leigh KE, Briggs JAG, van Gils MJ, Smith KGC, Bradley JR, Smith C, Doffinger R, Ceron-Gutierrez L, Barcenas-Morales G, Pollock DD, Goldstein RA, Smielewska A, Skittrall JP, Gouliouris T, Goodfellow IG, Gkrania-Klotsas E, Illingworth CJR, McCoy LE, Gupta RK. Kemp SA, et al. Nature. 2021 Apr;592(7853):277-282. doi: 10.1038/s41586-021-03291-y. Epub 2021 Feb 5. Nature. 2021. PMID: 33545711 Free PMC article.
Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England.
Vöhringer HS, Sanderson T, Sinnott M, De Maio N, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani CV, Gonçalves S, Jackson DK, Johnston I, Jung AW, Saint C, Sillitoe J, Suciu M, Goldman N, Panovska-Griffiths J; Wellcome Sanger Institute COVID-19 Surveillance Team; COVID-19 Genomics UK (COG-UK) Consortium*; Birney E, Volz E, Funk S, Kwiatkowski D, Chand M, Martincorena I, Barrett JC, Gerstung M. Vöhringer HS, et al. Nature. 2022 Jun;606(7915):E18. doi: 10.1038/s41586-022-04887-8. Nature. 2022. PMID: 35701578 Free PMC article. No abstract available.
Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning.
Nickbakhsh S, Hughes J, Christofidis N, Griffiths E, Shaaban S, Enright J, Smollett K, Nomikou K, Palmalux N, Tong L, Carmichael S, Sreenu VB, Orton R, Goldstein EJ, Tomb RM; COVID-19 Genomics UK (COG-UK) Consortium; Templeton K, Gunson RN, da Silva Filipe A, Milosevic C, Thomson E, Robertson DL, Holden MTG, Illingworth CJR, Smith-Palmer A. Nickbakhsh S, et al. Sci Rep. 2022 Jul 19;12(1):11735. doi: 10.1038/s41598-022-15661-1. Sci Rep. 2022. PMID: 35853960 Free PMC article.
GA4GH: International policies and standards for data sharing across genomic research and healthcare.
Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SOM, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Auvil JMG, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CWL, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJM, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen … See abstract for full author list ➔ Rehm HL, et al. Among authors: bonfield jk. Cell Genom. 2021 Nov 10;1(2):100029. doi: 10.1016/j.xgen.2021.100029. Cell Genom. 2021. PMID: 35072136 Free PMC article.
46 results