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The European Nucleotide Archive in 2017.
Silvester N, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L, Cleland I, Harrison PW, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Menchi M, Reddy K, Pakseresht N, Rajan J, Rossello M, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Silvester N, et al. Among authors: keane t. Nucleic Acids Res. 2018 Jan 4;46(D1):D36-D40. doi: 10.1093/nar/gkx1125. Nucleic Acids Res. 2018. PMID: 29140475 Free PMC article.
Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux.
Petty NK, Feltwell T, Pickard D, Clare S, Toribio AL, Fookes M, Roberts K, Monson R, Nair S, Kingsley RA, Bulgin R, Wiles S, Goulding D, Keane T, Corton C, Lennard N, Harris D, Willey D, Rance R, Yu L, Choudhary JS, Churcher C, Quail MA, Parkhill J, Frankel G, Dougan G, Salmond GP, Thomson NR. Petty NK, et al. Among authors: keane t. PLoS Pathog. 2011 Apr;7(4):e1002018. doi: 10.1371/journal.ppat.1002018. Epub 2011 Apr 7. PLoS Pathog. 2011. PMID: 21490962 Free PMC article.
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.
Variation in genome-wide mutation rates within and between human families.
Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P; 1000 Genomes Project. Conrad DF, et al. Nat Genet. 2011 Jun 12;43(7):712-4. doi: 10.1038/ng.862. Nat Genet. 2011. PMID: 21666693 Free PMC article.
The 1000 Genomes Project: data management and community access.
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P; 1000 Genomes Project Consortium. Clarke L, et al. Nat Methods. 2012 Apr 27;9(5):459-62. doi: 10.1038/nmeth.1974. Nat Methods. 2012. PMID: 22543379 Free PMC article.
Integrative annotation of variants from 1092 humans: application to cancer genomics.
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium; Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Khurana E, et al. Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587. Science. 2013. PMID: 24092746 Free PMC article.
htsget: a protocol for securely streaming genomic data.
Kelleher J, Lin M, Albach CH, Birney E, Davies R, Gourtovaia M, Glazer D, Gonzalez CY, Jackson DK, Kemp A, Marshall J, Nowak A, Senf A, Tovar-Corona JM, Vikhorev A, Keane TM; GA4GH Streaming Task Team. Kelleher J, et al. Bioinformatics. 2019 Jan 1;35(1):119-121. doi: 10.1093/bioinformatics/bty492. Bioinformatics. 2019. PMID: 29931085 Free PMC article.
The European Nucleotide Archive in 2018.
Harrison PW, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Holt S, Hussein A, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Milano A, Pakseresht N, Rajan J, Reddy K, Richards E, Rosello M, Silvester N, Smirnov D, Toribio AL, Vijayaraja S, Cochrane G. Harrison PW, et al. Among authors: keane t. Nucleic Acids Res. 2019 Jan 8;47(D1):D84-D88. doi: 10.1093/nar/gky1078. Nucleic Acids Res. 2019. PMID: 30395270 Free PMC article.
The European Nucleotide Archive in 2019.
Amid C, Alako BTF, Balavenkataraman Kadhirvelu V, Burdett T, Burgin J, Fan J, Harrison PW, Holt S, Hussein A, Ivanov E, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martinez-Villacorta J, Milano A, Pakseresht A, Rahman N, Rajan J, Reddy K, Richards E, Smirnov D, Sokolov A, Vijayaraja S, Cochrane G. Amid C, et al. Among authors: keane t. Nucleic Acids Res. 2020 Jan 8;48(D1):D70-D76. doi: 10.1093/nar/gkz1063. Nucleic Acids Res. 2020. PMID: 31722421 Free PMC article.
Refget: standardized access to reference sequences.
Yates AD, Adams J, Chaturvedi S, Davies RM, Laird M, Leinonen R, Nag R, Sheffield NC, Hofmann O, Keane TM. Yates AD, et al. Bioinformatics. 2021 Dec 22;38(1):299-300. doi: 10.1093/bioinformatics/btab524. Bioinformatics. 2021. PMID: 34260694 Free PMC article.
669 results