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Efficient storage of high throughput DNA sequencing data using reference-based compression.
Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E. Hsi-Yang Fritz M, et al. Genome Res. 2011 May;21(5):734-40. doi: 10.1101/gr.114819.110. Epub 2011 Jan 18. Genome Res. 2011. PMID: 21245279 Free PMC article.
FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community.
Harrison PW, Fan J, Richardson D, Clarke L, Zerbino D, Cochrane G, Archibald AL, Schmidt CJ, Flicek P. Harrison PW, et al. Anim Genet. 2018 Dec;49(6):520-526. doi: 10.1111/age.12736. Epub 2018 Oct 12. Anim Genet. 2018. PMID: 30311252 Free PMC article.
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. Bowers RM, et al. Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893. Nat Biotechnol. 2017. PMID: 28787424 Free PMC article.
Plant specimen contextual data consensus.
Hoopen PT, Walls RL, Cannon EK, Cochrane G, Cole J, Johnston A, Karsch-Mizrachi I, Yilmaz P. Hoopen PT, et al. Gigascience. 2016 Dec 1;5(1):1-4. doi: 10.1093/gigascience/giw002. Gigascience. 2016. PMID: 28369359 Free PMC article.
Archiving next generation sequencing data.
Shumway M, Cochrane G, Sugawara H. Shumway M, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D870-1. doi: 10.1093/nar/gkp1078. Epub 2009 Dec 3. Nucleic Acids Res. 2010. PMID: 19965774 Free PMC article.
The European Nucleotide Archive.
Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Ten Hoopen P, Vaughan R, Zalunin V, Cochrane G. Leinonen R, et al. Nucleic Acids Res. 2011 Jan;39(Database issue):D28-31. doi: 10.1093/nar/gkq967. Epub 2010 Oct 23. Nucleic Acids Res. 2011. PMID: 20972220 Free PMC article.
Content discovery and retrieval services at the European Nucleotide Archive.
Silvester N, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Ten Hoopen P, Kay S, Leinonen R, Li W, Liu X, Lopez R, Pakseresht N, Pallreddy S, Plaister S, Radhakrishnan R, Rossello M, Senf A, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Silvester N, et al. Nucleic Acids Res. 2015 Jan;43(Database issue):D23-9. doi: 10.1093/nar/gku1129. Epub 2014 Nov 17. Nucleic Acids Res. 2015. PMID: 25404130 Free PMC article.
The European Bioinformatics Institute in 2018: tools, infrastructure and training.
Cook CE, Lopez R, Stroe O, Cochrane G, Brooksbank C, Birney E, Apweiler R. Cook CE, et al. Nucleic Acids Res. 2019 Jan 8;47(D1):D15-D22. doi: 10.1093/nar/gky1124. Nucleic Acids Res. 2019. PMID: 30445657 Free PMC article.
The international nucleotide sequence database collaboration.
Karsch-Mizrachi I, Takagi T, Cochrane G; International Nucleotide Sequence Database Collaboration. Karsch-Mizrachi I, et al. Nucleic Acids Res. 2018 Jan 4;46(D1):D48-D51. doi: 10.1093/nar/gkx1097. Nucleic Acids Res. 2018. PMID: 29190397 Free PMC article.
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