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Text mining for biology--the way forward: opinions from leading scientists.
Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, Rebholz-Schuhmann D, Shatkay H, Valencia A. Altman RB, et al. Genome Biol. 2008;9 Suppl 2(Suppl 2):S7. doi: 10.1186/gb-2008-9-s2-s7. Epub 2008 Sep 1. Genome Biol. 2008. PMID: 18834498 Free PMC article.
SnapShot: S-Phase Entry and Exit.
Burgess A, Vuong J, Marzec KA, Nicolai de Lichtenberg U, O'Donoghue SI, Jensen LJ. Burgess A, et al. Among authors: o donoghue si. Cell. 2019 Oct 17;179(3):802-802.e1. doi: 10.1016/j.cell.2019.09.031. Cell. 2019. PMID: 31626778 Free article.
Reflect: augmented browsing for the life scientist.
Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R. Pafilis E, et al. Nat Biotechnol. 2009 Jun;27(6):508-10. doi: 10.1038/nbt0609-508. Nat Biotechnol. 2009. PMID: 19513049 Free article. No abstract available.
Martini: using literature keywords to compare gene sets.
Soldatos TG, O'Donoghue SI, Satagopam VP, Jensen LJ, Brown NP, Barbosa-Silva A, Schneider R. Soldatos TG, et al. Nucleic Acids Res. 2010 Jan;38(1):26-38. doi: 10.1093/nar/gkp876. Epub 2009 Oct 25. Nucleic Acids Res. 2010. PMID: 19858102 Free PMC article.
A roadmap for the functional annotation of protein families: a community perspective.
de Crécy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O'Donoghue S, Orengo C, O'Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J. de Crécy-Lagard V, et al. Database (Oxford). 2022 Aug 12;2022:baac062. doi: 10.1093/database/baac062. Database (Oxford). 2022. PMID: 35961013 Free PMC article.
Aquaria: simplifying discovery and insight from protein structures.
O'Donoghue SI, Sabir KS, Kalemanov M, Stolte C, Wellmann B, Ho V, Roos M, Perdigão N, Buske FA, Heinrich J, Rost B, Schafferhans A. O'Donoghue SI, et al. Nat Methods. 2015 Feb;12(2):98-9. doi: 10.1038/nmeth.3258. Nat Methods. 2015. PMID: 25633501 No abstract available.
59 results