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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. Among authors: karp pd. Database (Oxford). 2022 Aug 12;2022:baac062. doi: 10.1093/database/baac062. Database (Oxford). 2022. PMID: 35961013 Free PMC article.
The COMBREX project: design, methodology, and initial results.
Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S. Anton BP, et al. PLoS Biol. 2013;11(8):e1001638. doi: 10.1371/journal.pbio.1001638. Epub 2013 Aug 27. PLoS Biol. 2013. PMID: 24013487 Free PMC article.
Groups: knowledge spreadsheets for symbolic biocomputing.
Travers M, Paley SM, Shrager J, Holland TA, Karp PD. Travers M, et al. Among authors: karp pd. Database (Oxford). 2013 Sep 14;2013:bat061. doi: 10.1093/database/bat061. Print 2013. Database (Oxford). 2013. PMID: 24037025 Free PMC article.
The past, present and future of genome-wide re-annotation.
Ouzounis CA, Karp PD. Ouzounis CA, et al. Among authors: karp pd. Genome Biol. 2002;3(2):COMMENT2001. doi: 10.1186/gb-2002-3-2-comment2001. Epub 2002 Jan 31. Genome Biol. 2002. PMID: 11864365 Free PMC article. Review.
Multidimensional annotation of the Escherichia coli K-12 genome.
Karp PD, Keseler IM, Shearer A, Latendresse M, Krummenacker M, Paley SM, Paulsen I, Collado-Vides J, Gama-Castro S, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spínola MI, Bonavides-Martinez C, Ingraham J. Karp PD, et al. Nucleic Acids Res. 2007;35(22):7577-90. doi: 10.1093/nar/gkm740. Epub 2007 Oct 16. Nucleic Acids Res. 2007. PMID: 17940092 Free PMC article.
An advanced web query interface for biological databases.
Latendresse M, Karp PD. Latendresse M, et al. Among authors: karp pd. Database (Oxford). 2010 Jul 6;2010:baq006. doi: 10.1093/database/baq006. Database (Oxford). 2010. PMID: 20624715 Free PMC article.
149 results