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Items: 1 to 20 of 40

1.

The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.

Galperin MY, Fernández-Suárez XM.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1-8. doi: 10.1093/nar/gkr1196. Epub 2011 Dec 5.

2.

The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis.

Li JW, Robison K, Martin M, Sjödin A, Usadel B, Young M, Olivares EC, Bolser DM.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1313-7. doi: 10.1093/nar/gkr1058. Epub 2011 Nov 15.

3.

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation.

Wilkinson MD, Vandervalk B, McCarthy L.

J Biomed Semantics. 2011 Oct 24;2(1):8. doi: 10.1186/2041-1480-2-8.

4.

Chipster: user-friendly analysis software for microarray and other high-throughput data.

Kallio MA, Tuimala JT, Hupponen T, Klemelä P, Gentile M, Scheinin I, Koski M, Käki J, Korpelainen EI.

BMC Genomics. 2011 Oct 14;12:507. doi: 10.1186/1471-2164-12-507.

5.

War of ontology worlds: mathematics, computer code, or Esperanto?

Rzhetsky A, Evans JA.

PLoS Comput Biol. 2011 Sep;7(9):e1002191. doi: 10.1371/journal.pcbi.1002191. Epub 2011 Sep 29.

6.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO.

Nat Biotechnol. 2011 May;29(5):415-20. doi: 10.1038/nbt.1823.

7.

Semantics-based composition of EMBOSS services.

Lamprecht AL, Naujokat S, Margaria T, Steffen B.

J Biomed Semantics. 2011 Mar 7;2 Suppl 1:S5. doi: 10.1186/2041-1480-2-S1-S5.

8.

BIO::Phylo-phyloinformatic analysis using perl.

Vos RA, Caravas J, Hartmann K, Jensen MA, Miller C.

BMC Bioinformatics. 2011 Feb 27;12:63. doi: 10.1186/1471-2105-12-63.

9.

Community-driven computational biology with Debian Linux.

Möller S, Krabbenhöft HN, Tille A, Paleino D, Williams A, Wolstencroft K, Goble C, Holland R, Belhachemi D, Plessy C.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S5. doi: 10.1186/1471-2105-11-S12-S5.

10.

Towards BioDBcore: a community-defined information specification for biological databases.

Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group.

Nucleic Acids Res. 2011 Jan;39(Database issue):D7-10. doi: 10.1093/nar/gkq1173. Epub 2010 Nov 18.

11.

The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research.

Tenenbaum JD, Whetzel PL, Anderson K, Borromeo CD, Dinov ID, Gabriel D, Kirschner B, Mirel B, Morris T, Noy N, Nyulas C, Rubenson D, Saxman PR, Singh H, Whelan N, Wright Z, Athey BD, Becich MJ, Ginsburg GS, Musen MA, Smith KA, Tarantal AF, Rubin DL, Lyster P.

J Biomed Inform. 2011 Feb;44(1):137-45. doi: 10.1016/j.jbi.2010.10.003. Epub 2010 Oct 16.

12.

Adding a little reality to building ontologies for biology.

Lord P, Stevens R.

PLoS One. 2010 Sep 3;5(9):e12258. doi: 10.1371/journal.pone.0012258.

13.

The BioPAX community standard for pathway data sharing.

Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD.

Nat Biotechnol. 2010 Sep;28(9):935-42. doi: 10.1038/nbt.1666. Epub 2010 Sep 9. Erratum in: Nat Biotechnol. 2010 Dec;28(12):1308. Nat Biotechnol. 2012 Apr;30(4):365. Reubenacker, Oliver [corrected to Ruebenacker, Oliver].

14.

BioXSD: the common data-exchange format for everyday bioinformatics web services.

Kalas M, Puntervoll P, Joseph A, Bartaseviciūte E, Töpfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, Rapacki K, Jonassen I.

Bioinformatics. 2010 Sep 15;26(18):i540-6. doi: 10.1093/bioinformatics/btq391.

15.

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Goecks J, Nekrutenko A, Taylor J; Galaxy Team.

Genome Biol. 2010;11(8):R86. doi: 10.1186/gb-2010-11-8-r86. Epub 2010 Aug 25.

16.

myExperiment: a repository and social network for the sharing of bioinformatics workflows.

Goble CA, Bhagat J, Aleksejevs S, Cruickshank D, Michaelides D, Newman D, Borkum M, Bechhofer S, Roos M, Li P, De Roure D.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W677-82. doi: 10.1093/nar/gkq429. Epub 2010 May 25.

17.

BioCatalogue: a universal catalogue of web services for the life sciences.

Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W689-94. doi: 10.1093/nar/gkq394. Epub 2010 May 19.

18.

The EMBRACE web service collection.

Pettifer S, Ison J, Kalas M, Thorne D, McDermott P, Jonassen I, Liaquat A, Fernández JM, Rodriguez JM; INB-Partners, Pisano DG, Blanchet C, Uludag M, Rice P, Bartaseviciute E, Rapacki K, Hekkelman M, Sand O, Stockinger H, Clegg AB, Bongcam-Rudloff E, Salzemann J, Breton V, Attwood TK, Cameron G, Vriend G.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W683-8. doi: 10.1093/nar/gkq297. Epub 2010 May 12.

19.

The Ontology Lookup Service: bigger and better.

Côté R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W155-60. doi: 10.1093/nar/gkq331. Epub 2010 May 11.

20.

phyloXML: XML for evolutionary biology and comparative genomics.

Han MV, Zmasek CM.

BMC Bioinformatics. 2009 Oct 27;10:356. doi: 10.1186/1471-2105-10-356.

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