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References for PMC Articles for PubMed (Select 17062145)


Taverna: a tool for building and running workflows of services.

Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W729-32.


Quantitative assessment of dictionary-based protein named entity tagging.

Liu H, Hu ZZ, Torii M, Wu C, Friedman C.

J Am Med Inform Assoc. 2006 Sep-Oct;13(5):497-507. Epub 2006 Jun 23.


Aetiology-specific patterns in end-stage heart failure patients identified by functional annotation and classification of microarray data.

Beisvag V, Lehre PK, Midelfart H, Aass H, Geiran O, Sandvik AK, Laegreid A, Komorowski J, Ellingsen O.

Eur J Heart Fail. 2006 Jun;8(4):381-9. Epub 2006 Jun 6.


The Gene Ontology (GO) project in 2006.

Gene Ontology Consortium.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D322-6.


Microarray data analysis: from disarray to consolidation and consensus.

Allison DB, Cui X, Page GP, Sabripour M.

Nat Rev Genet. 2006 Jan;7(1):55-65. Review. Erratum in: Nat Rev Genet. 2006 May;7(5):406.


GeneCruiser: a web service for the annotation of microarray data.

Liefeld T, Reich M, Gould J, Zhang P, Tamayo P, Mesirov JP.

Bioinformatics. 2005 Sep 15;21(18):3681-2. Epub 2005 Jul 19.


Ontological analysis of gene expression data: current tools, limitations, and open problems.

Khatri P, Drăghici S.

Bioinformatics. 2005 Sep 15;21(18):3587-95. Epub 2005 Jun 30.


FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.

Al-Shahrour F, Díaz-Uriarte R, Dopazo J.

Bioinformatics. 2004 Mar 1;20(4):578-80. Epub 2004 Jan 22.


The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.

Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D262-6.


GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data.

Martínez-Cruz LA, Rubio A, Martínez-Chantar ML, Labarga A, Barrio I, Podhorski A, Segura V, Sevilla Campo JL, Avila MA, Mato JM.

Bioinformatics. 2003 Nov 1;19(16):2158-60.


Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate.

Draghici S, Khatri P, Bhavsar P, Shah A, Krawetz SA, Tainsky MA.

Nucleic Acids Res. 2003 Jul 1;31(13):3775-81.


GeneLynx mouse: integrated portal to the mouse genome.

Lenhard B, Wahlestedt C, Wasserman WW.

Genome Res. 2003 Jun;13(6B):1501-4.


GoMiner: a resource for biological interpretation of genomic and proteomic data.

Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, Weinstein JN.

Genome Biol. 2003;4(4):R28. Epub 2003 Mar 25.


The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum.

Bioinformatics. 2003 Mar 1;19(4):524-31.


SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.

Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA.

Nucleic Acids Res. 2003 Jan 1;31(1):219-23.


NetAffx: Affymetrix probesets and annotations.

Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, Siani-Rose MA.

Nucleic Acids Res. 2003 Jan 1;31(1):82-6.


BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data.

Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, Peterson C.

Genome Biol. 2002 Jul 15;3(8):SOFTWARE0003. Epub 2002 Jul 15.


Rat Genome Database (RGD): mapping disease onto the genome.

Twigger S, Lu J, Shimoyama M, Chen D, Pasko D, Long H, Ginster J, Chen CF, Nigam R, Kwitek A, Eppig J, Maltais L, Maglott D, Schuler G, Jacob H, Tonellato PJ.

Nucleic Acids Res. 2002 Jan 1;30(1):125-8.


Comparisons of predictive values of binary medical diagnostic tests for paired designs.

Leisenring W, Alonzo T, Pepe MS.

Biometrics. 2000 Jun;56(2):345-51.


Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G.

Nat Genet. 2000 May;25(1):25-9. No abstract available.

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