PubMed

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.

Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP.

Genome Biol. 2008;9 Suppl 1:S2. Epub 2008 Jun 27.PMID: 18613946 [PubMed - indexed for MEDLINE]Related articlesFree article

Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy.

Kim WK, Krumpelman C, Marcotte EM.

Genome Biol. 2008;9 Suppl 1:S5. Epub 2008 Jun 27.PMID: 18613949 [PubMed - indexed for MEDLINE]Related articlesFree article

An en masse phenotype and function prediction system for Mus musculus.

Taşan M, Tian W, Hill DP, Gibbons FD, Blake JA, Roth FP.

Genome Biol. 2008;9 Suppl 1:S8. Epub 2008 Jun 27.PMID: 18613952 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting gene function in a hierarchical context with an ensemble of classifiers.

Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, Troyanskaya OG.

Genome Biol. 2008;9 Suppl 1:S3. Epub 2008 Jun 27.PMID: 18613947 [PubMed - indexed for MEDLINE]Related articlesFree article

Information theory applied to the sparse gene ontology annotation network to predict novel gene function.

Tao Y, Sam L, Li J, Friedman C, Lussier YA.

Bioinformatics. 2007 Jul 1;23(13):i529-38.PMID: 17646340 [PubMed - indexed for MEDLINE]Related articlesFree article

Incorporating functional inter-relationships into protein function prediction algorithms.

Pandey G, Myers CL, Kumar V.

BMC Bioinformatics. 2009 May 12;10:142.PMID: 19435516 [PubMed - indexed for MEDLINE]Related articlesFree article

Consistent probabilistic outputs for protein function prediction.

Obozinski G, Lanckriet G, Grant C, Jordan MI, Noble WS.

Genome Biol. 2008;9 Suppl 1:S6. Epub 2008 Jun 27.PMID: 18613950 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparative gene prediction in human and mouse.

Parra G, Agarwal P, Abril JF, Wiehe T, Fickett JW, Guigó R.

Genome Res. 2003 Jan;13(1):108-17.PMID: 12529313 [PubMed - indexed for MEDLINE]Related articlesFree article

PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data.

Hawkins T, Chitale M, Luban S, Kihara D.

Proteins. 2009 Feb 15;74(3):566-82.PMID: 18655063 [PubMed - indexed for MEDLINE]Related articles

Integrative approaches to the prediction of protein functions based on the feature selection.

Ko S, Lee H.

BMC Bioinformatics. 2009 Dec 31;10:455.PMID: 20043848 [PubMed - in process]Related articlesFree article

Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome.

Buza TJ, McCarthy FM, Burgess SC.

BMC Genomics. 2007 Nov 19;8:425.PMID: 18021451 [PubMed - indexed for MEDLINE]Related articlesFree article

Globally predicting protein functions based on co-expressed protein-protein interaction networks and ontology taxonomy similarities.

Zhu M, Gao L, Guo Z, Li Y, Wang D, Wang J, Wang C.

Gene. 2007 Apr 15;391(1-2):113-9. Epub 2006 Dec 22.PMID: 17289301 [PubMed - indexed for MEDLINE]Related articles

PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data.

Bréhélin L, Dufayard JF, Gascuel O.

BMC Bioinformatics. 2008 Oct 16;9:440.PMID: 18925948 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting protein linkages in bacteria: which method is best depends on task.

Karimpour-Fard A, Leach SM, Gill RT, Hunter LE.

BMC Bioinformatics. 2008 Sep 24;9:397.PMID: 18816389 [PubMed - indexed for MEDLINE]Related articlesFree article

The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation.

Yu C, Zavaljevski N, Desai V, Johnson S, Stevens FJ, Reifman J.

BMC Bioinformatics. 2008 Jan 25;9:52.PMID: 18221520 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of evolutionarily conserved interologs in Mus musculus.

Yellaboina S, Dudekula DB, Ko MSh.

BMC Genomics. 2008 Oct 8;9:465.PMID: 18842131 [PubMed - indexed for MEDLINE]Related articlesFree article

Hierarchical multi-label prediction of gene function.

Barutcuoglu Z, Schapire RE, Troyanskaya OG.

Bioinformatics. 2006 Apr 1;22(7):830-6. Epub 2006 Jan 12.PMID: 16410319 [PubMed - indexed for MEDLINE]Related articlesFree article

Probabilistic protein function prediction from heterogeneous genome-wide data.

Nariai N, Kolaczyk ED, Kasif S.

PLoS One. 2007 Mar 28;2(3):e337.PMID: 17396164 [PubMed - in process]Related articlesFree article

The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks.

Hsing M, Byler KG, Cherkasov A.

BMC Syst Biol. 2008 Sep 16;2:80.PMID: 18796161 [PubMed - indexed for MEDLINE]Related articlesFree article

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function.

Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q.

Genome Biol. 2008;9 Suppl 1:S4. Epub 2008 Jun 27.PMID: 18613948 [PubMed - indexed for MEDLINE]Related articlesFree article