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A traveling salesman approach for predicting protein functions.

Johnson O, Liu J.

Source Code Biol Med. 2006 Oct 12;1:3.PMID: 17147783 [PubMed]Related articlesFree article

Faster and more accurate global protein function assignment from protein interaction networks using the MFGO algorithm.

Sun S, Zhao Y, Jiao Y, Yin Y, Cai L, Zhang Y, Lu H, Chen R, Bu D.

FEBS Lett. 2006 Mar 20;580(7):1891-6. Epub 2006 Feb 28.PMID: 16516894 [PubMed - indexed for MEDLINE]Related articles

ClusFCM: an algorithm for predicting protein functions using homologies and protein interactions.

Nguyen C, Mannino M, Gardiner K, Cios KJ.

J Bioinform Comput Biol. 2008 Feb;6(1):203-22.PMID: 18324753 [PubMed - indexed for MEDLINE]Related articles

Protein functional class prediction using global encoding of amino acid sequence.

Li X, Liao B, Shu Y, Zeng Q, Luo J.

J Theor Biol. 2009 Nov 21;261(2):290-3. Epub 2009 Jul 23.PMID: 19631664 [PubMed - in process]Related articles

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

A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge.

Cho YR, Shi L, Ramanathan M, Zhang A.

BMC Bioinformatics. 2008 Sep 18;9:382.PMID: 18801191 [PubMed - indexed for MEDLINE]Related articlesFree article

Improving protein function prediction methods with integrated literature data.

Gabow AP, Leach SM, Baumgartner WA, Hunter LE, Goldberg DS.

BMC Bioinformatics. 2008 Apr 15;9:198.PMID: 18412966 [PubMed - indexed for MEDLINE]Related articlesFree article

Inferring protein-protein interactions from multiple protein domain combinations.

Kanaan SP, Huang C, Wuchty S, Chen DZ, Izaguirre JA.

Methods Mol Biol. 2009;541:43-59. Review.PMID: 19381530 [PubMed - indexed for MEDLINE]Related articles

Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies.

DiMaggio PA Jr, McAllister SR, Floudas CA, Feng XJ, Rabinowitz JD, Rabitz HA.

BMC Bioinformatics. 2008 Oct 27;9:458.PMID: 18954459 [PubMed - indexed for MEDLINE]Related articlesFree article

A structural approach for finding functional modules from large biological networks.

Mete M, Tang F, Xu X, Yuruk N.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S19.PMID: 18793464 [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

Message-passing algorithms for the prediction of protein domain interactions from protein-protein interaction data.

Iqbal M, Freitas AA, Johnson CG, Vergassola M.

Bioinformatics. 2008 Sep 15;24(18):2064-70. Epub 2008 Jul 17.PMID: 18641010 [PubMed - indexed for MEDLINE]Related articlesFree article

Markov clustering versus affinity propagation for the partitioning of protein interaction graphs.

Vlasblom J, Wodak SJ.

BMC Bioinformatics. 2009 Mar 30;10:99.PMID: 19331680 [PubMed - indexed for MEDLINE]Related articlesFree article

Diffusion kernel-based logistic regression models for protein function prediction.

Lee H, Tu Z, Deng M, Sun F, Chen T.

OMICS. 2006 Spring;10(1):40-55.PMID: 16584317 [PubMed - indexed for MEDLINE]Related articles

GAIA: a gram-based interaction analysis tool--an approach for identifying interacting domains in yeast.

Zhang KX, Ouellette BF.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S60.PMID: 19208164 [PubMed - indexed for MEDLINE]Related articlesFree article

A domain-based approach to predict protein-protein interactions.

Singhal M, Resat H.

BMC Bioinformatics. 2007 Jun 13;8:199.PMID: 17567909 [PubMed - indexed for MEDLINE]Related articlesFree article

Ensemble non-negative matrix factorization methods for clustering protein-protein interactions.

Greene D, Cagney G, Krogan N, Cunningham P.

Bioinformatics. 2008 Aug 1;24(15):1722-8. Epub 2008 Jun 12.PMID: 18556670 [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

Widely predicting specific protein functions based on protein-protein interaction data and gene expression profile.

Gao L, Li X, Guo Z, Zhu M, Li Y, Rao S.

Sci China C Life Sci. 2007 Feb;50(1):125-34.PMID: 17393093 [PubMed - indexed for MEDLINE]Related articles

Using indirect protein-protein interactions for protein complex prediction.

Chua HN, Ning K, Sung WK, Leong HW, Wong L.

J Bioinform Comput Biol. 2008 Jun;6(3):435-66.PMID: 18574858 [PubMed - indexed for MEDLINE]Related articles