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Evaluation of clustering algorithms for protein-protein interaction networks.

Brohée S, van Helden J.

BMC Bioinformatics. 2006 Nov 6;7:488.PMID: 17087821 [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

An automated method for finding molecular complexes in large protein interaction networks.

Bader GD, Hogue CW.

BMC Bioinformatics. 2003 Jan 13;4:2. Epub 2003 Jan 13.PMID: 12525261 [PubMed - indexed for MEDLINE]Related articlesFree article

Combining functional and topological properties to identify core modules in protein interaction networks.

Lubovac Z, Gamalielsson J, Olsson B.

Proteins. 2006 Sep 1;64(4):948-59.PMID: 16794996 [PubMed - indexed for MEDLINE]Related articles

Identification of functional modules in a PPI network by clique percolation clustering.

Zhang S, Ning X, Zhang XS.

Comput Biol Chem. 2006 Dec;30(6):445-51. Epub 2006 Nov 13.PMID: 17098476 [PubMed - indexed for MEDLINE]Related articles

GIBA: a clustering tool for detecting protein complexes.

Moschopoulos CN, Pavlopoulos GA, Schneider R, Likothanassis SD, Kossida S.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S11.PMID: 19534736 [PubMed - indexed for MEDLINE]Related articlesFree article

Revealing biological modules via graph summarization.

Navlakha S, Schatz MC, Kingsford C.

J Comput Biol. 2009 Feb;16(2):253-64.PMID: 19183002 [PubMed - indexed for MEDLINE]Related articles

Protein complex prediction via cost-based clustering.

King AD, Przulj N, Jurisica I.

Bioinformatics. 2004 Nov 22;20(17):3013-20. Epub 2004 Jun 4.PMID: 15180928 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein complex prediction based on mutually exclusive interactions in protein interaction network.

Jung SH, Jang WH, Hur HY, Hyun B, Han DS.

Genome Inform. 2008;21:77-88.PMID: 19425149 [PubMed - indexed for MEDLINE]Related articlesFree article

Super paramagnetic clustering of protein sequences.

Tetko IV, Facius A, Ruepp A, Mewes HW.

BMC Bioinformatics. 2005 Apr 1;6:82.PMID: 15804359 [PubMed - indexed for MEDLINE]Related articlesFree article

Modifying the DPClus algorithm for identifying protein complexes based on new topological structures.

Li M, Chen JE, Wang JX, Hu B, Chen G.

BMC Bioinformatics. 2008 Sep 25;9:398.PMID: 18816408 [PubMed - indexed for MEDLINE]Related articlesFree article

Clustering proteins from interaction networks for the prediction of cellular functions.

Brun C, Herrmann C, Guénoche A.

BMC Bioinformatics. 2004 Jul 13;5:95.PMID: 15251039 [PubMed - indexed for MEDLINE]Related articlesFree article

Growing functional modules from a seed protein via integration of protein interaction and gene expression data.

Maraziotis IA, Dimitrakopoulou K, Bezerianos A.

BMC Bioinformatics. 2007 Oct 23;8:408.PMID: 17956603 [PubMed - indexed for MEDLINE]Related articlesFree article

The interactome as a tree--an attempt to visualize the protein-protein interaction network in yeast.

Lu H, Zhu X, Liu H, Skogerbø G, Zhang J, Zhang Y, Cai L, Zhao Y, Sun S, Xu J, Bu D, Chen R.

Nucleic Acids Res. 2004 Sep 8;32(16):4804-11. Print 2004.PMID: 15356297 [PubMed - indexed for MEDLINE]Related articlesFree article

Are scale-free networks robust to measurement errors?

Lin N, Zhao H.

BMC Bioinformatics. 2005 May 16;6:119.PMID: 15904487 [PubMed - indexed for MEDLINE]Related articlesFree article

Interaction graph mining for protein complexes using local clique merging.

Li XL, Tan SH, Foo CS, Ng SK.

Genome Inform. 2005;16(2):260-9.PMID: 16901108 [PubMed - indexed for MEDLINE]Related articles

Identifying protein complexes directly from high-throughput TAP data with Markov random fields.

Rungsarityotin W, Krause R, Schödl A, Schliep A.

BMC Bioinformatics. 2007 Dec 19;8:482.PMID: 18093306 [PubMed - indexed for MEDLINE]Related articlesFree article

A unified representation of multiprotein complex data for modeling interaction networks.

Ding C, He X, Meraz RF, Holbrook SR.

Proteins. 2004 Oct 1;57(1):99-108.PMID: 15326596 [PubMed - indexed for MEDLINE]Related articles

High-quality binary protein interaction map of the yeast interactome network.

Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabási AL, Tavernier J, Hill DE, Vidal M.

Science. 2008 Oct 3;322(5898):104-10. Epub 2008 Aug 21.PMID: 18719252 [PubMed - indexed for MEDLINE]Related articlesFree article

Estimating the parameters of a model for protein-protein interaction graphs.

Deshmukh V, Cannings C, Thomas A.

Math Med Biol. 2006 Dec;23(4):279-95. Epub 2006 Jul 20.PMID: 16857705 [PubMed - indexed for MEDLINE]Related articles