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A novel functional module detection algorithm for protein-protein interaction networks.

Hwang W, Cho YR, Zhang A, Ramanathan M.

Algorithms Mol Biol. 2006 Dec 5;1:24.PMID: 17147822 [PubMed]Related articlesFree article

CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions.

Hwang W, Cho YR, Zhang A, Ramanathan M.

BMC Bioinformatics. 2008 Jan 29;9:64.PMID: 18230159 [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

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

Semantic integration to identify overlapping functional modules in protein interaction networks.

Cho YR, Hwang W, Ramanathan M, Zhang A.

BMC Bioinformatics. 2007 Jul 24;8:265.PMID: 17650343 [PubMed - indexed for MEDLINE]Related articlesFree article

RRW: repeated random walks on genome-scale protein networks for local cluster discovery.

Macropol K, Can T, Singh AK.

BMC Bioinformatics. 2009 Sep 9;10:283.PMID: 19740439 [PubMed - indexed for MEDLINE]Related articlesFree article

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

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

An in silico method for detecting overlapping functional modules from composite biological networks.

Maraziotis IA, Dimitrakopoulou K, Bezerianos A.

BMC Syst Biol. 2008 Nov 1;2:93.PMID: 18976494 [PubMed - indexed for MEDLINE]Related articlesFree article

Assessing significance of connectivity and conservation in protein interaction networks.

Koyutürk M, Szpankowski W, Grama A.

J Comput Biol. 2007 Jul-Aug;14(6):747-64.PMID: 17691892 [PubMed - indexed for MEDLINE]Related articles

An ensemble framework for clustering protein-protein interaction networks.

Asur S, Ucar D, Parthasarathy S.

Bioinformatics. 2007 Jul 1;23(13):i29-40.PMID: 17646309 [PubMed - indexed for MEDLINE]Related articlesFree article

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.

Huttenhower C, Flamholz AI, Landis JN, Sahi S, Myers CL, Olszewski KL, Hibbs MA, Siemers NO, Troyanskaya OG, Coller HA.

BMC Bioinformatics. 2007 Jul 12;8:250.PMID: 17626636 [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

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

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

Inferring modules of functionally interacting proteins using the Bond Energy Algorithm.

Watanabe RL, Morett E, Vallejo EE.

BMC Bioinformatics. 2008 Jun 17;9:285.PMID: 18559112 [PubMed - indexed for MEDLINE]Related articlesFree article

A hybrid graph-theoretic method for mining overlapping functional modules in large sparse protein interaction networks.

Zhang S, Liu HW, Ning XM, Zhang XS.

Int J Data Min Bioinform. 2009;3(1):68-84.PMID: 19432377 [PubMed - indexed for MEDLINE]Related articles

Modularization of biochemical networks based on classification of Petri net t-invariants.

Grafahrend-Belau E, Schreiber F, Heiner M, Sackmann A, Junker BH, Grunwald S, Speer A, Winder K, Koch I.

BMC Bioinformatics. 2008 Feb 8;9:90.PMID: 18257938 [PubMed - indexed for MEDLINE]Related articlesFree article

Searching for functional gene modules with interaction component models.

Parkkinen JA, Kaski S.

BMC Syst Biol. 2010 Jan 25;4:4.PMID: 20100324 [PubMed - in process]Related articlesFree article

Detection of functional modules from protein interaction networks.

Pereira-Leal JB, Enright AJ, Ouzounis CA.

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