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Decomposition of overlapping protein complexes: a graph theoretical method for analyzing static and dynamic protein associations.

Zotenko E, Guimarães KS, Jothi R, Przytycka TM.

Algorithms Mol Biol. 2006 Apr 26;1(1):7.PMID: 16722537 [PubMed]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

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

From pull-down data to protein interaction networks and complexes with biological relevance.

Zhang B, Park BH, Karpinets T, Samatova NF.

Bioinformatics. 2008 Apr 1;24(7):979-86. Epub 2008 Feb 26.PMID: 18304937 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein evolution on a human signaling network.

Cui Q, Purisima EO, Wang E.

BMC Syst Biol. 2009 Feb 18;3:21.PMID: 19226461 [PubMed - indexed for MEDLINE]Related articlesFree article

Uncovering Biological Network Function via Graphlet Degree Signatures.

Milenkoviæ T, Pržulj N.

Cancer Inform. 2008;6:257-273. Epub 2008 Apr 14.PMID: 19259413 [PubMed - as supplied by publisher]Related articlesFree article

Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks.

Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I.

BMC Bioinformatics. 2007 Jul 10;8:243.PMID: 17620146 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein networking: insights into global functional organization of proteomes.

Pieroni E, de la Fuente van Bentem S, Mancosu G, Capobianco E, Hirt H, de la Fuente A.

Proteomics. 2008 Feb;8(4):799-816. Review.PMID: 18297653 [PubMed - indexed for MEDLINE]Related articles

ProtNet: a tool for stochastic simulations of protein interaction networks dynamics.

Bernaschi M, Castiglione F, Ferranti A, Gavrila C, Tinti M, Cesareni G.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S4.PMID: 17430571 [PubMed - indexed for MEDLINE]Related articlesFree article

The unfoldomics decade: an update on intrinsically disordered proteins.

Dunker AK, Oldfield CJ, Meng J, Romero P, Yang JY, Chen JW, Vacic V, Obradovic Z, Uversky VN.

BMC Genomics. 2008 Sep 16;9 Suppl 2:S1.PMID: 18831774 [PubMed - indexed for MEDLINE]Related articlesFree article

Information flow analysis of interactome networks.

Missiuro PV, Liu K, Zou L, Ross BC, Zhao G, Liu JS, Ge H.

PLoS Comput Biol. 2009 Apr;5(4):e1000350. Epub 2009 Apr 10.PMID: 19503817 [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

The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles.

Durek P, Walther D.

BMC Syst Biol. 2008 Nov 25;2:100.PMID: 19032748 [PubMed - indexed for MEDLINE]Related articlesFree article

Dynamic networks from hierarchical bayesian graph clustering.

Park Y, Moore C, Bader JS.

PLoS One. 2010 Jan 11;5(1):e8118.PMID: 20084108 [PubMed - in process]Related articlesFree article

Detecting conserved interaction patterns in biological networks.

Koyutürk M, Kim Y, Subramaniam S, Szpankowski W, Grama A.

J Comput Biol. 2006 Sep;13(7):1299-322.PMID: 17037960 [PubMed - indexed for MEDLINE]Related articles

Biological process linkage networks.

Dotan-Cohen D, Letovsky S, Melkman AA, Kasif S.

PLoS One. 2009;4(4):e5313. Epub 2009 Apr 23.PMID: 19390589 [PubMed - indexed for MEDLINE]Related articlesFree article

Discovering functional interaction patterns in protein-protein interaction networks.

Turanalp ME, Can T.

BMC Bioinformatics. 2008 Jun 11;9:276.PMID: 18547430 [PubMed - indexed for MEDLINE]Related articlesFree article

A core-attachment based method to detect protein complexes in PPI networks.

Wu M, Li X, Kwoh CK, Ng SK.

BMC Bioinformatics. 2009 Jun 2;10:169.PMID: 19486541 [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

Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages.

Del Sol A, Araúzo-Bravo MJ, Amoros D, Nussinov R.

Genome Biol. 2007;8(5):R92.PMID: 17531094 [PubMed - indexed for MEDLINE]Related articlesFree article