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Items: 1 to 20 of 174

1.

Revealing biological modules via graph summarization.

Navlakha S, Schatz MC, Kingsford C.

J Comput Biol. 2009 Feb;16(2):253-64. doi: 10.1089/cmb.2008.11TT.

PMID:
19183002
2.

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.

3.

Evaluation of clustering algorithms for protein-protein interaction networks.

Brohée S, van Helden J.

BMC Bioinformatics. 2006 Nov 6;7:488.

4.

A novel subgradient-based optimization algorithm for blockmodel functional module identification.

Wang Y, Qian X.

BMC Bioinformatics. 2013;14 Suppl 2:S23. doi: 10.1186/1471-2105-14-S2-S23. Epub 2013 Jan 21.

5.

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

Vlasblom J, Wodak SJ.

BMC Bioinformatics. 2009 Mar 30;10:99. doi: 10.1186/1471-2105-10-99.

6.

Efficient and accurate Greedy Search Methods for mining functional modules in protein interaction networks.

He J, Li C, Ye B, Zhong W.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S19. doi: 10.1186/1471-2105-13-S10-S19.

7.

A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification.

Yu L, Gao L, Li K, Zhao Y, Chiu DK.

Comput Biol Chem. 2011 Oct 12;35(5):298-307. doi: 10.1016/j.compbiolchem.2011.07.005. Epub 2011 Jul 20.

PMID:
22000801
8.

Detection of functional modules from protein interaction networks with an enhanced random walk based algorithm.

Cai B, Wang H, Zheng H, Wang H.

Int J Comput Biol Drug Des. 2011;4(3):290-306. doi: 10.1504/IJCBDD.2011.041416. Epub 2011 Jul 21.

PMID:
21778561
9.

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
10.

Finding molecular complexes through multiple layer clustering of protein interaction networks.

Andreopoulos B, An A, Huang X, Wang X.

Int J Bioinform Res Appl. 2007;3(1):65-85.

PMID:
18048173
11.

Detecting functional modules in the yeast protein-protein interaction network.

Chen J, Yuan B.

Bioinformatics. 2006 Sep 15;22(18):2283-90. Epub 2006 Jul 12.

PMID:
16837529
12.

Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins.

Cho YR, Zhang A.

BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S3. doi: 10.1186/1471-2105-11-S3-S3.

13.

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
14.

Modular organization of protein interaction networks.

Luo F, Yang Y, Chen CF, Chang R, Zhou J, Scheuermann RH.

Bioinformatics. 2007 Jan 15;23(2):207-14. Epub 2006 Nov 8. Erratum in: Bioinformatics. 2007 Apr 1;23(7):916.

PMID:
17092991
15.

Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data.

Li M, Wu X, Wang J, Pan Y.

BMC Bioinformatics. 2012 May 23;13:109. doi: 10.1186/1471-2105-13-109.

16.

Identification of functional modules in a PPI network by bounded diameter clustering.

Sohaee N, Forst CV.

J Bioinform Comput Biol. 2010 Dec;8(6):929-43.

PMID:
21121019
17.

Identifying similar functional modules by a new hybrid spectral clustering method.

Madani S, Faez K, Aminghafari M.

IET Syst Biol. 2012 Oct;6(5):175-86. doi: 10.1049/iet-syb.2010.0066.

PMID:
23101872
18.

ACC-FMD: ant colony clustering for functional module detection in protein-protein interaction networks.

Ji J, Liu H, Zhang A, Liu Z, Liu C.

Int J Data Min Bioinform. 2015;11(3):331-63.

PMID:
26333266
19.

Algorithms for effective querying of compound graph-based pathway databases.

Dogrusoz U, Cetintas A, Demir E, Babur O.

BMC Bioinformatics. 2009 Nov 16;10:376. doi: 10.1186/1471-2105-10-376.

20.

Predicting protein complexes from weighted protein-protein interaction graphs with a novel unsupervised methodology: Evolutionary enhanced Markov clustering.

Theofilatos K, Pavlopoulou N, Papasavvas C, Likothanassis S, Dimitrakopoulos C, Georgopoulos E, Moschopoulos C, Mavroudi S.

Artif Intell Med. 2015 Mar;63(3):181-9. doi: 10.1016/j.artmed.2014.12.012. Epub 2015 Feb 18.

PMID:
25765008

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