Evaluation of clustering algorithms for protein-protein interaction networks
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* Corresponding author: Sylvain Brohée sylvain@scmbb.ulb.ac.be
BMC Bioinformatics 2006, 7:488 doi:10.1186/1471-2105-7-488
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An overlapping module identification method in protein-protein interaction networks Xuesong Wang, Lijing Li, Yuhu Cheng BMC Bioinformatics 2012, 13(Suppl 7):S4 (8 May 2012) |
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Xia Wang, Junjie Yue, Xianwen Ren, Yuelan Wang, Mingfeng Tan, Beiping Li, Long Liang Theoretical Biology and Medical Modelling 2011, 8:47 (22 December 2011) |
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Which clustering algorithm is better for predicting protein complexes? Charalampos N Moschopoulos, Georgios A Pavlopoulos, Ernesto Iacucci, Jan Aerts, Spiridon Likothanassis, Reinhard Schneider, Sophia Kossida BMC Research Notes 2011, 4:549 (20 December 2011) |
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Annie Glatigny, Lise Mathieu, Christopher J Herbert, Geneviève Dujardin, Brigitte Meunier, Marie-Hélène Mucchielli-Giorgi BMC Systems Biology 2011, 5:173 (25 October 2011) |
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Proceedings
A binary matrix factorization algorithm for protein complex prediction Shikui Tu, Runsheng Chen, Lei Xu Proteome Science 2011, 9(Suppl 1):S18 (14 October 2011) |
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Proceedings
NWE: Node-weighted expansion for protein complex prediction using random walk distances Osamu Maruyama, Ayaka Chihara Proteome Science 2011, 9(Suppl 1):S14 (14 October 2011) |
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Proceedings
Ontology integration to identify protein complex in protein interaction networks Bo Xu, Hongfei Lin, Zhihao Yang Proteome Science 2011, 9(Suppl 1):S7 (14 October 2011) |
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Research article
Biological interaction networks are conserved at the module level Guy E Zinman, Shan Zhong, Ziv Bar-Joseph BMC Systems Biology 2011, 5:134 (23 August 2011) |
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Methodology article
A comparison of the functional modules identified from time course and static PPI network data Xiwei Tang, Jianxin Wang, Binbin Liu, Min Li, Gang Chen, Yi Pan BMC Bioinformatics 2011, 12:339 (15 August 2011) |
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Dynamical Basis for Drug Resistance of HIV-1 Protease Yi Mao BMC Structural Biology 2011, 11:31 (8 July 2011) |
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George D Kritikos, Charalampos Moschopoulos, Michalis Vazirgiannis, Sophia Kossida BMC Bioinformatics 2011, 12:239 (16 June 2011) |
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Andrés F Flórez, Daeui Park, Jong Bhak, Byoung-Chul Kim, Allan Kuchinsky, John H Morris, Jairo Espinosa, Carlos Muskus BMC Bioinformatics 2010, 11:484 (27 September 2010) |
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Proceedings
Determining modular organization of protein interaction networks by maximizing modularity density Shihua Zhang, Xue-Mei Ning, Chris Ding, Xiang-Sun Zhang BMC Systems Biology 2010, 4(Suppl 2):S10 (13 September 2010) |
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Response of the mosquito protein interaction network to dengue infection Xiang Guo, Yao Xu, Guowu Bian, Andrew D Pike, Yan Xie, Zhiyong Xi BMC Genomics 2010, 11:380 (16 June 2010) |
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Research
Computational approaches for detecting protein complexes from protein interaction networks: a survey Xiaoli Li, Min Wu, Chee-Keong Kwoh, See-Kiong Ng BMC Genomics 2010, 11(Suppl 1):S3 (10 February 2010) |
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Methodology article
Algorithms for effective querying of compound graph-based pathway databases Ugur Dogrusoz, Ahmet Cetintas, Emek Demir, Ozgun Babur BMC Bioinformatics 2009, 10:376 (16 November 2009) |
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Arabidopsis gene co-expression network and its functional modules Linyong Mao, John L Van Hemert, Sudhansu Dash, Julie A Dickerson BMC Bioinformatics 2009, 10:346 (21 October 2009) |
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RRW: repeated random walks on genome-scale protein networks for local cluster discovery Kathy Macropol, Tolga Can, Ambuj K Singh BMC Bioinformatics 2009, 10:283 (9 September 2009) |
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Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell Antonio Marco, Ignacio Marín BMC Systems Biology 2009, 3:69 (15 July 2009) |
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Proceedings
GIBA: a clustering tool for detecting protein complexes Charalampos N Moschopoulos, Georgios A Pavlopoulos, Reinhard Schneider, Spiridon D Likothanassis, Sophia Kossida BMC Bioinformatics 2009, 10(Suppl 6):S11 (16 June 2009) |
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Methodology article
A core-attachment based method to detect protein complexes in PPI networks Min Wu, Xiaoli Li, Chee-Keong Kwoh, See-Kiong Ng BMC Bioinformatics 2009, 10:169 (2 June 2009) |
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Methodology article
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs James Vlasblom, Shoshana J Wodak BMC Bioinformatics 2009, 10:99 (30 March 2009) |
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Proceedings
Identification of functional modules based on transcriptional regulation structure Etienne Birmelé, Mohamed Elati, Céline Rouveirol, Christophe Ambroise BMC Proceedings 2008, 2(Suppl 4):S4 (17 December 2008) |
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Research article
An in silico method for detecting overlapping functional modules from composite biological networks Ioannis A Maraziotis, Konstantina Dimitrakopoulou, Anastasios Bezerianos BMC Systems Biology 2008, 2:93 (1 November 2008) |
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Database
FUNYBASE: a FUNgal phYlogenomic dataBASE Sylvain Marthey, Gabriela Aguileta, François Rodolphe, Annie Gendrault, Tatiana Giraud, Elisabeth Fournier, Manuela Lopez-Villavicencio, Angélique Gautier, Marc-Henri Lebrun, Hélène Chiapello BMC Bioinformatics 2008, 9:456 (27 October 2008) |
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Methodology article
Modifying the DPClus algorithm for identifying protein complexes based on new topological structures Min Li, Jian-er Chen, Jian-xin Wang, Bin Hu, Gang Chen BMC Bioinformatics 2008, 9:398 (25 September 2008) |
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Research article
Discovering functional interaction patterns in protein-protein interaction networks Mehmet E Turanalp, Tolga Can BMC Bioinformatics 2008, 9:276 (11 June 2008) |
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Research article
Rekin's Janky, Jacques van Helden BMC Bioinformatics 2008, 9:37 (23 January 2008) |
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Method
Consistent dissection of the protein interaction network by combining global and local metrics Chunlin Wang, Chris Ding, Qiaofeng Yang, Stephen R Holbrook Genome Biology 2007, 8:R271 (21 December 2007) A new network decomposition method is proposed that uses both a global metric and a local metric to identify protein interaction modules in the protein interaction network. |
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Research article
Identifying protein complexes directly from high-throughput TAP data with Markov random fields Wasinee Rungsarityotin, Roland Krause, Arno Schödl, Alexander Schliep BMC Bioinformatics 2007, 8:482 (19 December 2007) |
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Research article
A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality G Traver Hart, Insuk Lee, Edward M Marcotte BMC Bioinformatics 2007, 8:236 (2 July 2007) |