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Semantic integration to identify overlapping functional modules in protein interaction networks
Young-Rae Cho, Woochang Hwang, Murali Ramanathan, Aidong Zhang
BMC Bioinformatics. 2007; 8: 265. Published online 2007 July 24. doi: 10.1186/1471-2105-8-265
PMCID:
PMC1971074
Abstract Full Text PDF–397K Supplementary Material

Is Cited by the Following 14 Articles in this Archive:

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 Res Notes. 2011; 4: 549. Published online 2011 December 20. doi: 10.1186/1756-0500-4-549
PMCID:
PMC3267700
Abstract Full Text PDF–389K Supplementary Material
Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation
Ágoston Mihalik, Peter Csermely
PLoS Comput Biol. 2011 October; 7(10): e1002187. Published online 2011 October 13. doi: 10.1371/journal.pcbi.1002187
PMCID:
PMC3192799
Abstract Full Text PDF–1.7M Supplementary Material
Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme
George D Kritikos, Charalampos Moschopoulos, Michalis Vazirgiannis, Sophia Kossida
BMC Bioinformatics. 2011; 12: 239. Published online 2011 June 16. doi: 10.1186/1471-2105-12-239
PMCID:
PMC3230908
Abstract Full Text PDF–853K
GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns
Xinan Yang, Jianrong Li, Younghee Lee, Yves A. Lussier
Bioinformatics. 2011 May 15; 27(10): 1444–1446. Published online 2011 March 17. doi: 10.1093/bioinformatics/btr142
PMCID:
PMC3087953
Abstract Full Text PDF–403K Supplementary Material
Recent advances in clustering methods for protein interaction networks
Jianxin Wang, Min Li, Youping Deng, Yi Pan
BMC Genomics. 2010; 11(Suppl 3): S10. Published online 2010 December 1. doi: 10.1186/1471-2164-11-S3-S10
PMCID:
PMC2999340
Abstract Full Text PDF–597K
Identifying protein complexes from interaction networks based on clique percolation and distance restriction
Jianxin Wang, Binbin Liu, Min Li, Yi Pan
BMC Genomics. 2010; 11(Suppl 2): S10. Published online 2010 November 2. doi: 10.1186/1471-2164-11-S2-S10
PMCID:
PMC2975417
Abstract Full Text PDF–976K
PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes
Khader Shameer, Lalima L Madan, Shivamurthy Veeranna, Balasubramanian Gopal, Ramanathan Sowdhamini
BMC Bioinformatics. 2010; 11: 473. Published online 2010 September 22. doi: 10.1186/1471-2105-11-473
PMCID:
PMC2955050
Abstract Full Text PDF–884K Supplementary Material
Investigating the validity of current network analysis on static conglomerate networks by protein network stratification
Minlu Zhang, Long J Lu
BMC Bioinformatics. 2010; 11: 466. Published online 2010 September 16. doi: 10.1186/1471-2105-11-466
PMCID:
PMC2949894
Abstract Full Text PDF–3.7M Supplementary Material
Determining modular organization of protein interaction networks by maximizing modularity density
Shihua Zhang, Xue-Mei Ning, Chris Ding, Xiang-Sun Zhang
BMC Syst Biol. 2010; 4(Suppl 2): S10. Published online 2010 September 13. doi: 10.1186/1752-0509-4-S2-S10
PMCID:
PMC2982684
Abstract Full Text PDF–885K
Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins
Young-Rae Cho, Aidong Zhang
BMC Bioinformatics. 2010; 11(Suppl 3): S3. Published online 2010 April 29. doi: 10.1186/1471-2105-11-S3-S3
PMCID:
PMC2863062
Abstract Full Text PDF–658K
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. Published online 2010 February 10. doi: 10.1186/1471-2164-11-S1-S3
PMCID:
PMC2822531
Abstract Full Text
Semantic Similarity in Biomedical Ontologies
Catia Pesquita, Daniel Faria, André O. Falcão, Phillip Lord, Francisco M. Couto
PLoS Comput Biol. 2009 July; 5(7): e1000443. Published online 2009 July 31. doi: 10.1371/journal.pcbi.1000443
PMCID:
PMC2712090
Abstract Full Text PDF–277K
An in silico method for detecting overlapping functional modules from composite biological networks
Ioannis A Maraziotis, Konstantina Dimitrakopoulou, Anastasios Bezerianos
BMC Syst Biol. 2008; 2: 93. Published online 2008 November 1. doi: 10.1186/1752-0509-2-93
PMCID:
PMC2600641
Abstract Full Text PDF–1.0M
A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge
Young-Rae Cho, Lei Shi, Murali Ramanathan, Aidong Zhang
BMC Bioinformatics. 2008; 9: 382. Published online 2008 September 18. doi: 10.1186/1471-2105-9-382
PMCID:
PMC2570367
Abstract Full Text PDF–447K Supplementary Material
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