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Volumn 26, Issue 2, 2014, Pages 261-277

Survey: Functional module detection from protein-protein interaction networks

Author keywords

clustering algorithm; computation approach; functional module detection; Protein protein interaction network

Indexed keywords

BIOLOGICAL MECHANISMS; CLASSIFICATION SYSTEM; COMPUTATIONAL APPROACH; FUNCTIONAL MODULE DETECTIONS; FUNCTIONAL MODULES; PERFORMANCE COMPARISON; PROTEIN-PROTEIN INTERACTION NETWORKS; RELATIONSHIP NETWORKS;

EID: 84891785632     PISSN: 10414347     EISSN: None     Source Type: Journal    
DOI: 10.1109/TKDE.2012.225     Document Type: Article
Times cited : (103)

References (98)
  • 1
    • 0037370373 scopus 로고    scopus 로고
    • Proteomics: The first decade and beyond
    • DOI 10.1038/ng1106
    • S.D. Patternson and R.H. Aebersold, Proteomics: The First Decade and Beyond, Nature Genetics, vol. 33, pp. 311-323, 2003. (Pubitemid 36278841)
    • (2003) Nature Genetics , vol.33 , Issue.SUPPL. , pp. 311-323
    • Patterson, S.D.1    Aebersold, R.H.2
  • 5
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • DOI 10.1038/nature01511
    • R. Aebersold and M. Mann, Mass Spectrometry-Based Proteomics, Nature, vol. 422, pp. 198-207, 2003. (Pubitemid 36362757)
    • (2003) Nature , vol.422 , Issue.6928 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 7
    • 0034622925 scopus 로고    scopus 로고
    • Printing proteins as microarrays for high-throughput function determination
    • G. Macbeath and S.L. Schreiber, Printing Proteins as Microarrays for High-Throughput Function Determination, Science, vol. 289, pp. 1760-1763, 2000.
    • (2000) Science , vol.289 , pp. 1760-1763
    • Macbeath, G.1    Schreiber, S.L.2
  • 10
    • 2942549190 scopus 로고    scopus 로고
    • Prebind and textomy-mining the biomedical literature for protein-protein interactions using a support vector machine
    • article 11
    • I. Donaldson et al., PreBIND and Textomy-Mining the Biomedical Literature for Protein-Protein Interactions Using a Support Vector Machine, BMC Bioinformatics, vol. 4, article 11, 2003.
    • (2003) BMC Bioinformatics , vol.4
    • Donaldson, I.1
  • 11
    • 13344278672 scopus 로고    scopus 로고
    • Content-rich biological network constructed by mining pubmed abstracts
    • article 147
    • H. Chen and B. Sharp, Content-Rich Biological Network Constructed by Mining Pubmed Abstracts, BMC Bioinformatics, vol. 5, article 147, 2004.
    • (2004) BMC Bioinformatics , vol.5
    • Chen, H.1    Sharp, B.2
  • 12
    • 10244245424 scopus 로고    scopus 로고
    • BioRAT: Extracting biological information from full-length papers
    • DOI 10.1093/bioinformatics/bth386
    • D. Corney et al., BioRAT: Extracting Biological Information from Full-Length Papers, Bioinformatics, vol. 20, pp. 3206-3213, 2004. (Pubitemid 39619210)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3206-3213
    • Corney, D.P.A.1    Buxton, B.F.2    Langdon, W.B.3    Jones, D.T.4
  • 13
    • 57749107003 scopus 로고    scopus 로고
    • The current status and the prospect of bioinformatics
    • C.T. Zhang, The Current Status and the Prospect of Bioinformatics, World Science Technology Research & Development, vol. 22, no. 6, pp. 17-20, 2000.
    • (2000) World Science Technology Research & Development , vol.22 , Issue.6 , pp. 17-20
    • Zhang, C.T.1
  • 14
    • 0032828715 scopus 로고    scopus 로고
    • A generic protein purification method for protein complex characterization and proteome exploration
    • DOI 10.1038/13732
    • G. Rigaut, A. Shevchenko, B. Rutz, M. Wilm, and M. Mann, A Generic Protein Purification Method for Protein Complex Characterization and Proteome Exploration, Nature Biotechnology, vol. 17, no. 10, pp. 1030-1032, 1999. (Pubitemid 29474865)
    • (1999) Nature Biotechnology , vol.17 , Issue.10 , pp. 1030-1032
    • Rigaut, G.1    Shevchenko, A.2    Rutz, B.3    Wilm, M.4    Mann, M.5    Seraphin, B.6
  • 15
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • A.C. Gavin et al., Functional Organization of the Yeast Proteome by Systematic Analysis of Protein Complexes, Nature, vol. 415, no. 6868, pp. 141-147, 2002.
    • (2002) Nature , vol.415 , Issue.6868 , pp. 141-147
    • Gavin, A.C.1
  • 19
    • 38449114820 scopus 로고    scopus 로고
    • Discovering protein complexes in dense reliable neighborhoods of protein interaction networks
    • X. Li, C. Foo, and S. Ng, Discovering Protein Complexes in Dense Reliable Neighborhoods of Protein Interaction Networks, Computational Systems Bioinformatics, vol. 6, pp. 157-168, 2007.
    • (2007) Computational Systems Bioinformatics , vol.6 , pp. 157-168
    • Li, X.1    Foo, C.2    Ng, S.3
  • 20
    • 0035826155 scopus 로고    scopus 로고
    • Exploring complex networks
    • DOI 10.1038/35065725
    • S.H. Strogatz, Exploring Complex Networks, Nature, vol. 410, pp. 268-276, 2001. (Pubitemid 32216604)
    • (2001) Nature , vol.410 , Issue.6825 , pp. 268-276
    • Strogatz, S.H.1
  • 21
    • 34250322596 scopus 로고    scopus 로고
    • Evolution at the system level: The natural history of protein interaction networks
    • DOI 10.1016/j.tree.2007.04.004, PII S0169534707001310
    • M.P. Stumpf et al., Evolution at the Systems Level: The Natural History of Protein Interaction Networks, Trends Ecology Evolution, vol. 22, no. 7, pp. 366-373, 2007. (Pubitemid 46920549)
    • (2007) Trends in Ecology and Evolution , vol.22 , Issue.7 , pp. 366-373
    • Stumpf, M.P.H.1    Kelly, W.P.2    Thorne, T.3    Wiuf, C.4
  • 22
    • 0034721164 scopus 로고    scopus 로고
    • Error and attack tolerance of complex networks
    • DOI 10.1038/35019019
    • R. Albert, H. Jeong, and A.L. Barabasi, Error and Attack Tolerance of Complex Networks, Nature, vol. 406, pp. 378-382, 2000. (Pubitemid 30625551)
    • (2000) Nature , vol.406 , Issue.6794 , pp. 378-382
    • Albert, R.1    Jeong, H.2    Barabasi, A.-L.3
  • 23
    • 32144441867 scopus 로고    scopus 로고
    • Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large-scale organization and robustness
    • DOI 10.1002/pmic.200500228
    • D. Li et al., Protein Interaction Networks of Saccharomyces Cerevisiae, Caenorhabditis Elegans and Drosophila Melanogaster: Large-Scale Organization and Robustness, Proteomics, vol. 6, no. 2, pp. 456-461, 2006. (Pubitemid 43208025)
    • (2006) Proteomics , vol.6 , Issue.2 , pp. 456-461
    • Li, D.1    Li, J.2    Ouyang, S.3    Wang, J.4    Wu, S.5    Wan, P.6    Zhu, Y.7    Xu, X.8    He, F.9
  • 25
    • 36248936497 scopus 로고    scopus 로고
    • The road to modularity
    • DOI 10.1038/nrg2267, PII NRG2267
    • G.P. Wagner, M. Pavlicev, and J.M. Cheverud, The Road to Modularity, Nature Rev. Genetics, vol. 8, no. 12, pp. 921-931, 2007. (Pubitemid 350129175)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.12 , pp. 921-931
    • Wagner, G.P.1    Pavlicev, M.2    Cheverud, J.M.3
  • 26
    • 41149147660 scopus 로고    scopus 로고
    • Growing functional modules from a seed protein via integration of protein interaction and gene expression data
    • article 408
    • I. Maraziotis, K. Dimitrakopoulou, and A. Bezerianos, Growing Functional Modules from a Seed Protein via Integration of Protein Interaction and Gene Expression Data, BMC Bioinformatics, vol. 8, article 408, 2007.
    • (2007) BMC Bioinformatics , vol.8
    • Maraziotis, I.1    Dimitrakopoulou, K.2    Bezerianos, A.3
  • 27
    • 34548742517 scopus 로고    scopus 로고
    • Identification of functional modules using network topology and high-throughput data
    • article 8
    • I. Ulitsky and R. Shamir, Identification of Functional Modules Using Network Topology and High-Throughput Data, BMC Systems Biology, vol. 1, article 8, 2007.
    • (2007) BMC Systems Biology , vol.1
    • Ulitsky, I.1    Shamir, R.2
  • 28
    • 33748464764 scopus 로고    scopus 로고
    • Combining functional and topological properties to identify core modules in protein interaction networks
    • DOI 10.1002/prot.21071
    • Z. Lubovac, J. Gamalielsson, and B. Olsson, Combining Functional and Topological Properties to Identify Core Modules in Protein Interaction Networks, Proteins, vol. 64, pp. 948-959, 2006. (Pubitemid 44420936)
    • (2006) Proteins: Structure, Function and Genetics , vol.64 , Issue.4 , pp. 948-959
    • Lubovac, Z.1    Gamalielsson, J.2    Olsson, B.3
  • 29
    • 10244264813 scopus 로고    scopus 로고
    • Protein complex prediction via cost-based clustering
    • DOI 10.1093/bioinformatics/bth351
    • A.D. King, N. Przulj, and I. Jurisica, Protein Complex Prediction via Cost-Based Clustering, Bioinformatics, vol. 20, no. 17, pp. 3013-3020, 2004. (Pubitemid 39619193)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3013-3020
    • King, A.D.1    Przulj, N.2    Jurisica, I.3
  • 30
    • 39749149026 scopus 로고    scopus 로고
    • Cascade: A novel quasi all paths-based network analysis algorithm for clustering biological interactions
    • article 64
    • W. Hwang, Y.R. Cho, A.D. Zhang, and M. Ramanathan, CASCADE: A Novel Quasi All Paths-Based Network Analysis Algorithm for Clustering Biological Interactions, BMC Bioinformatics, vol. 9, article 64, 2008.
    • (2008) BMC Bioinformatics , vol.9
    • Hwang, W.1    Cho, Y.R.2    Zhang, A.D.3    Ramanathan, M.4
  • 31
    • 28944431509 scopus 로고    scopus 로고
    • The choice of optimal distance measure in genome-wide data sets
    • G. Glazko, A. Gordon, and A. Mushegian, The Choice of Optimal Distance Measure in Genome-Wide Data Sets, Bioinformatics, vol. 21, no. S3, pp. iii3-iii11, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.S3 , pp. 33-311
    • Glazko, G.1    Gordon, A.2    Mushegian, A.3
  • 32
    • 1442329655 scopus 로고    scopus 로고
    • Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network
    • C. Brun, F. Chevenet, D. Martin, J. Wojcik, A. Guenoche, and B. Jacq, Functional Classification of Proteins for the Prediction of Cellular Function from a Protein-Protein Interaction Network, Genome Research, vol. 5, 2003.
    • (2003) Genome Research , vol.5
    • Brun, C.1    Chevenet, F.2    Martin, D.3    Wojcik, J.4    Guenoche, A.5    Jacq, B.6
  • 35
    • 33745486211 scopus 로고    scopus 로고
    • A topological measurement for weighted protein interaction network
    • DOI 10.1109/CSB.2005.8, 1498028, Proceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005
    • P. Pei and A.D. Zhang, A Topological Measurement for Weighted Protein Interaction Network, Proc. 16th IEEE Computational Systems Bioinformatics Conf., pp. 268-278, 2005. (Pubitemid 43959594)
    • (2005) Proceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005 , vol.2005 , pp. 268-278
    • Pei, P.1    Zhang, A.2
  • 36
    • 34547852262 scopus 로고    scopus 로고
    • An ensemble framework for clustering protein-protein interaction networks
    • S. Asur, D. Ucar, and S. Parthasarathy, An Ensemble Framework for Clustering Protein-Protein Interaction Networks, Bioinformatics, vol. 23, pp. i29-i40, 2007.
    • (2007) Bioinformatics , vol.23 , pp. 129-140
    • Asur, S.1    Ucar, D.2    Parthasarathy, S.3
  • 37
    • 33751165252 scopus 로고    scopus 로고
    • A two-step approach for clustering proteins based on protein interaction profile
    • DOI 10.1109/BIBE.2005.10, 1544467, Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering
    • P. Pei and A.D. Zhang, A Two-Step Approach for Clustering Proteins Based on Protein Interaction Profile, Proc. Fifth IEEE Symp. Bioinformatics and Bioeng. (BIBE '05), pp. 201-209, 2005. (Pubitemid 44773507)
    • (2005) Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering , vol.2005 , pp. 201-209
    • Pei, P.1    Zhang, A.2
  • 38
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • DOI 10.1038/35075138
    • H. Jeong, S.P. Mason, A.L. Barabasi, and Z.N. Oltvai, Lethality and Centrality in Protein Networks, Nature, vol. 411, no. 6833, pp. 41-42, 2001. (Pubitemid 32428180)
    • (2001) Nature , vol.411 , Issue.6833 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.-L.3    Oltvai, Z.N.4
  • 39
    • 27744469130 scopus 로고    scopus 로고
    • High-betweenness proteins in the yeast protein interaction network
    • DOI 10.1155/JBB.2005.96
    • M.P. Joy, A. Brock, D.E. Ingber, and S. Huang, High-Betweenness Proteins in the Yeast Protein Interaction Network, J. Biomedicine Biotechnology, vol. 2, pp. 96-103, 2005. (Pubitemid 41627865)
    • (2005) Journal of Biomedicine and Biotechnology , vol.2005 , Issue.2 , pp. 96-103
    • Joy, M.P.1    Brock, A.2    Ingber, D.E.3    Huang, S.4
  • 40
    • 34247622363 scopus 로고    scopus 로고
    • The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics
    • DOI 10.1371/journal.pcbi.0030059
    • H. Yu, P.M. Kim, E. Sprecher, V. Trifonov, and M. Gerstein, The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics, Plos Computational Biology, vol. 3, pp. 713-720, 2007. (Pubitemid 46683453)
    • (2007) PLoS Computational Biology , vol.3 , Issue.4 , pp. 713-720
    • Yu, H.1    Kim, P.M.2    Sprecher, E.3    Trifonov, V.4    Gerstein, M.5
  • 42
    • 26944450851 scopus 로고    scopus 로고
    • Subgraph centrality in complex networks
    • E. Estrada and R. velazquez, Subgraph Centrality in Complex Networks, Physical Rev. E, vol. 71, pp. 56-103, 2005.
    • (2005) Physical Rev. e , vol.71 , pp. 56-103
    • Estrada, E.1    Velazquez, R.2
  • 44
    • 33947109414 scopus 로고    scopus 로고
    • A "seed-refine" algorithm for detecting protein complexes from protein interaction data
    • DOI 10.1109/TNB.2007.891900
    • P. Pei and A.D. Zhang, A Seed-Refine Algorithm for Detecting Protein Complexes from Protein Interaction Data, IEEE Trans. Nanobioscience, vol. 6, no. 1, pp. 43-50, Mar. 2007. (Pubitemid 46397111)
    • (2007) IEEE Transactions on Nanobioscience , vol.6 , Issue.1 , pp. 43-50
    • Pei, P.1    Zhang, A.2
  • 46
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • article 2
    • G.D. Bader and C.W. Hogue, An Automated Method for Finding Molecular Complexes in Large Protein Interaction Networks, BMC Bioinformatics, vol. 4, article 2, 2003.
    • (2003) BMC Bioinformatics , vol.4
    • Bader, G.D.1    Hogue, C.W.2
  • 47
    • 79956189444 scopus 로고    scopus 로고
    • Mine: Module identification in networks
    • article 192
    • K. Rhrissorrakrai and K.C. Gunsalus, MINE: Module Identification in Networks, BMC Bioinformatics, vol. 12, article 192, 2011.
    • (2011) BMC Bioinformatics , vol.12
    • Rhrissorrakrai, K.1    Gunsalus, K.C.2
  • 48
    • 33645830948 scopus 로고    scopus 로고
    • Cfinder: Locating cliques and overlapping modules in biological networks
    • B. Adamcsek, G. Palla, I.J. Farkas, I. Derenyi, and T. Vicsek, CFinder: Locating Cliques and Overlapping Modules in Biological Networks, Bioinformatics, vol. 22, no. 8, pp. 1021-1023, 2006.
    • (2006) Bioinformatics , vol.22 , Issue.8 , pp. 1021-1023
    • Adamcsek, B.1    Palla, G.2    Farkas, I.J.3    Derenyi, I.4    Vicsek, T.5
  • 49
    • 20444504323 scopus 로고    scopus 로고
    • Uncovering the overlapping community structure of complex networks in nature and society
    • P. Gergely, D. Imre, F. Illes, and V. Tamas, Uncovering the Overlapping Community Structure of Complex Networks in Nature and Society, Nature, vol. 435, pp. 814-818, 2005.
    • (2005) Nature , vol.435 , pp. 814-818
    • Gergely, P.1    Imre, D.2    Illes, F.3    Tamas, V.4
  • 50
    • 33744805096 scopus 로고    scopus 로고
    • Development and implementation of an algorithm for detection of protein complexes in large interaction networks
    • article 207
    • M. Altaf-UI-adim et al., Development and Implementation of an Algorithm for Detection of Protein Complexes in Large Interaction Networks, BMC Bioinformatics, vol. 7, article 207, 2006.
    • (2006) BMC Bioinformatics , vol.7
    • Altaf-Ui-Adim, M.1
  • 51
    • 33748579201 scopus 로고    scopus 로고
    • Interaction graph mining for protein complexes using local clique merging
    • X.L. Li, S.H. Tan, C.S. Foo, and S.K. Ng, Interaction Graph Mining for Protein Complexes Using Local Clique Merging, Genome Informatics, vol. 16, no. 2, pp. 260-269, 2005.
    • (2005) Genome Informatics , vol.16 , Issue.2 , pp. 260-269
    • Li, X.L.1    Tan, S.H.2    Foo, C.S.3    Ng, S.K.4
  • 53
    • 49649104565 scopus 로고    scopus 로고
    • A structural approach for finding functional modules from large biological networks
    • article S19
    • M. Mete, F. Tang, X. Xu, and N. Yuruk, A Structural Approach for Finding Functional Modules from Large Biological Networks, BMC Bioinformatics, vol. 9, article S19, 2008.
    • (2008) BMC Bioinformatics , vol.9
    • Mete, M.1    Tang, F.2    Xu, X.3    Yuruk, N.4
  • 55
    • 18144393488 scopus 로고    scopus 로고
    • Clique percolation in random networks
    • I. Derenyi, G. Palla, and T. Vicsek, Clique Percolation in random Networks, Physical Rev. Letter, vol. 94, pp. 160-202, 2005.
    • (2005) Physical Rev. Letter , vol.94 , pp. 160-202
    • Derenyi, I.1    Palla, G.2    Vicsek, T.3
  • 58
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • DOI 10.1126/science.1073374
    • E. Ravasz, A.L. Somera, D.A. Mongru, Z.N. Oltvai, and A.L. Barabasi, Hierarchical Organization of Modularity in Metabolic Networks, Science, vol. 297, pp. 1551-1555, 2002. (Pubitemid 34971002)
    • (2002) Science , vol.297 , Issue.5586 , pp. 1551-1555
    • Ravasz, E.1    Somera, A.L.2    Mongru, D.A.3    Oltvai, Z.N.4    Barabasi, A.-L.5
  • 59
    • 0037345719 scopus 로고    scopus 로고
    • Subnetwork hierarchies of biochemical pathways
    • DOI 10.1093/bioinformatics/btg033
    • P. Holme, M. Huss, and H. Jeong, Subnetwork Hierarchies of Biochemical Pathways, Bioinformatics, vol. 19, pp. 532-538, 2003. (Pubitemid 36342252)
    • (2003) Bioinformatics , vol.19 , Issue.4 , pp. 532-538
    • Holme, P.1    Huss, M.2    Jeong, H.3
  • 60
    • 13844264514 scopus 로고    scopus 로고
    • Iterative cluster analysis of protein interaction data
    • DOI 10.1093/bioinformatics/bti021
    • V. Arnau, S. Mars, and I. Marin, Iterative Cluster Analysis of Protein Interaction Data, Bioinformatics, vol. 21, no. 3, pp. 364-378, 2005. (Pubitemid 40246608)
    • (2005) Bioinformatics , vol.21 , Issue.3 , pp. 364-378
    • Arnau, V.1    Mars, S.2    Marin, I.3
  • 61
    • 77955358462 scopus 로고    scopus 로고
    • Jerarca: Efficient analysis of complex networks using hierarchical clustering
    • R. Aldecoa and I. Marin, Jerarca: Efficient Analysis of Complex Networks Using Hierarchical Clustering, PLoS ONE, vol. 5, no. 7, p. e11585, 2010.
    • (2010) PLoS ONE , vol.5 , Issue.7
    • Aldecoa, R.1    Marin, I.2
  • 62
    • 34547422722 scopus 로고    scopus 로고
    • Efficient modularization of weighted protein interaction networks using k-hop graph reduction
    • DOI 10.1109/BIBE.2006.253347, 4019672, Proceedings - Sixth IEEE Symposium on BioInformatics and BioEngineering, BIBE 2006
    • Y.R. Cho, W. Hwang, and A.D. Zhang, Efficient Modularization of Weighted Protein Interaction Networks Using k-Hop Graph Reduction, Proc. Sixth IEEE Symp. Bioinformatics and Bioeng. (BIBM), pp. 289-298, 2006. (Pubitemid 47159430)
    • (2006) Proceedings - Sixth IEEE Symposium on BioInformatics and BioEngineering, BIBE 2006 , pp. 289-298
    • Cho, Y.-R.1    Hwang, W.2    Zhang, A.3
  • 63
    • 33847172327 scopus 로고    scopus 로고
    • Clustering by passing messages between data points
    • DOI 10.1126/science.1136800
    • B.J. Frey and D. Dueck, Clustering by Passing Messages between Data Points, Science, vol. 15, no. 5814, pp. 972-976, 2007. (Pubitemid 46281181)
    • (2007) Science , vol.315 , Issue.5814 , pp. 972-976
    • Frey, B.J.1    Dueck, D.2
  • 64
    • 65849100458 scopus 로고    scopus 로고
    • Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
    • article 99
    • J. Vlasblom and S.J. Wodak, Markov Clustering versus Affinity Propagation for the Partitioning of Protein Interaction Graphs, BMC Bioinformatics, vol. 10, article 99, 2009.
    • (2009) BMC Bioinformatics , vol.10
    • Vlasblom, J.1    Wodak, S.J.2
  • 65
    • 25444490121 scopus 로고    scopus 로고
    • The use of edge-betweenness clustering to investigate biological function in protein interaction networks
    • article 39
    • R. Dunn, F. Dudbridge, and C.M. Sanderson, The Use of Edge-Betweenness Clustering to Investigate Biological Function in Protein Interaction Networks, BMC Bioinformatics, vol. 6, article 39, 2005.
    • (2005) BMC Bioinformatics , vol.6
    • Dunn, R.1    Dudbridge, F.2    Sanderson, C.M.3
  • 67
    • 0005924596 scopus 로고    scopus 로고
    • Graph clustering by flow simulation
    • Center for Math. and Computer Science (CWI)
    • S. Van Dongen, Graph Clustering by Flow Simulation, PhD thesis, Center for Math. and Computer Science (CWI), 2000.
    • (2000) PhD Thesis
    • Van Dongen, S.1
  • 68
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • A.J. Enright, S. Van Dongen, and C.A. Ouzounis, An Efficient Algorithm for Large-Scale Detection of Protein Families, Nucleic Acids Research, vol. 30, no. 7, pp. 1575-1584, 2002. (Pubitemid 34679732)
    • (2002) Nucleic Acids Research , vol.30 , Issue.7 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 70
    • 34248397539 scopus 로고    scopus 로고
    • A novel functional module detection algorithm for protein-protein interaction networks
    • W. Hwang, Y.R. Cho, A. Zhang, and M. Ramanathan, A Novel Functional Module Detection Algorithm for Protein-Protein Interaction Networks, Algorithms for Molecular Biology, vol. 1, p. 24, 2006.
    • (2006) Algorithms for Molecular Biology , vol.1 , pp. 24
    • Hwang, W.1    Cho, Y.R.2    Zhang, A.3    Ramanathan, M.4
  • 71
    • 34548511546 scopus 로고    scopus 로고
    • Semantic integration to identify overlapping functional modules in protein interaction networks
    • article 265
    • Y.R. Cho, W. Hwang, M. Ramanathan, and A.D. Zhang, Semantic Integration to Identify Overlapping Functional Modules in Protein Interaction Networks, BMC Bioinformatics, vol. 8, article 265, 2007.
    • (2007) BMC Bioinformatics , vol.8
    • Cho, Y.R.1    Hwang, W.2    Ramanathan, M.3    Zhang, A.D.4
  • 72
    • 69249226348 scopus 로고    scopus 로고
    • A max-flow based approach to the identification of protein complexes using protein interaction and microarray data
    • J. Feng, R. Jiang, and T. Jiang, A Max-Flow Based Approach to the Identification of Protein Complexes Using Protein Interaction and Microarray Data, Computational Systems Bioinformatics, vol. 7, pp. 51-62, 2008.
    • (2008) Computational Systems Bioinformatics , vol.7 , pp. 51-62
    • Feng, J.1    Jiang, R.2    Jiang, T.3
  • 73
    • 41349102114 scopus 로고    scopus 로고
    • Spectral analysis of protein-protein interactions in drosophila melanogaster
    • C. Kamp and K. Christensen, Spectral Analysis of Protein-Protein Interactions in Drosophila Melanogaster, Physical Rev., vol. 71, no. 4, p. 041911, 2005.
    • (2005) Physical Rev. , vol.71 , Issue.4 , pp. 041911
    • Kamp, C.1    Christensen, K.2
  • 74
    • 33748202182 scopus 로고    scopus 로고
    • Functional clustering of yeast proteins from the protein-protein interaction network
    • article 355
    • T.Z. Sen and R.L. Jernigan, Functional Clustering of Yeast Proteins from the Protein-Protein Interaction Network, BMC Bioinformatics, vol. 7, article 355, 2006.
    • (2006) BMC Bioinformatics , vol.7
    • Sen, T.Z.1    Jernigan, R.L.2
  • 75
    • 77956339150 scopus 로고    scopus 로고
    • Spectral clustering for detecting protein complexes in protein-protein interaction (ppi) networks
    • G. Qin and L. Gao, Spectral Clustering for Detecting Protein Complexes in Protein-Protein Interaction (PPI) Networks, Math. and Computer Modeling, vol. 52, pp. 2066-2074, 2010.
    • (2010) Math. and Computer Modeling , vol.52 , pp. 2066-2074
    • Qin, G.1    Gao, L.2
  • 76
    • 77958537453 scopus 로고    scopus 로고
    • Diffusion model based spectral clustering for protein-protein interaction networks
    • K. Inoue, W. Li, and H. Kurata, Diffusion Model Based Spectral Clustering for Protein-Protein Interaction Networks, PLoS ONE, vol. 5, no. 9, p. e12623, 2010.
    • (2010) PLoS ONE , vol.5 , Issue.9
    • Inoue, K.1    Li, W.2    Kurata, H.3
  • 77
    • 46249126321 scopus 로고    scopus 로고
    • Protein complex identification by supervised graph local clustering
    • Y.J. Qi, F. Balem, C. Faloutsos, J. Klein-Seetharaman, and Z. Bar-Joseph, Protein Complex Identification by Supervised Graph Local Clustering, Bioinformatics, vol. 24, no. 13, pp. 250-268, 2008.
    • (2008) Bioinformatics , vol.24 , Issue.13 , pp. 250-268
    • Qi, Y.J.1    Balem, F.2    Faloutsos, C.3    Klein-Seetharaman, J.4    Bar-Joseph, Z.5
  • 78
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • A.C. Gavin et al., Proteome Survey Reveals Modularity of the Yeast Cell Machinery, Nature, vol. 440, pp. 631-636, 2006.
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.C.1
  • 79
    • 59649099220 scopus 로고    scopus 로고
    • Predicting protein complexes from ppi data: A core-attachment approach
    • H.C. Leung, S.M. Yiu, Q. Xiang, and F.Y. Chin, Predicting Protein Complexes from PPI Data: A Core-Attachment Approach, J. Computational Biology, vol. 16, no. 2, pp. 133-144, 2009.
    • (2009) J. Computational Biology , vol.16 , Issue.2 , pp. 133-144
    • Leung, H.C.1    Yiu, S.M.2    Xiang, Q.3    Chin, F.Y.4
  • 80
    • 67649518162 scopus 로고    scopus 로고
    • A core-attachment based method to detect protein complexes in ppi networks
    • article 169
    • M. Wu, X.L. Li, C.K. Kwoh, and S.K. Ng, A Core-Attachment Based Method to Detect Protein Complexes in PPI Networks, BMC Bioinformatics, vol. 10, article 169, 2009.
    • (2009) BMC Bioinformatics , vol.10
    • Wu, M.1    Li, X.L.2    Kwoh, C.K.3    Ng, S.K.4
  • 81
    • 84855901999 scopus 로고    scopus 로고
    • Predicting protein complexes in protein interaction networks using a core-attachment algorithm based on graph communicability
    • X.K. Ma and L. Gao, Predicting Protein Complexes in Protein Interaction Networks Using a Core-Attachment Algorithm Based on Graph Communicability, Information Sciences, vol. 189, pp. 233-254, 2012.
    • (2012) Information Sciences , vol.189 , pp. 233-254
    • Ma, X.K.1    Gao, L.2
  • 83
    • 80053426106 scopus 로고    scopus 로고
    • Clustering ppi network based on functional flow model through artificial bee colony algorithm
    • S. Wu, X.J. Lei, and J.F. Tian, Clustering PPI Network Based on Functional Flow Model through Artificial Bee Colony Algorithm, Proc. Seventh Int'l Conf. Natural Computation, pp. 92-96, 2011.
    • (2011) Proc. Seventh Int'l Conf. Natural Computation , pp. 92-96
    • Wu, S.1    Lei, X.J.2    Tian, J.F.3
  • 88
    • 13444272070 scopus 로고    scopus 로고
    • The biomolecular interaction network database and related tools 2005 update
    • C. Alfarano et al., The Biomolecular Interaction Network Database and Related Tools 2005 Update, Nucleic Acids Research, vol. 33, pp. D418-D424, 2005.
    • (2005) Nucleic Acids Research , vol.33 , pp. 418-424
    • Alfarano, C.1
  • 90
    • 33846073818 scopus 로고    scopus 로고
    • Mint: The molecular interaction database
    • C. Andrew et al., MINT: The Molecular Interaction Database, Nucleic Acids Research, vol. 35, pp. D572-D574, 2007.
    • (2007) Nucleic Acids Research , vol.35 , pp. 572-574
    • Andrew, C.1
  • 91
    • 33846047770 scopus 로고    scopus 로고
    • Intact-open source resource for molecular interaction data
    • S. Kerrien et al., IntAct - Open Source Resource for Molecular Interaction Data, Nucleic Acids Research, vol. 35, pp. D561-D565, 2007.
    • (2007) Nucleic Acids Research , vol.35 , pp. 561-565
    • Kerrien, S.1
  • 92
    • 33644877439 scopus 로고    scopus 로고
    • Human protein reference database-2006 update
    • G.R. Mishra1, M. Suresh1, and K. Kumaran, Human Protein Reference Database - 2006 Update, Nucleic Acids Research, vol. 34, pp. D411-D414, 2006.
    • (2006) Nucleic Acids Research , vol.34 , pp. 411-414
    • Mishra, G.R.1    Suresh, M.2    Kumaran, K.3
  • 93
    • 76749150479 scopus 로고    scopus 로고
    • Computational approaches for detecting protein complexes from protein interaction networks: A survey
    • article S3
    • X.L. Li, M. Wu, C.K. Kwoh, and S.K. Ng, Computational Approaches for Detecting Protein Complexes from Protein Interaction Networks: A Survey, BMC Genomics, vol. 11, no. suppl. 1, article S3, 2010.
    • (2010) BMC Genomics , vol.11 , Issue.SUPPL. 1
    • Li, X.L.1    Wu, M.2    Kwoh, C.K.3    Ng, S.K.4
  • 95
    • 77957935946 scopus 로고    scopus 로고
    • Models and algorithms for alignment of biological networks
    • X.L. Guo, L. Gao, and X. Chen, Models and Algorithms for Alignment of Biological Networks, J. Software, vol. 21, no. 9, pp. 2089-2106, 2010.
    • (2010) J. Software , vol.21 , Issue.9 , pp. 2089-2106
    • Guo, X.L.1    Gao, L.2    Chen, X.3
  • 96
    • 33846680167 scopus 로고    scopus 로고
    • Identification of conserved protein complexes based on a model of protein network evolution
    • E. Hirsh and R. Sharan, Identification of Conserved Protein Complexes Based on a Model of Protein Network Evolution, Bioinformatics, vol. 23, no. 2, pp. e170-e176, 2006.
    • (2006) Bioinformatics , vol.23 , Issue.2 , pp. 170-176
    • Hirsh, E.1    Sharan, R.2
  • 98
    • 34547840254 scopus 로고    scopus 로고
    • Identification of functional modules from conserved ancestral protein-protein interactions
    • J. Dutkowski and J. Tiuryn, Identification of Functional Modules from Conserved Ancestral Protein-Protein Interactions, Bioinformatics, vol. 23, no. 13, pp. 149-158, 2007.
    • (2007) Bioinformatics , vol.23 , Issue.13 , pp. 149-158
    • Dutkowski, J.1    Tiuryn, J.2


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