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Volumn 11, Issue SUPPL. 3, 2010, Pages

Recent advances in clustering methods for protein interaction networks

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL ACTIVITY; CELL FUNCTION; CLUSTER ANALYSIS; COMPUTER PROGRAM; MATHEMATICAL ANALYSIS; PREDICTION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; SYSTEMS BIOLOGY; ALGORITHM; CHEMISTRY; METABOLISM; PROTEIN ANALYSIS; PROTEIN BINDING;

EID: 78649679994     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-S3-S10     Document Type: Article
Times cited : (114)

References (125)
  • 1
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • 12000970
    • von Mering C, Krause R, Sne B, et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417(6887):399-403. 12000970.
    • (2002) Nature , vol.417 , Issue.6887 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Sne, B.3
  • 2
    • 34249945479 scopus 로고    scopus 로고
    • Specificity in protein interactions and its relationship with sequence diversity and coevolution
    • 1876561, 17468399
    • Hakes L, Lovell SC, Oliver SG, et al. Specificity in protein interactions and its relationship with sequence diversity and coevolution. PNAS 2007, 104(19):7999-8004. 1876561, 17468399.
    • (2007) PNAS , vol.104 , Issue.19 , pp. 7999-8004
    • Hakes, L.1    Lovell, S.C.2    Oliver, S.G.3
  • 4
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong H, Mason S, Barabási AL, et al. Lethality and centrality in protein networks. Nature 2001, 411(6833):41-42.
    • (2001) Nature , vol.411 , Issue.6833 , pp. 41-42
    • Jeong, H.1    Mason, S.2    Barabási, A.L.3
  • 5
    • 0345600247 scopus 로고    scopus 로고
    • A protein interaction map of Drosophila melanogaster
    • Giot L, et al. A protein interaction map of Drosophila melanogaster. Science 2003, 302:1727-1736.
    • (2003) Science , vol.302 , pp. 1727-1736
    • Giot, L.1
  • 6
    • 9144264169 scopus 로고    scopus 로고
    • A map of the interactome network of the metazoan
    • 1698949, 14704431
    • Li S, Armstrong C, Bertin N. A map of the interactome network of the metazoan. Science 2004, 303(5657):540-543. 1698949, 14704431.
    • (2004) Science , vol.303 , Issue.5657 , pp. 540-543
    • Li, S.1    Armstrong, C.2    Bertin, N.3
  • 7
    • 0034887573 scopus 로고    scopus 로고
    • Scale-free behavior in protein domain networks
    • Wuchty S. Scale-free behavior in protein domain networks. Mollecular Biology and Evolution 2001, 18(9):1694-1702.
    • (2001) Mollecular Biology and Evolution , vol.18 , Issue.9 , pp. 1694-1702
    • Wuchty, S.1
  • 8
    • 12944331889 scopus 로고    scopus 로고
    • Small-world network approach to identify key residues in protein-protein interaction
    • del Sol A, O'Meara P. Small-world network approach to identify key residues in protein-protein interaction. Proteins 2004, 58(3):672-682.
    • (2004) Proteins , vol.58 , Issue.3 , pp. 672-682
    • del Sol, A.1    O'Meara, P.2
  • 9
    • 17444396776 scopus 로고    scopus 로고
    • Topology of small-world networks of protein-protein complex structures
    • del Sol A, Fujihashi H, O'Meara P. Topology of small-world networks of protein-protein complex structures. Bioinformatics 2005, 21(8):1311-131.
    • (2005) Bioinformatics , vol.21 , Issue.8 , pp. 1311-2131
    • del Sol, A.1    Fujihashi, H.2    O'Meara, P.3
  • 10
    • 33751255087 scopus 로고    scopus 로고
    • Evaluation of clustering algorithms for protein-protein interaction networks
    • 1397874, 16448555
    • Brohée S, van Helden J. Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 2006, 7:48. 1397874, 16448555.
    • (2006) BMC Bioinformatics , vol.7 , pp. 48
    • Brohée, S.1    van Helden, J.2
  • 11
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • 218723, 14517352
    • Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. PNAS 2003, 100:12123-12128. 218723, 14517352.
    • (2003) PNAS , vol.100 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.A.2
  • 12
    • 0038074373 scopus 로고    scopus 로고
    • Topological structure analysis of the protein-protein interaction network in budding yeast
    • 154226, 12711690
    • Bu D, Zhao Y, Cai L, et al. Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Research 2003, 31(9):2443-2450. 154226, 12711690.
    • (2003) Nucleic Acids Research , vol.31 , Issue.9 , pp. 2443-2450
    • Bu, D.1    Zhao, Y.2    Cai, L.3
  • 13
    • 42949105070 scopus 로고    scopus 로고
    • An Algorithm for Finding Functional Modules and Protein Complexes in Protein-Protein Interaction Networks
    • doi:10.1155/2008/86027
    • Cui G, Chen Y, Huang DS, Han K. An Algorithm for Finding Functional Modules and Protein Complexes in Protein-Protein Interaction Networks. Journal of Biomedicine and Biotechnology 2008, 1-10. doi:10.1155/2008/86027.
    • (2008) Journal of Biomedicine and Biotechnology , pp. 1-10
    • Cui, G.1    Chen, Y.2    Huang, D.S.3    Han, K.4
  • 14
    • 15944412875 scopus 로고    scopus 로고
    • Identification of functional modules in protein complexes via hyperclique pattern discovery
    • Xiong H, He X, Ding C, et al. Identification of functional modules in protein complexes via hyperclique pattern discovery. Pacific Symposium on Biocomputing 2005, 10:221-232.
    • (2005) Pacific Symposium on Biocomputing , vol.10 , pp. 221-232
    • Xiong, H.1    He, X.2    Ding, C.3
  • 15
    • 2942552459 scopus 로고    scopus 로고
    • An Automated method for finding molecular complexes in large protein interaction networks
    • 149346, 12525261
    • Bader GD, Hogue CW. An Automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2. 149346, 12525261.
    • (2003) BMC Bioinformatics , vol.4 , pp. 2
    • Bader, G.D.1    Hogue, C.W.2
  • 16
    • 33845955474 scopus 로고    scopus 로고
    • Inferring topology from clustering coefficients in protein-protein interaction networks
    • 1361790, 16401345
    • Friedel C, Zimmer R. Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinformatics 2006, 7-519. 1361790, 16401345.
    • (2006) BMC Bioinformatics , pp. 7-519
    • Friedel, C.1    Zimmer, R.2
  • 17
    • 78649679358 scopus 로고    scopus 로고
    • http://www.cytoscape.org/
  • 18
    • 33749541272 scopus 로고    scopus 로고
    • Prediction of protein complexes based on protein interaction data and functional annotation data using kernel methods
    • Zhang S, Ning X, Liu H, Zhang X. Prediction of protein complexes based on protein interaction data and functional annotation data using kernel methods. ICIC 2006, Lecture Notes in Bioinformatics 4115:514-524.
    • ICIC 2006, Lecture Notes in Bioinformatics , vol.4115 , pp. 514-524
    • Zhang, S.1    Ning, X.2    Liu, H.3    Zhang, X.4
  • 19
    • 38449101120 scopus 로고    scopus 로고
    • Integration of biological networks and gene expression data using Cytoscape
    • Cline MS, Smoot M, Cerami E, et al. Integration of biological networks and gene expression data using Cytoscape. NatProtoc 2007, 2(10):2366-2382.
    • (2007) NatProtoc , vol.2 , Issue.10 , pp. 2366-2382
    • Cline, M.S.1    Smoot, M.2    Cerami, E.3
  • 20
    • 38849128078 scopus 로고    scopus 로고
    • Identifying protein complexes directly from high-throughput TAP data with Markov random fields
    • 2222659, 18093306
    • Rungsarityotin W, Krause R, Schödl A, Schliep A. Identifying protein complexes directly from high-throughput TAP data with Markov random fields. BMC Bioinformatics 2007, 8:482. 2222659, 18093306.
    • (2007) BMC Bioinformatics , vol.8 , pp. 482
    • Rungsarityotin, W.1    Krause, R.2    Schödl, A.3    Schliep, A.4
  • 21
    • 33744805096 scopus 로고    scopus 로고
    • Development and implementation of an algorithm for detection of protein complexes in large interaction networks
    • 1473204, 16613608
    • Altaf-UI-Amin M, Shinbo Y, Mihara K, et al. Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics 2006, 7:207. 1473204, 16613608.
    • (2006) BMC Bioinformatics , vol.7 , pp. 207
    • Altaf-UI-Amin, M.1    Shinbo, Y.2    Mihara, K.3
  • 22
    • 54349096842 scopus 로고    scopus 로고
    • Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
    • 2570695, 18816408
    • Li M, Chen J, Wang JX, et al. Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. BMC Bioinformatics 2008, 9:398. 2570695, 18816408.
    • (2008) BMC Bioinformatics , vol.9 , pp. 398
    • Li, M.1    Chen, J.2    Wang, J.X.3
  • 23
    • 1842580761 scopus 로고    scopus 로고
    • A Functional and topological characterization of protein interaction networks
    • Yook S, Oltvai Z, Barabási. A Functional and topological characterization of protein interaction networks. Proteomics 2004, 4(4):928-942.
    • (2004) Proteomics , vol.4 , Issue.4 , pp. 928-942
    • Yook, S.1    Oltvai, Z.2    Barabási3
  • 26
    • 78649649061 scopus 로고    scopus 로고
    • The betweenness centrality of biological networks. Master of Science in Computer Science
    • September 16
    • Narayanan S. The betweenness centrality of biological networks. Master of Science in Computer Science. Virginia Polytechnic Institute and State University 2005, September 16.
    • (2005) Virginia Polytechnic Institute and State University
    • Narayanan, S.1
  • 27
    • 0037062448 scopus 로고    scopus 로고
    • Community structure in social and biological networks
    • 122977, 12060727
    • Girvan M, Newman M. Community structure in social and biological networks. PNAS 2002, 99:7821-7826. 122977, 12060727.
    • (2002) PNAS , vol.99 , pp. 7821-7826
    • Girvan, M.1    Newman, M.2
  • 28
    • 37649028224 scopus 로고    scopus 로고
    • Finding and evaluating community structure in networks
    • Newman M, Girvan M. Finding and evaluating community structure in networks. Physical Review E 2004, 69(2):1-16.
    • (2004) Physical Review E , vol.69 , Issue.2 , pp. 1-16
    • Newman, M.1    Girvan, M.2
  • 29
    • 1542357701 scopus 로고    scopus 로고
    • Defining and identifying communities in networks
    • 365677, 14981240
    • Radicchi F, Castellano C, Cecconi F. Defining and identifying communities in networks. PNAS 2004, 101(9):2658-2663. 365677, 14981240.
    • (2004) PNAS , vol.101 , Issue.9 , pp. 2658-2663
    • Radicchi, F.1    Castellano, C.2    Cecconi, F.3
  • 30
    • 33748701649 scopus 로고    scopus 로고
    • Detecting functional modules in the yeast protein-protein interaction network
    • Chen JC, Yuan B. Detecting functional modules in the yeast protein-protein interaction network. Bioinformatics 2006, 22(18):2283-229.
    • (2006) Bioinformatics , vol.22 , Issue.18 , pp. 2283-3229
    • Chen, J.C.1    Yuan, B.2
  • 31
    • 33846681448 scopus 로고    scopus 로고
    • Modular organization of protein interaction networks
    • Luo F, Yang Y, Chen CF, et al. Modular organization of protein interaction networks. Bioinformatics 2007, 23(2):207-214.
    • (2007) Bioinformatics , vol.23 , Issue.2 , pp. 207-214
    • Luo, F.1    Yang, Y.2    Chen, C.F.3
  • 32
    • 25444490121 scopus 로고    scopus 로고
    • The use of edge-betweenness clustering to investigate biological function in protein interaction networks
    • 555937, 15740614
    • Ruth D, Frank D, Christopher M. The use of edge-betweenness clustering to investigate biological function in protein interaction networks. BMC Bioinformatics 2005, 6:39. 555937, 15740614.
    • (2005) BMC Bioinformatics , vol.6 , pp. 39
    • Ruth, D.1    Frank, D.2    Christopher, M.3
  • 33
    • 43049151837 scopus 로고    scopus 로고
    • Hierarchical structure and the prediction of missing links in networks
    • Clauset A, Moore C, Newman M. Hierarchical structure and the prediction of missing links in networks. Nature 2008, 453:98-101.
    • (2008) Nature , vol.453 , pp. 98-101
    • Clauset, A.1    Moore, C.2    Newman, M.3
  • 34
    • 38049081211 scopus 로고    scopus 로고
    • Betweenness-based decomposition methods for social and biological networks
    • Leeds, Leeds University Press, Barber S, Baxter PD, Mardia KV, &Walls RE
    • Pinney J, Westhead D. Betweenness-based decomposition methods for social and biological networks. Interdisciplinary Statistics and Bioinformatics 2006, 87-90. Leeds, Leeds University Press, Barber S, Baxter PD, Mardia KV, &Walls RE.
    • (2006) Interdisciplinary Statistics and Bioinformatics , pp. 87-90
    • Pinney, J.1    Westhead, D.2
  • 36
    • 38049036713 scopus 로고    scopus 로고
    • A parallel edge-betweenness clustering tool for protein-protein interaction networks
    • Yang Q, Lonardi S. A parallel edge-betweenness clustering tool for protein-protein interaction networks. International Journal of Data Mining and Bioinformatics 2007, 1(3):241-247.
    • (2007) International Journal of Data Mining and Bioinformatics , vol.1 , Issue.3 , pp. 241-247
    • Yang, Q.1    Lonardi, S.2
  • 37
    • 17444396776 scopus 로고    scopus 로고
    • Topology of small-world networks of protein-protein complex structures
    • del Sol A, Fujihashi H, O'Meara P. Topology of small-world networks of protein-protein complex structures. Bioinformatics 2005, 21(8):1311-1315.
    • (2005) Bioinformatics , vol.21 , Issue.8 , pp. 1311-1315
    • del Sol, A.1    Fujihashi, H.2    O'Meara, P.3
  • 38
    • 33947619951 scopus 로고    scopus 로고
    • Graph theory and networks in biology
    • Mason O, Verwoerd M. Graph theory and networks in biology. IET Systems Biology 2006, 1(2):89-119.
    • (2006) IET Systems Biology , vol.1 , Issue.2 , pp. 89-119
    • Mason, O.1    Verwoerd, M.2
  • 40
    • 67650160441 scopus 로고    scopus 로고
    • Hierarchical organization of functional modules in weighted protein interaction networks using clustering coefficient
    • LNBI 5542
    • Li M, Wang JX, Chen J, Pan Y. Hierarchical organization of functional modules in weighted protein interaction networks using clustering coefficient. ISBRA2009 75-86. LNBI 5542.
    • ISBRA2009 , pp. 75-86
    • Li, M.1    Wang, J.X.2    Chen, J.3    Pan, Y.4
  • 41
    • 40449109730 scopus 로고    scopus 로고
    • Consistent dissection of the protein interaction network by combining global and local metrics
    • 2246273, 18154653
    • Wang C, Ding C, Yang Q, Holbrook SR. Consistent dissection of the protein interaction network by combining global and local metrics. Genome Biology 2007, 8:R271. 2246273, 18154653.
    • (2007) Genome Biology , vol.8
    • Wang, C.1    Ding, C.2    Yang, Q.3    Holbrook, S.R.4
  • 42
    • 0034515528 scopus 로고    scopus 로고
    • A clustering algorithm based graph connectivity
    • Hartuv E, Shamir R. A clustering algorithm based graph connectivity. Information Processing Letters 2000, 76:175-181.
    • (2000) Information Processing Letters , vol.76 , pp. 175-181
    • Hartuv, E.1    Shamir, R.2
  • 43
    • 1342330546 scopus 로고    scopus 로고
    • Functional topology in a network of protein interactions
    • Pržulj N, Wigle DA, Jurisica I. Functional topology in a network of protein interactions. Bioinformatics 2004, 20(3):340-348.
    • (2004) Bioinformatics , vol.20 , Issue.3 , pp. 340-348
    • Pržulj, N.1    Wigle, D.A.2    Jurisica, I.3
  • 44
    • 13844264514 scopus 로고    scopus 로고
    • Iterative cluster analysis of protein interaction data
    • Arnau V, Mars S, Marín I. Iterative cluster analysis of protein interaction data. Bioinformatics 2005, 21:364-378.
    • (2005) Bioinformatics , vol.21 , pp. 364-378
    • Arnau, V.1    Mars, S.2    Marín, I.3
  • 45
  • 46
    • 55949137146 scopus 로고    scopus 로고
    • Clustering complex networks and biological networks by nonnegative matrix factorization with various similarity measures
    • Wang RS, Zhang SH, Wang Y, et al. Clustering complex networks and biological networks by nonnegative matrix factorization with various similarity measures. Neurocomputing 2008, 72:134-141.
    • (2008) Neurocomputing , vol.72 , pp. 134-141
    • Wang, R.S.1    Zhang, S.H.2    Wang, Y.3
  • 47
    • 67349144761 scopus 로고    scopus 로고
    • On the similarity metric and the distance metric
    • Chen S, Ma B, Zhang K. On the similarity metric and the distance metric. Theoretical Computer Science 2009, 410:2365-2376.
    • (2009) Theoretical Computer Science , vol.410 , pp. 2365-2376
    • Chen, S.1    Ma, B.2    Zhang, K.3
  • 48
    • 34548511546 scopus 로고    scopus 로고
    • Semantic integration to identify overlapping functional modules in protein interaction networks
    • 1971074, 17650343
    • Cho YR, Hwang W, Ramanmathan M, Zhang AD. Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics 2007, 8:265. 1971074, 17650343.
    • (2007) BMC Bioinformatics , vol.8 , pp. 265
    • Cho, Y.R.1    Hwang, W.2    Ramanmathan, M.3    Zhang, A.D.4
  • 49
    • 10244264813 scopus 로고    scopus 로고
    • Protein complex prediction via cost-based clustering
    • King AD, Pržulj N, Jurisica I. Protein complex prediction via cost-based clustering. Bioinformatics 2004, 20(17):3013-302.
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3013-3302
    • King, A.D.1    Pržulj, N.2    Jurisica, I.3
  • 50
    • 14644396645 scopus 로고    scopus 로고
    • Functional cartography of complex metabolic networks
    • 2175124, 15729348
    • Guimera R, Amaral Nunes LA. Functional cartography of complex metabolic networks. Nature 2005, 433:895-900. 2175124, 15729348.
    • (2005) Nature , vol.433 , pp. 895-900
    • Guimera, R.1    Amaral Nunes, L.A.2
  • 52
    • 36348985751 scopus 로고    scopus 로고
    • Maximizing Modularity is hard
    • e-print arXiv:physics/0608255
    • Brandes U, Delling D, Gaertler M, et al. Maximizing Modularity is hard. e-print arXiv:physics/0608255.
    • Brandes, U.1    Delling, D.2    Gaertler, M.3
  • 53
    • 41349117788 scopus 로고    scopus 로고
    • Finding community structure in very large networks
    • 066111
    • Clauset A, Newman M, Moore C. Finding community structure in very large networks. Phys. Rev. E 2004, 70. 066111.
    • (2004) Phys. Rev. E , vol.70
    • Clauset, A.1    Newman, M.2    Moore, C.3
  • 54
    • 27244441304 scopus 로고    scopus 로고
    • Community detection in complex networks using extreme optimization
    • 027104
    • Duch J, Arenas A. Community detection in complex networks using extreme optimization. Physical Review E 2005, 72. 027104.
    • (2005) Physical Review E , vol.72
    • Duch, J.1    Arenas, A.2
  • 55
    • 33745012299 scopus 로고    scopus 로고
    • Modularity and community structure in networks
    • 1482622, 16723398
    • Newman. Modularity and community structure in networks. PNAS 2006, 103(23):8577-8582. 1482622, 16723398.
    • (2006) PNAS , vol.103 , Issue.23 , pp. 8577-8582
    • Newman1
  • 57
    • 78649648529 scopus 로고    scopus 로고
    • Identifying network communities with high resolution
    • Ruan JH, Zhang WX. Identifying network communities with high resolution. Physical Review E 2007, 4:1-14.
    • (2007) Physical Review E , vol.4 , pp. 1-14
    • Ruan, J.H.1    Zhang, W.X.2
  • 58
    • 34248397539 scopus 로고    scopus 로고
    • A novel functional module detection algorithm for protein-protein interaction networks
    • 1764415, 17147822
    • Hwang W, Cho Y, Zhang A. A novel functional module detection algorithm for protein-protein interaction networks. Algorithms for Molecular Biology 2006, 1:24. 1764415, 17147822.
    • (2006) Algorithms for Molecular Biology , vol.1 , pp. 24
    • Hwang, W.1    Cho, Y.2    Zhang, A.3
  • 59
    • 39749149026 scopus 로고    scopus 로고
    • CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions
    • 2253513, 18230159
    • Hwang W, Cho Y, Zhang A. CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions. BMC Bioinformatics 2008, 9:64. 2253513, 18230159.
    • (2008) BMC Bioinformatics , vol.9 , pp. 64
    • Hwang, W.1    Cho, Y.2    Zhang, A.3
  • 61
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • 101833, 11917018
    • Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research 2002, 30(7):1575-1584. 101833, 11917018.
    • (2002) Nucleic Acids Research , vol.30 , Issue.7 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 63
    • 65849100458 scopus 로고    scopus 로고
    • Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
    • 2682798, 19331680
    • Vlasblom J, Wodak SJ. Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. BMC Bioinformatics 2009, 10:99. 2682798, 19331680.
    • (2009) BMC Bioinformatics , vol.10 , pp. 99
    • Vlasblom, J.1    Wodak, S.J.2
  • 65
    • 49649104565 scopus 로고    scopus 로고
    • A structural approach for finding functional modules from large biological networks
    • Mete M, Tang F, Xu X, Yuruk N. A structural approach for finding functional modules from large biological networks. BMC Bioinformatics 2008 9(Suppl 9):S19.
    • BMC Bioinformatics 2008 , vol.9 , Issue.SUPPL 9
    • Mete, M.1    Tang, F.2    Xu, X.3    Yuruk, N.4
  • 66
    • 65449131622 scopus 로고    scopus 로고
    • Core and periphery structures in protein interaction networks
    • 2681073, 19426456
    • Luo F, Li B, Wan XF, Scheuermann RH. Core and periphery structures in protein interaction networks. BMC Bioinformatics 2009, 10(Suppl 4):S8. 2681073, 19426456.
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL 4
    • Luo, F.1    Li, B.2    Wan, X.F.3    Scheuermann, R.H.4
  • 67
    • 0001396345 scopus 로고    scopus 로고
    • Models of core/periphery structures
    • Borgatii SP, Everett MG. Models of core/periphery structures. Social Networks 1999, 21:375-395.
    • (1999) Social Networks , vol.21 , pp. 375-395
    • Borgatii, S.P.1    Everett, M.G.2
  • 69
    • 20444504323 scopus 로고    scopus 로고
    • Uncoverring the overlapping community structure of complex networks in nature and society
    • Palla G, Dernyi I, Farkas I, et al. Uncoverring the overlapping community structure of complex networks in nature and society. Nature 2005, 435(7043):814-818.
    • (2005) Nature , vol.435 , Issue.7043 , pp. 814-818
    • Palla, G.1    Dernyi, I.2    Farkas, I.3
  • 70
    • 33645830948 scopus 로고    scopus 로고
    • CFinder: locating cliques and overlapping modules in biological networks
    • Adamcsek B, Palla G, Farkas I, et al. CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 2006, 22(8):1021-1023.
    • (2006) Bioinformatics , vol.22 , Issue.8 , pp. 1021-1023
    • Adamcsek, B.1    Palla, G.2    Farkas, I.3
  • 71
    • 30644463216 scopus 로고    scopus 로고
    • Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastatis
    • Jonsson P, Cavanna T, Zicha D, Bates P. Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastatis. BMC Bioinformmatics 2006, 7:2.
    • (2006) BMC Bioinformmatics , vol.7 , pp. 2
    • Jonsson, P.1    Cavanna, T.2    Zicha, D.3    Bates, P.4
  • 72
    • 33751229605 scopus 로고    scopus 로고
    • Identification of functional modules in a PPI network by clique percolation clustering
    • Zhang S, Ning X, Zhang X. Identification of functional modules in a PPI network by clique percolation clustering. Computational Biology and Chemistry 2006, 30:445-451.
    • (2006) Computational Biology and Chemistry , vol.30 , pp. 445-451
    • Zhang, S.1    Ning, X.2    Zhang, X.3
  • 74
    • 33645761859 scopus 로고    scopus 로고
    • Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast
    • Zhang C, Liu S, Zhou Y. Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast. J Proteome Res 2006, 5(4):801-7.
    • (2006) J Proteome Res , vol.5 , Issue.4 , pp. 801-807
    • Zhang, C.1    Liu, S.2    Zhou, Y.3
  • 75
    • 33748579201 scopus 로고    scopus 로고
    • Interaction Graph mining for protein complexes using local clique merging
    • Li XL, Tan SH, Foo CS, et al. Interaction Graph mining for protein complexes using local clique merging. Genome Informatics 2005, 16:260-269.
    • (2005) Genome Informatics , vol.16 , pp. 260-269
    • Li, X.L.1    Tan, S.H.2    Foo, C.S.3
  • 76
    • 38449114820 scopus 로고    scopus 로고
    • Discovering protein complexes in dense reliable neighborhoods of protein interaction networks
    • August
    • Li XL, Foo CS, Ng SK. Discovering protein complexes in dense reliable neighborhoods of protein interaction networks. Proc LSS Comput Syst Bioinform Conf 2007, 6:157-168. August.
    • (2007) Proc LSS Comput Syst Bioinform Conf , vol.6 , pp. 157-168
    • Li, X.L.1    Foo, C.S.2    Ng, S.K.3
  • 77
    • 34248396293 scopus 로고    scopus 로고
    • Decomposition of overlapping protein complexes a graph theoretical method for analyzing static and dynamic protein association
    • 1481596, 16722537
    • Zotenko E, Guimarães K, Jothi R. Decomposition of overlapping protein complexes a graph theoretical method for analyzing static and dynamic protein association. Algorithms for Molecular Biology 2006, 1:7. 1481596, 16722537.
    • (2006) Algorithms for Molecular Biology , vol.1 , pp. 7
    • Zotenko, E.1    Guimarães, K.2    Jothi, R.3
  • 78
    • 41549118299 scopus 로고
    • The intersection graphs of subtrees in trees are exactly the chordal graphs
    • Gavril F. The intersection graphs of subtrees in trees are exactly the chordal graphs. Journal of Combinatorial Theory (B) 1974, 16:47-56.
    • (1974) Journal of Combinatorial Theory (B) , vol.16 , pp. 47-56
    • Gavril, F.1
  • 81
    • 33947109414 scopus 로고    scopus 로고
    • A seed-refine algorithm for detecting protein complexes from protein interaction data
    • Pei P, Zhang A. A seed-refine algorithm for detecting protein complexes from protein interaction data. IEEE Transactions on Nanobioscience 2007, 6(1):43-50.
    • (2007) IEEE Transactions on Nanobioscience , vol.6 , Issue.1 , pp. 43-50
    • Pei, P.1    Zhang, A.2
  • 83
    • 13444282425 scopus 로고    scopus 로고
    • The Stanford Microarray Database accommodates additional microarray platforms and data formats
    • Ball CA, et al. The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acid Research 2005, 33:D580-D582.
    • (2005) Nucleic Acid Research , vol.33
    • Ball, C.A.1
  • 85
    • 33751166180 scopus 로고    scopus 로고
    • Identification of overlapping community structure in complex networks using fuzzy c-means clustering
    • Zhang S, Wang RS, Zhang XS. Identification of overlapping community structure in complex networks using fuzzy c-means clustering. PHYSICA 374(1).
    • PHYSICA , vol.374 , Issue.1
    • Zhang, S.1    Wang, R.S.2    Zhang, X.S.3
  • 86
    • 59449103335 scopus 로고    scopus 로고
    • Detect overlapping and hierarchical community structure in networks
    • Shen H, Cheng X, Cai K, Hu MB. Detect overlapping and hierarchical community structure in networks. Physica A 2009, 388:1706-1712.
    • (2009) Physica A , vol.388 , pp. 1706-1712
    • Shen, H.1    Cheng, X.2    Cai, K.3    Hu, M.B.4
  • 87
    • 64549145094 scopus 로고    scopus 로고
    • Detecting the overlapping and hierarchical community structure in complex networks
    • Lancichinetti A, Fortunato S, Kertesz J. Detecting the overlapping and hierarchical community structure in complex networks. New Journal of Physics 2009, 11:1-17.
    • (2009) New Journal of Physics , vol.11 , pp. 1-17
    • Lancichinetti, A.1    Fortunato, S.2    Kertesz, J.3
  • 89
    • 25444434087 scopus 로고    scopus 로고
    • AVID: an integrative framework for discovering functional relationships among proteins
    • 1177925, 15929793
    • Jiang T, Keating AE. AVID: an integrative framework for discovering functional relationships among proteins. BMC Bioinformatics 2005, 6:136. 1177925, 15929793.
    • (2005) BMC Bioinformatics , vol.6 , pp. 136
    • Jiang, T.1    Keating, A.E.2
  • 90
    • 39649083998 scopus 로고    scopus 로고
    • Integration of genomic data for inferring protein complexes from global protein-protein interaction networks
    • Man AND Cybernetics-Part B
    • Zheng H, Wang H, Glass DH. Integration of genomic data for inferring protein complexes from global protein-protein interaction networks. IEEE Transactions on Systems 2008, 38(1):5-16. Man AND Cybernetics-Part B.
    • (2008) IEEE Transactions on Systems , vol.38 , Issue.1 , pp. 5-16
    • Zheng, H.1    Wang, H.2    Glass, D.H.3
  • 91
    • 41349108025 scopus 로고    scopus 로고
    • From pull-down data to protein interaction networks and complexes with biological relevance
    • Zhang B, Park BH, Karpinets T, Samatova NF. From pull-down data to protein interaction networks and complexes with biological relevance. 2008, 24(7):979-986.
    • (2008) , vol.24 , Issue.7 , pp. 979-986
    • Zhang, B.1    Park, B.H.2    Karpinets, T.3    Samatova, N.F.4
  • 92
    • 46249128543 scopus 로고    scopus 로고
    • Identifying functional modules in protein-protein interaction networks: an integrated exact approach
    • Jul 1, 2718639, 18586718
    • Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Müller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 2008, 24(13):i223-31. Jul 1, 2718639, 18586718.
    • (2008) Bioinformatics , vol.24 , Issue.13
    • Dittrich, M.T.1    Klau, G.W.2    Rosenwald, A.3    Dandekar, T.4    Müller, T.5
  • 93
    • 67649568100 scopus 로고    scopus 로고
    • Protein complex prediction based on mutually exclusive interactions in protein interaction network
    • Jung SH, Jang W, Hur H, Hyun B, Han D. Protein complex prediction based on mutually exclusive interactions in protein interaction network. Genome Informatics 2008, 21:77-88.
    • (2008) Genome Informatics , vol.21 , pp. 77-88
    • Jung, S.H.1    Jang, W.2    Hur, H.3    Hyun, B.4    Han, D.5
  • 94
    • 0036141992 scopus 로고    scopus 로고
    • Relating whole-genome expression data with protein-protein interactions
    • 155252, 11779829
    • Jansen R, Greenbaum D, Gerstein M. Relating whole-genome expression data with protein-protein interactions. Genome Research 2002, 12:37-46. 155252, 11779829.
    • (2002) Genome Research , vol.12 , pp. 37-46
    • Jansen, R.1    Greenbaum, D.2    Gerstein, M.3
  • 95
    • 0038014879 scopus 로고    scopus 로고
    • Co-clustering of biological networks and gene expression data
    • Hanisch D, Zien A, Zimmer R, Lengauer T. Co-clustering of biological networks and gene expression data. Bioinformatics 2002, 18:S145-54.
    • (2002) Bioinformatics , vol.18
    • Hanisch, D.1    Zien, A.2    Zimmer, R.3    Lengauer, T.4
  • 96
    • 0000801240 scopus 로고    scopus 로고
    • Discovering regulatory and signalling circuits in molecular interaction networks
    • Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002, 18:S233-S240.
    • (2002) Bioinformatics , vol.18
    • Ideker, T.1    Ozier, O.2    Schwikowski, B.3    Siegel, A.F.4
  • 97
    • 34548742517 scopus 로고    scopus 로고
    • Identification of functional modules using network topology and high-throughput data
    • 1839897, 17408515
    • Ulitsky I, Shamir R. Identification of functional modules using network topology and high-throughput data. BMC Systems Biology 2007, 1:8. 1839897, 17408515.
    • (2007) BMC Systems Biology , vol.1 , pp. 8
    • Ulitsky, I.1    Shamir, R.2
  • 98
    • 0842309161 scopus 로고    scopus 로고
    • Discovering molecular pathways from protein interaction and gene expression data
    • Segal E, Wang H, Koller D. Discovering molecular pathways from protein interaction and gene expression data. Bioinformatics 2003, 19(Suppl 1):i264-71.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL 1
    • Segal, E.1    Wang, H.2    Koller, D.3
  • 99
    • 41149147660 scopus 로고    scopus 로고
    • Growing functional modules from a seed protein via integration of protein interaction and gene expression data
    • 2233647, 17956603
    • Maraziotis IA, Dimitrakopoulou K, Bezerianos A. Growing functional modules from a seed protein via integration of protein interaction and gene expression data. BMC Bioinformatics 2007, 8:408. 2233647, 17956603.
    • (2007) BMC Bioinformatics , vol.8 , pp. 408
    • Maraziotis, I.A.1    Dimitrakopoulou, K.2    Bezerianos, A.3
  • 101
    • 33646437012 scopus 로고    scopus 로고
    • Integrated analysis of multiple data sources reveals modular structure of biological networks
    • Lu H, Shi B, Wu G, et al. Integrated analysis of multiple data sources reveals modular structure of biological networks. Biochem Biophys Res Commun 2006, 345(1):302-9.
    • (2006) Biochem Biophys Res Commun , vol.345 , Issue.1 , pp. 302-309
    • Lu, H.1    Shi, B.2    Wu, G.3
  • 102
    • 65449141657 scopus 로고    scopus 로고
    • Identifying functional modules using expression profiles and confidence-scored protein interactions
    • 1 May
    • Ulitsky I, Shamir R. Identifying functional modules using expression profiles and confidence-scored protein interactions. Bioinformatics 2009, 25:1158-1164. 1 May.
    • (2009) Bioinformatics , vol.25 , pp. 1158-1164
    • Ulitsky, I.1    Shamir, R.2
  • 103
    • 33748464764 scopus 로고    scopus 로고
    • Combining functional and topological properties to identify core modules in protein interaction networks
    • Sep 1
    • Lubovac Z, Gamalielsson J, Olsson B. Combining functional and topological properties to identify core modules in protein interaction networks. Proteins. 2006, 64(4):948-59. Sep 1.
    • (2006) Proteins. , vol.64 , Issue.4 , pp. 948-959
    • Lubovac, Z.1    Gamalielsson, J.2    Olsson, B.3
  • 104
    • 46749134436 scopus 로고    scopus 로고
    • Discovering functional interaction patterns in protein-protein interaction networks
    • 2442100, 18547430
    • Turanalp ME, Can T. Discovering functional interaction patterns in protein-protein interaction networks. BMC Bioinformatics 2008, 9:276. 2442100, 18547430.
    • (2008) BMC Bioinformatics , vol.9 , pp. 276
    • Turanalp, M.E.1    Can, T.2
  • 105
    • 78649667284 scopus 로고    scopus 로고
    • http://psimap.com/index.php/
  • 107
    • 47849096998 scopus 로고    scopus 로고
    • Inferring modules of functionally interacting proteins using the Bond Energy Algorithm
    • 2474619, 18559112
    • Watanabe RL, Morett E, Vallejo EE. Inferring modules of functionally interacting proteins using the Bond Energy Algorithm. BMC Bioinformatics 2008, 9:285. 2474619, 18559112.
    • (2008) BMC Bioinformatics , vol.9 , pp. 285
    • Watanabe, R.L.1    Morett, E.2    Vallejo, E.E.3
  • 108
    • 0036931833 scopus 로고    scopus 로고
    • Cluster ensembles - a knowledge reuse framework for combining partitionings
    • AAAI
    • Strehl A, Ghosh J. Cluster ensembles - a knowledge reuse framework for combining partitionings. 2002, 93-98. AAAI.
    • (2002) , pp. 93-98
    • Strehl, A.1    Ghosh, J.2
  • 109
    • 34547852262 scopus 로고    scopus 로고
    • An ensemble framework for clustering protein-protein interaction networks
    • Asur S, Ucar D, Parthasarathy S. An ensemble framework for clustering protein-protein interaction networks. Bioinformatics 2007, 23(13):i29-i40.
    • (2007) Bioinformatics , vol.23 , Issue.13
    • Asur, S.1    Ucar, D.2    Parthasarathy, S.3
  • 110
    • 48249087654 scopus 로고    scopus 로고
    • Ensemble non-negative matrix factorization methods for clustering protein-protein interactions
    • Greene D, Cagney G, Krogan N, Cunningham P. Ensemble non-negative matrix factorization methods for clustering protein-protein interactions. Bioinformatics 2008, 24(15):1722-1728.
    • (2008) Bioinformatics , vol.24 , Issue.15 , pp. 1722-1728
    • Greene, D.1    Cagney, G.2    Krogan, N.3    Cunningham, P.4
  • 111
    • 0033592606 scopus 로고    scopus 로고
    • Learning the parts of objects by nonnegative matrix factorization
    • Lee DD, Seung HS. Learning the parts of objects by nonnegative matrix factorization. Nature 1999, 401:788-91.
    • (1999) Nature , vol.401 , pp. 788-791
    • Lee, D.D.1    Seung, H.S.2
  • 112
    • 55949137146 scopus 로고    scopus 로고
    • Clustering complex networks and biological networks by non-negative matrix factorization with various similarity measures
    • Wang R, Zhang S, Wang Y, Zhang XS, Chen L. Clustering complex networks and biological networks by non-negative matrix factorization with various similarity measures. Neurocomputing 2008, 72:134-141.
    • (2008) Neurocomputing , vol.72 , pp. 134-141
    • Wang, R.1    Zhang, S.2    Wang, Y.3    Zhang, X.S.4    Chen, L.5
  • 113
    • 9144242935 scopus 로고    scopus 로고
    • MIPS: analysis and annotation of proteins from whole genomes
    • 308826, 14681354
    • Mewes HW, Amid C, Arnold R, et al. MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Research 2004, 32:D41-D44. 308826, 14681354.
    • (2004) Nucleic Acids Research , vol.32
    • Mewes, H.W.1    Amid, C.2    Arnold, R.3
  • 114
    • 78649679890 scopus 로고    scopus 로고
    • http://www.geneontology.org/
  • 115
    • 34548407017 scopus 로고    scopus 로고
    • Discovering functions and revealing mechanisms at molecular level from biological networks
    • Zhang S, Jin G, Zhang XS, Chen L. Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics 2007, 7:2856-2869.
    • (2007) Proteomics , vol.7 , pp. 2856-2869
    • Zhang, S.1    Jin, G.2    Zhang, X.S.3    Chen, L.4
  • 116
    • 78649652691 scopus 로고    scopus 로고
    • Comparison of protein complexes predicted from PPI networks by DPClus and Newman clustering algorithms
    • Tuji H, Altaf-Ul-Amin M, Arita M, et al. Comparison of protein complexes predicted from PPI networks by DPClus and Newman clustering algorithms. IPSJDigital Courier 2006, 2:674-684.
    • (2006) IPSJDigital Courier , vol.2 , pp. 674-684
    • Tuji, H.1    Altaf-Ul-Amin, M.2    Arita, M.3
  • 117
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • 1847944, 17353930
    • Sharan R, Ulitsky I, Shamir R. Network-based prediction of protein function. Molecular Systems Biology 2007, 3:88. 1847944, 17353930.
    • (2007) Molecular Systems Biology , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 118
    • 0242268461 scopus 로고    scopus 로고
    • Predicting protein functions from redundancies in large-scale protein interaction networks
    • 240660, 14566057
    • Samanta MP, Liang S. Predicting protein functions from redundancies in large-scale protein interaction networks. PNAS 2003, 100(22):12579-12583. 240660, 14566057.
    • (2003) PNAS , vol.100 , Issue.22 , pp. 12579-12583
    • Samanta, M.P.1    Liang, S.2
  • 119
    • 47649107210 scopus 로고    scopus 로고
    • Protein function prediction from interaction networks using a random walk ranking algorithm
    • Freschi V. Protein function prediction from interaction networks using a random walk ranking algorithm. Bioinformatics and Bioengineering 2007, 42-48.
    • (2007) Bioinformatics and Bioengineering , pp. 42-48
    • Freschi, V.1
  • 121
    • 57549085034 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction networks
    • Jun; Chapter 8:Unit 8.2
    • Gomez SM, Choi K, Wu Y. Prediction of protein-protein interaction networks. Curr Protoc Bioinformatics 2008, Jun; Chapter 8:Unit 8.2.
    • (2008) Curr Protoc Bioinformatics
    • Gomez, S.M.1    Choi, K.2    Wu, Y.3
  • 122
    • 33645319955 scopus 로고    scopus 로고
    • Predicting interactions in protein networks by completing defective cliques
    • Yu H, Paccanaro A, Trifonov V, Gerstein M. Predicting interactions in protein networks by completing defective cliques. Bioinformatics 2006, 22(7):823-9.
    • (2006) Bioinformatics , vol.22 , Issue.7 , pp. 823-829
    • Yu, H.1    Paccanaro, A.2    Trifonov, V.3    Gerstein, M.4
  • 123
    • 51549118673 scopus 로고    scopus 로고
    • An Improved Method Based on Maximal Clique for Predicting Interactions in Protein Interaction Networks
    • Jianxin W, Zhao C, Min L. An Improved Method Based on Maximal Clique for Predicting Interactions in Protein Interaction Networks. BMEI2008 IEEE press 2008, 62-66.
    • (2008) BMEI2008 IEEE press , pp. 62-66
    • Jianxin, W.1    Zhao, C.2    Min, L.3
  • 124
    • 34248347402 scopus 로고    scopus 로고
    • Dynamical systems for discovering protein complexes and functional modules from biological networks
    • Li W, Liu Y, Huang HC, Peng Y, Lin Y, Ng WK, Ong KL. Dynamical systems for discovering protein complexes and functional modules from biological networks. IEEE/ACM Trans Comput Biol Bioinform 2007, 4(2):233-50.
    • (2007) IEEE/ACM Trans Comput Biol Bioinform , vol.4 , Issue.2 , pp. 233-250
    • Li, W.1    Liu, Y.2    Huang, H.C.3    Peng, Y.4    Lin, Y.5    Ng, W.K.6    Ong, K.L.7


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