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Volumn 5, Issue 7, 2010, Pages

Jerarca: Efficient analysis of complex networks using hierarchical clustering

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; BIOINFORMATICS; CLUSTER ANALYSIS; COMMUNITY STRUCTURE; COMPUTER NETWORK; COMPUTER PROGRAM; GENETIC ALGORITHM; PHYLOGENETIC TREE; PROTEIN PROTEIN INTERACTION; STATISTICAL ANALYSIS; ALGORITHM; BIOLOGY; METHODOLOGY; PHYSIOLOGY; SIGNAL TRANSDUCTION;

EID: 77955358462     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0011585     Document Type: Article
Times cited : (44)

References (28)
  • 1
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabási AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-114.
    • (2004) Nat Rev Genet , vol.5 , pp. 101-114
    • Barabási, A.L.1    Oltvai, Z.N.2
  • 2
    • 33748798478 scopus 로고    scopus 로고
    • Graph-based methods for analysing networks in cell biology
    • Aittokallio T, Schwikowski B (2006) Graph-based methods for analysing networks in cell biology. Brief Bioinform 7: 243-255.
    • (2006) Brief Bioinform , vol.7 , pp. 243-255
    • Aittokallio, T.1    Schwikowski, B.2
  • 3
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • Sharan R, Ulitsky I, Shamir R (2007) Network-based prediction of protein function. Mol Syst Biol 3: 88.
    • (2007) Mol Syst Biol , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 4
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • Spirin V, Mirny LA (2003) Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 100: 12123-12128.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.A.2
  • 5
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • Bader GD, Hogue CWV (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4: 2.
    • (2003) BMC Bioinformatics , vol.4 , pp. 2
    • Bader, G.D.1    Hogue, C.W.V.2
  • 6
    • 13244292287 scopus 로고    scopus 로고
    • Clustering proteins from interaction networks for the prediction of cellular functions
    • Brun C, Herrmann C, Guénoche A (2004) Clustering proteins from interaction networks for the prediction of cellular functions. BMC Bioinformatics 5: 95.
    • (2004) BMC Bioinformatics , vol.5 , pp. 95
    • Brun, C.1    Herrmann, C.2    Guénoche, A.3
  • 7
    • 0346156102 scopus 로고    scopus 로고
    • Detection of functional modules from protein interaction networks
    • Pereira-Leal JB, Enright AJ, Ouzounis CA (2004) Detection of functional modules from protein interaction networks. Proteins 54: 49-57.
    • (2004) Proteins , vol.54 , pp. 49-57
    • Pereira-Leal, J.B.1    Enright, A.J.2    Ouzounis, C.A.3
  • 8
    • 1342330546 scopus 로고    scopus 로고
    • Functional topology in a network of protein interactions
    • Pržulj N, Wigle DA, Jurisica I (2004) Functional topology in a network of protein interactions. Bioinformatics 20: 340-348.
    • (2004) Bioinformatics , vol.20 , pp. 340-348
    • Pržulj, N.1    Wigle, D.A.2    Jurisica, I.3
  • 9
    • 33744805096 scopus 로고    scopus 로고
    • Development and implementation of an algorithm for detection of protein complexes in large interaction networks
    • Altaf-Ul-Amin M, Shinbo Y, Mihara K, Kurokawa K, Kanaya S (2006) Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics 7: 207.
    • (2006) BMC Bioinformatics , vol.7 , pp. 207
    • Altaf-Ul-Amin, M.1    Shinbo, Y.2    Mihara, K.3    Kurokawa, K.4    Kanaya, S.5
  • 10
    • 37649028224 scopus 로고    scopus 로고
    • Finding and evaluating community structure in networks
    • Newman MEJ, Girvan M (2004) Finding and evaluating community structure in networks. Phys Rev E 69: 026113.
    • (2004) Phys Rev E , vol.69 , pp. 026113
    • Newman, M.E.J.1    Girvan, M.2
  • 11
    • 10244264813 scopus 로고    scopus 로고
    • Protein complex prediction via cost-based clustering
    • King AD, Pržulj N, Jurisica I (2004) Protein complex prediction via cost-based clustering. Bioinformatics 20: 3013-3020.
    • (2004) Bioinformatics , vol.20 , pp. 3013-3020
    • King, A.D.1    Pržulj, N.2    Jurisica, I.3
  • 12
    • 13844264514 scopus 로고    scopus 로고
    • Iterative cluster analysis of protein interaction data
    • Arnau V, Mars S, Marín I (2005) Iterative cluster analysis of protein interaction data. Bioinformatics 21: 364-378.
    • (2005) Bioinformatics , vol.21 , pp. 364-378
    • Arnau, V.1    Mars, S.2    Marín, I.3
  • 13
    • 0037417817 scopus 로고    scopus 로고
    • Modular organization of cellular networks
    • Rives AW, Galitski T (2003) Modular organization of cellular networks. Proc Natl Acad Sci U S A 100: 1128-1133.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 1128-1133
    • Rives, A.W.1    Galitski, T.2
  • 14
    • 4444281384 scopus 로고    scopus 로고
    • The interactome as a tree - an attempt to visualize the protein-protein interaction network in yeast
    • Lu H, Zhu X, Liu H, Skogerbø G, Zhang J, et al. (2004) The interactome as a tree - an attempt to visualize the protein-protein interaction network in yeast. Nucl Acids Res 32: 4804-4811.
    • (2004) Nucl Acids Res , vol.32 , pp. 4804-4811
    • Lu, H.1    Zhu, X.2    Liu, H.3    Skogerbø, G.4    Zhang, J.5
  • 15
    • 33847129641 scopus 로고    scopus 로고
    • Gene network interconnectedness and the generalized topological overlap measure
    • Yip AM, Horvath S (2007) Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics 8: 22.
    • (2007) BMC Bioinformatics , vol.8 , pp. 22
    • Yip, A.M.1    Horvath, S.2
  • 16
    • 33644779012 scopus 로고    scopus 로고
    • Comparative genomics and protein domain graph analyses link ubiquitination and RNA metabolism
    • Lucas JI, Arnau V, Marín I (2006) Comparative genomics and protein domain graph analyses link ubiquitination and RNA metabolism. J Mol Biol 357: 9-17.
    • (2006) J Mol Biol , vol.357 , pp. 9-17
    • Lucas, J.I.1    Arnau, V.2    Marín, I.3
  • 17
    • 38649130153 scopus 로고    scopus 로고
    • A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification
    • Marco A, Marín I (2007) A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification. BMC Bioinformatics 8: 442.
    • (2007) BMC Bioinformatics , vol.8 , pp. 442
    • Marco, A.1    Marín, I.2
  • 18
    • 68349130125 scopus 로고    scopus 로고
    • Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell
    • Marco A, Marín I (2009) Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell. BMC Syst Biol 3: 69.
    • (2009) BMC Syst Biol , vol.3 , pp. 69
    • Marco, A.1    Marín, I.2
  • 19
    • 0000825481 scopus 로고
    • A statistical method for evaluating systematic relationships
    • Sokal RR, Michenner CD (1958) A statistical method for evaluating systematic relationships. Univ Kansas Sci Bull 38: 1409-1438.
    • (1958) Univ Kansas Sci Bull , vol.38 , pp. 1409-1438
    • Sokal, R.R.1    Michenner, C.D.2
  • 20
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 22
    • 0000472542 scopus 로고
    • Estimating phylogenetics trees from distance matrices
    • Farris JS (1972) Estimating phylogenetics trees from distance matrices. Am Nat 106: 645-668.
    • (1972) Am Nat , vol.106 , pp. 645-668
    • Farris, J.S.1
  • 23
    • 27244456660 scopus 로고    scopus 로고
    • Finding local community structure in networks
    • Clauset A, Newman MEJ, Moore C (2005) Finding local community structure in networks. Phys Rev E 72: 026132.
    • (2005) Phys Rev E , vol.72 , pp. 026132
    • Clauset, A.1    Newman, M.E.J.2    Moore, C.3
  • 24
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
    • (2007) Mol Biol Evol , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 25
    • 38449101120 scopus 로고    scopus 로고
    • Integration of biological networks and gene expression data using Cytoscape
    • Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nature Protocols 2: 2366-2382.
    • (2007) Nature Protocols , vol.2 , pp. 2366-2382
    • Cline, M.S.1    Smoot, M.2    Cerami, E.3    Kuchinsky, A.4    Landys, N.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.