메뉴 건너뛰기




Volumn 4, Issue 1, 2011, Pages

Using graph theory to analyze biological networks

Author keywords

biological network; clustering analysis; graph theory; node ranking

Indexed keywords

CLUSTER ANALYSIS; DATA BASE; GENE REGULATORY NETWORK; GRAPH THEORY; HUMAN; MATHEMATICAL MODEL; METABOLISM; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; RECEIVER OPERATING CHARACTERISTIC; REVIEW; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

EID: 79955130092     PISSN: None     EISSN: 17560381     Source Type: Journal    
DOI: 10.1186/1756-0381-4-10     Document Type: Review
Times cited : (575)

References (169)
  • 2
    • 3242675407 scopus 로고    scopus 로고
    • Glutathione-S-transferase-fusion based assays for studying protein-protein interactions
    • Glutathione-S-transferase-fusion based assays for studying protein-protein interactions. HG Vikis KL Guan, Methods Mol Biol 2004 261 175 186
    • (2004) Methods Mol Biol , vol.261 , pp. 175-186
    • Vikis, H.G.1    Guan, K.L.2
  • 3
    • 0034841844 scopus 로고    scopus 로고
    • The tandem affinity purification (TAP) method: A general procedure of protein complex purification
    • DOI 10.1006/meth.2001.1183
    • The tandem affinity purification (TAP) method: a general procedure of protein complex purification. O Puig F Caspary G Rigaut B Rutz E Bouveret E Bragado-Nilsson M Wilm B Seraphin, Methods 2001 24 3 218 229 (Pubitemid 32846428)
    • (2001) Methods , vol.24 , Issue.3 , pp. 218-229
    • Puig, O.1    Caspary, F.2    Rigaut, G.3    Rutz, B.4    Bouveret, E.5    Bragado-Nilsson, E.6    Wilm, M.7    Seraphin, B.8
  • 7
    • 0036921994 scopus 로고    scopus 로고
    • Phage display: Practicalities and prospects
    • DOI 10.1023/A:1021215516430
    • Phage display: practicalities and prospects. WG Willats, Plant Mol Biol 2002 50 6 837 854 (Pubitemid 36034980)
    • (2002) Plant Molecular Biology , vol.50 , Issue.6 , pp. 837-854
    • Willats, W.G.T.1
  • 13
    • 0032894060 scopus 로고    scopus 로고
    • The Yeast Proteome Database (YPD): A model for the organization and presentation of genome-wide functional data
    • DOI 10.1093/nar/27.1.69
    • The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data. PE Hodges AH McKee BP Davis WE Payne JI Garrels, Nucleic Acids Res 1999 27 1 69 73 (Pubitemid 29209404)
    • (1999) Nucleic Acids Research , vol.27 , Issue.1 , pp. 69-73
    • Hodges, P.E.1    McKee, A.H.Z.2    Davis, B.P.3    Payne, W.E.4    Garrels, J.I.5
  • 20
    • 7244254458 scopus 로고    scopus 로고
    • HPID: The human protein interaction
    • DOI 10.1093/bioinformatics/bth253
    • HPID: the Human Protein Interaction Database. K Han B Park H Kim J Hong J Park, Bioinformatics 2004 20 15 2466 2470 (Pubitemid 39429921)
    • (2004) Bioinformatics , vol.20 , Issue.15 , pp. 2466-2470
    • Han, K.1    Park, B.2    Kim, H.3    Hong, J.4    Park, J.5
  • 21
    • 54949120007 scopus 로고    scopus 로고
    • DroID: The Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions
    • DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. J Yu S Pacifico G Liu RL Finley Jr, BMC Genomics 2008 9 461
    • (2008) BMC Genomics , vol.9 , pp. 461
    • Yu, J.1    Pacifico, S.2    Liu, G.3    Finley Jr., R.L.4
  • 24
    • 24644519490 scopus 로고    scopus 로고
    • The transcriptional landscape of the mammalian genome
    • The transcriptional landscape of the mammalian genome. Carninci Pea, Science 2005 309 1559 1563
    • (2005) Science , vol.309 , pp. 1559-1563
    • Pea, C.1
  • 25
    • 38549109487 scopus 로고    scopus 로고
    • NetworKIN: A resource for exploring cellular phosphorylation networks
    • NetworKIN: a resource for exploring cellular phosphorylation networks. Linding Rea, Nucleid Acids Res 2008 36 695 D699
    • (2008) Nucleid Acids Res , vol.36
    • Rea, L.1
  • 28
    • 0029960055 scopus 로고    scopus 로고
    • TRANSFAC: A database on transcription factors and their DNA binding sites
    • DOI 10.1093/nar/24.1.238
    • TRANSFAC: a database on transcription factors and their DNA binding sites. E Wingender P Dietze H Karas R Knuppel, Nucleic Acids Res 1996 24 1 238 241 (Pubitemid 26085775)
    • (1996) Nucleic Acids Research , vol.24 , Issue.1 , pp. 238-241
    • Wingender, E.1    Dietze, P.2    Karas, H.3    Knuppel, R.4
  • 30
    • 38049129809 scopus 로고    scopus 로고
    • A context-specific network of protein-DNA and protein-protein interactions reveals new regulatory motifs in human B cells
    • A context-specific network of protein-DNA and protein-protein interactions reveals new regulatory motifs in human B cells. C Lefebvre WK Lim K Basso R Dalla Favera A Califano, Lecture Notes in Bioinformatics (LNCS) 2007 4532 42 56
    • (2007) Lecture Notes in Bioinformatics (LNCS) , vol.4532 , pp. 42-56
    • Lefebvre, C.1    Lim, W.K.2    Basso, K.3    Dalla Favera, R.4    Califano, A.5
  • 32
    • 55749111058 scopus 로고    scopus 로고
    • Linear motif atlas for phosphorylation-dependent signaling
    • Linear motif atlas for phosphorylation-dependent signaling. ML Miller,, et al. Sci Signal 2008 1 35
    • (2008) Sci Signal , vol.1 , Issue.35
    • Miller, M.L.1
  • 33
    • 44149105911 scopus 로고    scopus 로고
    • PHOSIDA (phosphorylation site database): Management, structural and evolutionary investigation, and prediction of phosphosites
    • PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. F Gnad S Ren J Cox JV Olsen B Macek M Oroshi M Mann, Genome Biol 2007 8 11
    • (2007) Genome Biol , vol.8 , Issue.11
    • Gnad, F.1    Ren, S.2    Cox, J.3    Olsen, J.V.4    MacEk, B.5    Oroshi, M.6    Mann, M.7
  • 35
    • 33846090559 scopus 로고    scopus 로고
    • MiST: A microbial signal transduction database
    • MiST: a microbial signal transduction database. LE Ulrich IB Z, Nucleic Acids Res 2007 35 386 390
    • (2007) Nucleic Acids Res , vol.35 , pp. 4386-390
    • Ulrich, L.E.1    Z, I.B.2
  • 36
    • 0037208158 scopus 로고    scopus 로고
    • TRANSPATH®: An integrated database on signal transduction and a tool for array analysis
    • DOI 10.1093/nar/gkg089
    • TRANSPATH: an integrated database on signal transduction and a tool for array analysis. M Krull N Voss C Choi S Pistor A Potapov E Wingender, Nucleic Acids Res 2003 31 1 97 100 (Pubitemid 36150343)
    • (2003) Nucleic Acids Research , vol.31 , Issue.1 , pp. 97-100
    • Krull, M.1    Voss, N.2    Choi, C.3    Pistor, S.4    Potapov, A.5    Wingender, E.6
  • 37
    • 0034609791 scopus 로고    scopus 로고
    • The large-scale organization of metabolic networks
    • The large-scale organization of metabolic networks. H B Jeong R Tombor ZN Albert AL Oltvai, Nature 2000 407 651 654
    • (2000) Nature , vol.407 , pp. 651-654
    • Jeong, B.1    Tombor, R.2    Albert, Z.N.3    Oltvai, A.L.4
  • 39
    • 34548860112 scopus 로고    scopus 로고
    • The Edinburgh human metabolic network reconstruction and its functional analysis
    • The Edinburgh human metabolic network reconstruction and its functional analysis. H Ma A Mazein A Selkov E Selkov O Demin I Goryanin, Mol Syst Biol 2007 3 135
    • (2007) Mol Syst Biol , vol.3 , Issue.135
    • Ma, H.1    Mazein, A.2    Selkov, A.3    Selkov, E.4    Demin, O.5    Goryanin, I.6
  • 40
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • KEGG for representation and analysis of molecular networks involving diseases and drugs. M Kanehisa S Goto M Furumichi M Tanabe M Hirakawa, Nucleic Acids Res 38 Database 355 360
    • Nucleic Acids Res , Issue.38 DATABASE , pp. 4355-360
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5
  • 44
    • 0034615791 scopus 로고    scopus 로고
    • Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective
    • Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. CH Schilling D Letscher BO Palsson, J Theor Biol 2000 203 3 229 248
    • (2000) J Theor Biol , vol.203 , Issue.3 , pp. 229-248
    • Schilling, C.H.1    Letscher, D.2    Palsson, B.O.3
  • 45
    • 0034615788 scopus 로고    scopus 로고
    • Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis
    • Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. CH Schilling BO Palsson, J Theor Biol 2000 203 3 249 283
    • (2000) J Theor Biol , vol.203 , Issue.3 , pp. 249-283
    • Schilling, C.H.1    Palsson, B.O.2
  • 46
    • 0033136109 scopus 로고    scopus 로고
    • Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era
    • DOI 10.1021/bp990048k
    • Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. CH Schilling S Schuster BO Palsson R Heinrich, Biotechnol Prog 1999 15 3 296 303 (Pubitemid 29270673)
    • (1999) Biotechnology Progress , vol.15 , Issue.3 , pp. 296-303
    • Schilling, C.H.1    Schuster, S.2    Palsson, B.O.3    Heinrich, R.4
  • 47
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • DOI 10.1038/73786
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. S Schuster DA Fell T Dandekar, Nat Biotechnol 2000 18 3 326 332 (Pubitemid 30159487)
    • (2000) Nature Biotechnology , vol.18 , Issue.3 , pp. 326-332
    • Schuster, S.1    Fell, D.A.2    Dandekar, T.3
  • 48
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
    • DOI 10.1016/S0167-7799(98)01290-6, PII S0167779998012906
    • Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. S Schuster T Dandekar DA Fell, Trends Biotechnol 1999 17 2 53 60 (Pubitemid 29332898)
    • (1999) Trends in Biotechnology , vol.17 , Issue.2 , pp. 53-60
    • Schuster, S.1    Dandekar, T.2    Fell, D.A.3
  • 50
    • 0348049802 scopus 로고    scopus 로고
    • Systems biology markup language: Level 2 and beyond
    • Systems biology markup language: Level 2 and beyond. A Finney M Hucka, Biochemical Society transactions 2003 31 Pt 6 1472 1473 (Pubitemid 38031003)
    • (2003) Biochemical Society Transactions , vol.31 , Issue.6 , pp. 1472-1473
    • Finney, A.1    Hucka, M.2
  • 52
    • 0000554921 scopus 로고    scopus 로고
    • Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles
    • Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles. RP Murray RH S, Chem Inf Comput Sci 1999 39 928 942
    • (1999) Chem Inf Comput Sci , vol.39 , pp. 928-942
    • Murray, R.P.1    S, R.H.2
  • 53
    • 0035013293 scopus 로고    scopus 로고
    • Development of chemical markup language (CML) as a system for handling complex chemical content
    • DOI 10.1039/b008780g
    • Development of Chemical Markup Language (CML) as a System for Handling Complex Chemical Content. P Murray-Rust HS Rzepa M Wright, New J Chem 2001 618 634 (Pubitemid 32523097)
    • (2001) New Journal of Chemistry , vol.25 , Issue.4 , pp. 618-634
    • Murray-Rust, P.1    Rzepa, H.S.2    Wright, M.3
  • 60
    • 3042514191 scopus 로고    scopus 로고
    • Coexpresion analysis of human genes across many microarray data sets
    • DOI 10.1101/gr.1910904
    • Coexpression analysis of human genes across many microarray data sets. HK Lee AK Hsu J Sajdak J Qin P Pavlidis, Genome Res 2004 14 6 1085 1094 (Pubitemid 38811545)
    • (2004) Genome Research , vol.14 , Issue.6 , pp. 1085-1094
    • Lee, H.K.1    Hsu, A.K.2    Sajdak, J.3    Qin, J.4    Pavlidis, P.5
  • 64
    • 49449086368 scopus 로고    scopus 로고
    • Survival of the sparsest: Robust gene networks are parsimonious
    • Survival of the sparsest: robust gene networks are parsimonious. RD Leclerc, Mol Syst Biol 2008 4 213
    • (2008) Mol Syst Biol , vol.4 , pp. 213
    • Leclerc, R.D.1
  • 65
    • 34147120474 scopus 로고
    • A note on two problems in connexion with graphs
    • A note on two problems in connexion with graphs. EW Dijkstra, Numerische Mathematik 1959 1 269 271
    • (1959) Numerische Mathematik , vol.1 , pp. 269-271
    • Dijkstra, E.W.1
  • 66
    • 84945709831 scopus 로고
    • Algorithm 97
    • Algorithm 97. RW Floyd, Comm ACM 1962 5-6 345
    • (1962) Comm ACM , vol.56 , pp. 345
    • Floyd, R.W.1
  • 67
    • 84976668743 scopus 로고
    • Algorithm 457: Finding all cliques of an undirected graph
    • Algorithm 457: finding all cliques of an undirected graph. C Bron J Kerbosch, Commun ACM (ACM) 1973 16 9 575 577
    • (1973) Commun ACM (ACM) , vol.16 , Issue.9 , pp. 575-577
    • Bron, C.1    Kerbosch, J.2
  • 68
    • 76749163762 scopus 로고    scopus 로고
    • MIClique: An Algorithm to Identify Differentially Coexpressed Disease Gene Subset from Microarray Data
    • MIClique: An Algorithm to Identify Differentially Coexpressed Disease Gene Subset from Microarray Data. H Zhang X Song H Wang X Zhang, Journal of Biomedicine and Biotechnology 2009
    • (2009) Journal of Biomedicine and Biotechnology
    • Zhang, H.1    Song, X.2    Wang, H.3    Zhang, X.4
  • 72
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • DOI 10.1126/science.1073374
    • Hierarchical organization of modularity in metabolic networks. E Ravasz A Somera D Mongru Z Oltvai A-L Barabsi, Science 2002 297 1551 1555 (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
  • 74
    • 0037174670 scopus 로고    scopus 로고
    • Network motifs: Simple building blocks of complex networks
    • DOI 10.1126/science.298.5594.824
    • Network motifs: simple building blocks of complex networks. R Milo S Shen-Orr S Itzkovitz N Kashtan D Chklovskii U Alon, Science 2002 298 5594 824 827 (Pubitemid 35231534)
    • (2002) Science , vol.298 , Issue.5594 , pp. 824-827
    • Milo, R.1    Shen-Orr, S.2    Itzkovitz, S.3    Kashtan, N.4    Chklovskii, D.5    Alon, U.6
  • 75
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Network motifs in the transcriptional regulation network of Escherichia coli. S Shen-Orr R Milo S Mangan U Alon, Nat Genet 2002 31 64 68
    • (2002) Nat Genet , vol.31 , pp. 64-68
    • Shen-Orr, S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 76
    • 33745780500 scopus 로고    scopus 로고
    • Network motifs: Structure does not determine function
    • Network motifs: structure does not determine function. PJ Ingram MP Stumpf J Stark, BMC Genomics 2006 7 108
    • (2006) BMC Genomics , vol.7 , pp. 108
    • Ingram, P.J.1    Stumpf, M.P.2    Stark, J.3
  • 77
    • 50949092459 scopus 로고    scopus 로고
    • Why do hubs in the yeast protein interaction network tend to be essential: Re-examining the connection between the network topology and essentiality
    • Why do hubs in the yeast protein interaction network tend to be essential: re-examining the connection between the network topology and essentiality. E Zotenko J Mestre DP O'Leary TM Przytycka, PLoS Comput Biol 2008 4 1 16
    • (2008) PLoS Comput Biol , vol.4 , pp. 1-16
    • Zotenko, E.1    Mestre, J.2    O'Leary, D.P.3    Przytycka, T.M.4
  • 78
    • 56849091295 scopus 로고    scopus 로고
    • Network hubs buffer environmental variation in Saccharomyces cerevisiae
    • Network hubs buffer environmental variation in Saccharomyces cerevisiae. SF Levy ML S, PLoS Biol 2008 6 11
    • (2008) PLoS Biol , vol.6 , Issue.11
    • Levy, S.F.1    S, M.L.2
  • 79
    • 0042093610 scopus 로고    scopus 로고
    • The connectivity structure, giant strong component and centrality of metabolic networks
    • The connectivity structure, giant strong component and centrality of metabolic networks. H-W Ma A-P Z, Bioinformatics 2003 19 11
    • (2003) Bioinformatics , vol.19 , Issue.11
    • Ma, H.-W.1    Z, A.-P.2
  • 81
    • 47949110360 scopus 로고    scopus 로고
    • Centrality, Network Capacity, and Modularity as Parameters to Analyze the Core-Periphery Structure in Metabolic Networks
    • Centrality, Network Capacity, and Modularity as Parameters to Analyze the Core-Periphery Structure in Metabolic Networks. MR da Silva H Ma A-P Zeng, Proceedings of the IEEE 2008 96 8 1411 1420
    • (2008) Proceedings of the IEEE , vol.96 , Issue.8 , pp. 1411-1420
    • Da Silva, M.R.1    Ma, H.2    Zeng, A.-P.3
  • 83
    • 34547264299 scopus 로고    scopus 로고
    • Betweenness centrality of fractal and nonfractal scale-free model networks and tests on real networks
    • Betweenness centrality of fractal and nonfractal scale-free model networks and tests on real networks. M Kitsak S Havlin G Paul M Riccaboni F Pammolli HE Stanley, Phys Rev E 2007 75
    • (2007) Phys Rev e , vol.75
    • Kitsak, M.1    Havlin, S.2    Paul, G.3    Riccaboni, M.4    Pammolli, F.5    Stanley, H.E.6
  • 86
    • 46249127253 scopus 로고    scopus 로고
    • Identifying gene-disease associations using centrality on a literature mined gene-interaction network
    • Identifying gene-disease associations using centrality on a literature mined gene-interaction network. A zgür T Vu G Erkan DR Radev, Bioinformatics 2008 24 13 277 i285
    • (2008) Bioinformatics , vol.24 , Issue.13
    • Zgür, A.1    Vu, T.2    Erkan, G.3    Radev, D.R.4
  • 87
    • 77952961276 scopus 로고    scopus 로고
    • Network properties of human disease genes with pleiotropic effects
    • Network properties of human disease genes with pleiotropic effects. S Chavali F Barrenas K Kanduri M Benson, BMC Syst Bio 2010 4
    • (2010) BMC Syst Bio , vol.4
    • Chavali, S.1    Barrenas, F.2    Kanduri, K.3    Benson, M.4
  • 88
    • 0036083434 scopus 로고    scopus 로고
    • Characterization of the folding degree of proteins
    • Characterization of the folding degree of proteins. E Estrada, Bioinformatics 2002 18 697 704 (Pubitemid 34679116)
    • (2002) Bioinformatics , vol.18 , Issue.5 , pp. 697-704
    • Estrada, E.1
  • 89
    • 0035159445 scopus 로고    scopus 로고
    • Recent advances on the role of topological indices in drug discovery research
    • Recent advances on the role of topological indices in drug discovery research. E Estrada E Uriarte, Curr Med Chem 2001 8 1699 1714
    • (2001) Curr Med Chem , vol.8 , pp. 1699-1714
    • Estrada, E.1    Uriarte, E.2
  • 90
    • 77649338567 scopus 로고    scopus 로고
    • Generalized walks-based centrality measures for complex biological networks
    • Generalized walks-based centrality measures for complex biological networks. E Estrada, J Theor Biol 2010 263 4 556 565
    • (2010) J Theor Biol , vol.263 , Issue.4 , pp. 556-565
    • Estrada, E.1
  • 91
    • 34547874681 scopus 로고    scopus 로고
    • Developmental time windows for spatial growth generate multiple-cluster small-world networks
    • DOI 10.1140/epjb/e2007-00214-4
    • Developmental time windows for spatial growth generate multiple-cluster small-world networks. F Nisbach M K, Eur Phys J B 2007 58 185 191 (Pubitemid 47254951)
    • (2007) European Physical Journal B , vol.58 , Issue.2 , pp. 185-191
    • Nisbach, F.1    Kaiser, M.2
  • 92
    • 34249999887 scopus 로고    scopus 로고
    • Predicting the connectivity of primate cortical networks from topological and spatial node properties
    • Predicting the connectivity of primate cortical networks from topological and spatial node properties. LdF Costa M Kaiser CC Hilgetag, BMC Syst Bio 2007 1
    • (2007) BMC Syst Bio , vol.1
    • Costa, L.F.1    Kaiser, M.2    Hilgetag, C.C.3
  • 93
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • DOI 10.1038/35075138
    • Lethality and centrality in protein networks. H Jeong SP Mason A-L Barabasi ZN Oltvai, Nature 2001 411 6833 41 42 (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
  • 94
    • 16344381521 scopus 로고    scopus 로고
    • Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
    • DOI 10.1093/molbev/msi072
    • Comparative genomics of centrality and essentiality in three eukaryotic protein-protein interaction networks. M Hahn A K, Mol Biol Evol 2005 22 803 806 (Pubitemid 40471393)
    • (2005) Molecular Biology and Evolution , vol.22 , Issue.4 , pp. 803-806
    • Hahn, M.W.1    Kern, A.D.2
  • 98
    • 0002226683 scopus 로고    scopus 로고
    • Pajek - Program for Large Network Analysis
    • Pajek - Program for Large Network Analysis. V Batagelj A Mrvar, Connections 1998 21 47 57
    • (1998) Connections , vol.21 , pp. 47-57
    • Batagelj, V.1    Mrvar, A.2
  • 100
    • 27944493925 scopus 로고    scopus 로고
    • Scale-free networks in cell biology
    • Scale-free networks in cell biology. R Albert, Journal of Cell Science 2005 118
    • (2005) Journal of Cell Science , vol.118
    • Albert, R.1
  • 101
    • 72949090589 scopus 로고    scopus 로고
    • The powerful law of the power law and other myths in network biology
    • The powerful law of the power law and other myths in network biology. G Lima-Mendez J van Helden, Mol Biosyst 2009 5 12 1482 1493
    • (2009) Mol Biosyst , vol.5 , Issue.12 , pp. 1482-1493
    • Lima-Mendez, G.1    Van Helden, J.2
  • 102
    • 18744389789 scopus 로고    scopus 로고
    • Assortative Mixing in Networks
    • Assortative Mixing in Networks. MEJ Newman, Phys Rev Lett 2002 89 208701
    • (2002) Phys Rev Lett , vol.89 , pp. 208701
    • Newman, M.E.J.1
  • 103
    • 0038752085 scopus 로고    scopus 로고
    • Mixing patterns in networks
    • Mixing patterns in networks. MEJ Newman, Phys Rev 2003 67
    • (2003) Phys Rev , vol.67
    • Newman, M.E.J.1
  • 104
    • 43049149409 scopus 로고    scopus 로고
    • Networks: Teasing out the missing links
    • DOI 10.1038/453047a, PII 453047A
    • Networks: teasing out the missing links. S Redner, Nature 2008 453 47 48 (Pubitemid 351630319)
    • (2008) Nature , vol.453 , Issue.7191 , pp. 47-48
    • Redner, S.1
  • 105
    • 0000207615 scopus 로고
    • On the strength of connectedness of a random graph
    • On the strength of connectedness of a random graph. P Erdös A R, Acta Math Acad Sci Hungar 1961 12 261 267
    • (1961) Acta Math Acad Sci Hungar , vol.12 , pp. 261-267
    • Erdös, P.1    R, A.2
  • 106
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • DOI 10.1038/30918
    • Collective dynamics of 'small-world' networks. DJ Watts SH S, Nature 1998 393 440 442 (Pubitemid 28292183)
    • (1998) Nature , vol.393 , Issue.6684 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 107
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • Emergence of scaling in random networks. A-L Barabsi R A, Science 1999 286 509 512
    • (1999) Science , vol.286 , pp. 509-512
    • Barabsi, A.-L.1    A, R.2
  • 108
    • 12444301754 scopus 로고    scopus 로고
    • Structure and evolution of protein interaction networks: A statistical model for link dynamics and gene duplications
    • Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications. J Berg M Lassig A Wagner, BMC Evol Biol 2004 4 1 51
    • (2004) BMC Evol Biol , vol.4 , Issue.1 , pp. 51
    • Berg, J.1    Lassig, M.2    Wagner, A.3
  • 109
    • 70350482286 scopus 로고    scopus 로고
    • Evolution of biomolecular networks - Lessons from metabolic and protein interactions
    • Evolution of biomolecular networks - lessons from metabolic and protein interactions. T Yamada P B, Nature Rev Molecular Cell Biology 2009 10 791 803
    • (2009) Nature Rev Molecular Cell Biology , vol.10 , pp. 791-803
    • Yamada, T.1    B, P.2
  • 111
    • 33749164066 scopus 로고    scopus 로고
    • Pattern Classification, ch.10: Unsupervised learning and clustering
    • Pattern Classification, ch.10: Unsupervised learning and clustering. RO Duda PE Hart DG Stork, Wiley, New York 2001 571
    • (2001) Wiley, New York , pp. 571
    • Duda, R.O.1    Hart, P.E.2    Stork, D.G.3
  • 112
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • The neighbor-joining method: a new method for reconstructing phylogenetic trees. N Saitou M Nei, Mol Biol Evol 1987 4 4 406 425
    • (1987) Mol Biol Evol , vol.4 , Issue.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 113
  • 114
    • 70449448956 scopus 로고    scopus 로고
    • Threshold selection in gene co-expression networks using spectral graph theory techniques
    • Threshold selection in gene co-expression networks using spectral graph theory techniques. AD Perkins MA L, BMC Bioinformatics 2009 10
    • (2009) BMC Bioinformatics , vol.10
    • Perkins, A.D.1    L, M.A.2
  • 115
    • 0035375137 scopus 로고    scopus 로고
    • Computational analysis of microarray data
    • DOI 10.1038/35076576
    • Computational genetics: Computational analysis of microarray data. J Quackenbush, Nat Rev Genetics 2001 2 418 427 (Pubitemid 33673408)
    • (2001) Nature Reviews Genetics , vol.2 , Issue.6 , pp. 418-427
    • Quackenbush, J.1
  • 117
    • 0002510498 scopus 로고
    • Unweighted Pair Group Method with Arithmetic Mean
    • San Francisco: Freeman
    • Unweighted Pair Group Method with Arithmetic Mean. PHA Sneath RR Sokal, Numerical Taxonomy San Francisco: Freeman 1973 230 234
    • (1973) Numerical Taxonomy , pp. 230-234
    • Sneath, P.H.A.1    Sokal, R.R.2
  • 118
    • 0000028423 scopus 로고
    • A Quantitative Approach to a Problem in Classification
    • A Quantitative Approach to a Problem in Classification. CD Michener RR Sokal, Evolution 1957 11 2 130 162
    • (1957) Evolution , vol.11 , Issue.2 , pp. 130-162
    • Michener, C.D.1    Sokal, R.R.2
  • 119
    • 33749540417 scopus 로고    scopus 로고
    • Neighbor-joining revealed
    • DOI 10.1093/molbev/msl072
    • Neighbor-joining revealed. O Gascuel M Steel, Mol Biol Evol 2006 23 11 1997 2000 (Pubitemid 44536808)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.11 , pp. 1997-2000
    • Gascuel, O.1    Steel, M.2
  • 120
    • 34250285795 scopus 로고
    • U-Statistic Hierarchical Clustering
    • U-Statistic Hierarchical Clustering. R D'andrade, Psychometrika 1978 4 58 67
    • (1978) Psychometrika , vol.4 , pp. 58-67
    • D'Andrade, R.1
  • 121
    • 0014129195 scopus 로고
    • Hierarchical Clustering Schemes
    • Hierarchical Clustering Schemes. SC Johnson, Psychometrika 1967 2 241 254
    • (1967) Psychometrika , vol.2 , pp. 241-254
    • Johnson, S.C.1
  • 122
    • 0036645183 scopus 로고    scopus 로고
    • Interactively Exploring Hierarchical Clustering Results
    • Interactively Exploring Hierarchical Clustering Results. J Seo B Shneiderman, Computer 2002 35 7 80 86
    • (2002) Computer , vol.35 , Issue.7 , pp. 80-86
    • Seo, J.1    Shneiderman, B.2
  • 123
    • 33645324706 scopus 로고    scopus 로고
    • An interactive power analysis tool for microarray hypothesis testing and generation
    • An interactive power analysis tool for microarray hypothesis testing and generation. J Seo H Gordish-Dressman EP Hoffman, Bioinformatics 2006 22 7 808 814
    • (2006) Bioinformatics , vol.22 , Issue.7 , pp. 808-814
    • Seo, J.1    Gordish-Dressman, H.2    Hoffman, E.P.3
  • 124
    • 3242810318 scopus 로고    scopus 로고
    • MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
    • MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. S Kumar K Tamura M Nei, Brief Bioinform 2004 5 2 150 163
    • (2004) Brief Bioinform , vol.5 , Issue.2 , pp. 150-163
    • Kumar, S.1    Tamura, K.2    Nei, M.3
  • 125
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • DOI 10.1093/molbev/msm092
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura D J M Nei K S, Molecular Biology and Evolution 2007 24 1596 1599 (Pubitemid 47236692)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 126
    • 0036139211 scopus 로고    scopus 로고
    • MEGA2: Molecular evolutionary genetics analysis software
    • MEGA2: molecular evolutionary genetics analysis software. S Kumar K Tamura I Jakobsen M Nei, Bioinformatics 2001 17 12 1244 1245 (Pubitemid 33735359)
    • (2001) Bioinformatics , vol.17 , Issue.12 , pp. 1244-1245
    • Kumar, S.1    Tamura, K.2    Jakobsen, I.B.3    Nei, M.4
  • 127
    • 0028294049 scopus 로고
    • MEGA: Molecular evolutionary genetics analysis software for microcomputers
    • MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. S Kumar K Tamura M Nei, Comput Appl Biosci 1994 10 2 189 191 (Pubitemid 24125441)
    • (1994) Computer Applications in the Biosciences , vol.10 , Issue.2 , pp. 189-191
    • Kumar, S.1    Tamura, K.2    Nei, M.3
  • 130
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • An efficient algorithm for large-scale detection of protein families. AJ Enright S Van Dongen CA Ouzounis, Nucleic Acids Res 2002 30 7 1575 1584 (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
  • 132
    • 65449134296 scopus 로고    scopus 로고
    • Clustering algorithms for detecting functional modules in protein interaction networks
    • Clustering algorithms for detecting functional modules in protein interaction networks. L Gao PG Sun J Song, J Bioinform Comput Biol 2009 7 1 217 242
    • (2009) J Bioinform Comput Biol , vol.7 , Issue.1 , pp. 217-242
    • Gao, L.1    Sun, P.G.2    Song, J.3
  • 133
    • 26644466306 scopus 로고    scopus 로고
    • Improved K-means clustering algorithm for exploring local protein sequence motifs representing common structural property
    • DOI 10.1109/TNB.2005.853667
    • Improved K-means clustering algorithm for exploring local protein sequence motifs representing common structural property. W Zhong G Altun R Harrison PC Tai Y Pan, IEEE Trans Nanobioscience 2005 4 3 255 265 (Pubitemid 41441416)
    • (2005) IEEE Transactions on Nanobioscience , vol.4 , Issue.3 , pp. 255-265
    • Zhong, W.1    Altun, G.2    Harrison, R.3    Tai, P.C.4    Pan, Y.5
  • 134
    • 0005924596 scopus 로고    scopus 로고
    • Graph Clustering by Flow Simulation
    • University of Utrecht
    • Graph Clustering by Flow Simulation. S van Dogen, PhD thesis University of Utrecht 2000
    • (2000) PhD Thesis
    • Van Dogen, S.1
  • 135
    • 65849100458 scopus 로고    scopus 로고
    • Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
    • Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. J Vlasblom SJ Wodak, BMC Bioinformatics 2009 10 99
    • (2009) BMC Bioinformatics , vol.10 , pp. 99
    • Vlasblom, J.1    Wodak, S.J.2
  • 136
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • An efficient algorithm for large-scale detection of protein families. AJ Enright S Van Dongen CA Ouzounis, Nucleic Acids Res 2002 30 7 1575 1584 (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
  • 137
    • 0001457509 scopus 로고
    • Some Methods for classification and Analysis of Multivariate Observations
    • Berkeley, University of California Press
    • Some Methods for classification and Analysis of Multivariate Observations. B MacQueen, Proceedings of 5-th Berkeley Symposium on Mathematical Statistics and Probability Berkeley, University of California Press 1967 1 281 297
    • (1967) Proceedings of 5-th Berkeley Symposium on Mathematical Statistics and Probability , vol.1 , pp. 281-297
    • MacQueen, B.1
  • 138
    • 13244255357 scopus 로고    scopus 로고
    • Incremental genetic K-means algorithm and its application in gene expression data analysis
    • Incremental genetic K-means algorithm and its application in gene expression data analysis. Y Lu S Lu F Fotouhi Y Deng SJ Brown, BMC Bioinformatics 2004 5 172
    • (2004) BMC Bioinformatics , vol.5 , pp. 172
    • Lu, Y.1    Lu, S.2    Fotouhi, F.3    Deng, Y.4    Brown, S.J.5
  • 139
    • 33847172327 scopus 로고    scopus 로고
    • Clustering by passing messages between data points
    • DOI 10.1126/science.1136800
    • Clustering by passing messages between data points. BJ Frey D Dueck, Science 2007 315 5814 972 976 (Pubitemid 46281181)
    • (2007) Science , vol.315 , Issue.5814 , pp. 972-976
    • Frey, B.J.1    Dueck, D.2
  • 140
    • 10244264813 scopus 로고    scopus 로고
    • Protein complex prediction via cost-based clustering
    • DOI 10.1093/bioinformatics/bth351
    • Protein complex prediction via cost-based clustering. AD King N Przulj I Jurisica, Bioinformatics 2004 20 17 3013 3020 (Pubitemid 39619193)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3013-3020
    • King, A.D.1    Przulj, N.2    Jurisica, I.3
  • 141
  • 142
    • 76749150479 scopus 로고    scopus 로고
    • Computational approaches for detecting protein complexes from protein interaction networks: A survey
    • Computational approaches for detecting protein complexes from protein interaction networks: a survey. X Li M Wu CK Kwoh SK Ng, BMC Genomics 2010 11 Suppl 1 3
    • (2010) BMC Genomics , vol.11 , Issue.SUPPL. 1 , pp. 193
    • Li, X.1    Wu, M.2    Kwoh, C.K.3    Ng, S.K.4
  • 143
    • 33751255087 scopus 로고    scopus 로고
    • Evaluation of clustering algorithms for protein-protein interaction networks
    • Evaluation of clustering algorithms for protein-protein interaction networks. S Brohee J van Helden, BMC Bioinformatics 2006 7 488
    • (2006) BMC Bioinformatics , vol.7 , pp. 488
    • Brohee, S.1    Van Helden, J.2
  • 144
    • 65449162644 scopus 로고    scopus 로고
    • A survey of visualization tools for biological network analysis
    • A survey of visualization tools for biological network analysis. GA Pavlopoulos AL Wegener R Schneider, BioData Min 2008 1 12
    • (2008) BioData Min , vol.1 , pp. 12
    • Pavlopoulos, G.A.1    Wegener, A.L.2    Schneider, R.3
  • 147
    • 33745590867 scopus 로고    scopus 로고
    • ArrayCluster: An analytic tool for clustering, data visualization and module finder on gene expression profiles
    • DOI 10.1093/bioinformatics/btl129
    • ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles. R Yoshida T Higuchi S Imoto S Miyano, Bioinformatics 2006 22 1538 1539 (Pubitemid 43985329)
    • (2006) Bioinformatics , vol.22 , Issue.12 , pp. 1538-1539
    • Yoshida, R.1    Higuchi, T.2    Imoto, S.3    Miyano, S.4
  • 148
    • 28944452690 scopus 로고    scopus 로고
    • Medusa: A simple tool for interaction graph analysis
    • DOI 10.1093/bioinformatics/bti696
    • Medusa: a simple tool for interaction graph analysis. SD Hooper P Bork, Bioinformatics 2005 21 24 4432 4433 (Pubitemid 41782941)
    • (2005) Bioinformatics , vol.21 , Issue.24 , pp. 4432-4433
    • Hooper, S.D.1    Bork, P.2
  • 155
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • Comparative assessment of large-scale data sets of protein-protein interactions. C von Mering R Krause B Snel M Cornell SG Oliver S Fields P Bork, Nature 2002 417 6887 399 403 (Pubitemid 34563526)
    • (2002) Nature , vol.417 , Issue.6887 , pp. 399-403
    • Von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 156
    • 77956381678 scopus 로고    scopus 로고
    • Construction and analysis of protein-protein interaction networks
    • Construction and analysis of protein-protein interaction networks. K Raman, Autom Exp 2010 2 1 2
    • (2010) Autom Exp , vol.2 , Issue.1 , pp. 2
    • Raman, K.1
  • 159
    • 33746207758 scopus 로고    scopus 로고
    • Bacterial regulatory networks are extremely flexible in evolution
    • Bacterial regulatory networks are extremely flexible in evolution. I Lozada-Chavez SC Janga J Collado-Vides, Nucleic Acids Res 2006 34 12 3434 3445
    • (2006) Nucleic Acids Res , vol.34 , Issue.12 , pp. 3434-3445
    • Lozada-Chavez, I.1    Janga, S.C.2    Collado-Vides, J.3
  • 160
    • 33646113855 scopus 로고    scopus 로고
    • Evolutionary dynamics of prokaryotic transcriptional regulatory networks
    • Evolutionary dynamics of prokaryotic transcriptional regulatory networks. M Madan Babu SA Teichmann L Aravind, J Mol Biol 2006 358 2 614 633
    • (2006) J Mol Biol , vol.358 , Issue.2 , pp. 614-633
    • Madan Babu, M.1    Teichmann, S.A.2    Aravind, L.3
  • 162
    • 0041828241 scopus 로고    scopus 로고
    • Scaling laws in the functional content of genomes
    • DOI 10.1016/S0168-9525(03)00203-8
    • Scaling laws in the functional content of genomes. E van Nimwegen, Trends Genet 2003 19 9 479 484 (Pubitemid 37101085)
    • (2003) Trends in Genetics , vol.19 , Issue.9 , pp. 479-484
    • Van Nimwegen, E.1
  • 163
    • 0033555859 scopus 로고    scopus 로고
    • Emergent properties of networks of biological signaling pathways
    • Emergent properties of networks of biological signaling pathways. US Bhalla R Iyengar, Science 1999 283 5400 381 387
    • (1999) Science , vol.283 , Issue.5400 , pp. 381-387
    • Bhalla, U.S.1    Iyengar, R.2
  • 165
    • 0036578654 scopus 로고    scopus 로고
    • Topological and causal structure of the yeast transcriptional regulatory network
    • Topological and causal structure of the yeast transcriptional regulatory network. N Guelzim S Bottani P Bourgine F Kepes, Nat Genet 2002 31 1 60 63
    • (2002) Nat Genet , vol.31 , Issue.1 , pp. 60-63
    • Guelzim, N.1    Bottani, S.2    Bourgine, P.3    Kepes, F.4
  • 166
    • 0037316239 scopus 로고    scopus 로고
    • Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms
    • DOI 10.1093/bioinformatics/19.2.270
    • Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. H Ma AP Zeng, Bioinformatics 2003 19 2 270 277 (Pubitemid 36181913)
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 270-277
    • Ma, H.1    Zeng, A.-P.2
  • 168
    • 0038281450 scopus 로고    scopus 로고
    • Hierarchical analysis of dependency in metabolic networks
    • DOI 10.1093/bioinformatics/btg115
    • Hierarchical analysis of dependency in metabolic networks. J Gagneur DB Jackson G Casari, Bioinformatics 2003 19 8 1027 1034 (Pubitemid 36675825)
    • (2003) Bioinformatics , vol.19 , Issue.8 , pp. 1027-1034
    • Gagneur, J.1    Jackson, D.B.2    Casari, G.3
  • 169
    • 0037345719 scopus 로고    scopus 로고
    • Subnetwork hierarchies of biochemical pathways
    • DOI 10.1093/bioinformatics/btg033
    • Subnetwork hierarchies of biochemical pathways. P Holme M Huss H Jeong, Bioinformatics 2003 19 4 532 538 (Pubitemid 36342252)
    • (2003) Bioinformatics , vol.19 , Issue.4 , pp. 532-538
    • Holme, P.1    Huss, M.2    Jeong, H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.