메뉴 건너뛰기




Volumn 2, Issue 3, 2010, Pages 277-292

Algorithmic and analytical methods in network biology

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

EID: 79952196617     PISSN: 19395094     EISSN: 1939005X     Source Type: Journal    
DOI: 10.1002/wsbm.61     Document Type: Article
Times cited : (28)

References (132)
  • 3
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: a brief overview
    • Kitano H. Systems biology: a brief overview. Science 2002, 295:1662-1664.
    • (2002) Science , vol.295 , pp. 1662-1664
    • Kitano, H.1
  • 4
    • 0032524383 scopus 로고    scopus 로고
    • Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome
    • Wang DG, Fan JB, Siao CJ, Berno A, Young P, et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 1998, 280:1077-1082.
    • (1998) Science , vol.280 , pp. 1077-1082
    • Wang, D.G.1    Fan, J.B.2    Siao, C.J.3    Berno, A.4    Young, P.5
  • 6
    • 18144425478 scopus 로고    scopus 로고
    • A genome-wide scalable SNP genotyping assay using microarray technology
    • Gunderson KL, Steemers FJ, Lee G, Mendoza LG, Chee MS. A genome-wide scalable SNP genotyping assay using microarray technology. Nat Genet 2005, 37:549-554.
    • (2005) Nat Genet , vol.37 , pp. 549-554
    • Gunderson, K.L.1    Steemers, F.J.2    Lee, G.3    Mendoza, L.G.4    Chee, M.S.5
  • 7
    • 34347339520 scopus 로고    scopus 로고
    • Methods and strategies for analyzing copy number variation using DNA microarrays
    • Carter NP.Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet 2007, (suppl 7):39.
    • (2007) Nat Genet , Issue.SUPPL. 7 , pp. 39
    • Carter, N.P.1
  • 8
    • 0034910345 scopus 로고    scopus 로고
    • Navigating gene expression using microarrays-a technology review
    • Schulze A, Downward J. Navigating gene expression using microarrays-a technology review. Nat Cell Biol 2001, 3: E190-E195.
    • (2001) Nat Cell Biol , vol.3
    • Schulze, A.1    Downward, J.2
  • 9
    • 0036899286 scopus 로고    scopus 로고
    • From patterns to pathways: gene expression data analysis comes of age
    • Slonim DK. From patterns to pathways: gene expression data analysis comes of age. Nat Genet 2002, 32(suppl):502-508.
    • (2002) Nat Genet , vol.32 , Issue.SUPPL. , pp. 502-508
    • Slonim, D.K.1
  • 10
    • 0141920354 scopus 로고    scopus 로고
    • Comparing protein abundance and mRNA expression levels on a genomic scale
    • Greenbaum D, Colangelo C, Williams K, Gerstein M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 2003, 4(9) 117.
    • (2003) Genome Biol , vol.4 , Issue.9 , pp. 117
    • Greenbaum, D.1    Colangelo, C.2    Williams, K.3    Gerstein, M.4
  • 11
    • 23944483135 scopus 로고    scopus 로고
    • Post-transcriptional control of gene expression: a genome-wide perspective
    • Mata J, Marguerat S, Bähler J. Post-transcriptional control of gene expression: a genome-wide perspective. Trends Biochem Sci 2005, 30:506-514.
    • (2005) Trends Biochem Sci , vol.30 , pp. 506-514
    • Mata, J.1    Marguerat, S.2    Bähler, J.3
  • 14
    • 17644427718 scopus 로고    scopus 로고
    • Causal protein-signaling networks derived from multiparameter single-cell data
    • Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP. Causal protein-signaling networks derived from multiparameter single-cell data. Science 2005, 308:523-529.
    • (2005) Science , vol.308 , pp. 523-529
    • Sachs, K.1    Perez, O.2    Pe'er, D.3    Lauffenburger, D.A.4    Nolan, G.P.5
  • 15
    • 0035836765 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 2001, 98:4569-4574.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 4569-4574
    • Ito, T.1    Chiba, T.2    Ozawa, R.3    Yoshida, M.4    Hattori, M.5
  • 16
    • 0034841844 scopus 로고    scopus 로고
    • The tandem affinity purification (TAP) method: a general procedure of protein complex purification
    • Puig O, Caspary F, Rigaut G, Rutz B, Bouveret E, et al. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 2001, 24:218-229.
    • (2001) Methods , vol.24 , pp. 218-229
    • Puig, O.1    Caspary, F.2    Rigaut, G.3    Rutz, B.4    Bouveret, E.5
  • 17
    • 24144486554 scopus 로고    scopus 로고
    • Local modeling of global interactome networks
    • Scholtens D, Vidal M, Gentleman R. Local modeling of global interactome networks. Bioinformatics 2005, 21:3548-3557.
    • (2005) Bioinformatics , vol.21 , pp. 3548-3557
    • Scholtens, D.1    Vidal, M.2    Gentleman, R.3
  • 18
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering C, Krause R, Snel B, Cornell M, Oliver SG, et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417:399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5
  • 19
    • 0036141992 scopus 로고    scopus 로고
    • Relating wholegenome expression data with protein-protein interactions
    • Jansen R, Greenbaum D, GersteinM. Relating wholegenome expression data with protein-protein interactions. Genome Res 2002, 12:37-46.
    • (2002) Genome Res , vol.12 , pp. 37-46
    • Jansen, R.1    Greenbaum, D.2    Gerstein, M.3
  • 22
    • 13444278821 scopus 로고    scopus 로고
    • Reconstruction of cellular signalling networks and analysis of their properties
    • Papin JA, Hunter T, Palsson BO, Subramaniam S. Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol 2005, 6:99-111.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 99-111
    • Papin, J.A.1    Hunter, T.2    Palsson, B.O.3    Subramaniam, S.4
  • 23
    • 0036601150 scopus 로고    scopus 로고
    • Computational methods for the prediction of protein interactions
    • Valencia A, Pazos F. Computational methods for the prediction of protein interactions. Curr Opin Struct Biol 2002, 12:368-373.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 368-373
    • Valencia, A.1    Pazos, F.2
  • 25
    • 0042889111 scopus 로고    scopus 로고
    • Identification of functional links between genes using phylogenetic profiles
    • Wu J, Kasif S, DeLisi C. Identification of functional links between genes using phylogenetic profiles. Bioinformatics 2003, 19:1524-1530.
    • (2003) Bioinformatics , vol.19 , pp. 1524-1530
    • Wu, J.1    Kasif, S.2    DeLisi, C.3
  • 26
    • 29144461552 scopus 로고    scopus 로고
    • Predicting protein-protein interaction by searching evolutionary tree automorphism space
    • Jothi R, Kann MG, Przytycka TM. Predicting protein-protein interaction by searching evolutionary tree automorphism space. Bioinformatics 2005, 21(suppl 1):241-250.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1 , pp. 241-250
    • Jothi, R.1    Kann, M.G.2    Przytycka, T.M.3
  • 27
    • 0035177259 scopus 로고    scopus 로고
    • Similarity of phylogenetic trees as indicator of protein-protein interaction
    • Pazos F, Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng 2001, 14:609-614.
    • (2001) Protein Eng , vol.14 , pp. 609-614
    • Pazos, F.1    Valencia, A.2
  • 28
    • 0033736476 scopus 로고    scopus 로고
    • Genetic network inference: from co-expression clustering to reverse engineering
    • D'Haeseleer P, Liang S, Somogyi R. Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 2000, 16:707-726.
    • (2000) Bioinformatics , vol.16 , pp. 707-726
    • D'Haeseleer, P.1    Liang, S.2    Somogyi, R.3
  • 29
    • 0141993704 scopus 로고    scopus 로고
    • A Genecoexpression network for global discovery of conserved genetic modules
    • Stuart JM, Segal E, Koller D, Kim SK. A Genecoexpression network for global discovery of conserved genetic modules. Science 2003, 302:249-255.
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 32
    • 9444239213 scopus 로고    scopus 로고
    • A probabilistic functional network of yeast genes
    • Lee I, Date SV, Adai AT, Marcotte EM. A probabilistic functional network of yeast genes. Science 2004, 306:1555-1558.
    • (2004) Science , vol.306 , pp. 1555-1558
    • Lee, I.1    Date, S.V.2    Adai, A.T.3    Marcotte, E.M.4
  • 34
    • 36849004088 scopus 로고    scopus 로고
    • PathFinder: mining signal transduction pathway segments from protein-protein interaction networks
    • Bebek G, Yang J. PathFinder: mining signal transduction pathway segments from protein-protein interaction networks. BMC Bioinform 2007, 8:335.
    • (2007) BMC Bioinform , vol.8 , pp. 335
    • Bebek, G.1    Yang, J.2
  • 36
    • 33644550021 scopus 로고    scopus 로고
    • Structural systems biology: modelling protein interactions
    • Aloy P, Russell RB. Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 2006, 7:188-197.
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 188-197
    • Aloy, P.1    Russell, R.B.2
  • 37
    • 33644845048 scopus 로고    scopus 로고
    • Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships
    • Kim Y, Subramaniam S. Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships. Proteins 2006, 62:1115-1124.
    • (2006) Proteins , vol.62 , pp. 1115-1124
    • Kim, Y.1    Subramaniam, S.2
  • 38
    • 47249152384 scopus 로고    scopus 로고
    • Protein function prediction based on patterns in biological networks
    • Ki{dotless}raç M, Özsoyoǧlu G. Protein function prediction based on patterns in biological networks. Res Comput Mol Biol 2008, 197-213.
    • (2008) Res Comput Mol Biol , pp. 197-213
    • Kiraç, M.1    Özsoyoǧlu, G.2
  • 39
    • 0036568319 scopus 로고    scopus 로고
    • silico two-hybrid system for the selection of physically interacting protein pairs
    • Pazos F, Valencia A. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins Struct Function Genet 2002, 47:219-227.
    • (2002) Proteins Struct Function Genet , vol.47 , pp. 219-227
    • Pazos, F.1    Valencia, A.2
  • 40
    • 33745327144 scopus 로고    scopus 로고
    • An integrated approach to the prediction of domain-domain interactions
    • Lee H, Deng M, Sun F, Chen T. An integrated approach to the prediction of domain-domain interactions. BMC Bioinform 2006, 12:7.
    • (2006) BMC Bioinform , vol.12 , pp. 7
    • Lee, H.1    Deng, M.2    Sun, F.3    Chen, T.4
  • 41
    • 34548084807 scopus 로고    scopus 로고
    • Inferring protein domain interactions from databases of interacting proteins
    • Riley R, Lee C, Sabatti C, Eisenberg D. Inferring protein domain interactions from databases of interacting proteins. Genome Biol 2005, 6:R89.
    • (2005) Genome Biol , vol.6
    • Riley, R.1    Lee, C.2    Sabatti, C.3    Eisenberg, D.4
  • 42
    • 42949163440 scopus 로고    scopus 로고
    • Interrogating domain-domain interactions with parsimony based approaches
    • Guimaraes KS, Przytycka TM. Interrogating domain-domain interactions with parsimony based approaches. BMC Bioinform 2008, 9:171.
    • (2008) BMC Bioinform , vol.9 , pp. 171
    • Guimaraes, K.S.1    Przytycka, T.M.2
  • 43
    • 33748333117 scopus 로고    scopus 로고
    • Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain Interactions mediating protein-protein interactions
    • Jothi R, Cherukuri PF, Tasneem A, Przytycka TM. Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain Interactions mediating protein-protein interactions. J Mol Biol 2006, 362:861-875.
    • (2006) J Mol Biol , vol.362 , pp. 861-875
    • Jothi, R.1    Cherukuri, P.F.2    Tasneem, A.3    Przytycka, T.M.4
  • 46
    • 0037174671 scopus 로고    scopus 로고
    • Transcriptional regulatory networks in Saccharomyces cerevisiae
    • Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799-804.
    • (2002) Science , vol.298 , pp. 799-804
    • Lee, T.I.1    Rinaldi, N.J.2    Robert, F.3    Odom, D.T.4    Bar-Joseph, Z.5
  • 47
    • 0032616683 scopus 로고    scopus 로고
    • Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
    • Maui, HI
    • Akutsu T, Miyano S, Kuhara S. Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing, Maui, HI. 1999, 17-28.
    • (1999) Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing , pp. 17-28
    • Akutsu, T.1    Miyano, S.2    Kuhara, S.3
  • 48
    • 0035999984 scopus 로고    scopus 로고
    • Binary analysis and optimization-based normalization of gene expression data
    • Shmulevich I, Zhang W. Binary analysis and optimization-based normalization of gene expression data. Bioinformatics 2002, 18:555-565.
    • (2002) Bioinformatics , vol.18 , pp. 555-565
    • Shmulevich, I.1    Zhang, W.2
  • 49
    • 0038047901 scopus 로고    scopus 로고
    • On Learning Gene Regulatory Networks Under the Boolean Network Model
    • Lähdesmäki H, Shmulevich I, Yli-Harja O. On Learning Gene Regulatory Networks Under the Boolean Network Model. Machine Learning 2003, 52:147-167.
    • (2003) Machine Learning , vol.52 , pp. 147-167
    • Lähdesmäki, H.1    Shmulevich, I.2    Yli-Harja, O.3
  • 50
    • 0345504891 scopus 로고    scopus 로고
    • Crosstalk in plant cell signaling: structure and function of the genetic network
    • Genoud T, Métraux JP. Crosstalk in plant cell signaling: structure and function of the genetic network. Trends Plant Sci 1999, 4:503-507.
    • (1999) Trends Plant Sci , vol.4 , pp. 503-507
    • Genoud, T.1    Métraux, J.P.2
  • 51
    • 0842288337 scopus 로고    scopus 로고
    • Inferring cellular networks using probabilistic graphicalmodels
    • Friedman N. Inferring cellular networks using probabilistic graphicalmodels. Science 2004, 303:799-805.
    • (2004) Science , vol.303 , pp. 799-805
    • Friedman, N.1
  • 52
  • 53
    • 0842309206 scopus 로고    scopus 로고
    • Inferring gene networks from time series microarray data using dynamic Bayesian networks
    • Kim SY, Imoto S, Miyano S. Inferring gene networks from time series microarray data using dynamic Bayesian networks. Brief Bioinform 2003, 4:228-235.
    • (2003) Brief Bioinform , vol.4 , pp. 228-235
    • Kim, S.Y.1    Imoto, S.2    Miyano, S.3
  • 54
    • 0036184629 scopus 로고    scopus 로고
    • Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks
    • Shmulevich I, Dougherty ER, Kim S, Zhang W. Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 2002, 18:261-274.
    • (2002) Bioinformatics , vol.18 , pp. 261-274
    • Shmulevich, I.1    Dougherty, E.R.2    Kim, S.3    Zhang, W.4
  • 56
    • 1342330546 scopus 로고    scopus 로고
    • Functional topology in a network of protein interactions
    • Przulj N, Wigle DA, Jurisica I. Functional topology in a network of protein interactions. Bioinformatics 2004, 20:340-348.
    • (2004) Bioinformatics , vol.20 , pp. 340-348
    • Przulj, N.1    Wigle, D.A.2    Jurisica, I.3
  • 58
    • 0037460091 scopus 로고    scopus 로고
    • Evolving protein interaction networks through gene duplication
    • Pastor-Satorras R, Smith E, Solé RV. Evolving protein interaction networks through gene duplication. J Theor Biol 2003, 222:199-210.
    • (2003) J Theor Biol , vol.222 , pp. 199-210
    • Pastor-Satorras, R.1    Smith, E.2    Solé, R.V.3
  • 59
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • Spirin V, Mirny LA. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 2003, 100:12123-12128.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.A.2
  • 60
    • 0034515528 scopus 로고    scopus 로고
    • A clustering algorithm based on graph connectivity
    • Hartuv E, Shamir R. A clustering algorithm based on graph connectivity. Inform Processing Lett 2000, 76:175-181.
    • (2000) Inform Processing Lett , vol.76 , pp. 175-181
    • Hartuv, E.1    Shamir, R.2
  • 62
    • 34547672876 scopus 로고    scopus 로고
    • Assessing significance of connectivity and conservation in protein interaction networks
    • Koyutürk M, Szpankowski W, Grama A. Assessing significance of connectivity and conservation in protein interaction networks. J Comput Biol 2007, 14:747-764.
    • (2007) J Comput Biol , vol.14 , pp. 747-764
    • Koyutürk, M.1    Szpankowski, W.2    Grama, A.3
  • 63
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 64
    • 79956150970 scopus 로고    scopus 로고
    • Improved detection of overrepresentation of gene-ontology annotations with parent-child analysis
    • Grossmann S, Bauer S, Robinson PNN, Vingron M. Improved detection of overrepresentation of gene-ontology annotations with parent-child analysis. Bioinformatics 2007, 24:1650-1651.
    • (2007) Bioinformatics , vol.24 , pp. 1650-1651
    • Grossmann, S.1    Bauer, S.2    Robinson, P.N.N.3    Vingron, M.4
  • 65
    • 23144442351 scopus 로고    scopus 로고
    • VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data
    • Hsiao A, Ideker T, Olefsky JM, Subramaniam S. VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. Nucleic Acids Res 2005, 33:W627-W632.
    • (2005) Nucleic Acids Res , vol.33
    • Hsiao, A.1    Ideker, T.2    Olefsky, J.M.3    Subramaniam, S.4
  • 66
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform 2003, 4 2.
    • (2003) BMC Bioinform , vol.4 , pp. 2
    • Bader, G.D.1    Hogue, C.W.2
  • 67
    • 0142241336 scopus 로고    scopus 로고
    • Greedily building protein networks with confidence
    • Bader JS. Greedily building protein networks with confidence. Bioinformatics 2003, 19:1869-1874.
    • (2003) Bioinformatics , vol.19 , pp. 1869-1874
    • Bader, J.S.1
  • 68
    • 0033523989 scopus 로고    scopus 로고
    • Protein interaction maps for complete genomes based on gene fusion events
    • Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA. Protein interaction maps for complete genomes based on gene fusion events. Nature 1999, 402:86-90.
    • (1999) Nature , vol.402 , pp. 86-90
    • Enright, A.J.1    Iliopoulos, I.2    Kyrpides, N.C.3    Ouzounis, C.A.4
  • 69
    • 0038074373 scopus 로고    scopus 로고
    • Topological structure analysis of the protein-protein interaction network in budding yeast
    • Bu D, Zhao Y, Cai L, Xue H, Zhu X, et al. Topological structure analysis of the protein-protein interaction network in budding yeast. Nucl Acids Res 2003, 31:2443-2450.
    • (2003) Nucl Acids Res , vol.31 , pp. 2443-2450
    • Bu, D.1    Zhao, Y.2    Cai, L.3    Xue, H.4    Zhu, X.5
  • 70
    • 0038014879 scopus 로고    scopus 로고
    • Coclustering of biological networks and gene expression data
    • Hanisch D, Zien A, Zimmer R, Lengauer T. Coclustering of biological networks and gene expression data. Bioinformatics. 2002, 18(suppl 1):S145-S154.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Hanisch, D.1    Zien, A.2    Zimmer, R.3    Lengauer, T.4
  • 71
    • 33645732240 scopus 로고    scopus 로고
    • Modeling cellular machinery through biological network comparison
    • Sharan R, Ideker T. Modeling cellular machinery through biological network comparison. Nat Biotechnol 2006, 24:427-433.
    • (2006) Nat Biotechnol , vol.24 , pp. 427-433
    • Sharan, R.1    Ideker, T.2
  • 73
    • 0141593601 scopus 로고    scopus 로고
    • Conserved pathways within bacteria and yeast as revealed by global protein network alignment
    • Kelley BP, Sharan R, Karp RM, Sittler T, Root DE, et al. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci U S A 2003, 100:11394-11399.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 11394-11399
    • Kelley, B.P.1    Sharan, R.2    Karp, R.M.3    Sittler, T.4    Root, D.E.5
  • 74
    • 23844447959 scopus 로고    scopus 로고
    • Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
    • Sharan R, Ideker T, Kelley B, Shamir R, Karp RM. Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol 2005, 12:835-846.
    • (2005) J Comput Biol , vol.12 , pp. 835-846
    • Sharan, R.1    Ideker, T.2    Kelley, B.3    Shamir, R.4    Karp, R.M.5
  • 75
    • 33748257786 scopus 로고    scopus 로고
    • Graemlin: general and robust alignment of multiple large interaction networks
    • Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S. Graemlin: general and robust alignment of multiple large interaction networks. Genome Res 2006, 16:1169-1181.
    • (2006) Genome Res , vol.16 , pp. 1169-1181
    • Flannick, J.1    Novak, A.2    Srinivasan, B.S.3    McAdams, H.H.4    Batzoglou, S.5
  • 77
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • Barabasi AL, Albert R. Emergence of scaling in random networks. Science 1999, 286:509-512.
    • (1999) Science , vol.286 , pp. 509-512
    • Barabasi, A.L.1    Albert, R.2
  • 80
    • 34547558890 scopus 로고    scopus 로고
    • Not all scale-free networks are born equal: The role of the seed graph in PPI network evolution
    • Hormozdiari F, Berenbrink P, Przulj N, Sahinalp SC. Not all scale-free networks are born equal: The role of the seed graph in PPI network evolution. PLoS Comput Biol 2007, 3(7):e118.
    • (2007) PLoS Comput Biol , vol.3 , Issue.7
    • Hormozdiari, F.1    Berenbrink, P.2    Przulj, N.3    Sahinalp, S.C.4
  • 81
    • 12344273375 scopus 로고    scopus 로고
    • Modeling interactome: scale-free or geometric?
    • Przulj N, Corneil DG, Jurisica I. Modeling interactome: scale-free or geometric? Bioinformatics 2005, 20:3508.
    • (2005) Bioinformatics , vol.20 , pp. 3508
    • Przulj, N.1    Corneil, D.G.2    Jurisica, I.3
  • 82
    • 84962671739 scopus 로고    scopus 로고
    • Fast and accurate alignment of multiple protein networks
    • Kalaev M, Bafna V, Sharan R. Fast and accurate alignment of multiple protein networks. Res Comput Mol Biol 2008, 12:246-256.
    • (2008) Res Comput Mol Biol , vol.12 , pp. 246-256
    • Kalaev, M.1    Bafna, V.2    Sharan, R.3
  • 83
    • 14844305006 scopus 로고    scopus 로고
    • An efficient algorithm for detecting frequent subgraphs in biological networks
    • Koyutürk M, Grama A, Szpankowski W. An efficient algorithm for detecting frequent subgraphs in biological networks. Bioinformatics 2004, 20:200-207.
    • (2004) Bioinformatics , vol.20 , pp. 200-207
    • Koyutürk, M.1    Grama, A.2    Szpankowski, W.3
  • 85
    • 33646347364 scopus 로고    scopus 로고
    • QPath: a method for querying pathways in a protein-protein interaction network
    • Shlomi T, Segal D, Ruppin E, Sharan R. QPath: a method for querying pathways in a protein-protein interaction network. BMC Bioinform 2006, 7:199.
    • (2006) BMC Bioinform , vol.7 , pp. 199
    • Shlomi, T.1    Segal, D.2    Ruppin, E.3    Sharan, R.4
  • 86
    • 51349103135 scopus 로고    scopus 로고
    • QNet: a tool for querying protein interaction networks
    • Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, et al. QNet: a tool for querying protein interaction networks. J Comput Biol 2008, 15:913-925.
    • (2008) J Comput Biol , vol.15 , pp. 913-925
    • Dost, B.1    Shlomi, T.2    Gupta, N.3    Ruppin, E.4    Bafna, V.5
  • 88
    • 51349087811 scopus 로고    scopus 로고
    • Global alignment of multiple protein interaction networks with application to functional orthology detection
    • Singh R, Xu J, Berger B. Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc Nat Acad Sci 2008, 105:12763-12768.
    • (2008) Proc Nat Acad Sci , vol.105 , pp. 12763-12768
    • Singh, R.1    Xu, J.2    Berger, B.3
  • 89
    • 49549096179 scopus 로고    scopus 로고
    • Pairwise global alignment of protein interaction networks by matching neighborhood topology
    • Singh R, Xu J, Berger B. Pairwise global alignment of protein interaction networks by matching neighborhood topology. Res Comput Mol Biol 2007, 11:16-31.
    • (2007) Res Comput Mol Biol , vol.11 , pp. 16-31
    • Singh, R.1    Xu, J.2    Berger, B.3
  • 91
    • 0141484611 scopus 로고    scopus 로고
    • Evolutionary conservation of motif constituents in the yeast protein interaction network
    • Wuchty S, Oltvai ZN, Barabási AL. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet 2003, 35:176-179.
    • (2003) Nat Genet , vol.35 , pp. 176-179
    • Wuchty, S.1    Oltvai, Z.N.2    Barabási, A.L.3
  • 92
    • 33846672214 scopus 로고    scopus 로고
    • Biological network comparison using graphlet degree distribution
    • Przulj Natasa. Biological network comparison using graphlet degree distribution. Bioinformatics 2007, 23:e177-e183.
    • (2007) Bioinformatics , vol.23
    • Natasa, P.1
  • 93
    • 14744273317 scopus 로고    scopus 로고
    • Inferring network mechanisms: the Drosophila melanogaster protein interaction network
    • Middendorf M, Ziv E, Wiggins CH. Inferring network mechanisms: the Drosophila melanogaster protein interaction network. Proc Natl Acad Sci 2005, 102:3192-3197.
    • (2005) Proc Natl Acad Sci , vol.102 , pp. 3192-3197
    • Middendorf, M.1    Ziv, E.2    Wiggins, C.H.3
  • 94
    • 27844551326 scopus 로고    scopus 로고
    • Dynamic properties of network motifs contribute to biological network organization
    • Prill RJJ, Iglesias PAA, Levchenko A. Dynamic properties of network motifs contribute to biological network organization. PLoS Biol 2005, 3(11):e343.
    • (2005) PLoS Biol , vol.3 , Issue.11
    • Prill, R.J.J.1    Iglesias, P.A.A.2    Levchenko, A.3
  • 96
    • 33747893280 scopus 로고    scopus 로고
    • Annotating proteins by mining protein interaction networks
    • Ki{dotless}raçM, Özsoyoglu G, Yang J. Annotating proteins by mining protein interaction networks. Bioinformatics 2006, 22:e260-e270.
    • (2006) Bioinformatics , vol.22
    • Kiraç, M.1    Özsoyoglu, G.2    Yang, J.3
  • 97
    • 35748980569 scopus 로고    scopus 로고
    • Mining biological networks for unknown pathways
    • Çakmak A, Özsoyodlu G. Mining biological networks for unknown pathways. Bioinformatics 2007, 23:2775-2783.
    • (2007) Bioinformatics , vol.23 , pp. 2775-2783
    • Çakmak, A.1    Özsoyodlu, G.2
  • 100
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • Sharan R, Ulitsky I, Shamir R. Network-based prediction of protein function. Mol Syst Biol 2007, 3:88.
    • (2007) Mol Syst Biol , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 101
    • 0038699587 scopus 로고    scopus 로고
    • Global protein function prediction from proteinprotein interaction networks
    • Vázquez A, Flammini A, Maritan A, Vespignani A. Global protein function prediction from proteinprotein interaction networks. Nat Biotechnol 2003, 21:697-700.
    • (2003) Nat Biotechnol , vol.21 , pp. 697-700
    • Vázquez, A.1    Flammini, A.2    Maritan, A.3    Vespignani, A.4
  • 102
    • 0242268461 scopus 로고    scopus 로고
    • Predicting protein functions from redundancies in large-scale protein interaction networks
    • Samanta MP, Liang S. Predicting protein functions from redundancies in large-scale protein interaction networks. Proc Natl Acad Sci U S A 2003, 100:12579-12583.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 12579-12583
    • Samanta, M.P.1    Liang, S.2
  • 103
    • 0742304254 scopus 로고    scopus 로고
    • Prediction of protein function using protein-protein interaction data
    • Deng M, Zhang K,Mehta S, Chen T, Sun F. Prediction of protein function using protein-protein interaction data. J Comput Biol 2003, 10:947-960.
    • (2003) J Comput Biol , vol.10 , pp. 947-960
    • Deng, M.1    Zhang, K.2    Mehta, S.3    Chen, T.4    Sun, F.5
  • 104
    • 1542327694 scopus 로고    scopus 로고
    • Whole-genome annotation by using evidence integration in functional-linkage networks
    • Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, et al. Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A 2004, 101:2888-2893.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 2888-2893
    • Karaoz, U.1    Murali, T.M.2    Letovsky, S.3    Zheng, Y.4    Ding, C.5
  • 105
    • 41649119247 scopus 로고    scopus 로고
    • Protein networks in disease
    • Ideker T, Sharan R. Protein networks in disease. Genome Res 2008, 18:644-652.
    • (2008) Genome Res , vol.18 , pp. 644-652
    • Ideker, T.1    Sharan, R.2
  • 107
    • 33747035889 scopus 로고    scopus 로고
    • Predicting disease genes using protein-protein interactions
    • Oti M, Snel B, Huynen MA, Brunner HG. Predicting disease genes using protein-protein interactions. J Med Genet 2006, 43:691-698.
    • (2006) J Med Genet , vol.43 , pp. 691-698
    • Oti, M.1    Snel, B.2    Huynen, M.A.3    Brunner, H.G.4
  • 109
    • 22844450110 scopus 로고    scopus 로고
    • Systematic interpretation of genetic interactions using protein networks
    • KelleyR, Ideker T. Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 2005, 23:561-566.
    • (2005) Nat Biotechnol , vol.23 , pp. 561-566
    • Kelley, R.1    Ideker, T.2
  • 110
    • 0346095291 scopus 로고    scopus 로고
    • Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae
    • Ihmels J, Levy R, Barkai N. Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat Biotechnol 2004, 22:86-92.
    • (2004) Nat Biotechnol , vol.22 , pp. 86-92
    • Ihmels, J.1    Levy, R.2    Barkai, N.3
  • 112
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, et al. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 2004, 431:308-312.
    • (2004) Nature , vol.431 , pp. 308-312
    • Luscombe, N.M.1    Babu, M.M.2    Yu, H.3    Snyder, M.4    Teichmann, S.A.5
  • 113
    • 64349094767 scopus 로고    scopus 로고
    • Tissue specificity and the human protein interaction network
    • Bossi A, Lehner B. Tissue specificity and the human protein interaction network. Mol Syst Biol 2009, 5:260.
    • (2009) Mol Syst Biol , vol.5 , pp. 260
    • Bossi, A.1    Lehner, B.2
  • 114
    • 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, (supp. 1):S233-S240.
    • (2002) Bioinformatics , Issue.SUPP. 1
    • Ideker, T.1    Ozier, O.2    Schwikowski, B.3    Siegel, A.F.4
  • 115
    • 34248593385 scopus 로고    scopus 로고
    • Gene expression network analysis and applications to immunology
    • Nacu S, Critchley-Thorne R, Lee P, et al. Gene expression network analysis and applications to immunology. Bioinformatics 2007, 23:850-858.
    • (2007) Bioinformatics , vol.23 , pp. 850-858
    • Nacu, S.1    Critchley-Thorne, R.2    Lee, P.3
  • 116
    • 34347326247 scopus 로고    scopus 로고
    • Network-based analysis of affected biological processes in type 2 diabetes models
    • Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, et al. Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet 2007, 3:e96.
    • (2007) PLoS Genet , vol.3
    • Liu, M.1    Liberzon, A.2    Kong, S.W.3    Lai, W.R.4    Park, P.J.5
  • 117
    • 65449146537 scopus 로고    scopus 로고
    • Detecting diseasespecific dysregulated pathways via analysis of clinical expression profiles
    • Ulitsky I, Karp RM, Shamir R. Detecting diseasespecific dysregulated pathways via analysis of clinical expression profiles. Res Comput Mol Biol 2008, 12:347-359.
    • (2008) Res Comput Mol Biol , vol.12 , pp. 347-359
    • Ulitsky, I.1    Karp, R.M.2    Shamir, R.3
  • 118
    • 33847015674 scopus 로고    scopus 로고
    • Computational analysis of the synergy among multiple interacting genes
    • Anastassiou D. Computational analysis of the synergy among multiple interacting genes. Mol Syst Biol 2007, 3:83.
    • (2007) Mol Syst Biol , vol.3 , pp. 83
    • Anastassiou, D.1
  • 120
    • 40149090339 scopus 로고    scopus 로고
    • Identification of gene interactions associated with disease from gene expression data using synergy networks
    • Watkinson J,Wang X, Zheng T, Anastassiou D. Identification of gene interactions associated with disease from gene expression data using synergy networks. BMC Syst Biol 2008, 2:10.
    • (2008) BMC Syst Biol , vol.2 , pp. 10
    • Watkinson, J.1    Wang, X.2    Zheng, T.3    Anastassiou, D.4
  • 121
    • 66149156998 scopus 로고    scopus 로고
    • Discovery and scoring of protein interaction subnetworks discriminative of late stage human colon cancer
    • Nibbe RK, Markowitz S,Myeroff L, Ewing R, Chance M. Discovery and scoring of protein interaction subnetworks discriminative of late stage human colon cancer.Mol Cell Prot 2009.
    • (2009) Mol Cell Prot
    • Nibbe, R.K.1    Markowitz, S.2    Myeroff, L.3    Ewing, R.4    Chance, M.5
  • 123
    • 0036799752 scopus 로고    scopus 로고
    • Inferring domaindomain interactions from protein-protein interactions
    • Deng M, Mehta S, Sun F, Chen T. Inferring domaindomain interactions from protein-protein interactions. Genome Res 2002, 12:1540-1548.
    • (2002) Genome Res , vol.12 , pp. 1540-1548
    • Deng, M.1    Mehta, S.2    Sun, F.3    Chen, T.4
  • 124
    • 34548742517 scopus 로고    scopus 로고
    • Identification of functional modules using network topology and high-throughput data
    • Ulitsky I, Shamir R. Identification of functional modules using network topology and high-throughput data. BMC Syst Biol 2007, 1:8.
    • (2007) BMC Syst Biol , vol.1 , pp. 8
    • Ulitsky, I.1    Shamir, R.2
  • 127
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002, 30:1575-1584.
    • (2002) Nucleic Acids Res , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 129
    • 37749031255 scopus 로고    scopus 로고
    • Next generation sequencing transforms today's biology
    • Schuster C. Next generation sequencing transforms today's biology. Nature Methods 2008, 5:16-18.
    • (2008) Nature Methods , vol.5 , pp. 16-18
    • Schuster, C.1
  • 130
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5: 101-113.
    • (2004) Nat Rev Genet , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 131
    • 33644527950 scopus 로고    scopus 로고
    • The model organism as a system: integrating 'omics' data sets
    • Joyce AR, Palsson BØ. The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol 2006, 7: 198-210.
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 198-210
    • Joyce, A.R.1    Palsson, B.Ø.2
  • 132
    • 27144450537 scopus 로고    scopus 로고
    • Less is more in modelling large genetic networks
    • Bornholdt S. Less is more in modelling large genetic networks. Science 2005, 310: 449-451.
    • (2005) Science , vol.310 , pp. 449-451
    • Bornholdt, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.