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Volumn 1158, Issue , 2009, Pages 82-92

Global robustness and identifiability of random, scale-free, and small-world networks

Author keywords

Biochemical simulation; Network identifiability; Network robustness; Pathnet; Pathways; Reverse engineering

Indexed keywords

ANALYTIC METHOD; ARTICLE; CELL DIFFERENTIATION; GENE IDENTIFICATION; GENE LIBRARY; GENE STRUCTURE; GENETIC ALGORITHM; GENETIC ENGINEERING; GENETIC VARIABILITY; HELPER CELL; NETWORK LEARNING; PROCESS MODEL;

EID: 63849171480     PISSN: 00778923     EISSN: 17496632     Source Type: Book Series    
DOI: 10.1111/j.1749-6632.2008.03752.x     Document Type: Article
Times cited : (11)

References (41)
  • 1
    • 4444260067 scopus 로고    scopus 로고
    • Antibodies immobilized as arrays to profile protein post-translational modifications in mammalian cells
    • Ivanov, S.S. et al. 2004. Antibodies immobilized as arrays to profile protein post-translational modifications in mammalian cells. Mol. Cell Proteomics 3 : 788 795.
    • (2004) Mol. Cell Proteomics , vol.3 , pp. 788-795
    • Ivanov, S.S.1
  • 2
    • 33751314788 scopus 로고    scopus 로고
    • Current perspectives in protein array technology
    • Kricka, L.J. et al. 2006. Current perspectives in protein array technology. Ann. Clin. Biochem. 43 : 457 467.
    • (2006) Ann. Clin. Biochem. , vol.43 , pp. 457-467
    • Kricka, L.J.1
  • 3
    • 33644519040 scopus 로고    scopus 로고
    • Building mammalian signalling pathways with RNAi screens
    • Moffat, J. D.M. Sabatini. 2006. Building mammalian signalling pathways with RNAi screens. Nat. Rev. Mol. Cell Biol. 7 : 177 187.
    • (2006) Nat. Rev. Mol. Cell Biol. , vol.7 , pp. 177-187
    • Moffat, J.1    Sabatini, D.M.2
  • 4
    • 33746602343 scopus 로고    scopus 로고
    • Reconstructing gene regulatory networks: From random to scale-free connectivity
    • Wildenhain, J. E.J. Crampin. 2006. Reconstructing gene regulatory networks: from random to scale-free connectivity. IEE Proc. Syst. Biol. 153 : 247 256.
    • (2006) IEE Proc. Syst. Biol. , vol.153 , pp. 247-256
    • Wildenhain, J.1    Crampin, E.J.2
  • 6
    • 34447500056 scopus 로고    scopus 로고
    • The community structure of human cellular signaling network
    • Diao, Y. et al. 2007. The community structure of human cellular signaling network. J. Theor. Biol. 247 : 608 615.
    • (2007) J. Theor. Biol. , vol.247 , pp. 608-615
    • Diao, Y.1
  • 7
    • 33748523023 scopus 로고    scopus 로고
    • Topology of mammalian transcription networks
    • Potapov, A.P. et al. 2005. Topology of mammalian transcription networks. Genome Inform. 16 : 270 278.
    • (2005) Genome Inform. , vol.16 , pp. 270-278
    • Potapov, A.P.1
  • 8
    • 33845637127 scopus 로고    scopus 로고
    • Functional and evolutionary inference in gene networks: Does topology matter?
    • Siegal, M.L., D.E. Promislow A. Bergman. 2007. Functional and evolutionary inference in gene networks: does topology matter? Genetica 129 : 83 103.
    • (2007) Genetica , vol.129 , pp. 83-103
    • Siegal, M.L.1    Promislow, D.E.2    Bergman, A.3
  • 9
    • 33845955474 scopus 로고    scopus 로고
    • Inferring topology from clustering coefficients in protein-protein interaction networks
    • Friedel, C.C. R. Zimmer. 2006. Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinformatics 7 : 519.
    • (2006) BMC Bioinformatics , vol.7 , pp. 519
    • Friedel, C.C.1    Zimmer, R.2
  • 10
    • 12344273375 scopus 로고    scopus 로고
    • Modeling interactome: Scale-free or geometric?
    • Przulj, N., D.G. Corneil I. Jurisica. 2004. Modeling interactome: scale-free or geometric? Bioinformatics 20 : 3508 3515.
    • (2004) Bioinformatics , vol.20 , pp. 3508-3515
    • Przulj, N.1    Corneil, D.G.2    Jurisica, I.3
  • 11
    • 24944565272 scopus 로고    scopus 로고
    • Some protein interaction data do not exhibit power law statistics
    • Tanaka, R., T.M. Yi J. Doyle. 2005. Some protein interaction data do not exhibit power law statistics. FEBS Lett. 579 : 5140 5144.
    • (2005) FEBS Lett. , vol.579 , pp. 5140-5144
    • Tanaka, R.1    Yi, T.M.2    Doyle, J.3
  • 12
    • 14744273317 scopus 로고    scopus 로고
    • Inferring network mechanisms: The Drosophila melanogaster protein interaction network
    • Middendorf, M., E. Ziv C.H. Wiggins. 2005. Inferring network mechanisms: the Drosophila melanogaster protein interaction network. Proc. Natl. Acad. Sci. USA 102 : 3192 3197.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 3192-3197
    • Middendorf, M.1    Ziv, E.2    Wiggins, C.H.3
  • 13
    • 33746922321 scopus 로고    scopus 로고
    • Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence
    • Dwight Kuo, P., W. Banzhaf A. Leier. 2006. Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence. Biosystems 85 : 177 200.
    • (2006) Biosystems , vol.85 , pp. 177-200
    • Dwight Kuo, P.1    Banzhaf, W.2    Leier, A.3
  • 14
    • 32144441867 scopus 로고    scopus 로고
    • Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large-scale organization and robustness
    • Li, D. et al. 2006. Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: large-scale organization and robustness. Proteomics 6 : 456 461.
    • (2006) Proteomics , vol.6 , pp. 456-461
    • Li, D.1
  • 16
    • 29144470990 scopus 로고    scopus 로고
    • Topology, tinkering and evolution of the human transcription factor network
    • Rodriguez-Caso, C., M.A. Medina R.V. Sole. 2005. Topology, tinkering and evolution of the human transcription factor network. Febs J. 272 : 6423 6434.
    • (2005) Febs J. , vol.272 , pp. 6423-6434
    • Rodriguez-Caso, C.1    Medina, M.A.2    Sole, R.V.3
  • 17
    • 0034721164 scopus 로고    scopus 로고
    • Error and attack tolerance of complex networks
    • Albert, R., H. Jeong A.L. Barabasi. 2000. Error and attack tolerance of complex networks. Nature 406 : 378 382.
    • (2000) Nature , vol.406 , pp. 378-382
    • Albert, R.1    Jeong, H.2    Barabasi, A.L.3
  • 18
    • 33745242506 scopus 로고    scopus 로고
    • Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks
    • Balaji, S. et al. 2006. Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks. J. Mol. Biol. 360 : 204 212.
    • (2006) J. Mol. Biol. , vol.360 , pp. 204-212
    • Balaji, S.1
  • 19
  • 21
    • 18144412571 scopus 로고    scopus 로고
    • Optimization of robustness and connectivity in complex networks
    • Shargel, B. et al. 2003. Optimization of robustness and connectivity in complex networks. Phys. Rev. Lett. 90 : 068701.
    • (2003) Phys. Rev. Lett. , vol.90 , pp. 068701
    • Shargel, B.1
  • 22
    • 36249005452 scopus 로고    scopus 로고
    • CellFrame: A data structure for cell biology and construction of cell perturbation networks
    • Gong, Y. Z. Zhang. 2007. CellFrame: a data structure for cell biology and construction of cell perturbation networks. Ann. N. Y. Acad. Sci. 1115 : 249 266.
    • (2007) Ann. N. Y. Acad. Sci. , vol.1115 , pp. 249-266
    • Gong, Y.1    Zhang, Z.2
  • 23
    • 36248971654 scopus 로고    scopus 로고
    • Alternative pathway approach for automating analysis and validation of cell perturbation networks and design of perturbation experiments
    • Gong, Y. Z. Zhang. 2007. Alternative pathway approach for automating analysis and validation of cell perturbation networks and design of perturbation experiments. Ann. N. Y. Acad. Sci. 1115 : 267 285.
    • (2007) Ann. N. Y. Acad. Sci. , vol.1115 , pp. 267-285
    • Gong, Y.1    Zhang, Z.2
  • 24
    • 25844510799 scopus 로고    scopus 로고
    • Alternative signaling pathways: When, where and why?
    • Gong, Y. Z. Zhang. 2005. Alternative signaling pathways: when, where and why? FEBS Lett. 579 : 5265 5274.
    • (2005) FEBS Lett. , vol.579 , pp. 5265-5274
    • Gong, Y.1    Zhang, Z.2
  • 25
    • 0242541682 scopus 로고    scopus 로고
    • Shc-dependent pathway is redundant but dominant in MAPK cascade activation by EGF receptors: A modeling inference
    • Gong, Y. X. Zhao. 2003. Shc-dependent pathway is redundant but dominant in MAPK cascade activation by EGF receptors: a modeling inference. FEBS Lett. 554 : 467 472.
    • (2003) FEBS Lett. , vol.554 , pp. 467-472
    • Gong, Y.1    Zhao, X.2
  • 26
    • 2942694772 scopus 로고    scopus 로고
    • Artificial gene networks for objective comparison of analysis algorithms
    • Mendes, P., W. Sha K. Ye. 2003. Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics 19 (Suppl 2 II122 II129.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Mendes, P.1    Sha, W.2    Ye, K.3
  • 27
    • 33646346114 scopus 로고    scopus 로고
    • A method for the generation of standardized qualitative dynamical systems of regulatory networks
    • Mendoza, L. I. Xenarios. 2006. A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theor. Biol. Med. Model. 3 : 13.
    • (2006) Theor. Biol. Med. Model. , vol.3 , pp. 13
    • Mendoza, L.1    Xenarios, I.2
  • 28
    • 33745631242 scopus 로고    scopus 로고
    • The SBML ODE Solver Library: A native API for symbolic and fast numerical analysis of reaction networks
    • Machne, R. et al. 2006. The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics 22 : 1406 1407.
    • (2006) Bioinformatics , vol.22 , pp. 1406-1407
    • MacHne, R.1
  • 29
    • 33845355240 scopus 로고    scopus 로고
    • Hypothesis generation in signaling networks
    • Ruths, D.A. et al. 2006. Hypothesis generation in signaling networks. J. Comput. Biol. 13 : 1546 1557.
    • (2006) J. Comput. Biol. , vol.13 , pp. 1546-1557
    • Ruths, D.A.1
  • 30
    • 21144439147 scopus 로고    scopus 로고
    • Assessing computational tools for the discovery of transcription factor binding sites
    • Tompa, M. et al. 2005. Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol. 23 : 137 144.
    • (2005) Nat. Biotechnol. , vol.23 , pp. 137-144
    • Tompa, M.1
  • 31
    • 13244299124 scopus 로고    scopus 로고
    • Applying support vector machines for gene ontology based gene function prediction
    • Vinayagam, A. et al. 2004. Applying support vector machines for gene ontology based gene function prediction. BMC Bioinformatics 5 : 116.
    • (2004) BMC Bioinformatics , vol.5 , pp. 116
    • Vinayagam, A.1
  • 32
    • 41449088987 scopus 로고    scopus 로고
    • Beta 2-adrenergic receptor signaling and desensitization elucidated by quantitative modeling of real-time camp dynamics
    • Violin, J.D. et al. 2008. beta 2-adrenergic receptor signaling and desensitization elucidated by quantitative modeling of real-time camp dynamics. J. Biol. Chem. 283 : 2949 2961.
    • (2008) J. Biol. Chem. , vol.283 , pp. 2949-2961
    • Violin, J.D.1
  • 33
    • 39849102805 scopus 로고    scopus 로고
    • Regulation of sterol synthesis in eukaryotes
    • Espenshade, P.J. A.L. Hughes. 2007. Regulation of sterol synthesis in eukaryotes. Annu. Rev. Genet. 41 : 401 427.
    • (2007) Annu. Rev. Genet. , vol.41 , pp. 401-427
    • Espenshade, P.J.1    Hughes, A.L.2
  • 34
    • 33846807390 scopus 로고    scopus 로고
    • Alternative routes and mutational robustness in complex regulatory networks
    • Wagner, A. J. Wright. 2007. Alternative routes and mutational robustness in complex regulatory networks. Biosystems 88 : 163 172.
    • (2007) Biosystems , vol.88 , pp. 163-172
    • Wagner, A.1    Wright, J.2
  • 35
    • 25444489018 scopus 로고    scopus 로고
    • Systematic yeast synthetic lethal and synthetic dosage lethal screens identify genes required for chromosome segregation
    • Measday, V. et al. 2005. Systematic yeast synthetic lethal and synthetic dosage lethal screens identify genes required for chromosome segregation. Proc. Natl. Acad. Sci. USA 102 : 13956 13961.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 13956-13961
    • Measday, V.1
  • 36
    • 33644807842 scopus 로고    scopus 로고
    • Synthetic genetic array analysis in Saccharomyces cerevisiae
    • Tong, A.H. C. Boone. 2006. Synthetic genetic array analysis in Saccharomyces cerevisiae. Methods Mol. Biol. 313 : 171 192.
    • (2006) Methods Mol. Biol. , vol.313 , pp. 171-192
    • Tong, A.H.1    Boone, C.2
  • 37
    • 0242490789 scopus 로고    scopus 로고
    • Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: Insights from an identifiability analysis of an in silico network
    • Zak, D.E. et al. 2003. Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: insights from an identifiability analysis of an in silico network. Genome Res. 13 : 2396 2405.
    • (2003) Genome Res. , vol.13 , pp. 2396-2405
    • Zak, D.E.1
  • 38
    • 26844529251 scopus 로고    scopus 로고
    • A genetic basis for IFN-gamma production and T-bet expression in humans
    • Hohler, T. et al. 2005. A genetic basis for IFN-gamma production and T-bet expression in humans. J. Immunol. 175 : 5457 5462.
    • (2005) J. Immunol. , vol.175 , pp. 5457-5462
    • Hohler, T.1
  • 39
    • 33745699554 scopus 로고    scopus 로고
    • The T-box transcription factor T-bet in immunity and autoimmunity
    • Peng, S.L. 2006. The T-box transcription factor T-bet in immunity and autoimmunity. Cell Mol. Immunol. 3 : 87 95.
    • (2006) Cell Mol. Immunol. , vol.3 , pp. 87-95
    • Peng, S.L.1
  • 40
    • 0034677646 scopus 로고    scopus 로고
    • A novel transcription factor, T-bet, directs Th1 lineage commitment
    • Szabo, S.J. et al. 2000. A novel transcription factor, T-bet, directs Th1 lineage commitment. Cell 100 : 655 669.
    • (2000) Cell , vol.100 , pp. 655-669
    • Szabo, S.J.1
  • 41
    • 33747888564 scopus 로고    scopus 로고
    • Inferring functional pathways from multi-perturbation data
    • Yosef, N., A. Kaufman E. Ruppin. 2006. Inferring functional pathways from multi-perturbation data. Bioinformatics 22 : e539 e546.
    • (2006) Bioinformatics , vol.22
    • Yosef, N.1    Kaufman, A.2    Ruppin, E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.