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Volumn 11, Issue 4, 2010, Pages 297-307

Towards genome-scale signalling-network reconstructions

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE; NITRIC OXIDE;

EID: 77949773550     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg2750     Document Type: Review
Times cited : (101)

References (129)
  • 1
    • 77949772972 scopus 로고    scopus 로고
    • 2nd edn (eds Bradshaw, R. A. & Dennis, E. A.) Academic Press
    • Hyduke, D. R., Amundson, S. A. & Fornace, A. J. Jr. in Handbook of Cell Signaling 2nd edn Vol. 3 (eds Bradshaw, R. A. & Dennis, E. A.) 2107-2125 (Academic Press, 2009).
    • (2009) Handbook of Cell Signaling , vol.3 , pp. 2107-2125
    • Hyduke, D.R.1    Amundson, S.A.2    Jr J, F.A.3
  • 2
    • 32444449180 scopus 로고    scopus 로고
    • Small-molecule MDM2 antagonists reveal aberrant p53 signaling in cancer: Implications for therapy
    • Tovar, C. et al. Small-molecule MDM2 antagonists reveal aberrant p53 signaling in cancer: implications for therapy. Proc. Natl Acad. Sci. USA 103, 1888-1893 (2006).
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 1888-1893
    • Tovar, C.1
  • 4
    • 40649121691 scopus 로고    scopus 로고
    • DNA repair, damage signaling and carcinogenesis
    • Lavelle, C., Salles, B. & Wiesmuller, L. DNA repair, damage signaling and carcinogenesis. DNA Repair (Amst.) 7, 670-680 (2008).
    • (2008) DNA Repair (Amst.) , vol.7 , pp. 670-680
    • Lavelle, C.1    Salles, B.2    Wiesmuller, L.3
  • 5
    • 11144289688 scopus 로고    scopus 로고
    • The Crohn's disease protein, NOD2, requires RIP2 in order to induce ubiquitinylation of a novel site on NEMO
    • Abbott, D. W., Wilkins, A., Asara, J. M. & Cantley, L. C. The Crohn's disease protein, NOD2, requires RIP2 in order to induce ubiquitinylation of a novel site on NEMO. Curr. Biol. 14, 2217-2227 (2004).
    • (2004) Curr. Biol. , vol.14 , pp. 2217-2227
    • Abbott, D.W.1    Wilkins, A.2    Asara, J.M.3    Cantley, L.C.4
  • 6
    • 40149109180 scopus 로고    scopus 로고
    • Host-pathogen systems biology: Logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction
    • Franke, R. et al. Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction. BMC Syst. Biol. 2, 4 (2008).
    • (2008) BMC Syst. Biol. , vol.2 , pp. 4
    • Franke, R.1
  • 7
    • 44649117905 scopus 로고    scopus 로고
    • Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    • Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106-1117 (2008).
    • (2008) Cell , vol.133 , pp. 1106-1117
    • Chen, X.1
  • 8
    • 70149101589 scopus 로고    scopus 로고
    • Redefining the p53 response element
    • Wang, B., Xiao, Z. & Ren, E. C. Redefining the p53 response element. Proc. Natl Acad. Sci. USA 106, 14373-14378 (2009).
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 14373-14378
    • Wang, B.1    Xiao, Z.2    Ren, E.C.3
  • 9
    • 70350452746 scopus 로고    scopus 로고
    • Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks
    • Huang, S. S. & Fraenkel, E. Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci. Signal. 2, ra40 (2009).
    • (2009) Sci. Signal. , vol.2
    • Huang, S.S.1    Fraenkel, E.2
  • 10
    • 60149088848 scopus 로고    scopus 로고
    • Origins and mechanisms of miRNAs and siRNAs
    • Carthew, R. W. & Sontheimer, E. J. Origins and mechanisms of miRNAs and siRNAs. Cell 136, 642-655 (2009).
    • (2009) Cell , vol.136 , pp. 642-655
    • Carthew, R.W.1    Sontheimer, E.J.2
  • 11
    • 69749123311 scopus 로고    scopus 로고
    • Caught at its own game: Regulatory small RNA inactivated by an inducible transcript mimicking its target
    • Figueroa-Bossi, N., Valentini, M., Malleret, L. & Bossi, L. Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target. Genes Dev. 23, 2004-2015 (2009).
    • (2009) Genes Dev. , vol.23 , pp. 2004-2015
    • Figueroa-Bossi, N.1    Valentini, M.2    Malleret, L.3    Bossi, L.4
  • 12
    • 0033555859 scopus 로고    scopus 로고
    • Emergent properties of networks of biological signaling pathways
    • Bhalla, U. S. & Iyengar, R. Emergent properties of networks of biological signaling pathways. Science 283, 381-387 (1999).
    • (1999) Science , vol.283 , pp. 381-387
    • Bhalla, U.S.1    Iyengar, R.2
  • 13
    • 61449134182 scopus 로고    scopus 로고
    • Identification of potential pathway mediation targets in Toll-like receptor signaling
    • Li, F., Thiele, I., Jamshidi, N. & Palsson, B. Ø. Identification of potential pathway mediation targets in Toll-like receptor signaling. PLoS Comput. Biol. 5, e1000292 (2009).
    • (2009) PLoS Comput. Biol. , vol.5
    • Li, F.1    Thiele, I.2    Jamshidi, N.3    Palsson B.Ø4
  • 14
    • 33846910173 scopus 로고    scopus 로고
    • Global reconstruction of the human metabolic network based on genomic and bibliomic data
    • Duarte, N. C. et al. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl Acad. Sci. USA 104, 1777-1782 (2007).
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 1777-1782
    • Duarte, N.C.1
  • 15
    • 34347332311 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1,260 ORFs and thermodynamic information
    • Feist, A. M. et al. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1,260 ORFs and thermodynamic information. Mol. Syst. Biol. 3, 121 (2007).
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 121
    • Feist, A.M.1
  • 16
    • 53749085229 scopus 로고    scopus 로고
    • A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
    • Herrgard, M. J. et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotech. 26, 1155-1160 (2008).
    • (2008) Nature Biotech. , vol.26 , pp. 1155-1160
    • Herrgard, M.J.1
  • 17
    • 65649105134 scopus 로고    scopus 로고
    • Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction
    • Raghunathan, A., Reed, J., Shin, S., Palsson, B. & Daefler, S. Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC Syst. Biol. 3, 38 (2009).
    • (2009) BMC Syst. Biol. , vol.3 , pp. 38
    • Raghunathan, A.1    Reed, J.2    Shin, S.3    Palsson, B.4    Daefler, S.5
  • 18
    • 4544288672 scopus 로고    scopus 로고
    • Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data
    • Vo, T. D., Greenberg, H. J. & Palsson, B. Ø. Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J. Biol. Chem. 279, 39532-39540 (2004).
    • (2004) J. Biol. Chem. , vol.279 , pp. 39532-39540
    • Vo, T.D.1    Greenberg, H.J.2    Palsson B.Ø3
  • 19
    • 12144289400 scopus 로고    scopus 로고
    • A physical and functional map of the human TNF-α/NF-κB signal transduction pathway
    • Bouwmeester, T. et al. A physical and functional map of the human TNF-α/NF-κB signal transduction pathway. Nature Cell Biol. 6, 97-105 (2004).
    • (2004) Nature Cell Biol. , vol.6 , pp. 97-105
    • Bouwmeester, T.1
  • 20
    • 33947640043 scopus 로고    scopus 로고
    • Prediction of phenotype and gene expression for combinations of mutations
    • Carter, G. W. et al. Prediction of phenotype and gene expression for combinations of mutations. Mol. Syst. Biol. 3, 96 (2007).
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 96
    • Carter, G.W.1
  • 21
    • 0028859279 scopus 로고
    • Protein modules and signalling networks
    • Pawson, T. Protein modules and signalling networks. Nature 373, 573-580 (1995).
    • (1995) Nature , vol.373 , pp. 573-580
    • Pawson, T.1
  • 22
    • 38649138295 scopus 로고    scopus 로고
    • A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans
    • Lee, I. et al. A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nature Genet. 40, 181-188 (2008).
    • (2008) Nature Genet. , vol.40 , pp. 181-188
    • Lee, I.1
  • 23
    • 0037212568 scopus 로고    scopus 로고
    • Understanding complex signaling networks through models and metaphors
    • Bhalla, U. S. Understanding complex signaling networks through models and metaphors. Prog. Biophys. Mol. Biol. 81, 45-65 (2003).
    • (2003) Prog. Biophys. Mol. Biol. , vol.81 , pp. 45-65
    • Bhalla, U.S.1
  • 25
    • 0037433037 scopus 로고    scopus 로고
    • The Database of Quantitative Cellular Signaling: Management and analysis of chemical kinetic models of signaling networks
    • Sivakumaran, S., Hariharaputran, S., Mishra, J. & Bhalla, U. S. The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks. Bioinformatics 19, 408-415 (2003).
    • (2003) Bioinformatics , vol.19 , pp. 408-415
    • Sivakumaran, S.1    Hariharaputran, S.2    Mishra, J.3    Bhalla, U.S.4
  • 26
    • 33745435987 scopus 로고    scopus 로고
    • Circuit diagrams for biological networks
    • Kohn, K. W. & Aladjem, M. I. Circuit diagrams for biological networks. Mol. Syst. Biol. 2, 2006.0002 (2006).
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 2006
    • Kohn, K.W.1    Aladjem, M.I.2
  • 27
    • 33846326304 scopus 로고    scopus 로고
    • Genetic screening for signal transduction in the era of network biology
    • Friedman, A. & Perrimon, N. Genetic screening for signal transduction in the era of network biology. Cell 128, 225-231 (2007).
    • (2007) Cell , vol.128 , pp. 225-231
    • Friedman, A.1    Perrimon, N.2
  • 28
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabasi, A. L. & Oltvai, Z. N. Network biology: understanding the cell's functional organization. Nature Rev. Genet. 5, 101-113 (2004).
    • (2004) Nature Rev. Genet. , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 29
    • 50149090966 scopus 로고    scopus 로고
    • Variability and robustness in T cell activation from regulated heterogeneity in protein levels
    • Feinerman, O., Veiga, J., Dorfman, J. R., Germain, R. N. & Altan-Bonnet, G. Variability and robustness in T cell activation from regulated heterogeneity in protein levels. Science 321, 1081-1084 (2008).
    • (2008) Science , vol.321 , pp. 1081-1084
    • Feinerman, O.1    Veiga, J.2    Dorfman, J.R.3    Germain, R.N.4    Altan-Bonnet, G.5
  • 30
    • 38549140094 scopus 로고    scopus 로고
    • RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
    • Gama-Castro, S. et al. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 36, D120-D124 (2008).
    • (2008) Nucleic Acids Res. , vol.36
    • Gama-Castro, S.1
  • 31
    • 33745463739 scopus 로고    scopus 로고
    • A comprehensive map of the Toll-like receptor signaling network
    • Oda, K. & Kitano, H. A comprehensive map of the Toll-like receptor signaling network. Mol. Syst. Biol. 2, 2006.0015 (2006).
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 2006
    • Oda, K.1    Kitano, H.2
  • 33
    • 13444278821 scopus 로고    scopus 로고
    • Reconstruction of cellular signalling networks and analysis of their properties
    • Papin, J. A., Hunter, T., Palsson, B. Ø. & Subramaniam, S. Reconstruction of cellular signalling networks and analysis of their properties. Nature Rev. Mol. Cell Biol. 6, 99-111 (2005).
    • (2005) Nature Rev. Mol. Cell Biol. , vol.6 , pp. 99-111
    • Papin, J.A.1    Hunter, T.2    Palsson B.Ø3    Subramaniam, S.4
  • 34
    • 0344824417 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network
    • Famili, I., Forster, J., Nielsen, J. & Palsson, B. Ø. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc. Natl Acad. Sci. USA 100, 13134-13139 (2003).
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 13134-13139
    • Famili, I.1    Forster, J.2    Nielsen, J.3    Palsson B.Ø4
  • 35
    • 45149111660 scopus 로고    scopus 로고
    • The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
    • Feist, A. M. & Palsson, B. Ø. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nature Biotech. 26, 659-667 (2008).
    • (2008) Nature Biotech. , vol.26 , pp. 659-667
    • Feist, A.M.1    Palsson B.Ø2
  • 36
    • 69249102097 scopus 로고    scopus 로고
    • Genome-scale gene/reaction essentiality and synthetic lethality analysis
    • Suthers, P. F., Zomorrodi, A. & Maranas, C. D. Genome-scale gene/reaction essentiality and synthetic lethality analysis. Mol. Syst. Biol. 5, 301 (2009).
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 301
    • Suthers, P.F.1    Zomorrodi, A.2    Maranas, C.D.3
  • 37
    • 77950863401 scopus 로고    scopus 로고
    • Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli
    • 17 Oct doi:10.1016/j.ymben.2009.10.003
    • Feist, A. M. et al. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab. Eng. 17 Oct 2009 (doi:10.1016/j.ymben.2009.10.003).
    • (2009) Metab. Eng.
    • Feist, A.M.1
  • 38
    • 33745107471 scopus 로고    scopus 로고
    • Influence of metabolic network structure and function on enzyme evolution
    • Vitkup, D., Kharchenko, P. & Wagner, A. Influence of metabolic network structure and function on enzyme evolution. Genome Biol. 7, R39 (2006).
    • (2006) Genome Biol. , vol.7
    • Vitkup, D.1    Kharchenko, P.2    Wagner, A.3
  • 40
    • 33646337667 scopus 로고    scopus 로고
    • A methodology for the structural and functional analysis of signaling and regulatory networks
    • Klamt, S., Saez-Rodriguez, J., Lindquist, J. A., Simeoni, L. & Gilles, E. D. A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics 7, 56 (2006). This paper introduces the Boolean formalism for analysing large-scale signalling-network models.
    • (2006) BMC Bioinformatics , vol.7 , pp. 56
    • Klamt, S.1    Saez-Rodriguez, J.2    Lindquist, J.A.3    Simeoni, L.4    Gilles, E.D.5
  • 41
    • 70449370314 scopus 로고    scopus 로고
    • The transcription unit architecture of the Escherichia coli genome
    • Cho, B. K. et al. The transcription unit architecture of the Escherichia coli genome. Nature Biotech. 27, 1043-1049 (2009).
    • (2009) Nature Biotech. , vol.27 , pp. 1043-1049
    • Cho, B.K.1
  • 42
    • 34347250494 scopus 로고    scopus 로고
    • Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli
    • Hyduke, D. R., Jarboe, L. R., Tran, L. M., Chou, K. J. & Liao, J. C. Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli. Proc. Natl Acad. Sci. USA 104, 8484-8489 (2007).
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 8484-8489
    • Hyduke, D.R.1    Jarboe, L.R.2    Tran, L.M.3    Chou, K.J.4    Liao, J.C.5
  • 43
    • 41949119905 scopus 로고    scopus 로고
    • Determination of the Escherichia coli S-nitrosoglutathione response network using integrated biochemical and systems analysis
    • Jarboe, L. R., Hyduke, D. R., Tran, L. M., Chou, K. J. & Liao, J. C. Determination of the Escherichia coli S-nitrosoglutathione response network using integrated biochemical and systems analysis. J. Biol. Chem. 283, 5148-5157 (2008).
    • (2008) J. Biol. Chem. , vol.283 , pp. 5148-5157
    • Jarboe, L.R.1    Hyduke, D.R.2    Tran, L.M.3    Chou, K.J.4    Liao, J.C.5
  • 44
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr, S. S., Milo, R., Mangan, S. & Alon, U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet. 31, 64-68 (2002).
    • (2002) Nature Genet. , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 45
    • 20344379457 scopus 로고    scopus 로고
    • Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli
    • Balazsi, G., Barabasi, A. L. & Oltvai, Z. N. Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc. Natl Acad. Sci. USA 102, 7841-7846 (2005).
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 7841-7846
    • Balazsi, G.1    Barabasi, A.L.2    Oltvai, Z.N.3
  • 46
    • 63649099433 scopus 로고    scopus 로고
    • Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae
    • Christensen, T. S., Oliveira, A. P. & Nielsen, J. Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae. BMC Syst. Biol. 3, 7 (2009).
    • (2009) BMC Syst. Biol. , vol.3 , pp. 7
    • Christensen, T.S.1    Oliveira, A.P.2    Nielsen, J.3
  • 47
    • 3042816965 scopus 로고    scopus 로고
    • The JAK-STAT signaling network in the human B-cell: An extreme signaling pathway analysis
    • Papin, J. A. & Palsson, B. Ø. The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. Biophys. J. 87, 37-46 (2004).
    • (2004) Biophys. J. , vol.87 , pp. 37-46
    • Papin, J.A.1    Palsson B.Ø2
  • 48
    • 34548431024 scopus 로고    scopus 로고
    • A logical model provides insights into T cell receptor signaling
    • Saez-Rodriguez, J. et al. A logical model provides insights into T cell receptor signaling. PLoS Comput. Biol. 3, e163 (2007).
    • (2007) PLoS Comput. Biol. , vol.3
    • Saez-Rodriguez, J.1
  • 49
    • 0037069674 scopus 로고    scopus 로고
    • Unravelling the signal-transduction network in B lymphocytes
    • Sambrano, G. R. et al. Unravelling the signal-transduction network in B lymphocytes. Nature 420, 708-710 (2002).
    • (2002) Nature , vol.420 , pp. 708-710
    • Sambrano, G.R.1
  • 50
    • 58149183694 scopus 로고    scopus 로고
    • IUPHAR-DB: The IUPHAR database of G protein-coupled receptors and ion channels
    • Harmar, A. J. et al. IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels. Nucleic Acids Res. 37, D680-D685 (2009).
    • (2009) Nucleic Acids Res. , vol.37
    • Harmar, A.J.1
  • 51
    • 33750456519 scopus 로고    scopus 로고
    • Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    • Olsen, J. V. et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635-648 (2006).
    • (2006) Cell , vol.127 , pp. 635-648
    • Olsen, J.V.1
  • 52
    • 0041706156 scopus 로고    scopus 로고
    • A proteomics approach to understanding protein ubiquitination
    • Peng, J. et al. A proteomics approach to understanding protein ubiquitination. Nature Biotech. 21, 921-926 (2003).
    • (2003) Nature Biotech. , vol.21 , pp. 921-926
    • Peng, J.1
  • 53
    • 3543018486 scopus 로고    scopus 로고
    • Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses
    • Zhou, W., Ryan, J. J. & Zhou, H. Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses. J. Biol. Chem. 279, 32262-32268 (2004).
    • (2004) J. Biol. Chem. , vol.279 , pp. 32262-32268
    • Zhou, W.1    Ryan, J.J.2    Zhou, H.3
  • 54
    • 33846052595 scopus 로고    scopus 로고
    • SNAPPI-DB: A database and API of Structures iNterfaces and Alignments for Protein-Protein Interactions
    • Jefferson, E. R., Walsh, T. P., Roberts, T. J. & Barton, G. J. SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. Nucleic Acids Res. 35, D580-D589 (2007).
    • (2007) Nucleic Acids Res. , vol.35
    • Jefferson, E.R.1    Walsh, T.P.2    Roberts, T.J.3    Barton, G.J.4
  • 56
    • 38549173606 scopus 로고    scopus 로고
    • The BioGRID interaction database: 2008 update
    • Breitkreutz, B. J. et al. The BioGRID Interaction Database: 2008 update. Nucleic Acids Res. 36, D637-D640 (2008).
    • (2008) Nucleic Acids Res. , vol.36
    • Breitkreutz, B.J.1
  • 57
    • 1442335464 scopus 로고    scopus 로고
    • Topological analysis of mass-balanced signaling networks: A framework to obtain network properties including crosstalk
    • Papin, J. A. & Palsson, B. Ø. Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. J. Theor. Biol. 227, 283-297 (2004).
    • (2004) J. Theor. Biol. , vol.227 , pp. 283-297
    • Papin, J.A.1    Palsson B.Ø2
  • 58
    • 77949772254 scopus 로고    scopus 로고
    • Rapid evolution of functional complexity in a domain family
    • Ernst, A. et al. Rapid evolution of functional complexity in a domain family. Sci. Signal. 2, ra50 (2009).
    • (2009) Sci. Signal. , vol.2
    • Ernst, A.1
  • 59
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • Gavin, A. C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636 (2006).
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.C.1
  • 61
    • 34250878954 scopus 로고    scopus 로고
    • Mechanisms of specificity in protein phosphorylation
    • Ubersax, J. A. & Ferrell, J. E. J. Mechanisms of specificity in protein phosphorylation. Nature Rev. Mol. Cell Biol. 8, 530-541 (2007).
    • (2007) Nature Rev. Mol. Cell Biol. , vol.8 , pp. 530-541
    • Ubersax, J.A.1    Ferrell, J.E.J.2
  • 62
    • 28344456279 scopus 로고    scopus 로고
    • A genomic and functional inventory of deubiquitinating enzymes
    • Nijman, S. M. et al. A genomic and functional inventory of deubiquitinating enzymes. Cell 123, 773-786 (2005).
    • (2005) Cell , vol.123 , pp. 773-786
    • Nijman, S.M.1
  • 63
    • 63549148162 scopus 로고    scopus 로고
    • Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: A knowledge base, its mathematical formulation, and its functional characterization
    • Thiele, I., Jamshidi, N., Fleming, R. M. & Palsson, B. Ø. Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput. Biol. 5, e1000312 (2009).
    • (2009) PLoS Comput. Biol. , vol.5
    • Thiele, I.1    Jamshidi, N.2    Fleming, R.M.3    Palsson B.Ø4
  • 64
    • 58149481232 scopus 로고    scopus 로고
    • Properties of developmental gene regulatory networks
    • Davidson, E. H. & Levine, M. S. Properties of developmental gene regulatory networks. Proc. Natl Acad. Sci. USA 105, 20063-20066 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 20063-20066
    • Davidson, E.H.1    Levine, M.S.2
  • 65
    • 33746363486 scopus 로고    scopus 로고
    • Domains motifs, and scaffolds: The role of modular interactions in the evolution and wiring of cell signaling circuits
    • Bhattacharyya, R. P., Remenyi, A., Yeh, B. J. & Lim, W. A. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu. Rev. Biochem. 75, 655-680 (2006).
    • (2006) Annu. Rev. Biochem. , vol.75 , pp. 655-680
    • Bhattacharyya, R.P.1    Remenyi, A.2    Yeh, B.J.3    Lim, W.A.4
  • 66
    • 0037453510 scopus 로고    scopus 로고
    • Assembly of cell regulatory systems through protein interaction domains
    • Pawson, T. & Nash, P. Assembly of cell regulatory systems through protein interaction domains. Science 300, 445-452 (2003).
    • (2003) Science , vol.300 , pp. 445-452
    • Pawson, T.1    Nash, P.2
  • 67
    • 70350517075 scopus 로고    scopus 로고
    • Deciphering signaling outcomes from a system of complex networks
    • Hsueh, R. C. et al. Deciphering signaling outcomes from a system of complex networks. Sci. Signal. 2, ra22 (2009).
    • (2009) Sci. Signal. , vol.2
    • Hsueh, R.C.1
  • 68
    • 64349110975 scopus 로고    scopus 로고
    • Systems-level interactions between insulin-EGF networks amplify mitogenic signaling
    • Borisov, N. et al. Systems-level interactions between insulin-EGF networks amplify mitogenic signaling. Mol. Syst. Biol. 5, 256 (2009).
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 256
    • Borisov, N.1
  • 69
    • 49749106279 scopus 로고    scopus 로고
    • Linking the kinome and phosphorylome \ a comprehensive review of approaches to find kinase targets
    • Sopko, R. & Andrews, B. J. Linking the kinome and phosphorylome \ a comprehensive review of approaches to find kinase targets. Mol. Biosyst. 4, 920-933 (2008).
    • (2008) Mol. Biosyst. , vol.4 , pp. 920-933
    • Sopko, R.1    Andrews, B.J.2
  • 70
    • 44649153450 scopus 로고    scopus 로고
    • Rewiring the specificity of two-component signal transduction systems
    • Skerker, J. M. et al. Rewiring the specificity of two-component signal transduction systems. Cell 133, 1043-1054 (2008).
    • (2008) Cell , vol.133 , pp. 1043-1054
    • Skerker, J.M.1
  • 71
    • 0034625143 scopus 로고    scopus 로고
    • The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
    • Edwards, J. S. & Palsson, B. Ø. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc. Natl Acad. Sci. USA 97, 5528-5533 (2000).
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 5528-5533
    • Edwards, J.S.1    Palsson B.Ø2
  • 72
    • 67650573077 scopus 로고    scopus 로고
    • IBsu1103: A new genome-scale metabolic model of Bacillus subtilis based on SEED annotations
    • Henry, C. S., Zinner, J. F., Cohoon, M. P. & Stevens, R. L. iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biol. 10, R69 (2009).
    • (2009) Genome Biol. , vol.10
    • Henry, C.S.1    Zinner, J.F.2    Cohoon, M.P.3    Stevens, R.L.4
  • 73
    • 34447296697 scopus 로고    scopus 로고
    • Genome-scale analysis of Mannheimia succiniciproducens metabolism
    • Kim, T. Y. et al. Genome-scale analysis of Mannheimia succiniciproducens metabolism. Biotechnol. Bioeng. 97, 657-671 (2007).
    • (2007) Biotechnol. Bioeng. , vol.97 , pp. 657-671
    • Kim, T.Y.1
  • 74
    • 67549123519 scopus 로고    scopus 로고
    • Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets
    • Lee, D. S. et al. Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets. J. Bacteriol. 191, 4015-4024 (2009).
    • (2009) J. Bacteriol. , vol.191 , pp. 4015-4024
    • Lee, D.S.1
  • 75
    • 69249154275 scopus 로고    scopus 로고
    • Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum
    • Shinfuku, Y. et al. Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum. Microb. Cell Fact. 8, 43 (2009).
    • (2009) Microb. Cell Fact. , vol.8 , pp. 43
    • Shinfuku, Y.1
  • 76
    • 61449115916 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189
    • Suthers, P. F. et al. A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189. PLoS Comput. Biol. 5, e1000285 (2009).
    • (2009) PLoS Comput. Biol. , vol.5
    • Suthers, P.F.1
  • 77
    • 62149098396 scopus 로고    scopus 로고
    • A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola
    • Thomas, G. H. et al. A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola. BMC Syst. Biol. 3, 24 (2009).
    • (2009) BMC Syst. Biol. , vol.3 , pp. 24
    • Thomas, G.H.1
  • 79
    • 13544265458 scopus 로고    scopus 로고
    • Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus
    • Sheikh, K., Forster, J. & Nielsen, L. K. Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus. Biotechnol. Prog. 21, 112-121 (2005).
    • (2005) Biotechnol. Prog. , vol.21 , pp. 112-121
    • Sheikh, K.1    Forster, J.2    Nielsen, L.K.3
  • 81
    • 41049102359 scopus 로고    scopus 로고
    • Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks
    • Oliveira, A. P., Patil, K. R. & Nielsen, J. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. BMC Syst. Biol. 2, 17 (2008).
    • (2008) BMC Syst. Biol. , vol.2 , pp. 17
    • Oliveira, A.P.1    Patil, K.R.2    Nielsen, J.3
  • 82
    • 15744389378 scopus 로고    scopus 로고
    • A theoretical framework for detecting signal transfer routes in signalling networks
    • Zevedei-Oancea, I. & Schuster, S. A theoretical framework for detecting signal transfer routes in signalling networks. Comput. Chem. Eng. 29, 597-617 (2005).
    • (2005) Comput. Chem. Eng. , vol.29 , pp. 597-617
    • Zevedei-Oancea, I.1    Schuster, S.2
  • 83
    • 44949247269 scopus 로고    scopus 로고
    • Dynamic analysis of integrated signaling, metabolic, and regulatory networks
    • Min Lee, J., Gianchandani, E. P., Eddy, J. A. & Papin, J. A. Dynamic analysis of integrated signaling, metabolic, and regulatory networks. PLoS Comput. Biol. 4, e1000086 (2008).
    • (2008) PLoS Comput. Biol. , vol.4
    • Min Lee, J.1    Gianchandani, E.P.2    Eddy, J.A.3    Papin, J.A.4
  • 84
    • 40649117198 scopus 로고    scopus 로고
    • Dissection of the insulin signaling pathway via quantitative phosphoproteomics
    • Kruger, M. et al. Dissection of the insulin signaling pathway via quantitative phosphoproteomics. Proc. Natl Acad. Sci. USA 105, 2451-2456 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 2451-2456
    • Kruger, M.1
  • 85
    • 33846681448 scopus 로고    scopus 로고
    • Modular organization of protein interaction networks
    • Luo, F. et al. Modular organization of protein interaction networks. Bioinformatics 23, 207-214 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 207-214
    • Luo, F.1
  • 86
    • 23144466440 scopus 로고    scopus 로고
    • Metabolic PathFinding: Inferring relevant pathways in biochemical networks
    • Croes, D., Couche, F., Wodak, S. J. & van Helden, J. Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Res. 33, W326-W330 (2005).
    • (2005) Nucleic Acids Res. , vol.33
    • Croes, D.1    Couche, F.2    Wodak, S.J.3    Van Helden, J.4
  • 87
    • 48449102450 scopus 로고    scopus 로고
    • Hubba: Hub objects analyzer \ a framework of interactome hubs identification for network biology
    • Lin, C. Y. et al. Hubba: hub objects analyzer \ a framework of interactome hubs identification for network biology. Nucleic Acids Res. 36, W438-W443 (2008).
    • (2008) Nucleic Acids Res. , vol.36
    • Lin, C.Y.1
  • 88
    • 77949771945 scopus 로고    scopus 로고
    • Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks
    • in the press
    • Chang, R. L., Luo, F., Johnson, S. A. & Scheuermann, R. H. Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks. Int. J. Bioinform. Res. Appl. (in the press).
    • Int. J. Bioinform. Res. Appl.
    • Chang, R.L.1    Luo, F.2    Johnson, S.A.3    Scheuermann, R.H.4
  • 89
    • 33745764032 scopus 로고    scopus 로고
    • A computational framework for the topological analysis and targeted disruption of signal transduction networks
    • Dasika, M. S., Burgard, A. & Maranas, C. D. A computational framework for the topological analysis and targeted disruption of signal transduction networks. Biophys. J. 91, 382-398 (2006).
    • (2006) Biophys. J. , vol.91 , pp. 382-398
    • Dasika, M.S.1    Burgard, A.2    Maranas, C.D.3
  • 90
    • 65449186979 scopus 로고    scopus 로고
    • Fault tolerance in protein interaction networks: Stable bipartite subgraphs and redundant pathways
    • Brady, A., Maxwell, K., Daniels, N. & Cowen, L. J. Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways. PLoS ONE 4, e5364 (2009).
    • (2009) PLoS ONE , vol.4
    • Brady, A.1    Maxwell, K.2    Daniels, N.3    Cowen, L.J.4
  • 92
    • 67650841319 scopus 로고    scopus 로고
    • Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway
    • Krantz, M. et al. Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway. Mol. Syst. Biol. 5, 281 (2009).
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 281
    • Krantz, M.1
  • 94
    • 34249851523 scopus 로고    scopus 로고
    • Combinatorial RNAi for quantitative protein network analysis
    • Sahin, O. et al. Combinatorial RNAi for quantitative protein network analysis. Proc. Natl Acad. Sci. USA 104, 6579-6584 (2007).
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 6579-6584
    • Sahin, O.1
  • 95
    • 13244268322 scopus 로고    scopus 로고
    • A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
    • Green, M. L. & Karp, P. D. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 5, 76 (2004).
    • (2004) BMC Bioinformatics , vol.5 , pp. 76
    • Green, M.L.1    Karp, P.D.2
  • 96
    • 33846922557 scopus 로고    scopus 로고
    • A subsystems-based approach to the identification of drug targets in bacterial pathogens
    • Osterman, A. L. & Begley, T. P. A subsystems-based approach to the identification of drug targets in bacterial pathogens. Prog. Drug Res. 64, 131-170 (2007).
    • (2007) Prog. Drug Res. , vol.64 , pp. 131-170
    • Osterman, A.L.1    Begley, T.P.2
  • 97
    • 33646171940 scopus 로고    scopus 로고
    • Identifying metabolic enzymes with multiple types of association evidence
    • Kharchenko, P., Chen, L., Freund, Y., Vitkup, D. & Church, G. M. Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics 7, 177 (2006).
    • (2006) BMC Bioinformatics , vol.7 , pp. 177
    • Kharchenko, P.1    Chen, L.2    Freund, Y.3    Vitkup, D.4    Church, G.M.5
  • 98
    • 33751226921 scopus 로고    scopus 로고
    • Systems approach to refining genome annotation
    • Reed, J. L. et al. Systems approach to refining genome annotation. Proc. Natl Acad. Sci. USA 103, 17480-17484 (2006).
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 17480-17484
    • Reed, J.L.1
  • 99
    • 68149168970 scopus 로고    scopus 로고
    • Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments
    • Szczurek, E., Gat-Viks, I., Tiuryn, J. & Vingron, M. Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments. Mol. Syst. Biol. 5, 287 (2009).
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 287
    • Szczurek, E.1    Gat-Viks, I.2    Tiuryn, J.3    Vingron, M.4
  • 100
    • 64049083918 scopus 로고    scopus 로고
    • Protein-protein interaction as a predictor of subcellular location
    • Shin, C. J., Wong, S., Davis, M. J. & Ragan, M. A. Protein-protein interaction as a predictor of subcellular location. BMC Syst. Biol. 3, 28 (2009).
    • (2009) BMC Syst. Biol. , vol.3 , pp. 28
    • Shin, C.J.1    Wong, S.2    Davis, M.J.3    Ragan, M.A.4
  • 101
    • 22844450110 scopus 로고    scopus 로고
    • Systematic interpretation of genetic interactions using protein networks
    • Kelley, R. & Ideker, T. Systematic interpretation of genetic interactions using protein networks. Nature Biotech. 23, 561-566 (2005).
    • (2005) Nature Biotech. , vol.23 , pp. 561-566
    • Kelley, R.1    Ideker, T.2
  • 102
    • 43249117094 scopus 로고    scopus 로고
    • Functional maps of protein complexes from quantitative genetic interaction data
    • Bandyopadhyay, S., Kelley, R., Krogan, N. J. & Ideker, T. Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput. Biol. 4, e1000065 (2008).
    • (2008) PLoS Comput. Biol. , vol.4
    • Bandyopadhyay, S.1    Kelley, R.2    Krogan, N.J.3    Ideker, T.4
  • 103
    • 33847643207 scopus 로고    scopus 로고
    • Chemical combination effects predict connectivity in biological systems
    • Lehar, J. et al. Chemical combination effects predict connectivity in biological systems. Mol. Syst. Biol. 3, 80 (2007).
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 80
    • Lehar, J.1
  • 104
    • 65649100877 scopus 로고    scopus 로고
    • Reconstructing the ubiquitin network: Cross-talk with other systems and identification of novel functions
    • Venancio, T. M., Balaji, S., Iyer, L. M. & Aravind, L. Reconstructing the ubiquitin network: cross-talk with other systems and identification of novel functions. Genome Biol. 10, R33 (2009).
    • (2009) Genome Biol. , vol.10
    • Venancio, T.M.1    Balaji, S.2    Iyer, L.M.3    Aravind, L.4
  • 105
    • 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. Natl Acad. Sci. USA 105, 12763-12768 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 12763-12768
    • Singh, R.1    Xu, J.2    Berger, B.3
  • 106
    • 0141593601 scopus 로고    scopus 로고
    • Conserved pathways within bacteria and yeast as revealed by global protein network alignment
    • Kelley, B. P. et al. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl Acad. Sci. USA 100, 11394-11399 (2003).
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 11394-11399
    • Kelley, B.P.1
  • 107
    • 33644656793 scopus 로고    scopus 로고
    • Systematic identification of functional orthologs based on protein network comparison
    • Bandyopadhyay, S., Sharan, R. & Ideker, T. Systematic identification of functional orthologs based on protein network comparison. Genome Res. 16, 428-435 (2006).
    • (2006) Genome Res. , vol.16 , pp. 428-435
    • Bandyopadhyay, S.1    Sharan, R.2    Ideker, T.3
  • 108
    • 13844314048 scopus 로고    scopus 로고
    • Conserved patterns of protein interaction in multiple species
    • Sharan, R. et al. Conserved patterns of protein interaction in multiple species. Proc. Natl Acad. Sci. USA 102, 1974-1979 (2005).
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 1974-1979
    • Sharan, R.1
  • 109
    • 70349526350 scopus 로고    scopus 로고
    • Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases
    • Tan, C. S. et al. Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci. Signal. 2, ra39 (2009).
    • (2009) Sci. Signal. , vol.2
    • Tan, C.S.1
  • 110
    • 58149213932 scopus 로고    scopus 로고
    • Literature-curated protein interaction datasets
    • Cusick, M. E. et al. Literature-curated protein interaction datasets. Nature Methods 6, 39-46 (2009).
    • (2009) Nature Methods , vol.6 , pp. 39-46
    • Cusick, M.E.1
  • 111
    • 20344374161 scopus 로고    scopus 로고
    • Conserved modular design of an oxygen sensory/signaling network with species-specific output
    • Crosson, S., McGrath, P. T., Stephens, C., McAdams, H. H. & Shapiro, L. Conserved modular design of an oxygen sensory/signaling network with species-specific output. Proc. Natl Acad. Sci. USA 102, 8018-8023 (2005).
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 8018-8023
    • Crosson, S.1    McGrath, P.T.2    Stephens, C.3    McAdams, H.H.4    Shapiro, L.5
  • 112
    • 54249107599 scopus 로고    scopus 로고
    • Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast
    • Roguev, A. et al. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science 322, 405-410 (2008).
    • (2008) Science , vol.322 , pp. 405-410
    • Roguev, A.1
  • 113
    • 67649972198 scopus 로고    scopus 로고
    • Evolution of phosphoregulation: Comparison of phosphorylation patterns across yeast species
    • Beltrao, P. et al. Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol. 7, e1000134 (2009).
    • (2009) PLoS Biol. , vol.7
    • Beltrao, P.1
  • 114
    • 54249116230 scopus 로고
    • Genetic regulatory mechanisms in the synthesis of proteins
    • Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318-356 (1961)
    • (1961) J. Mol. Biol. , vol.3 , pp. 318-356
    • Jacob, F.1    Monod, J.2
  • 116
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • Covert, M. W., Knight, E. M., Reed, J. L., Herrgard, M. J. & Palsson, B. Ø. Integrating high-throughput and computational data elucidates bacterial networks. Nature 429, 92-96 (2004).
    • (2004) Nature , vol.429 , pp. 92-96
    • Covert, M.W.1    Knight, E.M.2    Reed, J.L.3    Herrgard, M.J.4    Palsson B.Ø5
  • 117
    • 33745178476 scopus 로고    scopus 로고
    • Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae
    • Herrgard, M. J., Lee, B. S., Portnoy, V. & Palsson, B. Ø. Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Res. 16, 627-635 (2006).
    • (2006) Genome Res. , vol.16 , pp. 627-635
    • Herrgard, M.J.1    Lee, B.S.2    Portnoy, V.3    Palsson B.Ø4
  • 119
    • 66149122278 scopus 로고    scopus 로고
    • Special feature: Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p
    • Moxley, J. F. et al. Special feature: linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc. Natl Acad. Sci. USA 106, 6477-6482 (2009).
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 6477-6482
    • Moxley, J.F.1
  • 120
    • 62649096826 scopus 로고    scopus 로고
    • Designing new cellular signaling pathways
    • Pryciak, P. M. Designing new cellular signaling pathways. Chem. Biol. 16, 249-254 (2009).
    • (2009) Chem. Biol. , vol.16 , pp. 249-254
    • Pryciak, P.M.1
  • 121
    • 67149113654 scopus 로고    scopus 로고
    • Engineering key components in a synthetic eukaryotic signal transduction pathway
    • Antunes, M. S. et al. Engineering key components in a synthetic eukaryotic signal transduction pathway. Mol. Syst. Biol. 5, 270 (2009).
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 270
    • Antunes, M.S.1
  • 122
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338 (2000).
    • (2000) Nature , vol.403 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 123
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • Gardner, T. S., Cantor, C. R. & Collins, J. J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339-342 (2000).
    • (2000) Nature , vol.403 , pp. 339-342
    • Gardner, T.S.1    Cantor, C.R.2    Collins, J.J.3
  • 124
    • 1442306167 scopus 로고    scopus 로고
    • Design of artificial cell-cell communication using gene and metabolic networks
    • Bulter, T. et al. Design of artificial cell-cell communication using gene and metabolic networks. Proc. Natl Acad. Sci. USA 101, 2299-2304 (2004).
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 2299-2304
    • Bulter, T.1
  • 125
    • 18344381476 scopus 로고    scopus 로고
    • A synthetic gene-metabolic oscillator
    • Fung, E. et al. A synthetic gene-metabolic oscillator. Nature 435, 118-122 (2005).
    • (2005) Nature , vol.435 , pp. 118-122
    • Fung, E.1
  • 126
    • 34547521789 scopus 로고    scopus 로고
    • Synthetic ecosystems based on airborne inter-and intrakingdom communication
    • Weber, W., Daoud-El Baba, M. & Fussenegger, M. Synthetic ecosystems based on airborne inter-and intrakingdom communication. Proc. Natl Acad. Sci. USA 104, 10435-10440 (2007).
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 10435-10440
    • Weber, W.1    Daoud-El Baba, M.2    Fussenegger, M.3
  • 127
    • 57049159362 scopus 로고    scopus 로고
    • A fast, robust and tunable synthetic gene oscillator
    • Stricker, J. et al. A fast, robust and tunable synthetic gene oscillator. Nature 456, 516-519 (2008).
    • (2008) Nature , vol.456 , pp. 516-519
    • Stricker, J.1
  • 128
    • 66349125024 scopus 로고    scopus 로고
    • Synthetic gene networks that count
    • Friedland, A. E. et al. Synthetic gene networks that count. Science 324, 1199-1202 (2009).
    • (2009) Science , vol.324 , pp. 1199-1202
    • Friedland, A.E.1
  • 129
    • 68449088806 scopus 로고    scopus 로고
    • Synthetic protein scaffolds provide modular control over metabolic flux
    • Dueber, J. E. et al. Synthetic protein scaffolds provide modular control over metabolic flux. Nature Biotech. 27, 753-759 (2009).
    • (2009) Nature Biotech. , vol.27 , pp. 753-759
    • Dueber, J.E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.