메뉴 건너뛰기




Volumn 13, Issue 117, 2016, Pages

Synthetic biology and regulatory networks: Where metabolic systems biology meets control engineering

Author keywords

Control engineering; Gene expression regulation; Metabolic engineering; Metabolic networks; Synthetic biology; Systems biology

Indexed keywords

BIOLOGY; ECONOMIC AND SOCIAL EFFECTS; GENE EXPRESSION; GENE EXPRESSION REGULATION; METABOLISM; ROBUST CONTROL; ROBUSTNESS (CONTROL SYSTEMS);

EID: 84969959743     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2015.1046     Document Type: Review
Times cited : (43)

References (170)
  • 1
    • 0025895183 scopus 로고
    • Toward a science of metabolic engineering
    • Bailey JE. 1991 Toward a science of metabolic engineering. Science 252, 1668-1675. (doi:10.1126/science.2047876)
    • (1991) Science , vol.252 , pp. 1668-1675
    • Bailey, J.E.1
  • 2
    • 84877315835 scopus 로고    scopus 로고
    • A community-driven global reconstruction of human metabolism
    • Thiele I et al. 2013 A community-driven global reconstruction of human metabolism. Nat. Biotechnol. 31, 419-425. (doi:10.1038/nbt.2488)
    • (2013) Nat. Biotechnol. , vol.31 , pp. 419-425
    • Thiele, I.1
  • 3
    • 0032600888 scopus 로고    scopus 로고
    • Metabolic fluxes and metabolic engineering
    • Stephanopoulos G. 1999 Metabolic fluxes and metabolic engineering. Metab. Eng. 1, 1-11. (doi:10.1006/mben.1998.0101)
    • (1999) Metab. Eng. , vol.1 , pp. 1-11
    • Stephanopoulos, G.1
  • 4
    • 0029055565 scopus 로고
    • The control of flux. Biochem
    • Kacser H, Burns JA, Fell DA. 1995 The control of flux. Biochem. Soc. Trans. 23, 341-366. (doi:10.1042/bst0230341)
    • (1995) Soc. Trans. , vol.23 , pp. 341-366
    • Kacser, H.1    Burns, J.A.2    Fell, D.A.3
  • 6
    • 0026000298 scopus 로고
    • Control-theory of regulatory cascades
    • Kahn D, Westerhoff HV. 1991 Control-theory of regulatory cascades. J. Theor. Biol. 153, 255-285. (doi:10.1016/S0022-5193(05)80426-6)
    • (1991) J. Theor. Biol. , vol.153 , pp. 255-285
    • Kahn, D.1    Westerhoff, H.V.2
  • 8
    • 84900303762 scopus 로고    scopus 로고
    • Optimizing genome-scale network reconstructions
    • Monk J, Nogales J, Palsson BO. 2014 Optimizing genome-scale network reconstructions. Nat. Biotechnol. 32, 447-452. (doi:10.1038/nbt.2870)
    • (2014) Nat. Biotechnol. , vol.32 , pp. 447-452
    • Monk, J.1    Nogales, J.2    Palsson, B.O.3
  • 9
    • 84879002382 scopus 로고    scopus 로고
    • Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli
    • McCloskey D, Palsson BO, Feist AM. 2013 Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol. Syst. Biol. 9, 661. (doi:10.1038/msb.2013.18)
    • (2013) Mol. Syst. Biol. , vol.9 , pp. 661
    • McCloskey, D.1    Palsson, B.O.2    Feist, A.M.3
  • 10
    • 18844392599 scopus 로고    scopus 로고
    • Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli
    • Alper H, Jin YS, Moxley JF, Stephanopoulos G. 2005 Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab. Eng. 7, 155-164. (doi:10.1016/j. ymben.2004.12.003)
    • (2005) Metab. Eng. , vol.7 , pp. 155-164
    • Alper, H.1    Jin, Y.S.2    Moxley, J.F.3    Stephanopoulos, G.4
  • 11
    • 84860822839 scopus 로고    scopus 로고
    • Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico
    • McAnulty MJ, Yen JY, Freedman BG, Senger RS. 2012 Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico. BMC Syst. Biol. 6, 42. (doi:10.1186/1752-0509-6-42)
    • (2012) BMC Syst. Biol. , vol.6 , pp. 42
    • McAnulty, M.J.1    Yen, J.Y.2    Freedman, B.G.3    Senger, R.S.4
  • 12
    • 77954699474 scopus 로고    scopus 로고
    • Systems metabolic engineering: Genome-scale models and beyond
    • Blazeck J, Alper H. 2010 Systems metabolic engineering: genome-scale models and beyond. Biotechnol. J. 5, 647-659. (doi:10.1002/biot. 200900247)
    • (2010) Biotechnol. J. , vol.5 , pp. 647-659
    • Blazeck, J.1    Alper, H.2
  • 13
    • 62649122977 scopus 로고    scopus 로고
    • Synthetic metabolism: Engineering biology at the protein and pathway scales
    • Martin CH, Nielsen DR, Solomon KV, Prather KLJ. 2009 Synthetic metabolism: engineering biology at the protein and pathway scales. Chem. Biol. 16, 277-286. (doi:10.1016/j.chembiol.2009.01.010)
    • (2009) Chem. Biol. , vol.16 , pp. 277-286
    • Martin, C.H.1    Nielsen, D.R.2    Solomon, K.V.3    Prather, K.L.J.4
  • 14
    • 33745454125 scopus 로고    scopus 로고
    • Synthetic biology: New engineering rules for an emerging discipline
    • Andrianantoandro E, Basu S, Karig DK, Weiss R. 2006 Synthetic biology: new engineering rules for an emerging discipline. Mol. Syst. Biol. 2, 28. (doi:10.1038/Msb4100073)
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 28
    • Andrianantoandro, E.1    Basu, S.2    Karig, D.K.3    Weiss, R.4
  • 15
    • 84864258391 scopus 로고    scopus 로고
    • Synthetic biology: An emerging engineering discipline
    • Cheng AA, Lu TK. 2012 Synthetic biology: an emerging engineering discipline. Annu. Rev. Biomed. Eng. 14, 155-178. (doi:10.1146/annurevbioeng-071811-150118)
    • (2012) Annu. Rev. Biomed. Eng. , vol.14 , pp. 155-178
    • Cheng, A.A.1    Lu, T.K.2
  • 16
    • 67650671869 scopus 로고    scopus 로고
    • Harnessing nature's toolbox: Regulatory elements for synthetic biology
    • Boyle PM, Silver PA. 2009 Harnessing nature's toolbox: regulatory elements for synthetic biology. J. R. Soc. Interface 6(Suppl. 4), S535-S546. (doi:10.1098/rsif.2008.0521.focus)
    • (2009) J. R. Soc. Interface , vol.6 , pp. S535-S546
    • Boyle, P.M.1    Silver, P.A.2
  • 17
    • 84862081641 scopus 로고    scopus 로고
    • Foundations for the design and implementation of synthetic genetic circuits
    • Slusarczyk AL, Lin A, Weiss R. 2012 Foundations for the design and implementation of synthetic genetic circuits. Nat. Rev. Genet. 13, 406-420. (doi:10.1038/nrg3227)
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 406-420
    • Slusarczyk, A.L.1    Lin, A.2    Weiss, R.3
  • 18
    • 77951107086 scopus 로고    scopus 로고
    • Synthetic biology: Applications come of age
    • Khalil AS, Collins JJ. 2010 Synthetic biology: applications come of age. Nat. Rev. Genet. 11, 367-379. (doi:10.1038/Nrg2775)
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 367-379
    • Khalil, A.S.1    Collins, J.J.2
  • 19
    • 66249088017 scopus 로고    scopus 로고
    • The second wave of synthetic biology: From modules to systems
    • Purnick PE, Weiss R. 2009 The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10, 410-422. (doi:10.1038/nrm2698)
    • (2009) Nat. Rev. Mol. Cell Biol. , vol.10 , pp. 410-422
    • Purnick, P.E.1    Weiss, R.2
  • 20
    • 69549091790 scopus 로고    scopus 로고
    • A systematic design method for robust synthetic biology to satisfy design specifications
    • Chen BS, Wu CH. 2009 A systematic design method for robust synthetic biology to satisfy design specifications. BMC Syst. Biol. 3, 66. (doi:10.1186/1752-0509-3-66)
    • (2009) BMC Syst. Biol. , vol.3 , Issue.66
    • Chen, B.S.1    Wu, C.H.2
  • 21
    • 84879101651 scopus 로고    scopus 로고
    • Synthetic biology: Advancing the design of diverse genetic systems
    • Wang YH, Wei KY, Smolke CD. 2013 Synthetic biology: advancing the design of diverse genetic systems. Annu. Rev. Chem. Biomol. 4, 69-102. (doi:10.1146/annurev-chembioeng-061312-103351)
    • (2013) Annu. Rev. Chem. Biomol. , vol.4 , pp. 69-102
    • Wang, Y.H.1    Wei, K.Y.2    Smolke, C.D.3
  • 22
  • 23
    • 0034024497 scopus 로고    scopus 로고
    • Improving lycopene production in Escherichia coli by engineering metabolic control
    • Farmer WR, Liao JC. 2000 Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol. 18, 533-537. (doi:10.1038/75398)
    • (2000) Nat. Biotechnol. , vol.18 , pp. 533-537
    • Farmer, W.R.1    Liao, J.C.2
  • 25
    • 84869420041 scopus 로고    scopus 로고
    • Synthetic biology and metabolic engineering
    • Stephanopoulos G. 2012 Synthetic biology and metabolic engineering. ACS Synth. Biol. 1, 514-525. doi:10.1021/Sb300094q)
    • (2012) ACS Synth. Biol. , vol.1 , pp. 514-525
    • Stephanopoulos, G.1
  • 26
    • 84859772410 scopus 로고    scopus 로고
    • Synthetic biology and the development of tools for metabolic engineering
    • Keasling JD. 2012 Synthetic biology and the development of tools for metabolic engineering. Metab. Eng. 14, 189-195. (doi:10.1016/j.ymben. 2012.01.004)
    • (2012) Metab. Eng. , vol.14 , pp. 189-195
    • Keasling, J.D.1
  • 27
    • 84859776222 scopus 로고    scopus 로고
    • The future of metabolic engineering and synthetic biology: Towards a systematic practice
    • Yadav VG, De Mey M, Lim CG, Ajikumar PK, Stephanopoulos G. 2012 The future of metabolic engineering and synthetic biology: towards a systematic practice. Metab. Eng. 14, 233-241. (doi:10.1016/j.ymben.2012.02.001)
    • (2012) Metab. Eng. , vol.14 , pp. 233-241
    • Yadav, V.G.1    De Mey, M.2    Lim, C.G.3    Ajikumar, P.K.4    Stephanopoulos, G.5
  • 28
    • 84859768457 scopus 로고    scopus 로고
    • Parts plus pipes: Synthetic biology approaches to metabolic engineering
    • Boyle PM, Silver PA. 2012 Parts plus pipes: synthetic biology approaches to metabolic engineering. Metab. Eng. 14, 223-232. (doi:10.1016/j.ymben. 2011.10.003)
    • (2012) Metab. Eng. , vol.14 , pp. 223-232
    • Boyle, P.M.1    Silver, P.A.2
  • 29
    • 84880084177 scopus 로고    scopus 로고
    • Synthetic biology and metabolic engineering approaches to produce biofuels
    • Rabinovitch-Deere CA, Oliver JWK, Rodriguez GM, Atsumi S. 2013 Synthetic biology and metabolic engineering approaches to produce biofuels. Chem. Rev. 113, 4611-4632. (doi:10.1021/cr300361t)
    • (2013) Chem. Rev. , vol.113 , pp. 4611-4632
    • Rabinovitch-Deere, C.A.1    Oliver, J.W.K.2    Rodriguez, G.M.3    Atsumi, S.4
  • 30
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr SS, Milo R, Mangan S, Alon U. 2002 Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31, 64-68. (doi:10.1038/ng881)
    • (2002) Nat. Genet. , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 32
    • 0034092437 scopus 로고    scopus 로고
    • How yeast cells synchronize their glycolytic oscillations: A perturbation analytic treatment
    • Bier M, Bakker BM, Westerhoff HV. 2000 How yeast cells synchronize their glycolytic oscillations: a perturbation analytic treatment. Biophys. J. 78, 1087-1093. (doi:10.1016/S0006-3495(00)76667-7)
    • (2000) Biophys. J. , vol.78 , pp. 1087-1093
    • Bier, M.1    Bakker, B.M.2    Westerhoff, H.V.3
  • 33
    • 84878237812 scopus 로고    scopus 로고
    • Systems biology, synthetic biology and control theory: A promising golden braid
    • Cury JER, Baldissera FL. 2013 Systems biology, synthetic biology and control theory: a promising golden braid. Annu. Rev. Control 37, 57-67. (doi:10.1016/j.arcontrol.2013.03.006)
    • (2013) Annu. Rev. Control , vol.37 , pp. 57-67
    • Cury, J.E.R.1    Baldissera, F.L.2
  • 34
    • 84951148708 scopus 로고    scopus 로고
    • Synthetic biology: A control engineering perspective
    • France, 24-27 June 2014
    • Prescott TP, Papachristodoulou A. 2014 Synthetic biology: a control engineering perspective. In European Control Conf., Strasbourg, France, 24-27 June 2014, pp. 1182-1186. (doi:10.1109/ECC.2014. 6862638)
    • (2014) European Control Conf., Strasbourg , pp. 1182-1186
    • Prescott, T.P.1    Papachristodoulou, A.2
  • 35
    • 77950805294 scopus 로고    scopus 로고
    • The control systems structures of energy metabolism
    • Cloutier M, Wellstead P. 2010 The control systems structures of energy metabolism. J. R. Soc. Interface 7, 651-665. (doi:10.1098/rsif.2009.0371)
    • (2010) J. R. Soc. Interface , vol.7 , pp. 651-665
    • Cloutier, M.1    Wellstead, P.2
  • 36
    • 84857050180 scopus 로고    scopus 로고
    • Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways
    • Michener JK, Thodey K, Liang JC, Smolke CD. 2012 Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metab. Eng. 14, 212-222. (doi:10.1016/j.ymben.2011.09.004)
    • (2012) Metab. Eng. , vol.14 , pp. 212-222
    • Michener, J.K.1    Thodey, K.2    Liang, J.C.3    Smolke, C.D.4
  • 37
    • 84859633048 scopus 로고    scopus 로고
    • Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids
    • Zhang FZ, Carothers JM, Keasling JD. 2012 Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat. Biotechnol. 30, 354-359. (doi:10.1038/nbt.2149)
    • (2012) Nat. Biotechnol. , vol.30 , pp. 354-359
    • Zhang, F.Z.1    Carothers, J.M.2    Keasling, J.D.3
  • 38
    • 39149113411 scopus 로고    scopus 로고
    • 2008 Modular cell biology: Retroactivity and insulation
    • Del Vecchio D, Ninfa AJ, Sontag ED. 2008 Modular cell biology: retroactivity and insulation. Mol. Syst. Biol. 4, 161. (doi:10.1038/msb4100204)
    • Mol. Syst. Biol. , vol.4 , pp. 161
    • Del Vecchio, D.1    Ninfa, A.J.2    Sontag, E.D.3
  • 39
    • 84871347056 scopus 로고    scopus 로고
    • Synthetic gene circuits for metabolic control: Design trade-offs and constraints
    • Oyarzun DA, Stan GB. 2012 Synthetic gene circuits for metabolic control: design trade-offs and constraints. J. R. Soc. Interface 10, 20120671. (doi:10.1098/rsif.2012.0671)
    • (2012) J. R. Soc. Interface , vol.10 , pp. 20120671
    • Oyarzun, D.A.1    Stan, G.B.2
  • 40
    • 14844358192 scopus 로고    scopus 로고
    • Ultrasensitivity and noise propagation in a synthetic transcriptional cascade
    • Hooshangi S, Thiberge S, Weiss R. 2005 Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc. Natl Acad. Sci. USA 102, 3581-3586. (doi:10.1073/pnas.0408507102)
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 3581-3586
    • Hooshangi, S.1    Thiberge, S.2    Weiss, R.3
  • 42
  • 43
    • 67449096729 scopus 로고    scopus 로고
    • Flux balance analysis of biological systems: Applications and challenges
    • Raman K, Chandra N. 2009 Flux balance analysis of biological systems: applications and challenges. Brief. Bioinform. 10, 435-449. (doi:10.1093/bib/bbp011)
    • (2009) Brief. Bioinform. , vol.10 , pp. 435-449
    • Raman, K.1    Chandra, N.2
  • 45
    • 84890484511 scopus 로고    scopus 로고
    • Nitrogen assimilation in Escherichia coli: Putting molecular data into a systems perspective
    • van Heeswijk WC, Westerhoff HV, Boogerd FC. 2013 Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. Microbiol. Mol. Biol. Rev 77, 628-695. (doi:10.1128/Mmbr.00025-13)
    • (2013) Microbiol. Mol. Biol. Rev , vol.77 , pp. 628-695
    • Van Heeswijk, W.C.1    Westerhoff, H.V.2    Boogerd, F.C.3
  • 48
    • 34249079154 scopus 로고    scopus 로고
    • Network motifs: Theory and experimental approaches
    • Alon U. 2007 Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8, 450-461. (doi:10.1038/nrg2102)
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 450-461
    • Alon, U.1
  • 50
    • 15044359242 scopus 로고    scopus 로고
    • Hierarchical and metabolic regulation of glucose influx in starved Saccharomyces cerevisiae
    • Rossell S, van der Weijden CC, Kruckeberg AL, Bakker BM, Westerhoff HV. 2005 Hierarchical and metabolic regulation of glucose influx in starved Saccharomyces cerevisiae. FEMS Yeast Res. 5, 611-619. doi:10.1016/j.femsyr.2004.11.003)
    • (2005) FEMS Yeast Res. , vol.5 , pp. 611-619
    • Rossell, S.1    Van Der Weijden, C.C.2    Kruckeberg, A.L.3    Bakker, B.M.4    Westerhoff, H.V.5
  • 51
    • 35648972123 scopus 로고    scopus 로고
    • The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels
    • Daran-Lapujade P et al. 2007 The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. Proc. Natl Acad. Sci. USA 104, 15 753-15 758. doi:10.1073/pnas.0707476104)
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 15753-15758
    • Daran-Lapujade, P.1
  • 52
    • 53749085229 scopus 로고    scopus 로고
    • A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
    • Herrgard MJ et al. 2008 A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat. Biotechnol. 26, 1155-1160. (doi:10.1038/nbt1492)
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1155-1160
    • Herrgard, M.J.1
  • 53
    • 0242487787 scopus 로고    scopus 로고
    • OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • Burgard AP, Pharkya P, Maranas CD. 2003 OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 84, 647-657. (doi:10.1002/bit.10803)
    • (2003) Biotechnol. Bioeng. , vol.84 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 54
    • 84895756673 scopus 로고    scopus 로고
    • K-OptForce: Integrating kinetics with flux balance analysis for strain design
    • Chowdhury A, Zomorrodi AR, Maranas CD. 2014 k-OptForce: integrating kinetics with flux balance analysis for strain design. PLoS Comput. Biol. 10, e1003487. (doi:10.1371/journal.pcbi.1003487)
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003487
    • Chowdhury, A.1    Zomorrodi, A.R.2    Maranas, C.D.3
  • 55
    • 80052573483 scopus 로고    scopus 로고
    • Large-scale bilevel strain design approaches and mixed-integer programming solution techniques
    • Kim J, Reed JL, Maravelias CT. 2011 Large-scale bilevel strain design approaches and mixed-integer programming solution techniques. PLoS ONE 6, e0024162. (doi:10.1371/journal.pone.0024162)
    • (2011) PLoS ONE , vol.6 , pp. e0024162
    • Kim, J.1    Reed, J.L.2    Maravelias, C.T.3
  • 56
    • 0034798879 scopus 로고    scopus 로고
    • Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments
    • Burgard AP, Vaidyaraman S, Maranas CD. 2001 Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments. Biotechnol. Progr. 17, 791-797. (doi:10.1021/Bp0100880)
    • (2001) Biotechnol. Progr. , vol.17 , pp. 791-797
    • Burgard, A.P.1    Vaidyaraman, S.2    Maranas, C.D.3
  • 57
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    • Mahadevan R, Schilling CH. 2003 The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 5, 264-276. (doi:10.1016/j.ymben.2003.09.002)
    • (2003) Metab. Eng. , vol.5 , pp. 264-276
    • Mahadevan, R.1    Schilling, C.H.2
  • 58
    • 0035824029 scopus 로고    scopus 로고
    • Regulation of gene expression in flux balance models of metabolism
    • Covert MW, Schilling CH, Palsson B. 2001 Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol. 213, 73-88. (doi:10.1006/jtbi.2001.2405)
    • (2001) J. Theor. Biol. , vol.213 , pp. 73-88
    • Covert, M.W.1    Schilling, C.H.2    Palsson, B.3
  • 59
    • 0037008673 scopus 로고    scopus 로고
    • Transcriptional regulation in constraints-based metabolic models of Escherichia coli
    • Covert MW, Palsson BO. 2002 Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J. Biol. Chem. 277, 28 058-28 064. (doi:10.1074/jbc.M201691200)
    • (2002) J. Biol. Chem. , vol.277 , pp. 28058-28064
    • Covert, M.W.1    Palsson, B.O.2
  • 60
    • 78649631909 scopus 로고    scopus 로고
    • The application of flux balance analysis in systems biology
    • Gianchandani EP, Chavali AK, Papin JA. 2010 The application of flux balance analysis in systems biology. Wires Syst. Biol. Med. 2, 372-382. (doi:10.1002/Wsbm.60)
    • (2010) Wires Syst. Biol. Med. , vol.2 , pp. 372-382
    • Gianchandani, E.P.1    Chavali, A.K.2    Papin, J.A.3
  • 61
    • 33748049119 scopus 로고    scopus 로고
    • Matrix formalism to describe functional states of transcriptional regulatory systems
    • Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BO. 2006 Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput. Biol. 2, e101. (doi:10.1371/journal.pcbi.0020101)
    • (2006) PLoS Comput. Biol. , vol.2 , pp. e101
    • Gianchandani, E.P.1    Papin, J.A.2    Price, N.D.3    Joyce, A.R.4    Palsson, B.O.5
  • 62
    • 34447523907 scopus 로고    scopus 로고
    • Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    • Schuetz R, Kuepfer L, Sauer U. 2007 Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol. Syst. Biol. 3, 119. (doi:10.1038/msb4100162)
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 119
    • Schuetz, R.1    Kuepfer, L.2    Sauer, U.3
  • 63
    • 43449132092 scopus 로고    scopus 로고
    • Is maximization of molar yield in metabolic networks favoured by evolution?
    • Schuster S, Pfeiffer T, Fell DA. 2008 Is maximization of molar yield in metabolic networks favoured by evolution? J. Theor. Biol. 252, 497-504. (doi:10.1016/j.jtbi.2007.12.008)
    • (2008) J. Theor. Biol. , vol.252 , pp. 497-504
    • Schuster, S.1    Pfeiffer, T.2    Fell, D.A.3
  • 67
    • 43449107085 scopus 로고    scopus 로고
    • Signalling control strength
    • Westerhoff HV. 2008 Signalling control strength. J. Theor. Biol. 252, 555-567. (doi:10.1016/j.jtbi. 2007.11.035)
    • (2008) J. Theor. Biol. , vol.252 , pp. 555-567
    • Westerhoff, H.V.1
  • 68
    • 0036708443 scopus 로고    scopus 로고
    • Dynamic flux balance analysis of diauxic growth in Escherichia coli
    • Mahadevan R, Edwards JS, Doyle FJ. 2002 Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys. J. 83, 1331-1340. (doi:10.1016/S0006-3495(02)73903-9)
    • (2002) Biophys. J. , vol.83 , pp. 1331-1340
    • Mahadevan, R.1    Edwards, J.S.2    Doyle, F.J.3
  • 70
    • 84911941359 scopus 로고    scopus 로고
    • Dynamic optimization of metabolic networks coupled with gene expression
    • Waldherr S, Oyarzun DA, Bockmayr A. 2015 Dynamic optimization of metabolic networks coupled with gene expression. J. Theor. Biol. 365, 469-485. (doi:10.1016/j.jtbi.2014.10.035)
    • (2015) J. Theor. Biol. , vol.365 , pp. 469-485
    • Waldherr, S.1    Oyarzun, D.A.2    Bockmayr, A.3
  • 71
    • 84945144145 scopus 로고    scopus 로고
    • Elucidating temporal resource allocation and diurnal dynamics in phototrophic metabolism using conditional FBA
    • Rugen M, Bockmayr A, Steuer R. 2015 Elucidating temporal resource allocation and diurnal dynamics in phototrophic metabolism using conditional FBA. Sci. Rep.-UK 5, 15247. (doi:10.1038/srep15247)
    • (2015) Sci. Rep.-UK , vol.5 , pp. 15247
    • Rugen, M.1    Bockmayr, A.2    Steuer, R.3
  • 74
    • 0027486853 scopus 로고
    • Modular analysis of the control of complex metabolic pathways
    • Schuster S, Kahn D, Westerhoff HV. 1993 Modular analysis of the control of complex metabolic pathways. Biophys. Chem. 48, 1-17. (doi:10.1016/0301-4622(93)80037-J)
    • (1993) Biophys. Chem. , vol.48 , pp. 1-17
    • Schuster, S.1    Kahn, D.2    Westerhoff, H.V.3
  • 75
    • 0025822783 scopus 로고
    • Quantitative assessment of regulation in metabolic systems
    • Hofmeyr JHS, Cornishbowden A. 1991 Quantitative assessment of regulation in metabolic systems. Eur. J. Biochem. 200, 223-236. (doi:10.1111/j. 1432-1033.1991.tb21071.x)
    • (1991) Eur. J. Biochem. , vol.200 , pp. 223-236
    • Hofmeyr, J.H.S.1    Cornishbowden, A.2
  • 76
    • 0034733820 scopus 로고    scopus 로고
    • Regulating the cellular economy of supply and demand
    • Hofmeyr JHS, Cornish-Bowden A. 2000 Regulating the cellular economy of supply and demand. FEBS Lett. 476, 47-51. (doi:10.1016/S0014-5793(00) 01668-9)
    • (2000) FEBS Lett. , vol.476 , pp. 47-51
    • Hofmeyr, J.H.S.1    Cornish-Bowden, A.2
  • 77
    • 84887889199 scopus 로고    scopus 로고
    • (Im)Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-expression regulation: Marrying control engineering with metabolic control analysis
    • He F, Fromion V, Westerhoff HV. 2013 (Im)Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-expression regulation: marrying control engineering with metabolic control analysis. BMC Syst. Biol. 7, 131. (doi:10.1186/1752-0509-7-131)
    • (2013) BMC Syst. Biol. , vol.7 , pp. 131
    • He, F.1    Fromion, V.2    Westerhoff, H.V.3
  • 78
    • 78650218972 scopus 로고    scopus 로고
    • Modeling of uncertainties in biochemical reactions
    • Miskovic L, Hatzimanikatis V. 2011 Modeling of uncertainties in biochemical reactions. Biotechnol. Bioeng. 108, 413-423. (doi:10.1002/bit.22932)
    • (2011) Biotechnol. Bioeng. , vol.108 , pp. 413-423
    • Miskovic, L.1    Hatzimanikatis, V.2
  • 79
    • 84929485233 scopus 로고    scopus 로고
    • A general framework for thermodynamically consistent parameterization and efficient sampling of enzymatic reactions
    • Saa P, Nielsen LK. 2015 A general framework for thermodynamically consistent parameterization and efficient sampling of enzymatic reactions. PLoS Comput. Biol. 11, e1004195. (doi:10.1371/journal. pcbi.1004195)
    • (2015) PLoS Comput. Biol. , vol.11 , pp. e1004195
    • Saa, P.1    Nielsen, L.K.2
  • 80
    • 84883800631 scopus 로고    scopus 로고
    • Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints
    • Chakrabarti A, Miskovic L, Soh KC, Hatzimanikatis V. 2013 Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints. Biotechnol. J. 8, 1043-1105. (doi:10.1002/biot.201300091)
    • (2013) Biotechnol. J. , vol.8 , pp. 1043-1105
    • Chakrabarti, A.1    Miskovic, L.2    Soh, K.C.3    Hatzimanikatis, V.4
  • 81
    • 84928723640 scopus 로고    scopus 로고
    • Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis
    • Oliveira AP, Ludwig C, Zampieri M, Weisser H, Aebersold R, Sauer U. 2015 Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis. Sci. Signal 8, rs4. (doi:10.1126/scisignal.2005768)
    • (2015) Sci. Signal , vol.8 , pp. rs4
    • Oliveira, A.P.1    Ludwig, C.2    Zampieri, M.3    Weisser, H.4    Aebersold, R.5    Sauer, U.6
  • 82
    • 84930642844 scopus 로고    scopus 로고
    • Posttranslational regulation of microbial metabolism
    • Kochanowski K, Sauer U, Noor E. 2015 Posttranslational regulation of microbial metabolism. Curr. Opin. Microbiol. 27, 10-17. (doi:10.1016/j.mib.2015.05.007)
    • (2015) Curr. Opin. Microbiol. , vol.27 , pp. 10-17
    • Kochanowski, K.1    Sauer, U.2    Noor, E.3
  • 83
    • 84943659706 scopus 로고    scopus 로고
    • Applications of computational modeling in metabolic engineering of yeast
    • Kerkhoven EJ, Lahtvee PJ, Nielsen J. 2015 Applications of computational modeling in metabolic engineering of yeast. FEMS Yeast Res. 15, 1-13. (doi:10.1111/1567-1364.12199)
    • (2015) FEMS Yeast Res. , vol.15 , pp. 1-13
    • Kerkhoven, E.J.1    Lahtvee, P.J.2    Nielsen, J.3
  • 84
    • 62049085905 scopus 로고    scopus 로고
    • Systems biology towards life in silico: Mathematics of the control of living cells
    • Westerhoff HV et al. 2009 Systems biology towards life in silico: mathematics of the control of living cells. J. Math. Biol. 58, 7-34. (doi:10.1007/s00285-008-0160-8)
    • (2009) J. Math. Biol. , vol.58 , pp. 7-34
    • Westerhoff, H.V.1
  • 85
    • 0001787632 scopus 로고
    • Regulatory responses and control analysis-assessment of the relative importance of internal effectors
    • New York, NY: Plenum Press
    • Sauro HM. 1990 Regulatory responses and control analysis-assessment of the relative importance of internal effectors. In Control of metabolic processes (ed. A Cornish-Bowden), pp. 225-230. New York, NY: Plenum Press.
    • (1990) Control of Metabolic Processes (Ed. A Cornish-Bowden) , pp. 225-230
    • Sauro, H.M.1
  • 86
    • 0035816464 scopus 로고    scopus 로고
    • Transcriptome meets metabolome: Hierarchical and metabolic regulation of the glycolytic pathway
    • ter Kuile BH, Westerhoff HV. 2001 Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway. FEBS Lett. 500, 169-171. (doi:10.1016/S0014-5793(01) 02613-8)
    • (2001) FEBS Lett. , vol.500 , pp. 169-171
    • Kuile, B.H.1    Westerhoff, H.V.2
  • 87
    • 0038487266 scopus 로고    scopus 로고
    • Transcriptional, translational and metabolic regulation of glycolysis in Lactococcus lactis subsp. Cremoris MG 1363 grown in continuous acidic cultures
    • Even S, Lindley ND, Cocaign-Bousquet M. 2003 Transcriptional, translational and metabolic regulation of glycolysis in Lactococcus lactis subsp. cremoris MG 1363 grown in continuous acidic cultures. Microbiology 149, 1935-1944. (doi:10.1099/mic.0.26146-0)
    • (2003) Microbiology , vol.149 , pp. 1935-1944
    • Even, S.1    Lindley, N.D.2    Cocaign-Bousquet, M.3
  • 88
    • 17444406291 scopus 로고    scopus 로고
    • The multifarious short-term regulation of ammonium assimilation of Escherichia coli: Dissection using an in silico replica
    • Bruggeman FJ, Boogerd FC, Westerhoff HV. 2005 The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica. FEBS J. 272, 1965-1985. (doi:10.1111/j.1742-4658.2005. 04626.x)
    • (2005) FEBS J. , vol.272 , pp. 1965-1985
    • Bruggeman, F.J.1    Boogerd, F.C.2    Westerhoff, H.V.3
  • 89
    • 33846017352 scopus 로고    scopus 로고
    • The nature of systems biology
    • Bruggeman FJ, Westerhoff HV. 2007 The nature of systems biology. Trends Microbiol. 15, 45-50. (doi:10.1016/j.tim.2006.11.003)
    • (2007) Trends Microbiol. , vol.15 , pp. 45-50
    • Bruggeman, F.J.1    Westerhoff, H.V.2
  • 91
    • 84881077601 scopus 로고    scopus 로고
    • Functional lysine modification by an intrinsically reactive primary glycolytic metabolite
    • Moellering RE, Cravatt BF. 2013 Functional lysine modification by an intrinsically reactive primary glycolytic metabolite. Science 341, 549-553. (doi:10.1126/science.1238327)
    • (2013) Science , vol.341 , pp. 549-553
    • Moellering, R.E.1    Cravatt, B.F.2
  • 93
    • 70349248100 scopus 로고    scopus 로고
    • Time-dependent regulation analysis dissects shifts between metabolic and gene-expression regulation during nitrogen starvation in baker's yeast
    • van Eunen K, Bouwman J, Lindenbergh A, Westerhoff HV, Bakker BM. 2009 Time-dependent regulation analysis dissects shifts between metabolic and gene-expression regulation during nitrogen starvation in baker's yeast. FEBS J. 276, 5521-5536. (doi:10.1111/j.1742-4658.2009. 07235.x)
    • (2009) FEBS J. , vol.276 , pp. 5521-5536
    • Van Eunen, K.1    Bouwman, J.2    Lindenbergh, A.3    Westerhoff, H.V.4    Bakker, B.M.5
  • 95
    • 0026640714 scopus 로고
    • Systems analysis of the tricarboxylic acid cycle in Dictyostelium discoideum. II. Control analysis
    • Albe KR, Wright BE. 1992 Systems analysis of the tricarboxylic acid cycle in Dictyostelium discoideum. II. Control analysis. J. Biol. Chem. 267, 3106-3114.
    • (1992) J. Biol. Chem. , vol.267 , pp. 3106-3114
    • Albe, K.R.1    Wright, B.E.2
  • 96
    • 83255187370 scopus 로고    scopus 로고
    • Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues
    • Araujo WL, Nunes-Nesi A, Nikoloski Z, Sweetlove LJ, Fernie AR. 2012 Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues. Plant Cell Environ. 35, 1-21. (doi:10.1111/j.1365-3040.2011.02332.x)
    • (2012) Plant Cell Environ. , vol.35 , pp. 1-21
    • Araujo, W.L.1    Nunes-Nesi, A.2    Nikoloski, Z.3    Sweetlove, L.J.4    Fernie, A.R.5
  • 97
    • 43649083387 scopus 로고    scopus 로고
    • Structural robustness of metabolic networks with respect to multiple knockouts
    • Behre J, Wilhelm T, von Kamp A, Ruppin E, Schuster S. 2008 Structural robustness of metabolic networks with respect to multiple knockouts. J. Theor. Biol. 252, 433-441. (doi:10.1016/j.jtbi. 2007.09.043)
    • (2008) J. Theor. Biol. , vol.252 , pp. 433-441
    • Behre, J.1    Wilhelm, T.2    Von Kamp, A.3    Ruppin, E.4    Schuster, S.5
  • 98
    • 41349112310 scopus 로고    scopus 로고
    • Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics
    • Kwon YK, Cho KH. 2008 Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics. Bioinformatics 24, 987-994. (doi:10.1093/bioinformatics/btn060)
    • (2008) Bioinformatics , vol.24 , pp. 987-994
    • Kwon, Y.K.1    Cho, K.H.2
  • 100
    • 84872042913 scopus 로고    scopus 로고
    • Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico
    • Quinton-Tulloch MJ, Bruggeman FJ, Snoep JL, Westerhoff HV. 2013 Trade-off of dynamic fragility but not of robustness in metabolic pathways in silico. FEBS J. 280, 160-173. (doi:10.1111/febs.12057)
    • (2013) FEBS J. , vol.280 , pp. 160-173
    • Quinton-Tulloch, M.J.1    Bruggeman, F.J.2    Snoep, J.L.3    Westerhoff, H.V.4
  • 102
    • 0033977087 scopus 로고    scopus 로고
    • Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs
    • Bakker BM, Westerhoff HV, Opperdoes FR, Michels PA. 2000 Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs. Mol. Biochem. Parasitol. 106, 1-10. (doi:10.1016/S0166-6851(99)00197-8)
    • (2000) Mol. Biochem. Parasitol. , vol.106 , pp. 1-10
    • Bakker, B.M.1    Westerhoff, H.V.2    Opperdoes, F.R.3    Michels, P.A.4
  • 103
    • 79955715337 scopus 로고    scopus 로고
    • A probabilistic approach to identify putative drug targets in biochemical networks
    • Murabito E, Smallbone K, Swinton J, Westerhoff HV, Steuer R. 2011 A probabilistic approach to identify putative drug targets in biochemical networks. J. R. Soc. Interface 8, 880-895. (doi:10.1098/rsif. 2010.0540)
    • (2011) J. R. Soc. Interface , vol.8 , pp. 880-895
    • Murabito, E.1    Smallbone, K.2    Swinton, J.3    Westerhoff, H.V.4    Steuer, R.5
  • 104
    • 0036227648 scopus 로고    scopus 로고
    • DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase i and DNA gyrase
    • Snoep JL, van der Weijden CC, Andersen HW, Westerhoff HV, Jensen PR. 2002 DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyrase. Eur. J. Biochem. 269, 1662-1669. (doi:10.1046/j.1432-1327.2002.02803.x)
    • (2002) Eur. J. Biochem. , vol.269 , pp. 1662-1669
    • Snoep, J.L.1    Van Der Weijden, C.C.2    Andersen, H.W.3    Westerhoff, H.V.4    Jensen, P.R.5
  • 105
    • 0024597907 scopus 로고
    • Control analysis of time-dependent metabolic systems
    • Acerenza L, Sauro HM, Kacser H. 1989 Control analysis of time-dependent metabolic systems. J. Theor. Biol. 137, 423-444. (doi:10.1016/S0022-5193(89)80038-4)
    • (1989) J. Theor. Biol. , vol.137 , pp. 423-444
    • Acerenza, L.1    Sauro, H.M.2    Kacser, H.3
  • 106
    • 0031099173 scopus 로고    scopus 로고
    • Control analysis of periodic phenomena in biological systems
    • Kholodenko BN, Demin OV, Westerhoff HV. 1997 Control analysis of periodic phenomena in biological systems. J. Phys. Chem. B 101, 2070-2081. (doi:10.1021/Jp962336u)
    • (1997) J. Phys. Chem. B , vol.101 , pp. 2070-2081
    • Kholodenko, B.N.1    Demin, O.V.2    Westerhoff, H.V.3
  • 107
    • 0001243061 scopus 로고    scopus 로고
    • Control analysis of stationary forced oscillations
    • Demin OV, Westerhoff HV, Kholodenko BN. 1999 Control analysis of stationary forced oscillations. J. Phys. Chem. B 103, 10 695-10 710. (doi:10.1021/jp991597b)
    • (1999) J. Phys. Chem. B , vol.103 , pp. 10695-10710
    • Demin, O.V.1    Westerhoff, H.V.2    Kholodenko, B.N.3
  • 108
    • 0036216077 scopus 로고    scopus 로고
    • Control analysis for autonomously oscillating biochemical networks
    • Reijenga KA, Westerhoff HV, Kholodenko BN, Snoep JL. 2002 Control analysis for autonomously oscillating biochemical networks. Biophys. J. 82, 99-108. (doi:10.1016/S0006-3495(02)75377-0)
    • (2002) Biophys. J. , vol.82 , pp. 99-108
    • Reijenga, K.A.1    Westerhoff, H.V.2    Kholodenko, B.N.3    Snoep, J.L.4
  • 109
    • 84902668956 scopus 로고    scopus 로고
    • Allosteric regulation of phosphofructokinase controls the emergence of glycolytic oscillations in isolated yeast cells
    • Gustavsson AK, van Niekerk DD, Adiels CB, Kooi B, Goksor M, Snoep JL. 2014 Allosteric regulation of phosphofructokinase controls the emergence of glycolytic oscillations in isolated yeast cells. FEBS J. 281, 2784-2793. (doi:10.1111/febs.12820)
    • (2014) FEBS J. , vol.281 , pp. 2784-2793
    • Gustavsson, A.K.1    Van Niekerk, D.D.2    Adiels, C.B.3    Kooi, B.4    Goksor, M.5    Snoep, J.L.6
  • 113
    • 0037466509 scopus 로고    scopus 로고
    • Sensitivity analysis of stoichiometric networks: An extension of metabolic control analysis to non-steady state trajectories
    • Ingalls BP, Sauro HM. 2003 Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories. J. Theor. Biol. 222, 23-36. (doi:10.1016/S0022-5193(03)00011-0)
    • (2003) J. Theor. Biol. , vol.222 , pp. 23-36
    • Ingalls, B.P.1    Sauro, H.M.2
  • 115
    • 0030573816 scopus 로고    scopus 로고
    • What bio technologists knew all along. .?
    • Westerhoff HV, Kell DB. 1996 What bio technologists knew all along. .? J. Theor. Biol. 182, 411-420. doi:10.1006/jtbi.1996.0181)
    • (1996) J. Theor. Biol. , vol.182 , pp. 411-420
    • Westerhoff, H.V.1    Kell, D.B.2
  • 117
    • 0028825813 scopus 로고
    • Protein burden in zymomonas-mobilis-negative flux and growth-control due to overproduction of glycolytic-enzymes
    • Snoep JL, Yomano LP, Westerhoff HV, Ingram LO. 1995 Protein burden in zymomonas-mobilis-negative flux and growth-control due to overproduction of glycolytic-enzymes. Microbiology 141, 2329-2337. doi:10.1099/13500872-141-9-2329)
    • (1995) Microbiology , vol.141 , pp. 2329-2337
    • Snoep, J.L.1    Yomano, L.P.2    Westerhoff, H.V.3    Ingram, L.O.4
  • 118
    • 84940592212 scopus 로고    scopus 로고
    • Dynamic metabolic engineering: New strategies for developing responsive cell factories
    • Brockman IM, Prather KLJ. 2015 Dynamic metabolic engineering: new strategies for developing responsive cell factories. Biotechnol. J. 10, 1360-1369. (doi:10.1002/biot.201400422)
    • (2015) Biotechnol. J. , vol.10 , pp. 1360-1369
    • Brockman, I.M.1    Prather, K.L.J.2
  • 120
    • 72249097352 scopus 로고    scopus 로고
    • Growth ratedependent global effects on gene expression in bacteria
    • Klumpp S, Zhang ZG, Hwa T. 2009 Growth ratedependent global effects on gene expression in bacteria. Cell 139, 1366-1375. (doi:10.1016/j.cell. 2009.12.001)
    • (2009) Cell , vol.139 , pp. 1366-1375
    • Klumpp, S.1    Zhang, Z.G.2    Hwa, T.3
  • 121
    • 84924370996 scopus 로고    scopus 로고
    • Mechanistic links between cellular trade-offs, gene expression, and growth
    • Weisse AY, Oyarzun DA, Danos V, Swain PS. 2015 Mechanistic links between cellular trade-offs, gene expression, and growth. Proc. Natl Acad. Sci. USA 112, E1038-E1047. (doi:10.1073/pnas. 1416533112)
    • (2015) Proc. Natl Acad. Sci. USA , vol.112 , pp. E1038-E1047
    • Weisse, A.Y.1    Oyarzun, D.A.2    Danos, V.3    Swain, P.S.4
  • 123
    • 0034712843 scopus 로고    scopus 로고
    • Robust perfect adaptation in bacterial chemotaxis through integral feedback control
    • Yi TM, Huang Y, Simon MI, Doyle J. 2000 Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc. Natl Acad. Sci. USA 97, 4649-4653. (doi:10.1073/pnas. 97.9.4649)
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 4649-4653
    • Yi, T.M.1    Huang, Y.2    Simon, M.I.3    Doyle, J.4
  • 124
    • 0036352423 scopus 로고    scopus 로고
    • Calcium homeostasis and parturient hypocalcemia: An integral feedback perspective
    • El-Samad H, Goff JP, Khammash M. 2002 Calcium homeostasis and parturient hypocalcemia: an integral feedback perspective. J. Theor. Biol. 214, 17-29. (doi:10.1006/jtbi.2001.2422)
    • (2002) J. Theor. Biol. , vol.214 , pp. 17-29
    • El-Samad, H.1    Goff, J.P.2    Khammash, M.3
  • 125
    • 67649669252 scopus 로고    scopus 로고
    • A systems-level analysis of perfect adaptation in yeast osmoregulation
    • Muzzey D, Gomez-Uribe CA, Mettetal JT, van Oudenaarden A. 2009 A systems-level analysis of perfect adaptation in yeast osmoregulation. Cell 138, 160-171. (doi:10.1016/j.cell.2009.04.047)
    • (2009) Cell , vol.138 , pp. 160-171
    • Muzzey, D.1    Gomez-Uribe, C.A.2    Mettetal, J.T.3    Van Oudenaarden, A.4
  • 126
    • 33846067658 scopus 로고    scopus 로고
    • DFBALQR: An optimal control approach to flux balance analysis
    • Uygun K, Matthew HWT, Huang YL. 2006 DFBALQR: an optimal control approach to flux balance analysis. Ind. Eng. Chem. Res. 45, 8554-8564. (doi:10.1021/Ie060218f )
    • (2006) Ind. Eng. Chem. Res. , vol.45 , pp. 8554-8564
    • Uygun, K.1    Matthew, H.W.T.2    Huang, Y.L.3
  • 127
    • 0027605597 scopus 로고
    • The regulatory strength-how to be precise about regulation and homeostasis
    • Kahn D, Westerhoff HV. 1993 The regulatory strength-how to be precise about regulation and homeostasis. Acta Biotheor. 41, 85-96. (doi:10.1007/Bf00712777)
    • (1993) Acta Biotheor. , vol.41 , pp. 85-96
    • Kahn, D.1    Westerhoff, H.V.2
  • 129
    • 0036441029 scopus 로고    scopus 로고
    • Prediction of temporal gene expression-metabolic optimization by re-distribution of enzyme activities
    • Klipp E, Heinrich R, Holzhutter HG. 2002 Prediction of temporal gene expression-metabolic optimization by re-distribution of enzyme activities. Eur. J. Biochem. 269, 5406-5413. (doi:10.1046/j. 1432-1033.2002.03223.x)
    • (2002) Eur. J. Biochem. , vol.269 , pp. 5406-5413
    • Klipp, E.1    Heinrich, R.2    Holzhutter, H.G.3
  • 131
    • 45849120994 scopus 로고    scopus 로고
    • Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways
    • Chin CS, Chubukov V, Jolly ER, DeRisi J, Li H. 2008 Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways. PLoS Biol. 6, 1343-1356. (doi:10.1371/journal.pbio. 0060146)
    • (2008) PLoS Biol. , vol.6 , pp. 1343-1356
    • Chin, C.S.1    Chubukov, V.2    Jolly, E.R.3    DeRisi, J.4    Li, H.5
  • 132
    • 84883288679 scopus 로고    scopus 로고
    • Dynamic optimization identifies optimal programmes for pathway regulation in prokaryotes
    • Bartl M, Kotzing M, Schuster S, Li P, Kaleta C. 2013 Dynamic optimization identifies optimal programmes for pathway regulation in prokaryotes. Nat. Commun. 4, 2243. (doi:10.1038/ncomms3243)
    • (2013) Nat. Commun. , vol.4 , pp. 2243
    • Bartl, M.1    Kotzing, M.2    Schuster, S.3    Li, P.4    Kaleta, C.5
  • 133
    • 70350400430 scopus 로고    scopus 로고
    • Sequential activation of metabolic pathways: A dynamic optimization approach
    • Oyarzun DA, Ingalls BP, Middleton RH, Kalamatianos D. 2009 Sequential activation of metabolic pathways: a dynamic optimization approach. Bull. Math. Biol. 71, 1851-1872. (doi:10.1007/s11538-009-9427-5)
    • (2009) Bull. Math. Biol. , vol.71 , pp. 1851-1872
    • Oyarzun, D.A.1    Ingalls, B.P.2    Middleton, R.H.3    Kalamatianos, D.4
  • 134
    • 77953609496 scopus 로고    scopus 로고
    • Modelling the optimal timing in metabolic pathway activation-use of Pontryagin's Maximum Principle and role of the Golden section
    • Bartl M, Li P, Schuster S. 2010 Modelling the optimal timing in metabolic pathway activation-use of Pontryagin's Maximum Principle and role of the Golden section. Biosystems 101, 67-77. (doi:10.1016/j.biosystems.2010.04.007)
    • (2010) Biosystems , vol.101 , pp. 67-77
    • Bartl, M.1    Li, P.2    Schuster, S.3
  • 135
    • 84891553151 scopus 로고    scopus 로고
    • Global dynamic optimization approach to predict activation in metabolic pathways
    • de Hijas-Liste GM, Klipp E, Balsa-Canto E, Banga JR. 2014 Global dynamic optimization approach to predict activation in metabolic pathways. BMC Syst. Biol. 8, 1. (doi:10.1186/1752-0509-8-1)
    • (2014) BMC Syst. Biol. , vol.8 , pp. 1
    • De Hijas-Liste, G.M.1    Klipp, E.2    Balsa-Canto, E.3    Banga, J.R.4
  • 136
    • 84872816956 scopus 로고    scopus 로고
    • Physical constraints on biological integral control design for homeostasis and sensory adaptation
    • Ang J, McMillen DR. 2013 Physical constraints on biological integral control design for homeostasis and sensory adaptation. Biophys. J. 104, 505-515. (doi:10.1016/j.bpj.2012.12.015)
    • (2013) Biophys. J. , vol.104 , pp. 505-515
    • Ang, J.1    McMillen, D.R.2
  • 137
    • 84867420739 scopus 로고    scopus 로고
    • A new approach to an old problem: Synthetic biology tools for human disease and metabolism
    • Burrill DR, Boyle PM, Silver PA. 2011 A new approach to an old problem: synthetic biology tools for human disease and metabolism. Cold Spring Harb. Symp. Quant. Biol. 76, 145-154. (doi:10.1101/sqb.2011.76.010686)
    • (2011) Cold Spring Harb. Symp. Quant. Biol. , vol.76 , pp. 145-154
    • Burrill, D.R.1    Boyle, P.M.2    Silver, P.A.3
  • 139
    • 84924239544 scopus 로고    scopus 로고
    • Negative feedback regulation of fatty acid production based on a malonyl-CoA sensor-actuator
    • Liu D, Xiao Y, Evans BS, Zhang F. 2015 Negative feedback regulation of fatty acid production based on a malonyl-CoA sensor-actuator. ACS Synth. Biol. 4, 132-140. (doi:10.1021/sb400158w)
    • (2015) ACS Synth. Biol. , vol.4 , pp. 132-140
    • Liu, D.1    Xiao, Y.2    Evans, B.S.3    Zhang, F.4
  • 140
    • 84905668376 scopus 로고    scopus 로고
    • Improving fatty acids production by engineering dynamic pathway regulation and metabolic control
    • Xu P, Li LY, Zhang FM, Stephanopoulos G, Koffas M. 2014 Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. Proc. Natl Acad. Sci. USA 111, 11 299-11 304. doi:10.1073/pnas. 1406401111)
    • (2014) Proc. Natl Acad. Sci. USA , vol.111 , pp. 11299-11304
    • Xu, P.1    Li, L.Y.2    Zhang, F.M.3    Stephanopoulos, G.4    Koffas, M.5
  • 141
    • 0033572810 scopus 로고    scopus 로고
    • Extensive regulation compromises the extent to which DNA gyrase controls DNA supercoiling and growth rate of Escherichia coli
    • Jensen PR, van der Weijden CC, Jensen LB, Westerhoff HV, Snoep JL. 1999 Extensive regulation compromises the extent to which DNA gyrase controls DNA supercoiling and growth rate of Escherichia coli. Eur. J. Biochem. 266, 865-877. (doi:10.1046/j.1432-1327.1999.00921.x)
    • (1999) Eur. J. Biochem. , vol.266 , pp. 865-877
    • Jensen, P.R.1    Van Der Weijden, C.C.2    Jensen, L.B.3    Westerhoff, H.V.4    Snoep, J.L.5
  • 142
    • 77957281370 scopus 로고
    • Hierarchies in control
    • Jensen PR et al. 1995 Hierarchies in control. J. Biol. Syst. 3, 139-144. (doi:10.1142/S02183 39095000137)
    • (1995) J. Biol. Syst. , vol.3 , pp. 139
    • Jensen, P.R.1
  • 143
    • 84929494299 scopus 로고    scopus 로고
    • Multiplex eukaryotic transcription (In) activation: Timing, bursting and cycling of a ratchet clock mechanism
    • Rybakova KN, Bruggeman FJ, Tomaszewska A, Mone MJ, Carlberg C, Westerhoff HV. 2015 Multiplex eukaryotic transcription (In) activation: timing, bursting and cycling of a ratchet clock mechanism. PLoS Comput. Biol. 11, e1004236. (doi:10.1371/journal.pcbi.1004236)
    • (2015) PLoS Comput. Biol. , vol.11 , pp. e1004236
    • Rybakova, K.N.1    Bruggeman, F.J.2    Tomaszewska, A.3    Mone, M.J.4    Carlberg, C.5    Westerhoff, H.V.6
  • 144
    • 84863092162 scopus 로고    scopus 로고
    • Design constraints on a synthetic metabolism
    • Bilgin T, Wagner A. 2012 Design constraints on a synthetic metabolism. PLoS ONE 7, e0039903. (doi:10.1371/journal.pone.0039903)
    • (2012) PLoS ONE , vol.7 , pp. e0039903
    • Bilgin, T.1    Wagner, A.2
  • 145
    • 77956870811 scopus 로고    scopus 로고
    • Structural synthetic biotechnology: From molecular structure to predictable design for industrial strain development
    • Chen Z, Wilmanns M, Zeng AP. 2010 Structural synthetic biotechnology: from molecular structure to predictable design for industrial strain development. Trends Biotechnol. 28, 534-542. (doi:10.1016/j. tibtech.2010.07.004)
    • (2010) Trends Biotechnol. , vol.28 , pp. 534-542
    • Chen, Z.1    Wilmanns, M.2    Zeng, A.P.3
  • 146
    • 47649125643 scopus 로고    scopus 로고
    • Allosteric regulation and catalysis emerge via a common route
    • Goodey NM, Benkovic SJ. 2008 Allosteric regulation and catalysis emerge via a common route. Nat. Chem. Biol. 4, 474-482. (doi:10.1038/Nchembio.98)
    • (2008) Nat. Chem. Biol. , vol.4 , pp. 474-482
    • Goodey, N.M.1    Benkovic, S.J.2
  • 147
    • 84924257528 scopus 로고    scopus 로고
    • Rational design of allosteric regulation of homoserine dehydrogenase by a non-natural inhibitor L-lysine
    • Chen Z, Rappert S, Zeng AP. 2013 Rational design of allosteric regulation of homoserine dehydrogenase by a non-natural inhibitor L-lysine. ACS Synth. Biol. 4, 126-131. (doi:10.1021/sb400133g)
    • (2013) ACS Synth. Biol. , vol.4 , pp. 126-131
    • Chen, Z.1    Rappert, S.2    Zeng, A.P.3
  • 149
    • 0029993759 scopus 로고    scopus 로고
    • Why and when channelling can decrease pool size at constant net flux in a simple dynamic channel
    • Mendes P, Kell DB, Westerhoff HV. 1996 Why and when channelling can decrease pool size at constant net flux in a simple dynamic channel. Biochim. Biophys. Acta 1289, 175-186. (doi:10.1016/0304-4165(95)00152-2)
    • (1996) Biochim. Biophys. Acta , vol.1289 , pp. 175-186
    • Mendes, P.1    Kell, D.B.2    Westerhoff, H.V.3
  • 150
    • 79960216783 scopus 로고    scopus 로고
    • Substrate channeling and enzyme complexes for biotechnological applications
    • Zhang YHP. 2011 Substrate channeling and enzyme complexes for biotechnological applications. Biotechnol. Adv. 29, 715-725. (doi:10.1016/j. biotechadv.2011.05.020)
    • (2011) Biotechnol. Adv. , vol.29 , pp. 715-725
    • Zhang, Y.H.P.1
  • 151
    • 84874095104 scopus 로고    scopus 로고
    • Self-assembly of synthetic metabolons through synthetic protein scaffolds: One-step purification, co-immobilization, and substrate channeling
    • You C, Zhang YHP. 2013 Self-assembly of synthetic metabolons through synthetic protein scaffolds: one-step purification, co-immobilization, and substrate channeling. ACS Synth. Biol. 2, 102-110. (doi:10.1021/sb300068g)
    • (2013) ACS Synth. Biol. , vol.2 , pp. 102-110
    • You, C.1    Zhang, Y.H.P.2
  • 153
    • 3242729569 scopus 로고    scopus 로고
    • Quantitative analysis of signaling networks
    • Sauro HM, Kholodenko BN. 2004 Quantitative analysis of signaling networks. Prog. Biophys. Mol. Biol. 86, 5-43. (doi:10.1016/j.pbiomolbio. 2004.03.002)
    • (2004) Prog. Biophys. Mol. Biol. , vol.86 , pp. 5-43
    • Sauro, H.M.1    Kholodenko, B.N.2
  • 154
    • 33847324364 scopus 로고    scopus 로고
    • Cross-talk and decision making in MAP kinase pathways
    • McClean MN, Mody A, Broach JR, Ramanathan S. 2007 Cross-talk and decision making in MAP kinase pathways. Nat. Genet. 39, 409-414. (doi:10.1038/Ng1957)
    • (2007) Nat. Genet. , vol.39 , pp. 409-414
    • McClean, M.N.1    Mody, A.2    Broach, J.R.3    Ramanathan, S.4
  • 155
    • 84878866199 scopus 로고    scopus 로고
    • Translational cross talk in gene networks
    • Mather WH, Hasty J, Tsimring LS, Williams RJ. 2013 Translational cross talk in gene networks. Biophys. J. 104, 2564-2572. (doi:10.1016/j.bpj.2013.04.049)
    • (2013) Biophys. J. , vol.104 , pp. 2564-2572
    • Mather, W.H.1    Hasty, J.2    Tsimring, L.S.3    Williams, R.J.4
  • 156
    • 84878155897 scopus 로고    scopus 로고
    • Computing life: Add logos to biology and bios to physics
    • Kolodkin A, Simeonidis E, Westerhoff HV. 2013 Computing life: add logos to biology and bios to physics. Prog. Biophys. Mol. Biol. 111, 69-74. (doi:10.1016/j.pbiomolbio.2012.10.003)
    • (2013) Prog. Biophys. Mol. Biol. , vol.111 , pp. 69-74
    • Kolodkin, A.1    Simeonidis, E.2    Westerhoff, H.V.3
  • 158
    • 84887620741 scopus 로고    scopus 로고
    • A control theoretic framework for modular analysis and design of biomolecular networks
    • Del Vecchio D. 2013 A control theoretic framework for modular analysis and design of biomolecular networks. Annu. Rev. Control 37, 333-345. (doi:10.1016/j.arcontrol.2013.09.011)
    • (2013) Annu. Rev. Control , vol.37 , pp. 333-345
    • Del Vecchio, D.1
  • 159
    • 25444468618 scopus 로고    scopus 로고
    • Noise in gene expression: Origins, consequences, and control
    • Raser JM, O'Shea EK. 2005 Noise in gene expression: origins, consequences, and control. Science 309, 2010-2013. (doi:10.1126/science.1105891)
    • (2005) Science , vol.309 , pp. 2010-2013
    • Raser, J.M.1    O'Shea, E.K.2
  • 160
    • 53549123008 scopus 로고    scopus 로고
    • Nature, nurture, or chance: Stochastic gene expression and its consequences
    • Raj A, van Oudenaarden A. 2008 Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135, 216-226. (doi:10.1016/j. cell.2008.09.050)
    • (2008) Cell , vol.135 , pp. 216-226
    • Raj, A.1    Van Oudenaarden, A.2
  • 162
    • 79953903095 scopus 로고    scopus 로고
    • Measuring retroactivity from noise in gene regulatory networks
    • Kim KH, Sauro HM. 2011 Measuring retroactivity from noise in gene regulatory networks. Biophys. J. 100, 1167-1177. (doi:10.1016/j.bpj. 2010.12.3737)
    • (2011) Biophys. J. , vol.100 , pp. 1167-1177
    • Kim, K.H.1    Sauro, H.M.2
  • 163
    • 34547177356 scopus 로고    scopus 로고
    • Stochastic fluctuations in metabolic pathways
    • Levine E, Hwa T. 2007 Stochastic fluctuations in metabolic pathways. Proc. Natl Acad. Sci. USA 104, 9224-9229. (doi:10.1073/pnas.0610987104)
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 9224-9229
    • Levine, E.1    Hwa, T.2
  • 164
    • 1542345686 scopus 로고    scopus 로고
    • Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks
    • Puchalka J, Kierzek AM. 2004 Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks. Biophys. J. 86, 1357-1372. (doi:10.1016/S0006-3495(04)74207-1)
    • (2004) Biophys. J. , vol.86 , pp. 1357-1372
    • Puchalka, J.1    Kierzek, A.M.2
  • 165
    • 84863825902 scopus 로고    scopus 로고
    • Influence of the feedback loops in the trp operon of B. Subtilis on the system dynamic response and noise amplitude
    • Zamora-Chimal C, Santillan M, Rodriguez-Gonzalez J. 2012 Influence of the feedback loops in the trp operon of B. subtilis on the system dynamic response and noise amplitude. J. Theor. Biol. 310, 119-131. (doi:10.1016/j.jtbi.2012.06.014)
    • (2012) J. Theor. Biol. , vol.310 , pp. 119-131
    • Zamora-Chimal, C.1    Santillan, M.2    Rodriguez-Gonzalez, J.3
  • 166
    • 60849112862 scopus 로고    scopus 로고
    • Stochastic control of metabolic pathways
    • Rocco A. 2009 Stochastic control of metabolic pathways. Phys. Biol. 6, 016002. (doi:10.1088/1478-3975/6/1/016002)
    • (2009) Phys. Biol. , vol.6 , pp. 016002
    • Rocco, A.1
  • 167
    • 77954143376 scopus 로고    scopus 로고
    • Sensitivity summation theorems for stochastic biochemical reaction systems
    • Kim KH, Sauro HM. 2010 Sensitivity summation theorems for stochastic biochemical reaction systems. Math. Biosci. 226, 109-119. (doi:10.1016/j.mbs.2010.04.004)
    • (2010) Math. Biosci. , vol.226 , pp. 109-119
    • Kim, K.H.1    Sauro, H.M.2
  • 168
    • 84924249049 scopus 로고    scopus 로고
    • Noise propagation in synthetic gene circuits for metabolic control
    • Oyarzun DA, Lugagne JB, Stan GB. 2014 Noise propagation in synthetic gene circuits for metabolic control. ACS Synth. Biol. 4, 116-125. (doi:10.1021/sb400126a)
    • (2014) ACS Synth. Biol. , vol.4 , pp. 116-125
    • Oyarzun, D.A.1    Lugagne, J.B.2    Stan, G.B.3
  • 169
    • 80053135296 scopus 로고    scopus 로고
    • Robust flux balance analysis of metabolic networks
    • San Francisco, CA, USA, 29 June-1 July 2011
    • Zavlanos MM, Julius AA. 2011 Robust flux balance analysis of metabolic networks. In 2011 American Control Conf., San Francisco, CA, USA, 29 June-1 July 2011, pp. 2915-2920.
    • (2011) 2011 American Control Conf. , pp. 2915-2920
    • Zavlanos, M.M.1    Julius, A.A.2
  • 170
    • 80053082267 scopus 로고    scopus 로고
    • Validation and invalidation of systems biology models using robustness analysis
    • Bates DG, Cosentino C. 2011 Validation and invalidation of systems biology models using robustness analysis. IET Syst. Biol. 5, 229-244. (doi:10.1049/iet-syb.2010.0072)
    • (2011) IET Syst. Biol. , vol.5 , pp. 229-244
    • Bates, D.G.1    Cosentino, C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.