메뉴 건너뛰기




Volumn 3, Issue 4, 2012, Pages e201210009-

Metabolic modelling in the development of cell factories by synthetic biology

Author keywords

Chassis; Constraint based; Flux; Kinetics; Simulation

Indexed keywords


EID: 84902133886     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.5936/csbj.201210009     Document Type: Short Survey
Times cited : (15)

References (97)
  • 1
    • 0347506028 scopus 로고    scopus 로고
    • It is all about metabolic fluxes
    • DOI 10.1128/JB.185.24.7031-7035.2003
    • Nielsen J (2003) It is all about metabolic fluxes. J Bacteriol 185: 7031-7035. (Pubitemid 37521234)
    • (2003) Journal of Bacteriology , vol.185 , Issue.24 , pp. 7031-7035
    • Nielsen, J.1
  • 2
    • 79961179947 scopus 로고    scopus 로고
    • Synergies between synthetic biology and metabolic engineering
    • Nielsen J, Keasling JD (2011) Synergies between synthetic biology and metabolic engineering. Nat Biotechnol 29: 693-695.
    • (2011) Nat Biotechnol , vol.29 , pp. 693-695
    • Nielsen, J.1    Keasling, J.D.2
  • 3
    • 0028108519 scopus 로고
    • Metabolic flux balancing: Basic concepts, scientific and practical use
    • Varma A, Palsson B (1994) Metabolic flux balancing: basic concepts, scientific and practical use. Nat Biotechnol 12: 994-998.
    • (1994) Nat Biotechnol , vol.12 , pp. 994-998
    • Varma, A.1    Palsson, B.2
  • 4
    • 0037385718 scopus 로고    scopus 로고
    • Genome-scale microbial in silico models: The constraints-based approach
    • DOI 10.1016/S0167-7799(03)00030-1, PII S0167779903000301
    • Price N, Papin J, Schilling C, Palsson B (2003) Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol 21: 162-169. (Pubitemid 36397984)
    • (2003) Trends in Biotechnology , vol.21 , Issue.4 , pp. 162-169
    • Price, N.D.1    Papin, J.A.2    Schilling, C.H.3    Palsson, B.O.4
  • 5
    • 70449592325 scopus 로고    scopus 로고
    • Enhancing sesquiterpene production in saccharomyces cerevisiae through in silico driven metabolic engineering
    • Asadollahi MA, Maury J, Patil KR, Schalk M, Clark A, Nielsen J (2009) Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab Eng 11: 328-334.
    • (2009) Metab Eng , vol.11 , pp. 328-334
    • Asadollahi, M.A.1    Maury, J.2    Patil, K.R.3    Schalk, M.4    Clark, A.5    Nielsen, J.6
  • 7
    • 79952106791 scopus 로고    scopus 로고
    • From zero to hero - Design-based systems metabolic engineering of corynebacterium glutamicum for l-lysine production
    • Becker J, Zelder O, Hafner S, Schroder H, Wittmann C (2011) From zero to hero - design-based systems metabolic engineering of Corynebacterium glutamicum for L-lysine production. Metab Eng 13: 159-68.
    • (2011) Metab Eng , vol.13 , pp. 159-168
    • Becker, J.1    Zelder, O.2    Hafner, S.3    Schroder, H.4    Wittmann, C.5
  • 8
    • 70349770739 scopus 로고    scopus 로고
    • Constraints-based genome-scale metabolic simulation for systems metabolic engineering
    • Park JM, Kim TY, Lee SY (2009) Constraints-based genome-scale metabolic simulation for systems metabolic engineering. Biotechnol Adv 27: 979-988.
    • (2009) Biotechnol Adv , vol.27 , pp. 979-988
    • Park, J.M.1    Kim, T.Y.2    Lee, S.Y.3
  • 9
    • 84863532131 scopus 로고    scopus 로고
    • Truncated branch and bound achieves efficient constraint-based genetic design
    • Egen D, Lun DS (2012) Truncated branch and bound achieves efficient constraint-based genetic design Bioinformatics 28: 1619-1623.
    • (2012) Bioinformatics , vol.28 , pp. 1619-1623
    • Egen, D.1    Lun, D.S.2
  • 10
    • 69249146187 scopus 로고    scopus 로고
    • Large-scale identification of genetic design strategies using local search
    • Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA et al. (2009) Large-scale identification of genetic design strategies using local search. Mol Syst Biol 5:296.
    • (2009) Mol Syst Biol , vol.5 , pp. 296
    • Lun, D.S.1    Rockwell, G.2    Guido, N.J.3    Baym, M.4    Kelner, J.A.5
  • 11
    • 84865075156 scopus 로고    scopus 로고
    • Flux variability scanning based on enforced objective flux for identifying gene amplification targets
    • Park JM, Park HM, Kim WJ, Kim HU, Kim TY (2012) Flux variability scanning based on enforced objective flux for identifying gene amplification targets. BMC Syst Biol 6:106.
    • (2012) BMC Syst Biol , vol.6 , pp. 106
    • Park, J.M.1    Park, H.M.2    Kim, W.J.3    Kim, H.U.4    Kim, T.Y.5
  • 12
    • 77952585143 scopus 로고    scopus 로고
    • Casop: A computational approach for strain optimization aiming at high productivity
    • Hadicke O, Klamt S (2010) CASOP: a computational approach for strain optimization aiming at high productivity. J Biotechnol 147: 88-101.
    • (2010) J Biotechnol , vol.147 , pp. 88-101
    • Hadicke, O.1    Klamt, S.2
  • 13
    • 74549189949 scopus 로고    scopus 로고
    • Flux design: In silico design of cell factories based on correlation of pathway fluxes to desired properties
    • Melzer G, Esfandabadi ME, Franco-Lara E, Wittmann C (2009) Flux Design: In silico design of cell factories based on correlation of pathway fluxes to desired properties. BMC Syst Biol 3:120.
    • (2009) BMC Syst Biol , vol.3 , pp. 120
    • Melzer, G.1    Esfandabadi, M.E.2    Franco-Lara, E.3    Wittmann, C.4
  • 14
    • 79551662521 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: The cobra toolbox v2.0
    • Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD et al. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6:1290-12307.
    • (2011) Nat Protoc , vol.6 , pp. 1290-12307
    • Schellenberger, J.1    Que, R.2    Fleming, R.M.3    Thiele, I.4    Orth, J.D.5
  • 15
    • 77950960250 scopus 로고    scopus 로고
    • Optflux: An open-source software platform for in silico metabolic engineering
    • Rocha I, Maia P, Evangelista P, Vilaca P, Soares S (2010) OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst Biol 4:45.
    • (2010) BMC Syst Biol , vol.4 , pp. 45
    • Rocha, I.1    Maia, P.2    Evangelista, P.3    Vilaca, P.4    Soares, S.5
  • 17
    • 0015989446 scopus 로고
    • Linear steady-state treatment of enzymatic chains - General properties, control and effector strength
    • Heinrich R, Rapoport TA (1974) Linear Steady-State Treatment of Enzymatic Chains - General Properties, Control and Effector Strength. Eur J Biochem 42: 89-95.
    • (1974) Eur J Biochem , vol.42 , pp. 89-95
    • Heinrich, R.1    Rapoport, T.A.2
  • 18
    • 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.
    • (2011) Biotechnol Bioeng , vol.108 , pp. 413-423
    • Miskovic, L.1    Hatzimanikatis, V.2
  • 19
    • 10044224601 scopus 로고    scopus 로고
    • Metabolic control analysis under uncertainty: Framework development and case studies
    • DOI 10.1529/biophysj.104.048090
    • Wang L, Birol I, Hatzimanikatis V (2004) Metabolic control analysis under uncertainty: framework development and case studies. BiophysJ87: 3750-3763. (Pubitemid 39602883)
    • (2004) Biophysical Journal , vol.87 , Issue.6 , pp. 3750-3763
    • Wang, L.1    Birol, I.2    Hatzimanikatis, V.3
  • 20
    • 84857702241 scopus 로고    scopus 로고
    • Metabolic ensemble modeling for strain engineers
    • Tan Y, Liao JC (2012) Metabolic ensemble modeling for strain engineers. Biotechnol J 7: 343-353.
    • (2012) Biotechnol J , vol.7 , pp. 343-353
    • Tan, Y.1    Liao, J.C.2
  • 21
    • 70149091494 scopus 로고    scopus 로고
    • Ensemble modeling for aromatic production in escherichia coli
    • Rizk ML, Liao JC (2009) Ensemble modeling for aromatic production in Escherichia coli. PLoS One 4: e6903.
    • (2009) PLoS One , vol.4
    • Rizk, M.L.1    Liao, J.C.2
  • 22
    • 0141684666 scopus 로고    scopus 로고
    • Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics
    • DOI 10.1016/S1096-7176(03)00025-9
    • Visser D, Heijnen JJ (2003) Dynamic simulation and metabolic re¬design of a branched pathway using linlog kinetics. Metab Eng 5: 164-176. (Pubitemid 37124115)
    • (2003) Metabolic Engineering , vol.5 , Issue.3 , pp. 164-176
    • Visser, D.1    Heijnen, J.J.2
  • 24
    • 33846617808 scopus 로고    scopus 로고
    • Bringing metabolic networks to life: Convenience rate law and thermodynamic constraints
    • Liebermeister W, Klipp E (2006) Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor BiolMedMod3: 41.
    • (2006) Theor BiolMedMod , vol.3 , pp. 41
    • Liebermeister, W.1    Klipp, E.2
  • 25
    • 0014733809 scopus 로고
    • Biochemical systems analysis. Iii. Dynamic solutions using a power-law approximation
    • Savageau M (1970) Biochemical systems analysis. III. Dynamic solutions using a power-law approximation. J Theor Biol 26:215-226.
    • (1970) J Theor Biol , vol.26 , pp. 215-226
    • Savageau, M.1
  • 26
    • 77952953154 scopus 로고    scopus 로고
    • Hybrid dynamic modeling of escherichia coli central metabolic network combining michaelis-menten and approximate kinetic equations
    • Costa RS, Machado D, Rocha I, Ferreira EC (2010) Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations. Biosystems. 100: 150-157.
    • (2010) Biosystems. , vol.100 , pp. 150-157
    • Costa, R.S.1    Machado, D.2    Rocha, I.3    Ferreira, E.C.4
  • 27
    • 58149156532 scopus 로고    scopus 로고
    • Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws - A promising method for speeding up the kinetic modelling of complex metabolic networks
    • Bulik S, Grimbs S, Huthmacher C, Selbig J, Holzhutter HG (2009) Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws - a promising method for speeding up the kinetic modelling of complex metabolic networks. FEBS J 276(2):410-424.
    • (2009) FEBS J , vol.276 , Issue.2 , pp. 410-424
    • Bulik, S.1    Grimbs, S.2    Huthmacher, C.3    Selbig, J.4    Holzhutter, H.G.5
  • 28
    • 79955137362 scopus 로고    scopus 로고
    • An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data
    • Canelas AB, Ras C, Ten Pierick A, van Gulik WM, Heijnen JJ (2011) An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data. Metab Eng 13: 294-306.
    • (2011) Metab Eng , vol.13 , pp. 294-306
    • Canelas, A.B.1    Ras, C.2    Ten Pierick, A.3    Van Gulik, W.M.4    Heijnen, J.J.5
  • 29
    • 79953162662 scopus 로고    scopus 로고
    • Escherichia coli w as a new platform strain for the enhanced production of l-valine by systems metabolic engineering
    • Park JH, Jang YS, Lee JW, Lee SY (2011) Escherichia coli W as a new platform strain for the enhanced production of L-valine by systems metabolic engineering. Biotechnol Bioeng 108: 1140-1147.
    • (2011) Biotechnol Bioeng , vol.108 , pp. 1140-1147
    • Park, J.H.1    Jang, Y.S.2    Lee, J.W.3    Lee, S.Y.4
  • 30
    • 29144524991 scopus 로고    scopus 로고
    • Engineering of solvent-tolerant pseudomonas putida S12 for bioproduction of phenol from glucose
    • DOI 10.1128/AEM.71.12.8221-8227.2005
    • Wierckx NJ, Ballerstedt H, de Bont JA, Wery J (2005) Engineering of solvent-tolerant Pseudomonas putida S12 for bioproduction of phenol from glucose. Appl Environ Microbiol 71: 8221-8227. (Pubitemid 41803948)
    • (2005) Applied and Environmental Microbiology , vol.71 , Issue.12 , pp. 8221-8227
    • Wierckx, N.J.P.1    Ballerstedt, H.2    De Bont, J.A.M.3    Wery, J.4
  • 31
    • 68049135724 scopus 로고    scopus 로고
    • Engineering alternative butanol production platforms in heterologous bacteria
    • Nielsen DR, Leonard E, Yoon SH, Tseng HC, Yuan C (2009) Engineering alternative butanol production platforms in heterologous bacteria. Metab Eng 11: 262-273.
    • (2009) Metab Eng , vol.11 , pp. 262-273
    • Nielsen, D.R.1    Leonard, E.2    Yoon, S.H.3    Tseng, H.C.4    Yuan, C.5
  • 32
    • 78751638661 scopus 로고    scopus 로고
    • Engineering cyanobacteria to generate high-value products
    • Ducat DC, Way JC, Silver PA (2011) Engineering cyanobacteria to generate high-value products. Trends Biotechnol 29: 95-103.
    • (2011) Trends Biotechnol , vol.29 , pp. 95-103
    • Ducat, D.C.1    Way, J.C.2    Silver, P.A.3
  • 33
    • 84863630261 scopus 로고    scopus 로고
    • Pathway engineering and synthetic biology using acetogens
    • Schiel-Bengelsdorf B, Diirre P (2012) Pathway engineering and synthetic biology using acetogens. FEBS Lett 586: 2191-2198.
    • (2012) FEBS Lett , vol.586 , pp. 2191-2198
    • Schiel-Bengelsdorf, B.1    Diirre, P.2
  • 34
    • 79955675417 scopus 로고    scopus 로고
    • Electrosynthesis of organic compounds from carbon dioxide is catalyzed by a diversity of acetogenic microorganisms
    • Nevin KP, Hensley SA, Franks AE, Summers ZM, Ou J (2011) Electrosynthesis of organic compounds from carbon dioxide is catalyzed by a diversity of acetogenic microorganisms. Appl Environ Microbiol 77: 2882-2886.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 2882-2886
    • Nevin, K.P.1    Hensley, S.A.2    Franks, A.E.3    Summers, Z.M.4    Ou, J.5
  • 35
    • 84859358212 scopus 로고    scopus 로고
    • Modelling cyanobacteria: From metabolism to integrative models of phototrophic growth
    • Steuer R, Knoop H, Machne R (2012) Modelling cyanobacteria: from metabolism to integrative models of phototrophic growth. J Exp Bot 63: 2259-2274.
    • (2012) J Exp Bot , vol.63 , pp. 2259-2274
    • Steuer, R.1    Knoop, H.2    Machne, R.3
  • 36
    • 67650573077 scopus 로고    scopus 로고
    • Ibsull03: A new genome-scale metabolic model of bacillus subtilis based on seed annotations
    • Henry CS, Zinner JF, Cohoon MP, Stevens RL (2009) iBsull03: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biol 10: R69.
    • (2009) Genome Biol , vol.10
    • Henry, C.S.1    Zinner, J.F.2    Cohoon, M.P.3    Stevens, R.L.4
  • 38
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • Thiele I, Palsson BO (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5: 93-121.
    • (2010) Nat Protoc , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.O.2
  • 39
    • 84859199206 scopus 로고    scopus 로고
    • Genome-scale metabolic reconstructions of pichia stipitis and pichia pastoris and in silico evaluation of their potentials
    • Caspeta L, Shoaie S, Agren R, Nookaew I, Nielsen J (2012) Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. BMC Syst Biol 6: 24.
    • (2012) BMC Syst Biol , vol.6 , pp. 24
    • Caspeta, L.1    Shoaie, S.2    Agren, R.3    Nookaew, I.4    Nielsen, J.5
  • 43
    • 0000029295 scopus 로고
    • On elementary flux modes in biochemical reaction systems at steady state
    • Schuster S, Hilgetag C (1994) On elementary flux modes in biochemical reaction systems at steady state. J Biol Syst 2: 165-182.
    • (1994) J Biol Syst , vol.2 , pp. 165-182
    • Schuster, S.1    Hilgetag, C.2
  • 44
    • 79951528622 scopus 로고    scopus 로고
    • Exploring metabolic pathways in genome-scale networks via generating flux modes
    • Rezola A, de Figueiredo LF, Brock M, Pey J, Podhorski A (2011) Exploring metabolic pathways in genome-scale networks via generating flux modes. Bioinformatics 27: 534-540.
    • (2011) Bioinformatics , vol.27 , pp. 534-540
    • Rezola, A.1    De Figueiredo, L.F.2    Brock, M.3    Pey, J.4    Podhorski, A.5
  • 45
    • 79961176618 scopus 로고    scopus 로고
    • Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks
    • Chan SH, Ji P (2011) Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks. Bioinformatics 27:2256-2262.
    • (2011) Bioinformatics , vol.27 , pp. 2256-2262
    • Chan, S.H.1    Ji, P.2
  • 46
    • 52949098408 scopus 로고    scopus 로고
    • Large-scale computation of elementary flux modes with bit pattern trees
    • Terzer M. Stelling J (2008) Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics 24: 2229-2235.
    • (2008) Bioinformatics , vol.24 , pp. 2229-2235
    • Terzer, M.1    Stelling, J.2
  • 47
    • 84856579358 scopus 로고    scopus 로고
    • Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms
    • Carbonell P, Fichera D, Pandit SB, Faulon JL (2012) Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Syst Biol 6: 10.
    • (2012) BMC Syst Biol , vol.6 , pp. 10
    • Carbonell, P.1    Fichera, D.2    Pandit, S.B.3    Faulon, J.L.4
  • 48
    • 8744224466 scopus 로고    scopus 로고
    • OptStrain: A computational framework for redesign of microbial production systems
    • DOI 10.1101/gr.2872004
    • Pharkya P, Burgard AP, Maranas CD (2004) OptStrain: a computational framework for redesign of microbial production systems. Genome Res 14: 2367-2376. (Pubitemid 39517344)
    • (2004) Genome Research , vol.14 , Issue.11 , pp. 2367-2376
    • Pharkya, P.1    Burgard, A.P.2    Maranas, C.D.3
  • 49
    • 70749083404 scopus 로고    scopus 로고
    • Inferring branching pathways in genome-scale metabolic networks
    • Pitkanen E, Jouhten P, Rousu J (2009) Inferring branching pathways in genome-scale metabolic networks. BMC Syst Biol 3:103.
    • (2009) BMC Syst Biol , vol.3 , pp. 103
    • Pitkanen, E.1    Jouhten, P.2    Rousu, J.3
  • 50
    • 77954188312 scopus 로고    scopus 로고
    • Finding metabolic pathways using atom tracking
    • Heath AP, Bennett GN, Kavraki LE (2010) Finding metabolic pathways using atom tracking. Bioinformatics 26: 1548-1555.
    • (2010) Bioinformatics , vol.26 , pp. 1548-1555
    • Heath, A.P.1    Bennett, G.N.2    Kavraki, L.E.3
  • 52
    • 78651301358 scopus 로고    scopus 로고
    • Computing atom mappings for biochemical reactions without subgraph isomorphism
    • Heinonen M, Lappalainen S, Mielikainen T, Rousu J (2011) Computing atom mappings for biochemical reactions without subgraph isomorphism. J Comput Biol 18: 43-58.
    • (2011) J Comput Biol , vol.18 , pp. 43-58
    • Heinonen, M.1    Lappalainen, S.2    Mielikainen, T.3    Rousu, J.4
  • 53
    • 33847797256 scopus 로고    scopus 로고
    • Thermodynamics-based metabolic flux analysis
    • DOI 10.1529/biophysj.106.093138
    • Henry CS, Broadbelt LJ, Hatzimanikatis V (2007) Thermodynamics-based metabolic flux analysis. Biophys J 92: 1792 - 1805. (Pubitemid 46393490)
    • (2007) Biophysical Journal , vol.92 , Issue.5 , pp. 1792-1805
    • Henry, C.S.1    Broadbelt, L.J.2    Hatzimanikatis, V.3
  • 54
    • 77953578214 scopus 로고    scopus 로고
    • Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate
    • Henry C S, Broadbelt L J, Hatzimanikatis V (2010) Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-Hydroxypropanoate Biotechnol Bioeng 106: 462- 473.
    • (2010) Biotechnol Bioeng , vol.106 , pp. 462-473
    • Henry, C.S.1    Broadbelt, L.J.2    Hatzimanikatis, V.3
  • 55
    • 51049107514 scopus 로고    scopus 로고
    • Group contribution method for thermodynamic analysis of complex metabolic networks
    • Jankowski MD, Henry CS, Broadbelt LJ, Hatzimanikatis V (2008) Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J 95: 1487-1499.
    • (2008) Biophys J , vol.95 , pp. 1487-1499
    • Jankowski, M.D.1    Henry, C.S.2    Broadbelt, L.J.3    Hatzimanikatis, V.4
  • 56
    • 84865136870 scopus 로고    scopus 로고
    • An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
    • Noor E, Bar-Even A, Flamholz A, Lubling Y, Davidi D et al. (2012) An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. Bioinformatics 28: 2037-2044.
    • (2012) Bioinformatics , vol.28 , pp. 2037-2044
    • Noor, E.1    Bar-Even, A.2    Flamholz, A.3    Lubling, Y.4    Davidi, D.5
  • 57
    • 84860819691 scopus 로고    scopus 로고
    • An in silico platform for the design of heterologous pathways in nonnative metabolite production
    • Chatsurachai S, Furusawa C, Shimizu H (2012) An in silico platform for the design of heterologous pathways in nonnative metabolite production. BMC Bioinformatics 13: 93.
    • (2012) BMC Bioinformatics , vol.13 , pp. 93
    • Chatsurachai, S.1    Furusawa, C.2    Shimizu, H.3
  • 59
    • 84869875863 scopus 로고    scopus 로고
    • Designing biological compartmentalization
    • In press
    • Chen AH, Silver PA (2012) Designing biological compartmentalization. Trends Cell Biol. In press.
    • (2012) Trends Cell Biol.
    • Chen, A.H.1    Silver, P.A.2
  • 60
    • 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.
    • (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
  • 61
    • 77955852574 scopus 로고    scopus 로고
    • A model for improving microbial biofuel production using a synthetic feedback loop
    • Dunlop MJ, Keasling JD, Mukhopadhyay A (2010) A model for improving microbial biofuel production using a synthetic feedback loop. Syst Synth Biol 4: 95-104.
    • (2010) Syst Synth Biol , vol.4 , pp. 95-104
    • Dunlop, M.J.1    Keasling, J.D.2    Mukhopadhyay, A.3
  • 62
    • 84858609338 scopus 로고    scopus 로고
    • Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology
    • Blount BA, Weenink T, Vasylechko S, Ellis T (2012) Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology. PLoS One 7: e33279.
    • (2012) PLoS One , vol.7
    • Blount, B.A.1    Weenink, T.2    Vasylechko, S.3    Ellis, T.4
  • 63
    • 84864634066 scopus 로고    scopus 로고
    • A synthetic biology framework for programming eukaryotic transcription functions
    • Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC et al. (2012) A synthetic biology framework for programming eukaryotic transcription functions. Cell 150: 647-658.
    • (2012) Cell , vol.150 , pp. 647-658
    • Khalil, A.S.1    Lu, T.K.2    Bashor, C.J.3    Ramirez, C.L.4    Pyenson, N.C.5
  • 64
    • 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. (Pubitemid 34977706)
    • (2002) Biophysical Journal , vol.83 , Issue.3 , pp. 1331-1340
    • Mahadevan, R.1    Edwards, J.S.2    Doyle III, F.J.3
  • 65
    • 33749996165 scopus 로고    scopus 로고
    • Optimization of fed-batch Saccharomyces cerevisiae fermentation using dynamic flux balance models
    • DOI 10.1021/bp060059v
    • Hjersted JL, Henson MA (2006) Optimization of fed-batch Saccharomyces cerevisiae fermentation using dynamic flux balance models. Biotechnol Prog 22: 1239-1248. (Pubitemid 44568797)
    • (2006) Biotechnology Progress , vol.22 , Issue.5 , pp. 1239-1248
    • Hjersted, J.L.1    Henson, M.A.2
  • 66
    • 79955987608 scopus 로고    scopus 로고
    • Expanding a dynamic flux balance model of yeast fermentation to genome-scale
    • Vargas FA, Pizarro F, Perez-Correa JR, Agosin E (2011) Expanding a dynamic flux balance model of yeast fermentation to genome-scale. BMC Syst Biol 5:75.
    • (2011) BMC Syst Biol , vol.5 , pp. 75
    • Vargas, F.A.1    Pizarro, F.2    Perez-Correa, J.R.3    Agosin, E.4
  • 67
    • 80455156250 scopus 로고    scopus 로고
    • Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in saccharomyces cerevisiae
    • Ghosh A, Zhao H, Price ND (2011) Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae. PLoS One 6: e27316.
    • (2011) PLoS One , vol.6
    • Ghosh, A.1    Zhao, H.2    Price, N.D.3
  • 68
    • 84865978199 scopus 로고    scopus 로고
    • Dynamic flux balance analysis of the metabolism of saccharomyces cerevisiae during the shift from fully respirative or respirofermentative metabolic states to anaerobiosis
    • doi: 10.1111/j.l742-4658.2012.08649.x
    • Jouhten P, Wiebe M, Penttila M (2012) Dynamic flux balance analysis of the metabolism of Saccharomyces cerevisiae during the shift from fully respirative or respirofermentative metabolic states to anaerobiosis. FEBS J doi: 10.1111/j.l742-4658.2012.08649.x.
    • (2012) FEBS J
    • Jouhten, P.1    Wiebe, M.2    Penttila, M.3
  • 69
    • 34447308322 scopus 로고    scopus 로고
    • Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture
    • DOI 10.1002/bit.21332
    • Hjersted JL, Henson MA, Mahadevan R (2007) Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture. Biotechnol Bioeng 97:1190-1204. (Pubitemid 47195316)
    • (2007) Biotechnology and Bioengineering , vol.97 , Issue.5 , pp. 1190-1204
    • Hjersted, J.L.1    Henson, M.A.2    Mahadevan, R.3
  • 70
    • 84864318798 scopus 로고    scopus 로고
    • Continuous modeling of metabolic networks with gene regulation in yeast and in vivo determination of rate parameters
    • Moisset P, Vaisman D, Cintolesi A, Urrutia J, Rapaport I (2012) Continuous modeling of metabolic networks with gene regulation in yeast and in vivo determination of rate parameters. Biotechnol Bioeng 109: 2325-2339.
    • (2012) Biotechnol Bioeng , vol.109 , pp. 2325-2339
    • Moisset, P.1    Vaisman, D.2    Cintolesi, A.3    Urrutia, J.4    Rapaport, I.5
  • 71
    • 77949385752 scopus 로고    scopus 로고
    • Bacterial adaptation through distributed sensing of metabolic fluxes
    • Kotte O, Zaugg JB, Heinemann M (2010) Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Syst Biol 6: 355.
    • (2010) Mol Syst Biol , vol.6 , pp. 355
    • Kotte, O.1    Zaugg, J.B.2    Heinemann, M.3
  • 72
    • 77954724818 scopus 로고    scopus 로고
    • Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing
    • Salimi F, Zhuang K, Mahadevan R (2010) Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing. Biotechnol J 5: 726-738.
    • (2010) Biotechnol J , vol.5 , pp. 726-738
    • Salimi, F.1    Zhuang, K.2    Mahadevan, R.3
  • 73
    • 84055200869 scopus 로고    scopus 로고
    • Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered escherichia coli
    • Bokinsky G, Peralta-Yahya PP, George A, Holmes BM, Steen EJ et al. (2011) Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. Proc Nad Acad Sci U SA 108: 19949-19954.
    • (2011) Proc Nad Acad Sci U SA , vol.108 , pp. 19949-19954
    • Bokinsky, G.1    Peralta-Yahya, P.P.2    George, A.3    Holmes, B.M.4    Steen, E.J.5
  • 74
    • 0242574984 scopus 로고    scopus 로고
    • In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism
    • DOI 10.1101/gr.1212003
    • Arita M (2003) In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Res 13: 2455-66. (Pubitemid 37428270)
    • (2003) Genome Research , vol.13 , Issue.11 , pp. 2455-2466
    • Arita, M.1
  • 75
    • 79954459893 scopus 로고    scopus 로고
    • Construction of an e. Coli genome-scale atom mapping model for mfa calculations
    • Ravikirthi P, Suthers PF, Maranas CD (2011) Construction of an E. Coli genome-scale atom mapping model for MFA calculations. Biotechnol Bioeng 108: 1372-1382.
    • (2011) Biotechnol Bioeng , vol.108 , pp. 1372-1382
    • Ravikirthi, P.1    Suthers, P.F.2    Maranas, C.D.3
  • 76
    • 4243829380 scopus 로고    scopus 로고
    • Bidirectional reaction steps in metabolic networks: IV. Optimal design of isotopomer labeling experiments
    • DOI 10.1002/(SICI)1097-0290(1999)66:2<86: :AID-BIT2>3.0.CO;2-A
    • Mollney M, Wiechert W, Kownatzki D, de Graaf AA (1999) Bidirectional reaction steps in metabolic networks: IV.Optimal design of isotopomer labeling experiments. Biotechnol Bioeng 66: 86-103. (Pubitemid 32262269)
    • (1999) Biotechnology and Bioengineering , vol.66 , Issue.2 , pp. 86-103
    • Mollney, M.1    Wiechert, W.2    Kownatzki, D.3    De Graaf, A.A.4
  • 77
    • 84856291750 scopus 로고    scopus 로고
    • Predicting outcomes of steady-state 13c isotope tracing experiments using monte carlo sampling
    • Schellenberger J, Zielinski DC, Choi W, Madireddi S, Portnoy V et al. (2012) Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling. BMC Syst Biol 6:9.
    • (2012) BMC Syst Biol , vol.6 , pp. 9
    • Schellenberger, J.1    Zielinski, D.C.2    Choi, W.3    Madireddi, S.4    Portnoy, V.5
  • 78
    • 33845679072 scopus 로고    scopus 로고
    • Elementary metabolite units (EMU): A novel framework for modeling isotopic distributions
    • DOI 10.1016/j.ymben.2006.09.001, PII S109671760600084X
    • Antoniewicz MR, Kelleher JK, Stephanopoulos G (2007) Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab Eng 9: 68-86. (Pubitemid 44960874)
    • (2007) Metabolic Engineering , vol.9 , Issue.1 , pp. 68-86
    • Antoniewicz, M.R.1    Kelleher, J.K.2    Stephanopoulos, G.3
  • 79
    • 84861008392 scopus 로고    scopus 로고
    • Rational design of 13c-labeling experiments for metabolic flux analysis in mammalian cells
    • Crown SB, Ahn WS, Antoniewicz MR (2012) Rational design of 13C-labeling experiments for metabolic flux analysis in mammalian cells. BMC Syst Biol 6: 43.
    • (2012) BMC Syst Biol , vol.6 , pp. 43
    • Crown, S.B.1    Ahn, W.S.2    Antoniewicz, M.R.3
  • 80
    • 56149101337 scopus 로고    scopus 로고
    • Fid: A software for ab initio structural identification of product ions from tandem mass spectrometric data
    • Heinonen M, Rantanen A, Mielikainen T, Kokkonen J, Kiuru J et al. (2008) FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data. Rapid Commun Mass Spectrom 22: 3043-3052.
    • (2008) Rapid Commun Mass Spectrom , vol.22 , pp. 3043-3052
    • Heinonen, M.1    Rantanen, A.2    Mielikainen, T.3    Kokkonen, J.4    Kiuru, J.5
  • 81
    • 77952302069 scopus 로고    scopus 로고
    • In silico fragmentation for computer assisted identification of metabolite mass spectra
    • WolfS, Schmidt S, Miiller-Hannemann M, Neumann S (2010) In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics 11: 148.
    • (2010) BMC Bioinformatics , vol.11 , pp. 148
    • Wolf, S.1    Schmidt, S.2    Miiller-Hannemann, M.3    Neumann, S.4
  • 82
    • 0029146299 scopus 로고
    • Biosynthetically directed fractional 13c-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism
    • Szyperski T (1995) Biosynthetically directed fractional 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism. Eur J Biochem 232: 433-448.
    • (1995) Eur J Biochem , vol.232 , pp. 433-448
    • Szyperski, T.1
  • 84
    • 1642538406 scopus 로고    scopus 로고
    • 13C constraints
    • DOI 10.1016/j.ab.2003.10.036
    • Fischer E, Zamboni N, Sauer U (2004) High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints. Anal Biochem 325: 308-316. (Pubitemid 38134368)
    • (2004) Analytical Biochemistry , vol.325 , Issue.2 , pp. 308-316
    • Fischer, E.1    Zamboni, N.2    Sauer, U.3
  • 85
    • 49549104162 scopus 로고    scopus 로고
    • Oxygen dependence of metabolic fluxes and energy generation of saccharomyces cerevisiae cen.Pk113-1a
    • Jouhten P, Rintala E, Huuskonen A, Tamminen A, Toivari M et al. (2008) Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A. BMC Syst Biol 2:60.
    • (2008) BMC Syst Biol , vol.2 , pp. 60
    • Jouhten, P.1    Rintala, E.2    Huuskonen, A.3    Tamminen, A.4    Toivari, M.5
  • 86
    • 45749090110 scopus 로고    scopus 로고
    • An analytic and systematic framework for estimating metabolic flux ratios from 13c tracer experiments
    • Rantanen A, Rousu J, Jouhten P, Zamboni N, Maaheimo H et al. (2008) An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments.BMC Bioinformatics 9: 266.
    • (2008) BMC Bioinformatics , vol.9 , pp. 266
    • Rantanen, A.1    Rousu, J.2    Jouhten, P.3    Zamboni, N.4    Maaheimo, H.5
  • 87
    • 25444489844 scopus 로고    scopus 로고
    • Fiatflux - A software for metabolic flux analysis from 13c-glucose experiments
    • Zamboni N, Fischer E, Sauer U (2005) FiatFlux - a software for metabolic flux analysis from 13C-glucose experiments.BMC Bioinformatics 6: 209.
    • (2005) BMC Bioinformatics , vol.6 , pp. 209
    • Zamboni, N.1    Fischer, E.2    Sauer, U.3
  • 88
    • 84855258472 scopus 로고    scopus 로고
    • The ethylmalonyl-coa pathway is used in place of the glyoxylate cycle by methylobacterium extorquens ami during growth on acetate
    • Schneider K, Peyraud R, Kiefer P, Christen P, Delmotte N (2012) The ethylmalonyl-CoA pathway is used in place of the glyoxylate cycle by Methylobacterium extorquens AMI during growth on acetate. J Biol Chem 287: 757-766.
    • (2012) J Biol Chem , vol.287 , pp. 757-766
    • Schneider, K.1    Peyraud, R.2    Kiefer, P.3    Christen, P.4    Delmotte, N.5
  • 90
    • 80052644208 scopus 로고    scopus 로고
    • Metabolite channeling and compartmentation in the human cell line age1. Hn determined by 13c labeling experiments and 13c metabolic flux analysis
    • Niklas J, Sandig V, Heinzle E (2011) Metabolite channeling and compartmentation in the human cell line AGE1 .HN determined by 13C labeling experiments and 13C metabolic flux analysis. J Biosci Bioengll2: 616-623.
    • (2011) J Biosci Bioengll , vol.2 , pp. 616-623
    • Niklas, J.1    Sandig, V.2    Heinzle, E.3
  • 91
    • 66949164842 scopus 로고    scopus 로고
    • Openflux: Efficient modelling software for 13c-based metabolic flux analysis
    • Quek LE, Wittmann C, Nielsen LK, Kromer JO (2009) OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis. Microb Cell Fact 8:25.
    • (2009) Microb Cell Fact , vol.8 , pp. 25
    • Quek, L.E.1    Wittmann, C.2    Nielsen, L.K.3    Kromer, J.O.4
  • 92
    • 25444467580 scopus 로고    scopus 로고
    • Large-scale 13c-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast
    • Blank LM, Kuepfer L, Sauer U (2005) Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol. 6: R49.
    • (2005) Genome Biol , vol.6
    • Blank, L.M.1    Kuepfer, L.2    Sauer, U.3
  • 93
    • 76749140314 scopus 로고    scopus 로고
    • Improved computational performance of mfa using elementary metabolite units and flux coupling
    • Suthers PF, Chang YJ, Maranas CD (2010) Improved computational performance of MFA using elementary metabolite units and flux coupling. Metab Eng 12: 123-128.
    • (2010) Metab Eng , vol.12 , pp. 123-128
    • Suthers, P.F.1    Chang, Y.J.2    Maranas, C.D.3
  • 94
    • 84860855750 scopus 로고    scopus 로고
    • Application of targeted proteomics to metabolically engineered escherichia coli
    • Singh P, Batth TS, Juminaga D, Dahl RH, Keasling JD et al. (2012) Application of targeted proteomics to metabolically engineered Escherichia coli. Proteomics 12: 1289-1299.
    • (2012) Proteomics , vol.12 , pp. 1289-1299
    • Singh, P.1    Batth, T.S.2    Juminaga, D.3    Dahl, R.H.4    Keasling, J.D.5
  • 97
    • 78650571311 scopus 로고    scopus 로고
    • Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux
    • Tan Y, Rivera JG, Contador CA, Asenjo JA, Liao JC (2011) Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux.Metab Eng 13: 60-75.
    • (2011) Metab Eng , vol.13 , pp. 60-75
    • Tan, Y.1    Rivera, J.G.2    Contador, C.A.3    Asenjo, J.A.4    Liao, J.C.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.