메뉴 건너뛰기




Volumn 25, Issue , 2014, Pages 63-71

Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways

Author keywords

Ensemble modeling; Metabolic engineering; Robustness; Synthetic biology

Indexed keywords

METABOLISM; ROBUSTNESS (CONTROL SYSTEMS);

EID: 84904296838     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2014.06.006     Document Type: Article
Times cited : (85)

References (39)
  • 2
    • 0033552946 scopus 로고    scopus 로고
    • Robustness in bacterial chemotaxis
    • Alon U., et al. Robustness in bacterial chemotaxis. Nature 1999, 397:168-171.
    • (1999) Nature , vol.397 , pp. 168-171
    • Alon, U.1
  • 3
    • 0033828273 scopus 로고    scopus 로고
    • Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways
    • Alves R., Savageau M.A. Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways. Bioinformatics 2000, 16:534-547.
    • (2000) Bioinformatics , vol.16 , pp. 534-547
    • Alves, R.1    Savageau, M.A.2
  • 4
    • 38049001166 scopus 로고    scopus 로고
    • Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
    • Atsumi S., et al. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 2008, 451:86-89.
    • (2008) Nature , vol.451 , pp. 86-89
    • Atsumi, S.1
  • 5
    • 0030797355 scopus 로고    scopus 로고
    • Robustness in simple biochemical networks
    • Barkai N., Leibler S. Robustness in simple biochemical networks. Nature 1997, 387:913-917.
    • (1997) Nature , vol.387 , pp. 913-917
    • Barkai, N.1    Leibler, S.2
  • 6
    • 84886947479 scopus 로고    scopus 로고
    • Synthetic non-oxidative glycolysis enables complete carbon conservation
    • Bogorad I.W., et al. Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature 2013, 502:693-697.
    • (2013) Nature , vol.502 , pp. 693-697
    • Bogorad, I.W.1
  • 7
    • 79960105112 scopus 로고    scopus 로고
    • Glycolytic oscillations and limits on robust efficiency
    • Chandra F.A., et al. Glycolytic oscillations and limits on robust efficiency. Science 2011, 333:187-192.
    • (2011) Science , vol.333 , pp. 187-192
    • Chandra, F.A.1
  • 8
    • 84886948663 scopus 로고    scopus 로고
    • Microbial production of short-chain alkanes
    • Choi Y.J., Lee S.Y. Microbial production of short-chain alkanes. Nature 2013, 502:571-574.
    • (2013) Nature , vol.502 , pp. 571-574
    • Choi, Y.J.1    Lee, S.Y.2
  • 9
    • 84887422015 scopus 로고    scopus 로고
    • Engineering dynamic pathway regulation using stress-response promoters
    • Dahl R.H., et al. Engineering dynamic pathway regulation using stress-response promoters. Nat. Biotechnol. 2013, 31:1039-1046.
    • (2013) Nat. Biotechnol. , vol.31 , pp. 1039-1046
    • Dahl, R.H.1
  • 10
    • 0033581959 scopus 로고    scopus 로고
    • Sustained oscillations in living cells
    • Danø S., et al. Sustained oscillations in living cells. Nature 1999, 402:320-322.
    • (1999) Nature , vol.402 , pp. 320-322
    • Danø, S.1
  • 11
    • 80051941601 scopus 로고    scopus 로고
    • Engineered reversal of the beta-oxidation cycle for the synthesis of fuels and chemicals
    • Dellomonaco C., et al. Engineered reversal of the beta-oxidation cycle for the synthesis of fuels and chemicals. Nature 2011, 476:355-359.
    • (2011) Nature , vol.476 , pp. 355-359
    • Dellomonaco, C.1
  • 12
    • 0034024497 scopus 로고    scopus 로고
    • Improving lycopene production in Escherichia coli by engineering metabolic control
    • Farmer W.R., Liao J.C. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol. 2000, 18:533-537.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 533-537
    • Farmer, W.R.1    Liao, J.C.2
  • 13
    • 84861429699 scopus 로고    scopus 로고
    • EQuilibrator-the biochemical thermodynamics calculator
    • Flamholz A., et al. eQuilibrator-the biochemical thermodynamics calculator. Nucleic Acids Res. 2012, 40:D770-D775.
    • (2012) Nucleic Acids Res. , vol.40
    • Flamholz, A.1
  • 14
    • 18344381476 scopus 로고    scopus 로고
    • A synthetic gene-metabolic oscillator
    • Fung E., et al. A synthetic gene-metabolic oscillator. Nature 2005, 435:118-122.
    • (2005) Nature , vol.435 , pp. 118-122
    • Fung, E.1
  • 15
    • 84878854426 scopus 로고    scopus 로고
    • Next generation biofuel engineering in prokaryotes
    • Gronenberg L.S., et al. Next generation biofuel engineering in prokaryotes. Curr. Opin. Chem. Biol. 2013, 17:462-471.
    • (2013) Curr. Opin. Chem. Biol. , vol.17 , pp. 462-471
    • Gronenberg, L.S.1
  • 16
    • 0000090169 scopus 로고
    • Pentose fermentation by Lactobacillus plantarum. I. The cleavage of xylulose 5-phosphate by phosphoketolase
    • Heath E.C., et al. Pentose fermentation by Lactobacillus plantarum. I. The cleavage of xylulose 5-phosphate by phosphoketolase. J. Biol. Chem. 1958, 231:1009-1029.
    • (1958) J. Biol. Chem. , vol.231 , pp. 1009-1029
    • Heath, E.C.1
  • 17
    • 79953889249 scopus 로고    scopus 로고
    • Conversion of proteins into biofuels by engineering nitrogen flux
    • Huo Y.X., et al. Conversion of proteins into biofuels by engineering nitrogen flux. Nat. Biotechnol. 2011, 29:346-351.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 346-351
    • Huo, Y.X.1
  • 18
    • 0023431472 scopus 로고
    • Genetic engineering of ethanol production in Escherichia coli
    • Ingram L.O., et al. Genetic engineering of ethanol production in Escherichia coli. Appl. Environ. Microbiol. 1987, 53:2420-2425.
    • (1987) Appl. Environ. Microbiol. , vol.53 , pp. 2420-2425
    • Ingram, L.O.1
  • 19
    • 34548825690 scopus 로고    scopus 로고
    • Towards a theory of biological robustness
    • Kitano H. Towards a theory of biological robustness. Mol. Syst. Biol. 2007, 3:137.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 137
    • Kitano, H.1
  • 20
    • 34948840834 scopus 로고    scopus 로고
    • Ensemble modeling for analysis of cell signaling dynamics
    • Kuepfer L., et al. Ensemble modeling for analysis of cell signaling dynamics. Nat. Biotechnol. 2007, 25:1001-1006.
    • (2007) Nat. Biotechnol. , vol.25 , pp. 1001-1006
    • Kuepfer, L.1
  • 21
    • 0642281331 scopus 로고    scopus 로고
    • Quantifying robustness of biochemical network models
    • Ma L., Iglesias P.A. Quantifying robustness of biochemical network models. BMC Bioinform. 2002, 3:38.
    • (2002) BMC Bioinform. , vol.3 , pp. 38
    • Ma, L.1    Iglesias, P.A.2
  • 22
    • 84883554005 scopus 로고    scopus 로고
    • A reverse glyoxylate shunt to build a non-native route from C4 to C2 in Escherichia coli
    • Mainguet S.E., et al. A reverse glyoxylate shunt to build a non-native route from C4 to C2 in Escherichia coli. Metab. Eng. 2013, 19:116-127.
    • (2013) Metab. Eng. , vol.19 , pp. 116-127
    • Mainguet, S.E.1
  • 23
    • 70149091494 scopus 로고    scopus 로고
    • Ensemble modeling for aromatic production in Escherichia coli
    • Rizk M.L., Liao J.C. Ensemble modeling for aromatic production in Escherichia coli. PLoS One 2009, 4:e6903.
    • (2009) PLoS One , vol.4
    • Rizk, M.L.1    Liao, J.C.2
  • 24
    • 0000210193 scopus 로고
    • Phosphorolytic cleavage of fructose-6-phosphate by fructose-6-phosphate phosphoketolase from Acetobacter xylinum
    • Schramm M., et al. Phosphorolytic cleavage of fructose-6-phosphate by fructose-6-phosphate phosphoketolase from Acetobacter xylinum. J. Biol. Chem. 1958, 233:1283-1288.
    • (1958) J. Biol. Chem. , vol.233 , pp. 1283-1288
    • Schramm, M.1
  • 25
    • 36949069407 scopus 로고
    • Formation of erythrose-4-phosphate and acetyl phosphate by a phosphorolytic cleavage of fructose-6-phosphate
    • Schramm M., Racker E. Formation of erythrose-4-phosphate and acetyl phosphate by a phosphorolytic cleavage of fructose-6-phosphate. Nature 1957, 179:1349-1350.
    • (1957) Nature , vol.179 , pp. 1349-1350
    • Schramm, M.1    Racker, E.2
  • 26
    • 15244353650 scopus 로고    scopus 로고
    • Improved methods for the mathematically controlled comparison of biochemical systems
    • Schwacke J.H., Voit E.O. Improved methods for the mathematically controlled comparison of biochemical systems. Theor. Biol. Med. Model. 2004, 1:1.
    • (2004) Theor. Biol. Med. Model. , vol.1 , pp. 1
    • Schwacke, J.H.1    Voit, E.O.2
  • 27
    • 75749125061 scopus 로고    scopus 로고
    • Microbial production of fatty-acid-derived fuels and chemicals from plant biomass
    • Steen E.J., et al. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 2010, 463:559-562.
    • (2010) Nature , vol.463 , pp. 559-562
    • Steen, E.J.1
  • 28
    • 4444322221 scopus 로고    scopus 로고
    • Robustness properties of circadian clock architectures
    • Stelling J., et al. Robustness properties of circadian clock architectures. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:13210-13215.
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 13210-13215
    • Stelling, J.1
  • 29
    • 0037079050 scopus 로고    scopus 로고
    • Metabolic network structure determines key aspects of functionality and regulation
    • Stelling J., et al. Metabolic network structure determines key aspects of functionality and regulation. Nature 2002, 420:190-193.
    • (2002) Nature , vol.420 , pp. 190-193
    • Stelling, J.1
  • 30
    • 4544346660 scopus 로고    scopus 로고
    • Robustness of cellular functions
    • Stelling J., et al. Robustness of cellular functions. Cell 2004, 118:675-685.
    • (2004) Cell , vol.118 , pp. 675-685
    • Stelling, J.1
  • 31
    • 33747061013 scopus 로고    scopus 로고
    • Structural kinetic modeling of metabolic networks
    • Steuer R., et al. Structural kinetic modeling of metabolic networks. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:11868-11873.
    • (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , pp. 11868-11873
    • Steuer, R.1
  • 32
    • 78650571311 scopus 로고    scopus 로고
    • Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux
    • Tan Y., et al. Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux. Metab. Eng. 2011, 13:60-75.
    • (2011) Metab. Eng. , vol.13 , pp. 60-75
    • Tan, Y.1
  • 33
    • 84857702241 scopus 로고    scopus 로고
    • Metabolic ensemble modeling for strain engineers
    • Tan Y., Liao J.C. Metabolic ensemble modeling for strain engineers. Biotechnol. J. 2012, 7:343-353.
    • (2012) Biotechnol. J. , vol.7 , pp. 343-353
    • Tan, Y.1    Liao, J.C.2
  • 34
    • 58749106454 scopus 로고    scopus 로고
    • Ensemble modeling of metabolic networks
    • Tran L.M., et al. Ensemble modeling of metabolic networks. Biophys. J. 2008, 95:5606-5617.
    • (2008) Biophys. J. , vol.95 , pp. 5606-5617
    • Tran, L.M.1
  • 35
    • 10044224601 scopus 로고    scopus 로고
    • Metabolic control analysis under uncertainty: framework development and case studies
    • Wang L., et al. Metabolic control analysis under uncertainty: framework development and case studies. Biophys. J. 2004, 87:3750-3763.
    • (2004) Biophys. J. , vol.87 , pp. 3750-3763
    • Wang, L.1
  • 36
    • 84859633048 scopus 로고    scopus 로고
    • Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids
    • Zhang F., et al. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat. Biotechnol. 2012, 30:354-359.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 354-359
    • Zhang, F.1
  • 37
    • 77950899704 scopus 로고    scopus 로고
    • Expanding metabolism for total biosynthesis of the nonnatural amino acid l-homoalanine
    • Zhang K., et al. Expanding metabolism for total biosynthesis of the nonnatural amino acid l-homoalanine. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:6234-6239.
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 6234-6239
    • Zhang, K.1
  • 38
    • 58549111802 scopus 로고    scopus 로고
    • Expanding metabolism for biosynthesis of nonnatural alcohols
    • Zhang K., et al. Expanding metabolism for biosynthesis of nonnatural alcohols. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:20653-20658.
    • (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 20653-20658
    • Zhang, K.1
  • 39
    • 0028953195 scopus 로고
    • Metabolic engineering of a pentose metabolism pathway in ethanologenic Zymomonas mobilis
    • Zhang M., et al. Metabolic engineering of a pentose metabolism pathway in ethanologenic Zymomonas mobilis. Science 1995, 267:240-243.
    • (1995) Science , vol.267 , pp. 240-243
    • Zhang, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.