메뉴 건너뛰기




Volumn 31, Issue 17, 2015, Pages 2844-2851

Genome-scale strain designs based on regulatory minimal cut sets

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL;

EID: 84940738929     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv217     Document Type: Article
Times cited : (24)

References (47)
  • 1
    • 84856566482 scopus 로고    scopus 로고
    • Minimal cut sets in a metabolic network are elementary modes in a dual network
    • Ballerstein K., et al. (2012). Minimal cut sets in a metabolic network are elementary modes in a dual network. Bioinformatics, 28, 381-387
    • (2012) Bioinformatics , vol.28 , pp. 381-387
    • Ballerstein, K.1
  • 2
    • 78049460641 scopus 로고    scopus 로고
    • Improved vanillin production in baker's yeast through in silico design
    • Brochado A.R., et al. (2010). Improved vanillin production in baker's yeast through in silico design. Microb. Cell Fact., 9, 84
    • (2010) Microb. Cell Fact , vol.9 , pp. 84
    • Brochado, A.R.1
  • 3
    • 0242487787 scopus 로고    scopus 로고
    • Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • Burgard A.P., et al. (2003). OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng., 84, 647-657
    • (2003) Biotechnol. Bioeng , vol.84 , pp. 647-657
    • Burgard, A.P.1
  • 4
    • 84455174703 scopus 로고    scopus 로고
    • Model-driven engineering of RNA devices to quantitatively program gene expression
    • Carothers J.M., et al. (2011). Model-driven engineering of RNA devices to quantitatively program gene expression. Science, 334, 1716-1719
    • (2011) Science , vol.334 , pp. 1716-1719
    • Carothers, J.M.1
  • 5
    • 84895756673 scopus 로고    scopus 로고
    • K-OptForce: Integrating kinetics with flux balance analysis for strain design
    • Chowdhury A., et al. (2014). k-OptForce: integrating kinetics with flux balance analysis for strain design. PLoS Comput. Biol., 10, e1003487
    • (2014) Plos Comput. Biol , vol.10 , pp. e1003487
    • Chowdhury, A.1
  • 6
    • 84877118199 scopus 로고    scopus 로고
    • Constraint-based strain design using continuous modifications (cosmos) of flux bounds finds new strategies for metabolic engineering
    • Cotten C., and Reed J.L. (2013). Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering. Biotechnol. J., 8, 595-604
    • (2013) Biotechnol. J. , vol.8 , pp. 595-604
    • Cotten, C.1    Reed, J.L.2
  • 7
    • 84903766210 scopus 로고    scopus 로고
    • Efficient search, mapping, and optimization of multiprotein genetic systems in diverse bacteria
    • Farasat I., et al. (2014). Efficient search, mapping, and optimization of multiprotein genetic systems in diverse bacteria. Mol. Syst. Biol., 10, 731
    • (2014) Mol. Syst. Biol , vol.10 , pp. 731
    • Farasat, I.1
  • 8
    • 34347332311 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction for Escherichia coli k-12 mg1655 that accounts for 1260 orfs, and thermodynamic information
    • Feist A.M., et al. (2007). A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs, and thermodynamic information. Mol. Syst. Biol., 3, 121
    • (2007) Mol. Syst. Biol , vol.3 , pp. 121
    • Feist, A.M.1
  • 9
    • 84877149255 scopus 로고    scopus 로고
    • SMET: Systematic multiple enzyme targeting-a method to rationally design optimal strains for target chemical overproduction
    • Flowers D., et al. (2013). SMET: systematic multiple enzyme targeting-a method to rationally design optimal strains for target chemical overproduction. Biotechnol. J., 8, 605-618
    • (2013) Biotechnol. J. , vol.8 , pp. 605-618
    • Flowers, D.1
  • 10
    • 25144505718 scopus 로고    scopus 로고
    • In silico design, and adaptive evolution of Escherichia coli for production of lactic acid
    • Fong S.S., et al. (2005). In silico design, and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol. Bioeng., 91, 643-648
    • (2005) Biotechnol. Bioeng , vol.91 , pp. 643-648
    • Fong, S.S.1
  • 11
    • 77952585143 scopus 로고    scopus 로고
    • Casop: A computational approach for strain optimization aiming at high productivity
    • Hädicke O., and 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
    • Hädicke, O.1    Klamt, S.2
  • 12
    • 79952103372 scopus 로고    scopus 로고
    • Computing complex metabolic intervention strategies using constrained minimal cut sets
    • Hädicke O., and Klamt S. (2011). Computing complex metabolic intervention strategies using constrained minimal cut sets. Metab. Eng., 13, 204-213
    • (2011) Metab. Eng , vol.13 , pp. 204-213
    • Hädicke, O.1    Klamt, S.2
  • 13
    • 84859772410 scopus 로고    scopus 로고
    • Synthetic biology, and the development of tools for metabolic engineering
    • Keasling J.D. (2012). Synthetic biology, and the development of tools for metabolic engineering. Metab. Eng., 14, 189-195
    • (2012) Metab. Eng , vol.14 , pp. 189-195
    • Keasling, J.D.1
  • 14
    • 77951552860 scopus 로고    scopus 로고
    • Optorf: Optimal metabolic, and regulatory perturbations for metabolic engineering of microbial strains
    • Kim J., and Reed J.L. (2010). OptORF: optimal metabolic, and regulatory perturbations for metabolic engineering of microbial strains. BMC Syst. Biol., 4, 53
    • (2010) BMC Syst. Biol , vol.4 , pp. 53
    • Kim, J.1    Reed, J.L.2
  • 15
    • 32144453095 scopus 로고    scopus 로고
    • Generalized concept of minimal cut sets in biochemical networks
    • Klamt S. (2006). Generalized concept of minimal cut sets in biochemical networks. BioSystems, 83, 233-247
    • (2006) BioSystems , vol.83 , pp. 233-247
    • Klamt, S.1
  • 16
    • 1042269472 scopus 로고    scopus 로고
    • Minimal cut sets in biochemical reaction networks
    • Klamt S., and Gilles E.D. (2004). Minimal cut sets in biochemical reaction networks. Bioinformatics, 20, 226-234
    • (2004) Bioinformatics , vol.20 , pp. 226-234
    • Klamt, S.1    Gilles, E.D.2
  • 17
    • 34447551397 scopus 로고    scopus 로고
    • Structural, and functional analysis of cellular networks with cellnetanalyzer
    • Klamt S., et al. (2007). Structural, and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol., 1, 2
    • (2007) BMC Syst. Biol , vol.1 , pp. 2
    • Klamt, S.1
  • 18
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    • Mahadevan R., and Schilling C.H. (2003). The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng., 5, 264-276
    • (2003) Metab. Eng , vol.5 , pp. 264-276
    • Mahadevan, R.1    Schilling, C.H.2
  • 19
    • 84879002382 scopus 로고    scopus 로고
    • Basic, and applied uses of genome-scale metabolic network reconstructions of Escherichia coli
    • McCloskey D., et al. (2013). Basic, and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol. Syst. Biol., 9, 661
    • (2013) Mol. Syst. Biol , vol.9 , pp. 661
    • McCloskey, D.1
  • 20
    • 74549189949 scopus 로고    scopus 로고
    • Flux design: In silico design of cell factories based on correlation of pathway fluxes to desired properties
    • Melzer G., et al. (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
  • 21
    • 78650218972 scopus 로고    scopus 로고
    • Modeling of uncertainties in biochemical reactions
    • Miskovic L., and 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
  • 22
    • 84900303762 scopus 로고    scopus 로고
    • Optimizing genome-scale network reconstructions
    • Monk J., et al. (2014). Optimizing genome-scale network reconstructions. Nat. Biotechnol., 32, 447-452
    • (2014) Nat. Biotechnol , vol.32 , pp. 447-452
    • Monk, J.1
  • 23
    • 84875625255 scopus 로고    scopus 로고
    • Fast thermodynamically constrained flux variability analysis
    • Muller A.C., and Bockmayr A. (2013). Fast thermodynamically constrained flux variability analysis. Bioinformatics, 29, 903-909
    • (2013) Bioinformatics , vol.29 , pp. 903-909
    • Muller, A.C.1    Bockmayr, A.2
  • 24
    • 80054755690 scopus 로고    scopus 로고
    • Genome-scale metabolic models of Saccharomyces cerevisiae
    • Nookaew I., et al. (2011). Genome-scale metabolic models of Saccharomyces cerevisiae. Methods Mol. Biol., 759, 445-463
    • (2011) Methods Mol. Biol , vol.759 , pp. 445-463
    • Nookaew, I.1
  • 25
    • 84865075156 scopus 로고    scopus 로고
    • Flux variability scanning based on enforced objective flux for identifying gene amplification targets
    • Park J.M., et al. (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
  • 26
    • 30044437327 scopus 로고    scopus 로고
    • Evolutionary programming as a platform for in silico metabolic engineering
    • Patil K.R., et al. (2005). Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics, 6, 308
    • (2005) BMC Bioinformatics , vol.6 , pp. 308
    • Patil, K.R.1
  • 27
    • 29544436058 scopus 로고    scopus 로고
    • An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems
    • Pharkya P., and Maranas C.D. (2006). An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab. Eng., 8, 1-13
    • (2006) Metab. Eng , vol.8 , pp. 1-13
    • Pharkya, P.1    Maranas, C.D.2
  • 28
    • 8744224466 scopus 로고    scopus 로고
    • OptStrain: A computational framework for redesign of microbial production systems
    • Pharkya P., et al. (2004). OptStrain: a computational framework for redesign of microbial production systems. Genome Res., 14, 2367-2376
    • (2004) Genome Res , vol.14 , pp. 2367-2376
    • Pharkya, P.1
  • 29
    • 78049253925 scopus 로고    scopus 로고
    • Deletion of genes encoding cytochrome oxidases, and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli k-12 mg1655
    • Portnoy V.A., et al. (2010). Deletion of genes encoding cytochrome oxidases, and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655. Appl. Environ. Microbiol., 76, 6529-6540
    • (2010) Appl. Environ. Microbiol , vol.76 , pp. 6529-6540
    • Portnoy, V.A.1
  • 30
    • 77954590959 scopus 로고    scopus 로고
    • Optforce: An optimization procedure for identifying all genetic manipulations leading to targeted overproductions
    • Ranganathan S., et al. (2010). OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Comput. Biol., 6, e1000744
    • (2010) Plos Comput. Biol , vol.6 , pp. e1000744
    • Ranganathan, S.1
  • 31
    • 84869027982 scopus 로고    scopus 로고
    • An integrated computational, and experimental study for overproducing fatty acids in Escherichia coli
    • Ranganathan S., et al. (2012). An integrated computational, and experimental study for overproducing fatty acids in Escherichia coli. Metab. Eng., 14, 687-704
    • (2012) Metab. Eng , vol.14 , pp. 687-704
    • Ranganathan, S.1
  • 32
    • 70349964350 scopus 로고    scopus 로고
    • Automated design of synthetic ribosome binding sites to control protein expression
    • Salis H.M., et al. (2009). Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol., 27, 946-950
    • (2009) Nat. Biotechnol , vol.27 , pp. 946-950
    • Salis, H.M.1
  • 33
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization, and analysis of complex metabolic networks
    • Schuster S., et al. (2000). A general definition of metabolic pathways useful for systematic organization, and analysis of complex metabolic networks. Nat. Biotechnol., 18, 326-332
    • (2000) Nat. Biotechnol , vol.18 , pp. 326-332
    • Schuster, S.1
  • 34
    • 84869420041 scopus 로고    scopus 로고
    • Synthetic biology, and metabolic engineering
    • Stephanopoulos G. (2012). Synthetic biology, and metabolic engineering. ACS Synth. Biol., 1, 514-525
    • (2012) ACS Synth. Biol , vol.1 , pp. 514-525
    • Stephanopoulos, G.1
  • 35
    • 58749106454 scopus 로고    scopus 로고
    • Ensemble modeling of metabolic networks
    • Tran L.M., et al. (2008). Ensemble modeling of metabolic networks Biophys. J., 95, 5606-5617
    • (2008) Biophys. J. , vol.95 , pp. 5606-5617
    • Tran, L.M.1
  • 36
    • 84864631184 scopus 로고    scopus 로고
    • Elucidating, and reprogramming Escherichia coli metabolisms for obligate anaerobic n-butanol, and isobutanol production
    • Trinh C.T. (2012). Elucidating, and reprogramming Escherichia coli metabolisms for obligate anaerobic n-butanol, and isobutanol production. Appl. Microbiol. Biotechnol., 95, 1083-1094
    • (2012) Appl. Microbiol. Biotechnol , vol.95 , pp. 1083-1094
    • Trinh, C.T.1
  • 37
    • 45749137679 scopus 로고    scopus 로고
    • Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses, and pentoses
    • Trinh C.T., et al. (2008). Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses, and pentoses. Appl. Environ. Microbiol., 74, 3634-3643
    • (2008) Appl. Environ. Microbiol , vol.74 , pp. 3634-3643
    • Trinh, C.T.1
  • 38
    • 58149154663 scopus 로고    scopus 로고
    • Elementary mode analysis: A useful metabolic pathway analysis tool for characterizing cellular metabolism
    • Trinh C.T., et al. (2009). Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl. Microbiol. Biotechnol., 81, 813-826
    • (2009) Appl. Microbiol. Biotechnol , vol.81 , pp. 813-826
    • Trinh, C.T.1
  • 39
    • 79961084093 scopus 로고    scopus 로고
    • Redesigning Escherichia coli metabolism for anaerobic production of isobutanol
    • Trinh C.T., et al. (2011). Redesigning Escherichia coli metabolism for anaerobic production of isobutanol. Appl. Environ. Microbiol., 77, 4894-4904
    • (2011) Appl. Environ. Microbiol , vol.77 , pp. 4894-4904
    • Trinh, C.T.1
  • 40
    • 84896731390 scopus 로고    scopus 로고
    • Enumeration of smallest intervention strategies in genome-scale metabolic networks
    • von Kamp A., and Klamt S. (2014). Enumeration of smallest intervention strategies in genome-scale metabolic networks. PLoS Comput. Biol., 10, e1003378
    • (2014) Plos Comput. Biol , vol.10 , pp. e1003378
    • Von Kamp, A.1    Klamt, S.2
  • 41
    • 33644817094 scopus 로고    scopus 로고
    • Metabolic engineering under uncertainty I: Framework development
    • Wang L., and Hatzimanikatis V. (2006). Metabolic engineering under uncertainty. I: framework development. Metab. Eng., 8, 133-141
    • (2006) Metab. Eng , vol.8 , pp. 133-141
    • Wang, L.1    Hatzimanikatis, V.2
  • 42
    • 84897149238 scopus 로고    scopus 로고
    • Integrating biological redesign: Where synthetic biology came from, and where it needs to go
    • Way J.C., et al. (2014). Integrating biological redesign: where synthetic biology came from, and where it needs to go. Cell, 157, 151-161
    • (2014) Cell , vol.157 , pp. 151-161
    • Way, J.C.1
  • 43
    • 80052021573 scopus 로고    scopus 로고
    • Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl- CoA
    • Xu P., et al. (2011). Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl- CoA. Metab. Eng., 13, 578-587
    • (2011) Metab. Eng , vol.13 , pp. 578-587
    • Xu, P.1
  • 44
    • 79955145774 scopus 로고    scopus 로고
    • Emilio: A fast algorithm for genome-scale strain design
    • Yang L., et al. (2011). EMILiO: a fast algorithm for genome-scale strain design. Metab. Eng., 13, 272
    • (2011) Metab. Eng , vol.13 , pp. 272
    • Yang, L.1
  • 45
    • 84921301913 scopus 로고    scopus 로고
    • Characterizing metabolic pathway diversification in the context of perturbation size
    • Yang L., et al. (2015). Characterizing metabolic pathway diversification in the context of perturbation size. Metab. Eng., 28, 114-122
    • (2015) Metab. Eng , vol.28 , pp. 114-122
    • Yang, L.1
  • 46
    • 79959374585 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli for direct production of 1, 4-butanediol
    • Yim H., et al. (2011). Metabolic engineering of Escherichia coli for direct production of 1, 4-butanediol. Nat. Chem. Biol., 7, 445-452
    • (2011) Nat. Chem. Biol , vol.7 , pp. 445-452
    • Yim, H.1
  • 47
    • 84869010163 scopus 로고    scopus 로고
    • Mathematical optimization applications in metabolic networks
    • Zomorrodi A.R., et al. (2012). Mathematical optimization applications in metabolic networks. Metab. Eng., 14, 672-686
    • (2012) Metab. Eng , vol.14 , pp. 672-686
    • Zomorrodi, A.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.