메뉴 건너뛰기




Volumn 7, Issue 6, 2012, Pages

Design constraints on a synthetic metabolism

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

EID: 84863092162     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0039903     Document Type: Article
Times cited : (8)

References (101)
  • 1
    • 66249088017 scopus 로고    scopus 로고
    • The second wave of synthetic biology: from modules to systems
    • Purnick PEM, Weiss R, (2009) The second wave of synthetic biology: from modules to systems. Nature reviews Molecular cell biology 10: 410-422. Available:http://www.ncbi.nlm.nih.gov/pubmed/19461664. Accessed 2011 Jun 10.
    • (2009) Nature reviews Molecular cell biology , vol.10 , pp. 410-422
    • Purnick, P.E.M.1    Weiss, R.2
  • 2
    • 79952645848 scopus 로고    scopus 로고
    • Informing biological design by integration of systems and synthetic biology
    • Smolke CD, Silver PA, (2011) Informing biological design by integration of systems and synthetic biology. Cell 144: 855-859. Available:http://www.ncbi.nlm.nih.gov/pubmed/21414477. Accessed 2011 Jun 10.
    • (2011) Cell , vol.144 , pp. 855-859
    • Smolke, C.D.1    Silver, P.A.2
  • 3
    • 28544440364 scopus 로고    scopus 로고
    • Reconstruction of genetic circuits
    • Sprinzak D, Elowitz MB, (2005) Reconstruction of genetic circuits. Nature 438: 443-448. Available:http://www.ncbi.nlm.nih.gov/pubmed/16306982. Accessed 2011 Jul 5.
    • (2005) Nature , vol.438 , pp. 443-448
    • Sprinzak, D.1    Elowitz, M.B.2
  • 4
    • 21344458620 scopus 로고    scopus 로고
    • Synthetic biology
    • Benner SA, Sismour AM, (2005) Synthetic biology. Nature Reviews Genetics 6: 533-543. Available:http://www.ncbi.nlm.nih.gov/pubmed/15995697. Accessed 2012 Jun 11.
    • (2005) Nature Reviews Genetics , vol.6 , pp. 533-543
    • Benner, S.A.1    Sismour, A.M.2
  • 5
    • 0642305408 scopus 로고    scopus 로고
    • Metabolic engineering: advances in modeling and intervention in health and disease
    • Yarmush ML, Banta S, (2003) Metabolic engineering: advances in modeling and intervention in health and disease. Annual review of biomedical engineering 5: 349-381. Available:http://www.ncbi.nlm.nih.gov/pubmed/14527316. Accessed 2012 Jun 11.
    • (2003) Annual review of biomedical engineering , vol.5 , pp. 349-381
    • Yarmush, M.L.1    Banta, S.2
  • 6
    • 0347364647 scopus 로고    scopus 로고
    • Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides
    • Smith HO, Hutchison CA, Pfannkoch C, Venter JC, (2003) Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proceedings of the National Academy of Sciences of the United States of America 100: 15440-15445. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=307586&tool=pmcentrez&rendertype=abstract. Accessed 2012 Jun 11.
    • (2003) Proceedings of the National Academy of Sciences of the United States of America , vol.100 , pp. 15440-15445
    • Smith, H.O.1    Hutchison, C.A.2    Pfannkoch, C.3    Venter, J.C.4
  • 7
    • 39449112551 scopus 로고    scopus 로고
    • Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome
    • (New York, NY)
    • Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, et al. (2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science (New York, NY) 319: 1215-1220. Available:http://www.ncbi.nlm.nih.gov/pubmed/18218864. Accessed 2011 Jul 11.
    • (2008) Science , vol.319 , pp. 1215-1220
    • Gibson, D.G.1    Benders, G.A.2    Andrews-Pfannkoch, C.3    Denisova, E.A.4    Baden-Tillson, H.5
  • 8
    • 77953584054 scopus 로고    scopus 로고
    • Creation of a bacterial cell controlled by a chemically synthesized genome
    • (New York, NY)
    • Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang R-Y, et al. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science (New York, NY) 329: 52-56. Available:http://www.ncbi.nlm.nih.gov/pubmed/20488990. Accessed 2011 Jul 17.
    • (2010) Science , vol.329 , pp. 52-56
    • Gibson, D.G.1    Glass, J.I.2    Lartigue, C.3    Noskov, V.N.4    Chuang, R.-Y.5
  • 10
    • 1142286362 scopus 로고    scopus 로고
    • Evolution. Transitions from nonliving to living matter
    • (New York, NY)
    • Rasmussen S, Chen L, Deamer D, Krakauer DC, Packard NH, et al. (2004) Evolution. Transitions from nonliving to living matter. Science (New York, NY) 303: 963-965. Available:http://www.ncbi.nlm.nih.gov/pubmed/14963315. Accessed 2011 Jul 27.
    • (2004) Science , vol.303 , pp. 963-965
    • Rasmussen, S.1    Chen, L.2    Deamer, D.3    Krakauer, D.C.4    Packard, N.H.5
  • 12
    • 58149168844 scopus 로고    scopus 로고
    • Spontaneous reaction silencing in metabolic optimization
    • Nishikawa T, Gulbahce N, Motter AE, (2008) Spontaneous reaction silencing in metabolic optimization. PLoS computational biology 4: e1000236. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2582435&=pmcentrez&rendertype=abstract. Accessed 2011 Jul 21.
    • (2008) PLoS computational biology , vol.4
    • Nishikawa, T.1    Gulbahce, N.2    Motter, A.E.3
  • 13
    • 33846108255 scopus 로고    scopus 로고
    • Towards synthesis of a minimal cell
    • Forster AC, Church GM, (2006) Towards synthesis of a minimal cell. Molecular systems biology 2: 45. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1681520&=pmcentrez&rendertype=abstract. Accessed 2011 Jun 12.
    • (2006) Molecular systems biology , vol.2 , pp. 45
    • Forster, A.C.1    Church, G.M.2
  • 14
    • 34247876090 scopus 로고    scopus 로고
    • Reduced genome of the thioautotrophic intracellular symbiont in a deep-sea clam, Calyptogena okutanii
    • CB
    • Kuwahara H, Yoshida T, Takaki Y, Shimamura S, Nishi S, et al. (2007) Reduced genome of the thioautotrophic intracellular symbiont in a deep-sea clam, Calyptogena okutanii. Current biology?: CB 17: 881-886. Available:http://www.ncbi.nlm.nih.gov/pubmed/17493812. Accessed 2011 Jul 18.
    • (2007) Current biology? , vol.7 , pp. 881-886
    • Kuwahara, H.1    Yoshida, T.2    Takaki, Y.3    Shimamura, S.4    Nishi, S.5
  • 15
    • 0035479142 scopus 로고    scopus 로고
    • Deletional bias and the evolution of bacterial genomes
    • Mira A, Ochman H, Moran NA, (2001) Deletional bias and the evolution of bacterial genomes. Trends in Genetics 17: 589-596. Available:http://www.ncbi.nlm.nih.gov/pubmed/11585665. Accessed 2012 Jun 11.
    • (2001) Trends in Genetics , vol.17 , pp. 589-596
    • Mira, A.1    Ochman, H.2    Moran, N.A.3
  • 19
    • 66349139329 scopus 로고    scopus 로고
    • New microbial fuels: a biotech perspective
    • Rude MA, Schirmer A, (2009) New microbial fuels: a biotech perspective. Current opinion in microbiology 12: 274-281. Available:http://www.ncbi.nlm.nih.gov/pubmed/19447673. Accessed 2011 Jul 12.
    • (2009) Current opinion in microbiology , vol.12 , pp. 274-281
    • Rude, M.A.1    Schirmer, A.2
  • 21
    • 57049098094 scopus 로고    scopus 로고
    • Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels
    • Lee SK, Chou H, Ham TS, Lee TS, Keasling JD, (2008) Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels. Current opinion in biotechnology 19: 556-563. Available:http://www.ncbi.nlm.nih.gov/pubmed/18996194. Accessed 2011 Jul 5.
    • (2008) Current opinion in biotechnology , vol.19 , pp. 556-563
    • Lee, S.K.1    Chou, H.2    Ham, T.S.3    Lee, T.S.4    Keasling, J.D.5
  • 22
    • 0025895183 scopus 로고
    • Toward a science of metabolic engineering
    • Bailey JE, (1991) Toward a science of metabolic engineering. Science 252: 1668-1675. Available:http://www.ncbi.nlm.nih.gov/pubmed/2047876. Accessed 2012 Jun 11.
    • (1991) Science , vol.252 , pp. 1668-1675
    • Bailey, J.E.1
  • 23
    • 58249098522 scopus 로고    scopus 로고
    • Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol
    • Steen EJ, Chan R, Prasad N, Myers S, Petzold CJ, et al. (2008) Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol. Microbial cell factories 7: 36. Available:http://www.ncbi.nlm.nih.gov/pubmed/19055772. Accessed 2012 Jun 11.
    • (2008) Microbial cell factories , vol.7 , pp. 36
    • Steen, E.J.1    Chan, R.2    Prasad, N.3    Myers, S.4    Petzold, C.J.5
  • 24
    • 75749125061 scopus 로고    scopus 로고
    • Microbial production of fatty-acid-derived fuels and chemicals from plant biomass
    • Steen EJ, Kang Y, Bokinsky G, Hu Z, Schirmer A, et al. (2010) Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463: 559-562. Available:http://www.ncbi.nlm.nih.gov/pubmed/20111002. Accessed 2012 Jun 11.
    • (2010) Nature , vol.463 , pp. 559-562
    • Steen, E.J.1    Kang, Y.2    Bokinsky, G.3    Hu, Z.4    Schirmer, A.5
  • 25
    • 77955118014 scopus 로고    scopus 로고
    • Microbial Biosynthesis of Alkanes
    • Schirmer A, Rude MA, Li X, Popova E, del Cardayre SB, (2010) Microbial Biosynthesis of Alkanes. Science 329: 559-562. Available:http://www.sciencemag.org/cgi/doi/10.1126/science.1187936. Accessed 2010 Jul 30.
    • (2010) Science , vol.329 , pp. 559-562
    • Schirmer, A.1    Rude, M.A.2    Li, X.3    Popova, E.4    del Cardayre, S.B.5
  • 26
    • 78649716727 scopus 로고    scopus 로고
    • Manufacturing Molecules Through Metabolic Engineering
    • Keasling JD, (2010) Manufacturing Molecules Through Metabolic Engineering. Science 330: 1355-1358. Available:http://www.sciencemag.org/cgi/doi/10.1126/science.1193990. Accessed 2010 Dec 2.
    • (2010) Science , vol.330 , pp. 1355-1358
    • Keasling, J.D.1
  • 27
    • 46549087174 scopus 로고    scopus 로고
    • Importance of systems biology in engineering microbes for biofuel production
    • Mukhopadhyay A, Redding AM, Rutherford BJ, Keasling JD, (2008) Importance of systems biology in engineering microbes for biofuel production. Current opinion in biotechnology 19: 228-234. Available:http://www.ncbi.nlm.nih.gov/pubmed/18515068. Accessed 2011 Jul 11 July.
    • (2008) Current opinion in biotechnology , vol.19 , pp. 228-234
    • Mukhopadhyay, A.1    Redding, A.M.2    Rutherford, B.J.3    Keasling, J.D.4
  • 28
    • 77649202560 scopus 로고    scopus 로고
    • Synthetic Biology: Environmental Health Implications of a New Field
    • Schmidt CW, (2010) Synthetic Biology: Environmental Health Implications of a New Field. Environmental Health Perspectives 118: A118-A123.
    • (2010) Environmental Health Perspectives , vol.118
    • Schmidt, C.W.1
  • 29
    • 24944583078 scopus 로고    scopus 로고
    • Genetically modified organisms for the environment: stories of success and failure and what we have learned from them
    • Cases I, Lorenzo V, (2005) Genetically modified organisms for the environment: stories of success and failure and what we have learned from them. International microbiology 8: 213-222. Available:http://scielo.isciii.es/scielo.php?pid=S1139-67092005000300009&script=sci_abstract&tlng=e. Accessed 2011 Nov 28.
    • (2005) International microbiology , vol.8 , pp. 213-222
    • Cases, I.1    Lorenzo, V.2
  • 30
    • 0025866296 scopus 로고
    • Network rigidity and metabolic engineering in metabolite overproduction
    • Stephanopoulos G, Vallino JJ, (1991) Network rigidity and metabolic engineering in metabolite overproduction. Science 252: 1675-1681. Available:http://www.ncbi.nlm.nih.gov/pubmed/1904627. Accessed 2012 Jun 11.
    • (1991) Science , vol.252 , pp. 1675-1681
    • Stephanopoulos, G.1    Vallino, J.J.2
  • 31
    • 59949093124 scopus 로고    scopus 로고
    • Novel evolutionary engineering approach for accelerated utilization of glucose, xylose, and arabinose mixtures by engineered Saccharomyces cerevisiae strains
    • Wisselink HW, Toirkens MJ, Wu Q, Pronk JT, van Maris AJ a, (2009) Novel evolutionary engineering approach for accelerated utilization of glucose, xylose, and arabinose mixtures by engineered Saccharomyces cerevisiae strains. Applied and environmental microbiology 75: 907-914. Available:http://www.ncbi.nlm.nih.gov/pubmed/19074603. Accessed 2012 Jun 11.
    • (2009) Applied and environmental microbiology , vol.75 , pp. 907-914
    • Wisselink, H.W.1    Toirkens, M.J.2    Wu, Q.3    Pronk, J.T.4    van Maris, A.J.5
  • 32
    • 80052975908 scopus 로고    scopus 로고
    • Engineering Biological Systems with Synthetic RNA Molecules
    • Liang JC, Bloom RJ, Smolke CD, (2011) Engineering Biological Systems with Synthetic RNA Molecules. Molecular Cell 43: 915-926. Available:http://linkinghub.elsevier.com/retrieve/pii/S1097276511006447. Accessed 2011 Sep 19.
    • (2011) Molecular Cell , vol.43 , pp. 915-926
    • Liang, J.C.1    Bloom, R.J.2    Smolke, C.D.3
  • 33
    • 38749110064 scopus 로고    scopus 로고
    • Defossiling fuel: how synthetic biology can transform biofuel production
    • Savage DF, Way J, Silver PA, (2008) Defossiling fuel: how synthetic biology can transform biofuel production. ACS Chemical Biology 3: 13-16.
    • (2008) ACS Chemical Biology , vol.3 , pp. 13-16
    • Savage, D.F.1    Way, J.2    Silver, P.A.3
  • 34
    • 1942499454 scopus 로고    scopus 로고
    • Advanced sequencing technologies: methods and goals
    • Shendure J, Mitra RD, Varma C, Church GM, (2004) Advanced sequencing technologies: methods and goals. Nature reviews Genetics 5: 335-344. Available:http://www.ncbi.nlm.nih.gov/pubmed/15143316. Accessed 2011 Jul 16.
    • (2004) Nature reviews Genetics , vol.5 , pp. 335-344
    • Shendure, J.1    Mitra, R.D.2    Varma, C.3    Church, G.M.4
  • 35
    • 71849115077 scopus 로고    scopus 로고
    • Genome engineering
    • Carr PA, Church GM, (2009) Genome engineering. Nature biotechnology 27: 1151-1162. Available:http://www.ncbi.nlm.nih.gov/pubmed/20010598. Accessed 2011 Jul 27.
    • (2009) Nature biotechnology , vol.27 , pp. 1151-1162
    • Carr, P.A.1    Church, G.M.2
  • 36
    • 0034519221 scopus 로고    scopus 로고
    • Robustness analysis of the Escherichia coli metabolic network
    • Edwards JS, Palsson BO, (2000) Robustness analysis of the Escherichia coli metabolic network. Biotechnology Progress 16: 927-939.
    • (2000) Biotechnology Progress , vol.16 , pp. 927-939
    • Edwards, J.S.1    Palsson, B.O.2
  • 37
    • 2942579562 scopus 로고    scopus 로고
    • Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions
    • Edwards JS, Palsson BO, (2000) Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC bioinformatics 1: 1.
    • (2000) BMC Bioinformatics , vol.1 , pp. 1
    • Edwards, J.S.1    Palsson, B.O.2
  • 42
    • 0142152457 scopus 로고    scopus 로고
    • Description and Interpretation of Adaptive Evolution of Escherichia coli K-12 MG1655 by Using a Genome-Scale In Silico Metabolic Model
    • Fong SS, Marciniak JY, Palsson BØ, (2003) Description and Interpretation of Adaptive Evolution of Escherichia coli K-12 MG1655 by Using a Genome-Scale In Silico Metabolic Model. Journal Of Bacteriology 185: 6400-6408.
    • (2003) Journal Of Bacteriology , vol.185 , pp. 6400-6408
    • Fong, S.S.1    Marciniak, J.Y.2    Palsson, BØ.3
  • 43
    • 25844495901 scopus 로고    scopus 로고
    • Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states
    • Fong S, Joyce A, (2005) Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome research 15: 1365-1372. Available:http://genome.cshlp.org/content/15/10/1365.short. Accessed 2011 Nov 28.
    • (2005) Genome research , vol.15 , pp. 1365-1372
    • Fong, S.1    Joyce, A.2
  • 44
    • 79551662521 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
    • Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, et al. (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nature Protocols 2: 1290-1307.
    • (2007) Nature Protocols , vol.2 , pp. 1290-1307
    • Schellenberger, J.1    Que, R.2    Fleming, R.M.T.3    Thiele, I.4    Orth, J.D.5
  • 47
    • 74549117172 scopus 로고    scopus 로고
    • Evolutionary plasticity and innovations in complex metabolic reaction networks
    • e1000613
    • Matias Rodrigues JF, Wagner A, (2009) Evolutionary plasticity and innovations in complex metabolic reaction networks. PLoS computational biology 5: e1000613.
    • (2009) PLoS Computational Biology , vol.5
    • Matias Rodrigues, J.F.1    Wagner, A.2
  • 50
    • 0004087397 scopus 로고
    • Probabilistic Inference Using Markov Chain Monte Carlo Methods
    • Neal RM, (1993) Probabilistic Inference Using Markov Chain Monte Carlo Methods. Intelligence 62: 144.
    • (1993) Intelligence , vol.62 , pp. 144
    • Neal, R.M.1
  • 51
    • 0002595470 scopus 로고
    • Generation of random points uniformly distributed in hyperellipsoids
    • doi:10.1109/CCA.1992.269770
    • Li XR, (1992) Generation of random points uniformly distributed in hyperellipsoids. Proc First IEEE Conference on Control Applications. p. 654-658 vol.2 doi:10.1109/CCA.1992.269770.
    • (1992) Proc First IEEE Conference on Control Applications , vol.2 , pp. 654-658
    • Li, X.R.1
  • 54
    • 33847268619 scopus 로고    scopus 로고
    • Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology
    • Ciliberti S, Martin OC, Wagner A, (2007) Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology. PLoS Computational Biology 3: 10.
    • (2007) PLoS Computational Biology , vol.3 , pp. 10
    • Ciliberti, S.1    Martin, O.C.2    Wagner, A.3
  • 55
    • 42349100173 scopus 로고    scopus 로고
    • The chemical genomic portrait of yeast: uncovering a phenotype for all genes
    • (New York, NY)
    • Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S, et al. (2008) The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science (New York, NY) 320: 362-365. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2794835&=pmcentrez&rendertype=abstract. Accessed 2011 Jul 18.
    • (2008) Science , vol.320 , pp. 362-365
    • Hillenmeyer, M.E.1    Fung, E.2    Wildenhain, J.3    Pierce, S.E.4    Hoon, S.5
  • 56
    • 76649143066 scopus 로고    scopus 로고
    • Genes involved in long-chain alkene biosynthesis in Micrococcus luteus
    • Beller HR, Goh E-B, Keasling JD, (2010) Genes involved in long-chain alkene biosynthesis in Micrococcus luteus. Applied and environmental microbiology 76: 1212-1223. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2820947&=pmcentrez&rendertype=abstract. Accessed 2011 Apr 3.
    • (2010) Applied and environmental microbiology , vol.76 , pp. 1212-1223
    • Beller, H.R.1    Goh, E.-B.2    Keasling, J.D.3
  • 57
    • 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 AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular systems biology 3: 121.
    • (2007) Molecular Systems Biology , vol.3 , pp. 121
    • Feist, A.M.1    Henry, C.S.2    Reed, J.L.3    Krummenacker, M.4    Joyce, A.R.5
  • 59
    • 0002322469 scopus 로고
    • On a test of whether one of two random variables is stochastically larger than the other
    • Mann HB, Whitney DR, (1947) On a test of whether one of two random variables is stochastically larger than the other. The Annals of Mathematical Statistics 18: 50-60.
    • (1947) The Annals of Mathematical Statistics , vol.18 , pp. 50-60
    • Mann, H.B.1    Whitney, D.R.2
  • 60
    • 0031832290 scopus 로고    scopus 로고
    • Genetically engineered Saccharomyces yeast capable of effective cofermentation of glucose and xylose
    • Ho NWY, Chen Z, Brainard AP, (1998) Genetically engineered Saccharomyces yeast capable of effective cofermentation of glucose and xylose. Applied and Environmental Microbiology 64: 1852-1859.
    • (1998) Applied and Environmental Microbiology , vol.64 , pp. 1852-1859
    • Ho, N.W.Y.1    Chen, Z.2    Brainard, A.P.3
  • 61
    • 35348934254 scopus 로고    scopus 로고
    • Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data
    • Oh Y-K, Palsson BO, Park SM, Schilling CH, Mahadevan R, (2007) Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. The Journal of biological chemistry 282: 28791-28799. Available:http://www.ncbi.nlm.nih.gov/pubmed/17573341. Accessed 2011 Aug 3.
    • (2007) The Journal of biological chemistry , vol.282 , pp. 28791-28799
    • Oh, Y.-K.1    Palsson, B.O.2    Park, S.M.3    Schilling, C.H.4    Mahadevan, R.5
  • 62
    • 77953807608 scopus 로고    scopus 로고
    • Abundant Indispensable Redundancies in Cellular Metabolic Networks
    • Wang Z, Zhang J, (2009) Abundant Indispensable Redundancies in Cellular Metabolic Networks. Genome biology and evolution 2009: 23-33.
    • (2009) Genome Biology and Evolution , vol.2009 , pp. 23-33
    • Wang, Z.1    Zhang, J.2
  • 63
    • 84863097762 scopus 로고    scopus 로고
    • The Cell
    • Cooper GM, (2008) The Cell. Cell 77: 67-109.
    • (2008) Cell , vol.77 , pp. 67-109
    • Cooper, G.M.1
  • 64
    • 79960610255 scopus 로고    scopus 로고
    • Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs
    • Wessely F, Bartl M, Guthke R, Li P, Schuster S, et al. (2011) Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Molecular Systems Biology 7: 515.
    • (2011) Molecular Systems Biology , vol.7 , pp. 515
    • Wessely, F.1    Bartl, M.2    Guthke, R.3    Li, P.4    Schuster, S.5
  • 65
    • 77951552860 scopus 로고    scopus 로고
    • OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains
    • Kim J, Reed JL, (2010) OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. BMC systems biology 4: 53.
    • (2010) BMC Systems Biology , vol.4 , pp. 53
    • Kim, J.1    Reed, J.L.2
  • 66
    • 51949107835 scopus 로고    scopus 로고
    • Progress in Metabolic Engineering of Saccharomyces cerevisiae
    • Nevoigt E, (2008) Progress in Metabolic Engineering of Saccharomyces cerevisiae. Microbiology and molecular biology reviews MMBR 72: 379-412.
    • (2008) Microbiology and Molecular Biology Reviews MMBR , vol.72 , pp. 379-412
    • Nevoigt, E.1
  • 67
    • 63949086729 scopus 로고    scopus 로고
    • Alcoholic fermentation of xylose and mixed sugars using recombinant Saccharomyces cerevisiae engineered for xylose utilization
    • Madhavan A, Tamalampudi S, Srivastava A, Fukuda H, Bisaria VS, et al. (2009) Alcoholic fermentation of xylose and mixed sugars using recombinant Saccharomyces cerevisiae engineered for xylose utilization. Applied Microbiology and Biotechnology 82: 1037-1047.
    • (2009) Applied Microbiology and Biotechnology , vol.82 , pp. 1037-1047
    • Madhavan, A.1    Tamalampudi, S.2    Srivastava, A.3    Fukuda, H.4    Bisaria, V.S.5
  • 68
    • 77953368385 scopus 로고    scopus 로고
    • Improved xylose and arabinose utilization by an industrial recombinant Saccharomyces cerevisiae strain using evolutionary engineering
    • Garcia Sanchez R, Karhumaa K, Fonseca C, Sànchez Nogué V, Almeida JR, et al. (2010) Improved xylose and arabinose utilization by an industrial recombinant Saccharomyces cerevisiae strain using evolutionary engineering. Biotechnology for biofuels 3: 13.
    • (2010) Biotechnology for Biofuels , vol.3 , pp. 13
    • Garcia Sanchez, R.1    Karhumaa, K.2    Fonseca, C.3    Sànchez Nogué, V.4    Almeida, J.R.5
  • 69
    • 72149123391 scopus 로고    scopus 로고
    • Construction of a xylose-fermenting Saccharomyces cerevisiae strain by combined approaches of genetic engineering, chemical mutagenesis and evolutionary adaptation
    • Liu E, Hu Y, (2010) Construction of a xylose-fermenting Saccharomyces cerevisiae strain by combined approaches of genetic engineering, chemical mutagenesis and evolutionary adaptation. Biochemical Engineering Journal 48: 204-210.
    • (2010) Biochemical Engineering Journal , vol.48 , pp. 204-210
    • Liu, E.1    Hu, Y.2
  • 70
    • 15844406532 scopus 로고    scopus 로고
    • Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. II. Dynamic response to famine and feast, activation of the methylglyoxal pathway and oscillatory behaviour
    • (Reading, England)
    • Weber J, Kayser A, Rinas U, (2005) Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. II. Dynamic response to famine and feast, activation of the methylglyoxal pathway and oscillatory behaviour. Microbiology (Reading, England) 151: 707-716. Available:http://www.ncbi.nlm.nih.gov/pubmed/15758217. Accessed 2011 Aug 24.
    • (2005) Microbiology , vol.151 , pp. 707-716
    • Weber, J.1    Kayser, A.2    Rinas, U.3
  • 71
    • 0026530031 scopus 로고
    • Production of vitamins, coenzymes and related biochemicals by biotechnological processes
    • Vandamme EJ, (1992) Production of vitamins, coenzymes and related biochemicals by biotechnological processes. Journal of chemical technology and biotechnology Oxford Oxfordshire 1986 53: 313-327 Available:http://doi.wiley.com/10.1002/chin.199229310.
    • (1992) Journal of Chemical Technology and Biotechnology Oxford Oxfordshire 1986 , vol.53 , pp. 313-327
    • Vandamme, E.J.1
  • 73
    • 12544258708 scopus 로고    scopus 로고
    • Botryococcus braunii: a rich source for hydrocarbons and related ether lipids
    • Metzger P, Largeau C, (2005) Botryococcus braunii: a rich source for hydrocarbons and related ether lipids. Applied Microbiology and Biotechnology 66: 486-496.
    • (2005) Applied Microbiology and Biotechnology , vol.66 , pp. 486-496
    • Metzger, P.1    Largeau, C.2
  • 75
    • 33744960597 scopus 로고    scopus 로고
    • Hap4 is not essential for activation of respiration at low specific growth rates in Saccharomyces cerevisiae
    • Raghevendran V, Patil KR, Olsson L, Nielsen J, (2006) Hap4 is not essential for activation of respiration at low specific growth rates in Saccharomyces cerevisiae. The Journal of Biological Chemistry 281: 12308-12314.
    • (2006) The Journal of Biological Chemistry , vol.281 , pp. 12308-12314
    • Raghevendran, V.1    Patil, K.R.2    Olsson, L.3    Nielsen, J.4
  • 77
    • 79953197942 scopus 로고    scopus 로고
    • Shifting the Fermentative/Oxidative Balance in Saccharomyces cerevisiae by Transcriptional Deregulation of Snf1 via Overexpression of the Upstream Activating Kinase Sak1p
    • Raab AM, Hlavacek V, Bolotina N, Lang C, (2011) Shifting the Fermentative/Oxidative Balance in Saccharomyces cerevisiae by Transcriptional Deregulation of Snf1 via Overexpression of the Upstream Activating Kinase Sak1p. Applied and Environmental Microbiology 77: 1981-1989.
    • (2011) Applied and Environmental Microbiology , vol.77 , pp. 1981-1989
    • Raab, A.M.1    Hlavacek, V.2    Bolotina, N.3    Lang, C.4
  • 78
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: evaluating the consequences of constraints
    • Price ND, Reed JL, Palsson BØ, (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nature reviews Microbiology 2: 886-897. Available:http://www.ncbi.nlm.nih.gov/pubmed/15494745. Accessed 2010 Jul 16.
    • (2004) Nature reviews Microbiology , vol.2 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, BØ.3
  • 79
    • 0142122303 scopus 로고    scopus 로고
    • Advances in flux balance analysis
    • Kauffman KJ, Prakash P, Edwards JS, (2003) Advances in flux balance analysis. Current Opinion in Biotechnology 14: 491-496. Available:http://linkinghub.elsevier.com/retrieve/pii/S0958166903001174. Accessed 2010 Jul 16.
    • (2003) Current Opinion in Biotechnology , vol.14 , pp. 491-496
    • Kauffman, K.J.1    Prakash, P.2    Edwards, J.S.3
  • 80
    • 33847314052 scopus 로고    scopus 로고
    • Parameter estimation using Simulated Annealing for S-system models of biochemical networks
    • Gonzalez OR, Küper C, Jung K, Naval PC, Mendoza E, (2007) Parameter estimation using Simulated Annealing for S-system models of biochemical networks. Bioinformatics 23: 480-486.
    • (2007) Bioinformatics , vol.23 , pp. 480-486
    • Gonzalez, O.R.1    Küper, C.2    Jung, K.3    Naval, P.C.4    Mendoza, E.5
  • 81
    • 33751204469 scopus 로고    scopus 로고
    • Optimization of a Stochastically Simulated Gene Network Model via Simulated Annealing
    • Tomshine J, Kaznessis YN, (2006) Optimization of a Stochastically Simulated Gene Network Model via Simulated Annealing. Biophysical Journal 91: 3196-3205.
    • (2006) Biophysical Journal , vol.91 , pp. 3196-3205
    • Tomshine, J.1    Kaznessis, Y.N.2
  • 83
    • 45949101960 scopus 로고    scopus 로고
    • A bilevel optimization algorithm to identify enzymatic capacity constraints in metabolic networks
    • Yang L, Mahadevan R, Cluett W, (2008) A bilevel optimization algorithm to identify enzymatic capacity constraints in metabolic networks. Computers & Chemical Engineering 32: 2072-2085.
    • (2008) Computers & Chemical Engineering , vol.32 , pp. 2072-2085
    • Yang, L.1    Mahadevan, R.2    Cluett, W.3
  • 84
    • 77950960250 scopus 로고    scopus 로고
    • OptFlux: an open-source software platform for in silico metabolic engineering
    • Rocha I, Maia P, Evangelista P, Vilaça P, Soares S, et al. (2010) OptFlux: an open-source software platform for in silico metabolic engineering. BMC systems biology 4: 45.
    • (2010) BMC Systems Biology , vol.4 , pp. 45
    • Rocha, I.1    Maia, P.2    Evangelista, P.3    Vilaça, P.4    Soares, S.5
  • 86
    • 30044437327 scopus 로고    scopus 로고
    • Evolutionary programming as a platform for in silico metabolic engineering
    • Patil KR, Rocha I, Förster J, Nielsen J, (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    Rocha, I.2    Förster, J.3    Nielsen, J.4
  • 87
    • 0034973362 scopus 로고    scopus 로고
    • Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems
    • Ebenhöh O, Heinrich R, (2001) Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems. Bulletin of Mathematical Biology 63: 21-55.
    • (2001) Bulletin of Mathematical Biology , vol.63 , pp. 21-55
    • Ebenhöh, O.1    Heinrich, R.2
  • 88
    • 0030860218 scopus 로고    scopus 로고
    • Genes and proteins of Escherichia coli K-12 (GenProtEC)
    • Riley M, (1997) Genes and proteins of Escherichia coli K-12 (GenProtEC). Nucleic Acids Research 25: 51-52.
    • (1997) Nucleic Acids Research , vol.25 , pp. 51-52
    • Riley, M.1
  • 90
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S, (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic acids research 28: 27-30.
    • (2000) Nucleic Acids Research , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 92
    • 0347990454 scopus 로고    scopus 로고
    • Evolution of minimal-gene-sets in host-dependent bacteria
    • Klasson L, (2004) Evolution of minimal-gene-sets in host-dependent bacteria. Trends in Microbiology 12: 37-43. Available:http://linkinghub.elsevier.com/retrieve/pii/S0966842X03003111. Accessed 2011 Jul 19.
    • (2004) Trends in Microbiology , vol.12 , pp. 37-43
    • Klasson, L.1
  • 96
    • 59249089471 scopus 로고    scopus 로고
    • Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
    • e1000344
    • Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, et al. (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS genetics 5: e1000344. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2617782&tool=pmcentrez&rendertype=abstract. Accessed 2011 Jul 21.
    • (2009) PLoS genetics , vol.5
    • Touchon, M.1    Hoede, C.2    Tenaillon, O.3    Barbe, V.4    Baeriswyl, S.5
  • 97
    • 62149098396 scopus 로고    scopus 로고
    • A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola
    • Thomas GH, Zucker J, Macdonald SJ, Sorokin A, Goryanin I, et al. (2009) A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola. BMC systems biology 3: 24. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2649895&tool=pmcentrez&rendertype=abstract. Accessed 2011 Jun 17.
    • (2009) BMC systems biology , vol.3 , pp. 24
    • Thomas, G.H.1    Zucker, J.2    Macdonald, S.J.3    Sorokin, A.4    Goryanin, I.5
  • 99
    • 17844405878 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation
    • Becker SA, Palsson BØ, (2005) Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC microbiology 5: 8. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1079855&tool=pmcentrez&rendertype=abstract. Accessed 2011 Jul 18.
    • (2005) BMC microbiology , vol.5 , pp. 8
    • Becker, S.A.1    Palsson, BØ.2
  • 100
    • 33645462347 scopus 로고    scopus 로고
    • Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri
    • 2006.0004
    • Feist AM, Scholten JCM, Palsson BØ, Brockman FJ, Ideker T, (2006) Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Molecular systems biology 2: 2006.0004. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1681478&tool=pmcentrez&rendertype=abstract. Accessed 2011 Jul 20.
    • (2006) Molecular systems biology , vol.2
    • Feist, A.M.1    Scholten, J.C.M.2    Palsson, BØ.3    Brockman, F.J.4    Ideker, T.5
  • 101
    • 34548861262 scopus 로고    scopus 로고
    • GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism
    • Beste DJV, Hooper T, Stewart G, Bonde B, Avignone-Rossa C, et al. (2007) GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism. Genome biology 8: R89. Available:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1929162&tool=pmcentrez&rendertype=abstract. Accessed 2011 Jun 14.
    • (2007) Genome biology , vol.8
    • Beste, D.J.V.1    Hooper, T.2    Stewart, G.3    Bonde, B.4    Avignone-Rossa, C.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.