메뉴 건너뛰기




Volumn 12, Issue 11, 2017, Pages 2823-2829

EcoSynther: A Customized Platform to Explore the Biosynthetic Potential in E. coli

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BACTERIAL GROWTH; BIOSYNTHESIS; ESCHERICHIA COLI K 12; NONHUMAN; ONLINE SYSTEM; PRIORITY JOURNAL; PROBABILITY; ESCHERICHIA COLI; GENETICS; METABOLIC ENGINEERING; METABOLISM; METABOLOMICS;

EID: 85034659963     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/acschembio.7b00605     Document Type: Article
Times cited : (11)

References (34)
  • 1
    • 84920937371 scopus 로고    scopus 로고
    • Computational methods in metabolic engineering for strain design
    • Long, M. R., Ong, W. K., and Reed, J. L. (2015) Computational methods in metabolic engineering for strain design Curr. Opin. Biotechnol. 34, 135-141 10.1016/j.copbio.2014.12.019
    • (2015) Curr. Opin. Biotechnol. , vol.34 , pp. 135-141
    • Long, M.R.1    Ong, W.K.2    Reed, J.L.3
  • 2
    • 84962333480 scopus 로고    scopus 로고
    • BioSynther: A customized biosynthetic potential explorer
    • Tu, W., Zhang, H., Liu, J., and Hu, Q.-N. (2016) BioSynther: a customized biosynthetic potential explorer Bioinformatics 32, 472-473 10.1093/bioinformatics/btv599
    • (2016) Bioinformatics , vol.32 , pp. 472-473
    • Tu, W.1    Zhang, H.2    Liu, J.3    Hu, Q.-N.4
  • 3
    • 84937459775 scopus 로고    scopus 로고
    • Engineered biosynthesis of natural products in heterologous hosts
    • Luo, Y., Li, B., Liu, D., Zhang, L., and Chen, Y. (2015) Engineered biosynthesis of natural products in heterologous hosts Chem. Soc. Rev. 44, 5265-5290 10.1039/C5CS00025D
    • (2015) Chem. Soc. Rev. , vol.44 , pp. 5265-5290
    • Luo, Y.1    Li, B.2    Liu, D.3    Zhang, L.4    Chen, Y.5
  • 4
    • 84952682854 scopus 로고    scopus 로고
    • CRISPR/Cas9 advances engineering of microbial cell factories
    • Jakociunas, T., Jensen, M., and Keasling, J. (2016) CRISPR/Cas9 advances engineering of microbial cell factories Metab. Eng. 34, 44-59 10.1016/j.ymben.2015.12.003
    • (2016) Metab. Eng. , vol.34 , pp. 44-59
    • Jakociunas, T.1    Jensen, M.2    Keasling, J.3
  • 5
    • 84857192122 scopus 로고    scopus 로고
    • Computational tools for the synthetic design of biochemical pathways
    • Medema, M., van Raaphorst, R., Takano, E., and Breitling, R. (2012) Computational tools for the synthetic design of biochemical pathways Nat. Rev. Microbiol. 10, 191-202 10.1038/nrmicro2717
    • (2012) Nat. Rev. Microbiol. , vol.10 , pp. 191-202
    • Medema, M.1    Van Raaphorst, R.2    Takano, E.3    Breitling, R.4
  • 6
    • 85016149190 scopus 로고    scopus 로고
    • KEGG: New perspectives on genomes, pathways, diseases and drugs
    • Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K. (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs Nucleic Acids Res. 45, D353-D361 10.1093/nar/gkw1092
    • (2017) Nucleic Acids Res. , vol.45 , pp. D353-D361
    • Kanehisa, M.1    Furumichi, M.2    Tanabe, M.3    Sato, Y.4    Morishima, K.5
  • 9
    • 80051936716 scopus 로고    scopus 로고
    • RxnFinder: Biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity
    • Hu, Q.-N., Deng, Z., Hu, H., Cao, D. S., and Liang, Y. Z. (2011) RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity Bioinformatics 27, 2465-2467 10.1093/bioinformatics/btr413
    • (2011) Bioinformatics , vol.27 , pp. 2465-2467
    • Hu, Q.-N.1    Deng, Z.2    Hu, H.3    Cao, D.S.4    Liang, Y.Z.5
  • 10
    • 79952604817 scopus 로고    scopus 로고
    • Evaluating Factors That Influence Microbial Synthesis Yields by Linear Regression with Numerical and Ordinal Variables
    • Colletti, P. F., Goyal, Y., Varman, A. M., Feng, X., Wu, B., and Tang, Y. J. (2011) Evaluating Factors That Influence Microbial Synthesis Yields by Linear Regression with Numerical and Ordinal Variables Biotechnol. Bioeng. 108, 893-902 10.1002/bit.22996
    • (2011) Biotechnol. Bioeng. , vol.108 , pp. 893-902
    • Colletti, P.F.1    Goyal, Y.2    Varman, A.M.3    Feng, X.4    Wu, B.5    Tang, Y.J.6
  • 11
    • 79959216987 scopus 로고    scopus 로고
    • Statistics-based model for prediction of chemical biosynthesis yield from Saccharomyces cerevisiae
    • Varman, A. M., Xiao, Y., Leonard, E., and Tang, Y. J. (2011) Statistics-based model for prediction of chemical biosynthesis yield from Saccharomyces cerevisiae Microb. Cell Fact. 10, 45 10.1186/1475-2859-10-45
    • (2011) Microb. Cell Fact. , vol.10 , pp. 45
    • Varman, A.M.1    Xiao, Y.2    Leonard, E.3    Tang, Y.J.4
  • 12
    • 84878862372 scopus 로고    scopus 로고
    • Metabolic tinker: An online tool for guiding the design of synthetic metabolic pathways
    • McClymont, K. and Soyer, O. S. (2013) Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways Nucleic Acids Res. 41, 113-121 10.1093/nar/gkt234
    • (2013) Nucleic Acids Res. , vol.41 , pp. 113-121
    • McClymont, K.1    Soyer, O.S.2
  • 14
    • 70749083404 scopus 로고    scopus 로고
    • Inferring branching pathways in genome-scale metabolic networks.
    • Pitkänen, E., Jouhten, P., and Rousu, J. (2009) Inferring branching pathways in genome-scale metabolic networks. BMC Syst. Biol. 3, 103 10.1186/1752-0509-3-103
    • (2009) BMC Syst. Biol. , vol.3 , pp. 103
    • Pitkänen, E.1    Jouhten, P.2    Rousu, J.3
  • 17
    • 67849083088 scopus 로고    scopus 로고
    • FMM: A web server for metabolic pathway reconstruction and comparative analysis
    • Chou, C.-H., Chang, W.-C., Chiu, C.-M., Huang, C.-C., and Huang, H.-D. (2009) FMM: a web server for metabolic pathway reconstruction and comparative analysis Nucleic Acids Res. 37, W129-W134 10.1093/nar/gkp264
    • (2009) Nucleic Acids Res. , vol.37 , pp. W129-W134
    • Chou, C.-H.1    Chang, W.-C.2    Chiu, C.-M.3    Huang, C.-C.4    Huang, H.-D.5
  • 18
    • 16344376028 scopus 로고    scopus 로고
    • Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)
    • Rahman, S. A., Advani, P., Schunk, R., Schrader, R., and Schomburg, D. (2005) Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC) Bioinformatics 21, 1189-1193 10.1093/bioinformatics/bti116
    • (2005) Bioinformatics , vol.21 , pp. 1189-1193
    • Rahman, S.A.1    Advani, P.2    Schunk, R.3    Schrader, R.4    Schomburg, D.5
  • 19
    • 85018511356 scopus 로고    scopus 로고
    • MRE: A web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind
    • Kuwahara, H., Alazmi, M., Cui, X., and Gao, X. (2016) MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind Nucleic Acids Res. 44, W217-W225 10.1093/nar/gkw342
    • (2016) Nucleic Acids Res. , vol.44 , pp. W217-W225
    • Kuwahara, H.1    Alazmi, M.2    Cui, X.3    Gao, X.4
  • 20
    • 80054069179 scopus 로고    scopus 로고
    • A comprehensive genome-scale reconstruction of Escherichia coli metabolism - 2011
    • Orth, J., Conrad, T., Feist, A., and Palsson, B. (2011) A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011 Mol. Syst. Biol. 7, 535-544 10.1038/msb.2011.65
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 535-544
    • Orth, J.1    Conrad, T.2    Feist, A.3    Palsson, B.4
  • 21
    • 79954741746 scopus 로고    scopus 로고
    • Increase of lycopene production by supplementing auxiliary carbon sources in metabolically engineered Escherichia coli
    • Kim, Y.-S., Lee, J.-H., Kim, N.-H., Yeom, S.-J., Kim, S.-W., and Oh, D.-K. (2011) Increase of lycopene production by supplementing auxiliary carbon sources in metabolically engineered Escherichia coli Appl. Microbiol. Biotechnol. 90, 489-497 10.1007/s00253-011-3091-z
    • (2011) Appl. Microbiol. Biotechnol. , vol.90 , pp. 489-497
    • Kim, Y.-S.1    Lee, J.-H.2    Kim, N.-H.3    Yeom, S.-J.4    Kim, S.-W.5    Oh, D.-K.6
  • 22
    • 18844392599 scopus 로고    scopus 로고
    • Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli
    • Alper, H., Jin, Y.-S., Moxley, J. F., and Stephanopoulos, G. (2005) Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli Metab. Eng. 7, 155-164 10.1016/j.ymben.2004.12.003
    • (2005) Metab. Eng. , vol.7 , pp. 155-164
    • Alper, H.1    Jin, Y.-S.2    Moxley, J.F.3    Stephanopoulos, G.4
  • 23
    • 84940751701 scopus 로고    scopus 로고
    • Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
    • King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., and Palsson, B. O. (2015) Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways PLoS Comput. Biol. 11, e1004321 10.1371/journal.pcbi.1004321
    • (2015) PLoS Comput. Biol. , vol.11 , pp. e1004321
    • King, Z.A.1    Dräger, A.2    Ebrahim, A.3    Sonnenschein, N.4    Lewis, N.E.5    Palsson, B.O.6
  • 24
    • 84883232076 scopus 로고    scopus 로고
    • Multivariate modular metabolic engineering of Escherichia coli to produce resveratrol from l-tyrosine
    • Wu, J., Liu, P., Fan, Y., Bao, H., Du, G., Zhou, J., and Chen, J. (2013) Multivariate modular metabolic engineering of Escherichia coli to produce resveratrol from l-tyrosine J. Biotechnol. 167, 404-411 10.1016/j.jbiotec.2013.07.030
    • (2013) J. Biotechnol. , vol.167 , pp. 404-411
    • Wu, J.1    Liu, P.2    Fan, Y.3    Bao, H.4    Du, G.5    Zhou, J.6    Chen, J.7
  • 25
    • 84958233208 scopus 로고    scopus 로고
    • Metabolic Assessment of E. Coli as a Biofactory for Commercial Products
    • Zhang, X., Tervo, C. J., and Reed, J. L. (2016) Metabolic Assessment of E. coli as a Biofactory for Commercial Products Metab. Eng. 35, 64-74 10.1016/j.ymben.2016.01.007
    • (2016) Metab. Eng. , vol.35 , pp. 64-74
    • Zhang, X.1    Tervo, C.J.2    Reed, J.L.3
  • 26
    • 77953329895 scopus 로고    scopus 로고
    • Prediction of novel synthetic pathways for the production of desired chemicals
    • Cho, A., Yun, H., Park, J. H., and Lee, S. Y. (2010) Prediction of novel synthetic pathways for the production of desired chemicals BMC Syst. Biol. 4, 35 10.1186/1752-0509-4-35
    • (2010) BMC Syst. Biol. , vol.4 , pp. 35
    • Cho, A.1    Yun, H.2    Park, J.H.3    Lee, S.Y.4
  • 29
    • 77749320898 scopus 로고    scopus 로고
    • What is flux balance analysis?
    • Orth, J. D., Thiele, I., and Palsson, B. Ø. (2010) What is flux balance analysis? Nat. Biotechnol. 28, 245-248 10.1038/nbt.1614
    • (2010) Nat. Biotechnol. , vol.28 , pp. 245-248
    • Orth, J.D.1    Thiele, I.2    Palsson, B.Ø.3
  • 30
    • 79958753912 scopus 로고    scopus 로고
    • Probabilistic pathway construction
    • Yousofshahi, M., Lee, K., and Hassoun, S. (2011) Probabilistic pathway construction Metab. Eng. 13, 435-444 10.1016/j.ymben.2011.01.006
    • (2011) Metab. Eng. , vol.13 , pp. 435-444
    • Yousofshahi, M.1    Lee, K.2    Hassoun, S.3
  • 31
    • 84881152495 scopus 로고    scopus 로고
    • COBRApy: COnstraints-Based Reconstruction and Analysis for Python
    • Ebrahim, A., Lerman, J. A., Palsson, B. O., and Hyduke, D. R. (2013) COBRApy: COnstraints-Based Reconstruction and Analysis for Python BMC Syst. Biol. 7, 74 10.1186/1752-0509-7-74
    • (2013) BMC Syst. Biol. , vol.7 , pp. 74
    • Ebrahim, A.1    Lerman, J.A.2    Palsson, B.O.3    Hyduke, D.R.4
  • 32
    • 77950863401 scopus 로고    scopus 로고
    • Model-driven evaluation of the production potential for growth- coupled products of Escherichia coli
    • Feist, A. M., Zielinski, D. C., and Orth, J. D. (2010) Model-driven evaluation of the production potential for growth- coupled products of Escherichia coli Metab. Eng. 12, 173-186 10.1016/j.ymben.2009.10.003
    • (2010) Metab. Eng. , vol.12 , pp. 173-186
    • Feist, A.M.1    Zielinski, D.C.2    Orth, J.D.3
  • 33
    • 0027223982 scopus 로고
    • Stoichiometric Interpretation of Escherichia coli Glucose Catabolism under Various Oxygenation Rates
    • VARMA, A., BOESCH, B. W., and PALSSON, B. (1993) Stoichiometric Interpretation of Escherichia coli Glucose Catabolism under Various Oxygenation Rates Appl. Environ. Microbiol. 59, 2465-2473
    • (1993) Appl. Environ. Microbiol. , vol.59 , pp. 2465-2473
    • Varma, A.1    Boesch, B.W.2    Palsson, B.3
  • 34
    • 0028146781 scopus 로고
    • Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110
    • VARMA, A. and PALSSON, B. O. (1994) Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110 Appl. Environ. Microbiol. 60, 3724-3731
    • (1994) Appl. Environ. Microbiol. , vol.60 , pp. 3724-3731
    • Varma, A.1    Palsson, B.O.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.