메뉴 건너뛰기




Volumn 10, Issue 1, 2015, Pages

Designing minimal microbial strains of desired functionality using a genetic algorithm

Author keywords

Elementary flux modes; Metabolic networks; Minimal cut sets; Strain optimization; Systems biology

Indexed keywords


EID: 84953635714     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/s13015-015-0060-6     Document Type: Article
Times cited : (6)

References (38)
  • 2
    • 57549102595 scopus 로고    scopus 로고
    • Genome-scale models of bacterial metabolism: reconstruction and applications
    • Durot M, Bourguignon P-Y, Schachter V. Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev. 2009;33(1):164-90.
    • (2009) FEMS Microbiol Rev , vol.33 , Issue.1 , pp. 164-190
    • Durot, M.1    Bourguignon, P.-Y.2    Schachter, V.3
  • 4
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • Thiele I, Palsson BØ. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc. 2010;5(1):93-121.
    • (2010) Nat Protoc , vol.5 , Issue.1 , pp. 93-121
    • Thiele, I.1    Palsson, B.2
  • 5
    • 73149122136 scopus 로고    scopus 로고
    • Applications of genome-scale metabolic reconstructions
    • Oberhardt MA, Palsson BØ, Papin JA. Applications of genome-scale metabolic reconstructions. Mol Syst Biol. 2009;5(1):320.
    • (2009) Mol Syst Biol. , vol.5 , Issue.1 , pp. 320
    • Oberhardt, M.A.1    Palsson, B.2    Papin, J.A.3
  • 6
    • 79957637424 scopus 로고    scopus 로고
    • A survey on methods for modeling and analyzing integrated biological networks
    • Tenazinha N, Vinga S. A survey on methods for modeling and analyzing integrated biological networks. IEEE/ACM Trans Comput Biol Bioinform (TCBB). 2011;8(4):943-58.
    • (2011) IEEE/ACM Trans Comput Biol Bioinform (TCBB) , vol.8 , Issue.4 , pp. 943-958
    • Tenazinha, N.1    Vinga, S.2
  • 7
  • 8
    • 0000029295 scopus 로고
    • On elementary flux modes in biochemical reaction systems at steady state
    • Schuster S, Hilgetag C. On elementary flux modes in biochemical reaction systems at steady state. J Biol Syst. 1994;2(02):165-82.
    • (1994) J Biol Syst , vol.2 , Issue.2 , pp. 165-182
    • Schuster, S.1    Hilgetag, C.2
  • 9
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • Schuster S, Fell DA, Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol. 2000;18(3):326-32.
    • (2000) Nat Biotechnol , vol.18 , Issue.3 , pp. 326-332
    • Schuster, S.1    Fell, D.A.2    Dandekar, T.3
  • 10
    • 0036039060 scopus 로고    scopus 로고
    • Combinatorial complexity of pathway analysis in metabolic networks
    • Klamt S, Stelling J. Combinatorial complexity of pathway analysis in metabolic networks. Mol Biol Rep. 2002;29(1-2):233-6.
    • (2002) Mol Biol Rep , vol.29 , Issue.1-2 , pp. 233-236
    • Klamt, S.1    Stelling, J.2
  • 11
    • 13244292328 scopus 로고    scopus 로고
    • Computation of elementary modes: a unifying framework and the new binary approach
    • Gagneur J, Klamt S. Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinform. 2004;5(1):175.
    • (2004) BMC Bioinform , vol.5 , Issue.1 , pp. 175
    • Gagneur, J.1    Klamt, S.2
  • 12
    • 52949098408 scopus 로고    scopus 로고
    • Large-scale computation of elementary flux modes with bit pattern trees
    • Terzer M, Stelling J. Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics. 2008;24(19):2229-35.
    • (2008) Bioinformatics , vol.24 , Issue.19 , pp. 2229-2235
    • Terzer, M.1    Stelling, J.2
  • 13
    • 84878346520 scopus 로고    scopus 로고
    • regEfmtool: speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic
    • Jungreuthmayer C, Ruckerbauer DE, Zanghellini J. regEfmtool: speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic. Biosystems. 2013;113(1):37-9.
    • (2013) Biosystems , vol.113 , Issue.1 , pp. 37-39
    • Jungreuthmayer, C.1    Ruckerbauer, D.E.2    Zanghellini, J.3
  • 14
    • 84919499768 scopus 로고    scopus 로고
    • Computing elementary flux modes involving a set of target reactions
    • David L, Bockmayr A. Computing elementary flux modes involving a set of target reactions. IEEE/ACM Trans Comput Biol Bioinform (TCBB). 2014;11(6):1099-107.
    • (2014) IEEE/ACM Trans Comput Biol Bioinform (TCBB) , vol.11 , Issue.6 , pp. 1099-1107
    • David, L.1    Bockmayr, A.2
  • 15
    • 45749137679 scopus 로고    scopus 로고
    • Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses
    • Trinh CT, Unrean P, Srienc F. Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses. Appl Environ Microbiol. 2008;74(12):3634-43.
    • (2008) Appl Environ Microbiol , vol.74 , Issue.12 , pp. 3634-3643
    • Trinh, C.T.1    Unrean, P.2    Srienc, F.3
  • 16
    • 79952103372 scopus 로고    scopus 로고
    • Computing complex metabolic intervention strategies using constrained minimal cut sets
    • Hädicke O, Klamt S. Computing complex metabolic intervention strategies using constrained minimal cut sets. Metab Eng. 2011;13(2):204-13.
    • (2011) Metab Eng , vol.13 , Issue.2 , pp. 204-213
    • Hädicke, O.1    Klamt, S.2
  • 17
    • 84864923763 scopus 로고    scopus 로고
    • Designing optimal cell factories: integer programming couples elementary mode analysis with regulation
    • Jungreuthmayer C, Zanghellini J. Designing optimal cell factories: integer programming couples elementary mode analysis with regulation. BMC Syst Biol. 2012;6(1):103.
    • (2012) BMC Syst Biol , vol.6 , Issue.1 , pp. 103
    • Jungreuthmayer, C.1    Zanghellini, J.2
  • 18
    • 84887038656 scopus 로고    scopus 로고
    • Comparison and improvement of algorithms for computing minimal cut sets
    • Jungreuthmayer C, Nair G, Klamt S, Zanghellini J. Comparison and improvement of algorithms for computing minimal cut sets. BMC Bioinform. 2013;14(1):318.
    • (2013) BMC Bioinform , vol.14 , Issue.1 , pp. 318
    • Jungreuthmayer, C.1    Nair, G.2    Klamt, S.3    Zanghellini, J.4
  • 19
    • 84856566482 scopus 로고    scopus 로고
    • Minimal cut sets in a metabolic network are elementary modes in a dual network
    • Ballerstein K, von Kamp A, Klamt S, Haus U-U. Minimal cut sets in a metabolic network are elementary modes in a dual network. Bioinformatics. 2012;28(3):381-7.
    • (2012) Bioinformatics , vol.28 , Issue.3 , pp. 381-387
    • Ballerstein, K.1    Kamp, A.2    Klamt, S.3    Haus, U.-U.4
  • 20
    • 84896731390 scopus 로고    scopus 로고
    • Enumeration of smallest intervention strategies in genome-scale metabolic networks
    • von Kamp A, Klamt S. Enumeration of smallest intervention strategies in genome-scale metabolic networks. PLoS Comput Biol. 2014;10(1):1003378.
    • (2014) PLoS Comput Biol , vol.10 , Issue.1 , pp. 1003378
    • Kamp, A.1    Klamt, S.2
  • 21
    • 84940738929 scopus 로고    scopus 로고
    • Genome-scale strain designs based on regulatory minimal cut sets
    • Mahadevan R, von Kamp A, Klamt S. Genome-scale strain designs based on regulatory minimal cut sets. Bioinformatics. 2015;31(17):2844-51.
    • (2015) Bioinformatics , vol.31 , Issue.17 , pp. 2844-2851
    • Mahadevan, R.1    von Kamp, A.2    Klamt, S.3
  • 23
    • 84899785053 scopus 로고    scopus 로고
    • Design of optimally constructed metabolic networks of minimal functionality
    • Ruckerbauer D, Jungreuthmayer C, Zanghellini J. Design of optimally constructed metabolic networks of minimal functionality. PLoS One. 2014;9(3):92583.
    • (2014) PLoS One , vol.9 , Issue.3 , pp. 92583
    • Ruckerbauer, D.1    Jungreuthmayer, C.2    Zanghellini, J.3
  • 24
    • 84884172916 scopus 로고    scopus 로고
    • Elementary flux modes in a nutshell: properties, calculation and applications
    • Zanghellini J, Ruckerbauer DE, Hanscho M, Jungreuthmayer C. Elementary flux modes in a nutshell: properties, calculation and applications. Biotechnol J. 2013;8(9):1009-16.
    • (2013) Biotechnol J , vol.8 , Issue.9 , pp. 1009-1016
    • Zanghellini, J.1    Ruckerbauer, D.E.2    Hanscho, M.3    Jungreuthmayer, C.4
  • 25
    • 1042269472 scopus 로고    scopus 로고
    • Minimal cut sets in biochemical reaction networks
    • Klamt S, Gilles ED. Minimal cut sets in biochemical reaction networks. Bioinformatics. 2004;20(2):226-34.
    • (2004) Bioinformatics , vol.20 , Issue.2 , pp. 226-234
    • Klamt, S.1    Gilles, E.D.2
  • 26
    • 0002338687 scopus 로고
    • A genetic algorithm tutorial
    • Whitley D. A genetic algorithm tutorial. Stat Comput. 1994;4(2):65-85.
    • (1994) Stat Comput , vol.4 , Issue.2 , pp. 65-85
    • Whitley, D.1
  • 27
    • 0001844324 scopus 로고
    • An overview of genetic algorithms: part 1. fundamentals
    • Beasley D, Martin R, Bull D. An overview of genetic algorithms: part 1. fundamentals. Univ Comput. 1993;15:58-58.
    • (1993) Univ Comput. , vol.15 , pp. 58
    • Beasley, D.1    Martin, R.2    Bull, D.3
  • 28
    • 84953634870 scopus 로고    scopus 로고
    • Computing minimal hitting sets with genetic algorithm
    • Technical report, DTIC Document
    • Li L, Yunfei J. Computing minimal hitting sets with genetic algorithm. Technical report, DTIC Document; 2002.
    • (2002)
    • Li, L.1    Yunfei, J.2
  • 29
    • 29144524121 scopus 로고    scopus 로고
    • An introduction to genetic algorithms
    • Mitchell M. An introduction to genetic algorithms. MIT press. 1998.
    • (1998) MIT press
    • Mitchell, M.1
  • 30
    • 84906095977 scopus 로고    scopus 로고
    • Fast computation of minimal cut sets in metabolic networks with a berge algorithm that utilizes binary bit pattern trees
    • Jungreuthmayer C, Beurton-Aimar M, Zanghellini J. Fast computation of minimal cut sets in metabolic networks with a berge algorithm that utilizes binary bit pattern trees. IEEE/ACM Trans Comput Biol Bioinform (TCBB). 2013;10(5):1.
    • (2013) IEEE/ACM Trans Comput Biol Bioinform (TCBB) , vol.10 , Issue.5 , pp. 1
    • Jungreuthmayer, C.1    Beurton-Aimar, M.2    Zanghellini, J.3
  • 31
    • 84866883709 scopus 로고
    • A comparative analysis of selection schemes used in genetic algorithms
    • Goldberg DE, Deb K. A comparative analysis of selection schemes used in genetic algorithms. Urbana. 1991;51:61801-2996.
    • (1991) Urbana , vol.51 , pp. 61801-62996
    • Goldberg, D.E.1    Deb, K.2
  • 32
    • 77950863401 scopus 로고    scopus 로고
    • Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli
    • Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng. 2010;12(3):173-86.
    • (2010) Metab Eng , vol.12 , Issue.3 , pp. 173-186
    • Feist, A.M.1    Zielinski, D.C.2    Orth, J.D.3    Schellenberger, J.4    Herrgard, M.J.5    Palsson, B.6
  • 33
    • 30044437327 scopus 로고    scopus 로고
    • Evolutionary programming as a platform for in silico metabolic engineering
    • Patil KR, Rocha I, Förster J, Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinform. 2005;6(1):308.
    • (2005) BMC Bioinform , vol.6 , Issue.1 , pp. 308
    • Patil, K.R.1    Rocha, I.2    Förster, J.3    Nielsen, J.4
  • 34
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of optimality in natural and perturbed metabolic networks
    • Segre D, Vitkup D, Church GM. Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci. 2002;99(23):15112-7.
    • (2002) Proc Natl Acad Sci , vol.99 , Issue.23 , pp. 15112-15117
    • Segre, D.1    Vitkup, D.2    Church, G.M.3
  • 35
    • 0242487787 scopus 로고    scopus 로고
    • Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • Burgard AP, Pharkya P, Maranas CD. Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng. 2003;84(6):647-57.
    • (2003) Biotechnol Bioeng , vol.84 , Issue.6 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 36
    • 77949495880 scopus 로고    scopus 로고
    • Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways
    • Tepper N, Shlomi T. Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics. 2010;26(4):536-43.
    • (2010) Bioinformatics , vol.26 , Issue.4 , pp. 536-543
    • Tepper, N.1    Shlomi, T.2
  • 37
    • 77951109180 scopus 로고    scopus 로고
    • Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design
    • Boghigian BA, Shi H, Lee K, Pfeifer BA. Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design. BMC Syst Biol. 2010;4(1):49.
    • (2010) BMC Syst Biol , vol.4 , Issue.1 , pp. 49
    • Boghigian, B.A.1    Shi, H.2    Lee, K.3    Pfeifer, B.A.4
  • 38
    • 34447551397 scopus 로고    scopus 로고
    • Structural and functional analysis of cellular networks with cellnetanalyzer
    • Klamt S, Saez-Rodriguez J, Gilles ED. Structural and functional analysis of cellular networks with cellnetanalyzer. BMC Syst Biol. 2007;1(1):2.
    • (2007) BMC Syst Biol , vol.1 , Issue.1 , pp. 2
    • Klamt, S.1    Saez-Rodriguez, J.2    Gilles, E.D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.