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Volumn 17, Issue 2, 2010, Pages 107-119

On algebraic properties of extreme pathways in metabolic networks

Author keywords

Algorithms; Biochemical networks; Linear algebra

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; ERYTHROCYTE; ESCHERICHIA COLI; HUMAN; METABOLISM; METHODOLOGY; SIGNAL TRANSDUCTION;

EID: 77249147418     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2009.0020     Document Type: Article
Times cited : (16)

References (34)
  • 1
    • 17544366029 scopus 로고    scopus 로고
    • Expa: Program for calculating extreme pathways in biochemical reaction networks
    • Bell, S., and Palsson, B. 2005. Expa: program for calculating extreme pathways in biochemical reaction networks. Bioinformatics 21, 1739-1740.
    • (2005) Bioinformatics , vol.21 , pp. 1739-1740
    • Bell, S.1    Palsson, B.2
  • 2
    • 0037406237 scopus 로고    scopus 로고
    • Development of network-based pathway definitions: The need to analyze real metabolic networks
    • Bernhard, O., Palsson, N.D.P., and Papin, J.A. 2003. Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends Biotechnol. 21, 195-198.
    • (2003) Trends Biotechnol , vol.21 , pp. 195-198
    • Bernhard, O.1    Palsson, N.D.P.2    Papin, J.A.3
  • 3
    • 1842525835 scopus 로고    scopus 로고
    • Fundamental Escherichia coli biochemical pathways for biomass and energy production: Creation of overall flux states
    • Carlson, R., and Srienc, F. 2004a. Fundamental Escherichia coli biochemical pathways for biomass and energy production: creation of overall flux states. Biotechnol. Bioeng. 86, 149-162.
    • (2004) Biotechnol. Bioeng , vol.86 , pp. 149-162
    • Carlson, R.1    Srienc, F.2
  • 4
    • 0347761259 scopus 로고    scopus 로고
    • Fundamental Escherichia coli biochemical pathways for biomass and energy production: Identification of reactions
    • Carlson, R., and Srienc, F. 2004b. Fundamental Escherichia coli biochemical pathways for biomass and energy production: identification of reactions. Biotechnol. Bioeng. 85, 1-19.
    • (2004) Biotechnol. Bioeng , vol.85 , pp. 1-19
    • Carlson, R.1    Srienc, F.2
  • 5
    • 84947909628 scopus 로고    scopus 로고
    • Double description method revisited
    • Deza, M., Euler, R., and Manoussakis I., Eds. Springer, New York
    • Fukuda, K., and Prodon, A. 1996. Double description method revisited, 91-111. In: Deza, M., Euler, R., and Manoussakis, I., Eds. Combinatorics and Computer Science. Springer, New York.
    • (1996) Combinatorics and Computer Science , pp. 91-111
    • Fukuda, K.1    Prodon, A.2
  • 6
    • 13244292328 scopus 로고    scopus 로고
    • Computation of elementary modes: A unifying framework and the new binary approach
    • Gagneur, J., and Klamt, S. 2004. Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinform. 5, 175.
    • (2004) BMC Bioinform , vol.5 , pp. 175
    • Gagneur, J.1    Klamt, S.2
  • 7
    • 0036039060 scopus 로고    scopus 로고
    • Combinatorial complexity of pathway analysis in metabolic networks
    • Klamt, S., and Stelling, J. 2002. Combinatorial complexity of pathway analysis in metabolic networks. Mol. Biol. Rep. 29, 233-236.
    • (2002) Mol. Biol. Rep , vol.29 , pp. 233-236
    • Klamt, S.1    Stelling, J.2
  • 8
    • 0037308505 scopus 로고    scopus 로고
    • Two approaches for metabolic pathway analysis
    • Klamt, S., and Stelling, J. 2003. Two approaches for metabolic pathway analysis. Trends Biotechnol. 21, 64-69.
    • (2003) Trends Biotechnol , vol.21 , pp. 64-69
    • Klamt, S.1    Stelling, J.2
  • 9
    • 0037316342 scopus 로고    scopus 로고
    • Flux analyzer: Exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps
    • Klamt, S., Stelling, J., Ginkel, M., et al. 2003. FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19, 261-269.
    • (2003) Bioinformatics , vol.19 , pp. 261-269
    • Klamt, S.1    Stelling, J.2    Ginkel, M.3
  • 10
    • 31144448020 scopus 로고    scopus 로고
    • Algorithmic approaches for computing elementary modes in large biochemical reaction networks
    • Klamt, S., Gagneur, J., and Von Kamp, A. 2005. Algorithmic approaches for computing elementary modes in large biochemical reaction networks. IEE Proc. Syst. Biol. 152, 249-255.
    • (2005) IEE Proc. Syst. Biol , vol.152 , pp. 249-255
    • Klamt, S.1    Gagneur, J.2    Von Kamp, A.3
  • 11
    • 34447551397 scopus 로고    scopus 로고
    • Structural and functional analysis of cellular networks with CellNetAnalyzer
    • Klamt, S., Saez-Rodriguez, J., and Gilles, E. D. 2007. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol. 1.
    • (2007) BMC Syst. Biol , pp. 1
    • Klamt, S.1    Saez-Rodriguez, J.2    Gilles, E.D.3
  • 12
    • 77249126295 scopus 로고    scopus 로고
    • Parallel extreme pathway computation for metabolic networks
    • Lee, L., Varner, J., and Ko, K. 2004. Parallel extreme pathway computation for metabolic networks. Static Anal. Symp. 33-50.
    • (2004) Static Anal. Symp. , pp. 33-50
    • Lee, L.1    Varner, J.2    Ko, K.3
  • 13
    • 0002043078 scopus 로고
    • The double description method
    • Kuhn, H., and Tucker, A., eds. Princeton University Press, Princeton, NJ
    • Motzkin, T., Raiffa, H., Thompson, G., et al. 1953. The double description method, 51-73. In: Kuhn, H., and Tucker, A., eds. Contributions to Theory of Games, Vol.II. Princeton University Press, Princeton, NJ.
    • (1953) Contributions to Theory of Games , vol.2 , pp. 51-73
    • Motzkin, T.1    Raiffa, H.2    Thompson, G.3
  • 14
    • 3342925846 scopus 로고    scopus 로고
    • Comparison of network-based pathway analysis methods
    • Papin, J., Stelling, J., Price, N. D., et al. 2004. Comparison of network-based pathway analysis methods. Trends Biotechnol. 22, 400-405.
    • (2004) Trends Biotechnol , vol.22 , pp. 400-405
    • Papin, J.1    Stelling, J.2    Price, N.D.3
  • 16
    • 36248982110 scopus 로고    scopus 로고
    • Modular decomposition of metabolic systems via null-space analysis
    • Poolman, M., Sebu, C., Pidcocle, M., et al. 2007. Modular decomposition of metabolic systems via null-space analysis. J. Theoret. Biol. 249, 691-705.
    • (2007) J. Theoret. Biol , vol.249 , pp. 691-705
    • Poolman, M.1    Sebu, C.2    Pidcocle, M.3
  • 18
    • 0034615791 scopus 로고    scopus 로고
    • Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective
    • Schilling, C.H., Letscher, D., and Palsson, B. 2000. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theoret. Biol. 203, 229-248.
    • (2000) J. Theoret. Biol , vol.203 , pp. 229-248
    • Schilling, C.H.1    Letscher, D.2    Palsson, B.3
  • 19
    • 0000029295 scopus 로고
    • On elementary flux modes in biochemical reaction systems at steady state
    • Schuster, S., and Hilgetag, C. 1994. On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst. 2, 165-182.
    • (1994) J. Biol. Syst , vol.2 , pp. 165-182
    • Schuster, S.1    Hilgetag, C.2
  • 20
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
    • Schuster, S., Dandekar, T., and Fell, D. 1999. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol. 17, 53-60.
    • (1999) Trends Biotechnol , vol.17 , pp. 53-60
    • Schuster, S.1    Dandekar, T.2    Fell, D.3
  • 21
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • Schuster, S., Fell, D., and Dandekar, T. 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    Fell, D.2    Dandekar, T.3
  • 22
    • 0036691976 scopus 로고    scopus 로고
    • Reaction routes in biochemical reaction systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism
    • Schuster, S., Hilgetag, C., Woods, J., et al. 2002. Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism. Math. Biol. 45, 153-181.
    • (2002) Math. Biol , vol.45 , pp. 153-181
    • Schuster, S.1    Hilgetag, C.2    Woods, J.3
  • 23
    • 0037079050 scopus 로고    scopus 로고
    • Metabolic network structure determines key aspects of functionality and regulation
    • Stelling, J., Klamt, S., Bettenbrock, K., et al. 2002. Metabolic network structure determines key aspects of functionality and regulation. Nature 420, 190-193.
    • (2002) Nature , vol.420 , pp. 190-193
    • Stelling, J.1    Klamt, S.2    Bettenbrock, K.3
  • 24
    • 52949098408 scopus 로고    scopus 로고
    • Large scale computation of elementary flux modes with bit pattern trees
    • doi: 10.1093=bioinformatics=btn401
    • Terzer, M., and Stelling, J. 2008. Large scale computation of elementary flux modes with bit pattern trees. Bioinformatics doi: 10.1093=bioinformatics= btn401.
    • (2008) Bioinformatics
    • Terzer, M.1    Stelling, J.2
  • 25
    • 33749448704 scopus 로고    scopus 로고
    • Design, construction and performance of the most efficient biomass producing E. coli bacterium
    • Trinh, C., Carlson, R., Wlaschin, A., et al. 2006. Design, construction and performance of the most efficient biomass producing E. coli bacterium. Metab. Eng. 8, 628-638.
    • (2006) Metab. Eng , vol.8 , pp. 628-638
    • Trinh, C.1    Carlson, R.2    Wlaschin, A.3
  • 26
    • 45749137679 scopus 로고    scopus 로고
    • A minimal Escherichia coli cell for most efficient ethanol production from hexoses and pentoses
    • Trinh, C., Unrean, P., and Srienc, F. 2008. A minimal Escherichia coli cell for most efficient ethanol production from hexoses and pentoses. Appl. Environ. Microbiol. 74, 3634-3643.
    • (2008) Appl. Environ. Microbiol , vol.74 , pp. 3634-3643
    • Trinh, C.1    Unrean, P.2    Srienc, F.3
  • 27
    • 34548406565 scopus 로고    scopus 로고
    • Enumerating constrained elementary flux vectors of metabolic networks
    • Urbanczik, R. 2007. Enumerating constrained elementary flux vectors of metabolic networks. IET Syst. Biol. 1, 274-279.
    • (2007) IET Syst. Biol , vol.1 , pp. 274-279
    • Urbanczik, R.1
  • 28
    • 27944471469 scopus 로고    scopus 로고
    • Functional stoichiometric analysis of metabolic networks
    • Urbanczik, R., and Wagner, C. 2005a. Functional stoichiometric analysis of metabolic networks. Bioinformatics 21, 4176-4180.
    • (2005) Bioinformatics , vol.21 , pp. 4176-4180
    • Urbanczik, R.1    Wagner, C.2
  • 29
    • 16344382935 scopus 로고    scopus 로고
    • An improved algorithm for stoichiometric network analysis: Theory and applications
    • Urbanczik, R., and Wagner, C. 2005b. An improved algorithm for stoichiometric network analysis: theory and applications. Bioinformatics 21, 1203-1210.
    • (2005) Bioinformatics , vol.21 , pp. 1203-1210
    • Urbanczik, R.1    Wagner, C.2
  • 30
    • 27544505746 scopus 로고    scopus 로고
    • Metablic pathway structures for recombinant protein synthesis in Escherichia coli
    • Vijayasankaran, N., Carlson, R., and Srienc, F. 2005. Metablic pathway structures for recombinant protein synthesis in Escherichia coli. Appl. Microbiol. Biotechnol. 68, 737-746.
    • (2005) Appl. Microbiol. Biotechnol , vol.68 , pp. 737-746
    • Vijayasankaran, N.1    Carlson, R.2    Srienc, F.3
  • 31
    • 33747856186 scopus 로고    scopus 로고
    • Metatool 5.0: Fast and flexible elementary modes analysis
    • Von Kamp, A., and Schuster, S. 2006. Metatool 5.0: fast and flexible elementary modes analysis. Bioinformatics 22, 1930-1931.
    • (2006) Bioinformatics , vol.22 , pp. 1930-1931
    • Von Kamp, A.1    Schuster, S.2
  • 32
    • 1442337345 scopus 로고    scopus 로고
    • Nullspace approach to determine the elementary modes of chemical reaction systems
    • Wagner, C. 2004. Nullspace approach to determine the elementary modes of chemical reaction systems. J. Phys. Chem. 108, 2425-2431.
    • (2004) J. Phys. Chem , vol.108 , pp. 2425-2431
    • Wagner, C.1
  • 33
    • 0035997009 scopus 로고    scopus 로고
    • Extreme pathway analysis of human red blood cell metabolism
    • Wiback, S., and Palsson, B. 2002. Extreme pathway analysis of human red blood cell metabolism. Biophys. J. 83, 808-818.
    • (2002) Biophys. J , vol.83 , pp. 808-818
    • Wiback, S.1    Palsson, B.2
  • 34
    • 36348959154 scopus 로고    scopus 로고
    • Estimation of the number of extreme pathways for metabolic networks
    • Yeung, M., Thiele, I., and Palsson, B. 2007. Estimation of the number of extreme pathways for metabolic networks. BMC Bioinform. 8.
    • (2007) BMC Bioinform , pp. 8
    • Yeung, M.1    Thiele, I.2    Palsson, B.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.