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Volumn 10, Issue SUPPL. 1, 2009, Pages

Analysis on relationship between extreme pathways and correlated reaction sets

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY RELATIONSHIP; CONSTRAINT-BASED MODELING; GENOME-SCALE METABOLIC NETWORK; METABOLIC NETWORK; POSSIBLE MECHANISMS; REGULATORY NETWORK; RELATED FUNCTIONS; TOPOLOGY INFORMATION;

EID: 60849128208     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S1-S58     Document Type: Article
Times cited : (4)

References (36)
  • 1
    • 31144435316 scopus 로고    scopus 로고
    • Towards multidimensional genome annotation
    • 10.1038/nrg1769 16418748
    • Reed JL Famili I Thiele I Palsson BO Towards multidimensional genome annotation Nat Rev Genet 2006, 7(2):130-141 10.1038/nrg1769 16418748
    • (2006) Nat Rev Genet , vol.7 , Issue.2 , pp. 130-141
    • Reed, J.L.1    Famili, I.2    Thiele, I.3    Palsson, B.O.4
  • 3
    • 0036001069 scopus 로고    scopus 로고
    • Metabolic modelling of microbes: The flux-balance approach
    • 10.1046/j.1462-2920.2002.00282.x 12000313
    • Edwards JS Covert M Palsson BO Metabolic modelling of microbes: The flux-balance approach Environ Microbiol 2002, 4(3):133-40 10.1046/ j.1462-2920.2002.00282.x 12000313
    • (2002) Environ Microbiol , vol.4 , Issue.3 , pp. 133-140
    • Edwards, J.S.1    Covert, M.2    Palsson, B.O.3
  • 4
    • 0037406843 scopus 로고    scopus 로고
    • Thirteen years of building constraint-based in silico models of Escherichia coli
    • 154396 12700248 10.1128/JB.185.9.2692-2699.2003
    • Reed JL Palsson BO Thirteen years of building constraint-based in silico models of Escherichia coli J Bacteriol 2003, 185(9):2692-2699 154396 12700248 10.1128/JB.185.9.2692-2699.2003
    • (2003) J Bacteriol , vol.185 , Issue.9 , pp. 2692-2699
    • Reed, J.L.1    Palsson, B.O.2
  • 5
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: Evaluating the consequences of constraints
    • 10.1038/nrmicro1023 15494745
    • Price ND Reed JL Palsson BO Genome-scale models of microbial cells: evaluating the consequences of constraints Nat Rev Microbiol 2004, 2(11):886-97 10.1038/nrmicro1023 15494745
    • (2004) Nat Rev Microbiol , vol.2 , Issue.11 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, B.O.3
  • 6
    • 0037424661 scopus 로고    scopus 로고
    • Constraints-based models: Regulation of gene expression reduces the steady-state solution space
    • 10.1006/jtbi.2003.3071 12642111
    • Covert MW Palsson BO Constraints-based models: Regulation of gene expression reduces the steady-state solution space J Theor Biol 2003, 221(3):309-325 10.1006/jtbi.2003.3071 12642111
    • (2003) J Theor Biol , vol.221 , Issue.3 , pp. 309-325
    • Covert, M.W.1    Palsson, B.O.2
  • 7
    • 0034447725 scopus 로고    scopus 로고
    • Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems
    • 10.1002/1097-0290(2000)71:4<286::AID-BIT1018>3.0.CO;2-R 11291038
    • Schilling CH Edwards JS Letscher D Palsson BO Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems Biotechnol Bioeng 2000, 71(4):286-306 10.1002/ 1097-0290(2000)71:4<286::AID-BIT1018>3.0.CO;2-R 11291038
    • (2000) Biotechnol Bioeng , vol.71 , Issue.4 , pp. 286-306
    • Schilling, C.H.1    Edwards, J.S.2    Letscher, D.3    Palsson, B.O.4
  • 8
    • 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
    • 10.1006/jtbi.2000.1073 10716907
    • Schilling CH Letscher D Palsson BO Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective J Theor Biol 2000, 203(3):229-248 10.1006/ jtbi.2000.1073 10716907
    • (2000) J Theor Biol , vol.203 , Issue.3 , pp. 229-248
    • Schilling, C.H.1    Letscher, D.2    Palsson, B.O.3
  • 9
    • 0032516028 scopus 로고    scopus 로고
    • The underlying pathway structure of biochemical reaction networks
    • 22464 9539712 10.1073/pnas.95.8.4193
    • Schilling CH Palsson BO The underlying pathway structure of biochemical reaction networks Proc Natl Acad Sci USA 1998, 95(8):4193-4198 22464 9539712 10.1073/pnas.95.8.4193
    • (1998) Proc Natl Acad Sci USA , vol.95 , Issue.8 , pp. 4193-4198
    • Schilling, C.H.1    Palsson, B.O.2
  • 10
  • 11
    • 0037304679 scopus 로고    scopus 로고
    • Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices
    • 1302660 12547764 10.1016/S0006-3495(03)74899-1
    • Price ND Reed JL Papin JA Famili I Palsson BO Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices Biophys J 2003, 84(2 Pt 1):794-804 1302660 12547764 10.1016/ S0006-3495(03)74899-1
    • (2003) Biophys J , vol.84 , Issue.2 PART 1 , pp. 794-804
    • Price, N.D.1    Reed, J.L.2    Papin, J.A.3    Famili, I.4    Palsson, B.O.5
  • 12
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • 10.1038/73786 10700151
    • 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 10.1038/73786 10700151
    • (2000) Nat Biotechnol , vol.18 , Issue.3 , pp. 326-332
    • Schuster, S.1    Fell, D.A.2    Dandekar, T.3
  • 13
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
    • 10.1016/S0167-7799(98)01290-6 10087604
    • Schuster S Dandekar T Fell DA Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering Trends Biotechnol 1999, 17(2):53-60 10.1016/ S0167-7799(98)01290-6 10087604
    • (1999) Trends Biotechnol , vol.17 , Issue.2 , pp. 53-60
    • Schuster, S.1    Dandekar, T.2    Fell, D.A.3
  • 14
    • 0000029295 scopus 로고
    • On elementary flux modes in biochemical reaction systems at steady state
    • 10.1142/S0218339094000131
    • Schuster S Hilgetag C On elementary flux modes in biochemical reaction systems at steady state Journal of Biological Systems (JBS) 1994, 2(2):165-182 10.1142/S0218339094000131
    • (1994) Journal of Biological Systems (JBS) , vol.2 , Issue.2 , pp. 165-182
    • Schuster, S.1    Hilgetag, C.2
  • 15
    • 0037308505 scopus 로고    scopus 로고
    • Two approaches for metabolic pathway analysis?
    • 10.1016/S0167-7799(02)00034-3 12573854
    • Klamt S Stelling J Two approaches for metabolic pathway analysis? Trends Biotechnol 2003, 21(2):64-9 10.1016/S0167-7799(02)00034-3 12573854
    • (2003) Trends Biotechnol , vol.21 , Issue.2 , pp. 64-69
    • Klamt, S.1    Stelling, J.2
  • 16
    • 8544223537 scopus 로고    scopus 로고
    • Hierarchical thinking in network biology: The unbiased modularization of biochemical networks
    • 10.1016/j.tibs.2004.10.001 15544950
    • Papin JA Reed JL Palsson BO Hierarchical thinking in network biology: the unbiased modularization of biochemical networks Trends Biochem Sci 2004, 29(12):641-647 10.1016/j.tibs.2004.10.001 15544950
    • (2004) Trends Biochem Sci , vol.29 , Issue.12 , pp. 641-647
    • Papin, J.A.1    Reed, J.L.2    Palsson, B.O.3
  • 17
    • 0037079050 scopus 로고    scopus 로고
    • Metabolic network structure determines key aspects of functionality and regulation
    • 10.1038/nature01166 12432396
    • Stelling J Klamt S Bettenbrock K Schuster S Gilles ED Metabolic network structure determines key aspects of functionality and regulation Nature 2002, 420(6912):190-3 10.1038/nature01166 12432396
    • (2002) Nature , vol.420 , Issue.6912 , pp. 190-193
    • Stelling, J.1    Klamt, S.2    Bettenbrock, K.3    Schuster, S.4    Gilles, E.D.5
  • 18
    • 0036100243 scopus 로고    scopus 로고
    • Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis
    • 186586 11997342
    • Price ND Papin JA Palsson BO Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis Genome Res 2002, 12(5):760-769 186586 11997342
    • (2002) Genome Res , vol.12 , Issue.5 , pp. 760-769
    • Price, N.D.1    Papin, J.A.2    Palsson, B.O.3
  • 19
    • 0036039060 scopus 로고    scopus 로고
    • Combinatorial complexity of pathway analysis in metabolic networks
    • 10.1023/A:1020390132244 12241063
    • Klamt S Stelling J Combinatorial complexity of pathway analysis in metabolic networks Mol Biol Rep 2002, 29(1-2):233-6 10.1023/ A:1020390132244 12241063
    • (2002) Mol Biol Rep , vol.29 , Issue.1-2 , pp. 233-236
    • Klamt, S.1    Stelling, J.2
  • 20
    • 36348959154 scopus 로고    scopus 로고
    • Estimation of the number of extreme pathways for metabolic networks
    • 2089122 17897474 10.1186/1471-2105-8-363
    • Yeung M Thiele I Palsson BO Estimation of the number of extreme pathways for metabolic networks BMC Bioinformatics 2007, 8:363 2089122 17897474 10.1186/1471-2105-8-363
    • (2007) BMC Bioinformatics , vol.8 , pp. 363
    • Yeung, M.1    Thiele, I.2    Palsson, B.O.3
  • 21
    • 1542288938 scopus 로고    scopus 로고
    • Global organization of metabolic fluxes in the bacterium Escherichia coli
    • 10.1038/nature02289 14985762
    • Almaas E Kovacs B Vicsek T Oltvai ZN Barabasi AL Global organization of metabolic fluxes in the bacterium Escherichia coli Nature 2004, 427(6977):839-43 10.1038/nature02289 14985762
    • (2004) Nature , vol.427 , Issue.6977 , pp. 839-843
    • Almaas, E.1    Kovacs, B.2    Vicsek, T.3    Oltvai, Z.N.4    Barabasi, A.L.5
  • 22
    • 34347258175 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox
    • 10.1038/nprot.2007.99 17406635
    • Becker SA Feist AM Mo ML Hannum G Palsson BO Herrgard MJ Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox Nat Protoc 2007, 2(3):727-738 10.1038/nprot.2007.99 17406635
    • (2007) Nat Protoc , vol.2 , Issue.3 , pp. 727-738
    • Becker, S.A.1    Feist, A.M.2    Mo, M.L.3    Hannum, G.4    Palsson, B.O.5    Herrgard, M.J.6
  • 23
    • 33747192003 scopus 로고    scopus 로고
    • Monte Carlo sampling and principal component analysis of flux distributions yield topological and modular information on metabolic networks
    • 10.1016/j.jtbi.2006.03.007 16860341
    • SarIyar B Perk S Akman U Hortacsu A Monte Carlo sampling and principal component analysis of flux distributions yield topological and modular information on metabolic networks Journal of Theoretical Biology 2006, 242(2):389-400 10.1016/j.jtbi.2006.03.007 16860341
    • (2006) Journal of Theoretical Biology , vol.242 , Issue.2 , pp. 389-400
    • SarIyar, B.1    Perk, S.2    Akman, U.3    Hortacsu, A.4
  • 24
    • 4644220226 scopus 로고    scopus 로고
    • Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: Assessment of correlated reaction subsets that comprise network states
    • 515326 15342562 10.1101/gr.2546004
    • Reed JL Palsson BO Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: Assessment of correlated reaction subsets that comprise network states Genome Res 2004, 14(9):1797-1805 515326 15342562 10.1101/gr.2546004
    • (2004) Genome Res , vol.14 , Issue.9 , pp. 1797-1805
    • Reed, J.L.1    Palsson, B.O.2
  • 25
    • 0035997009 scopus 로고    scopus 로고
    • Extreme Pathway Analysis of Human Red Blood Cell Metabolism
    • 1302188 12124266 10.1016/S0006-3495(02)75210-7
    • Wiback SJ Palsson BO Extreme Pathway Analysis of Human Red Blood Cell Metabolism Biophys J 2002, 83(2):808-818 1302188 12124266 10.1016/ S0006-3495(02)75210-7
    • (2002) Biophys J , vol.83 , Issue.2 , pp. 808-818
    • Wiback, S.J.1    Palsson, B.O.2
  • 26
    • 84874647148 scopus 로고    scopus 로고
    • E. coli, E. coli SBML
    • In Silico Organisms, E. coli, E. coli SBML http://gcrg.ucsd.edu/ In_Silico_Organisms/E_coli/E_coli_SBML
    • In Silico Organisms
  • 28
    • 0033567930 scopus 로고    scopus 로고
    • Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: Computer simulation and metabolic control analysis
    • 1220500 10477270 10.1042/0264-6021:3420597
    • Mulquiney PJ Kuchel PW Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: computer simulation and metabolic control analysis Biochem J 1999, 342(Pt 3):597-604 1220500 10477270 10.1042/0264-6021:3420597
    • (1999) Biochem J , vol.342 , Issue.PART 3 , pp. 597-604
    • Mulquiney, P.J.1    Kuchel, P.W.2
  • 29
    • 0025687613 scopus 로고
    • A comprehensive model of human erythrocyte metabolism: Extensions to include pH effects
    • 2082921
    • Lee ID Palsson BO A comprehensive model of human erythrocyte metabolism: extensions to include pH effects Biomed Biochim Acta 1990, 49(8-9):771-789 2082921
    • (1990) Biomed Biochim Acta , vol.49 , Issue.8-9 , pp. 771-789
    • Lee, I.D.1    Palsson, B.O.2
  • 30
    • 0024842144 scopus 로고
    • Metabolic dynamics in the human red cell. Part I - A comprehensive kinetic model
    • 10.1016/S0022-5193(89)80233-4 2630803
    • Joshi A Palsson BO Metabolic dynamics in the human red cell. Part I - A comprehensive kinetic model J Theor Biol 1989, 141(4):515-528 10.1016/ S0022-5193(89)80233-4 2630803
    • (1989) J Theor Biol , vol.141 , Issue.4 , pp. 515-528
    • Joshi, A.1    Palsson, B.O.2
  • 31
    • 0024799182 scopus 로고
    • Metabolic dynamics in the human red cell. Part II - Interactions with the environment
    • 10.1016/S0022-5193(89)80234-6 2630804
    • Joshi A Palsson BO Metabolic dynamics in the human red cell. Part II - Interactions with the environment J Theor Biol 1989, 141(4):529-545 10.1016/S0022-5193(89)80234-6 2630804
    • (1989) J Theor Biol , vol.141 , Issue.4 , pp. 529-545
    • Joshi, A.1    Palsson, B.O.2
  • 33
    • 3843128481 scopus 로고    scopus 로고
    • Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model
    • 442145 15197165 10.1101/gr.2250904
    • Duarte NC Herrgard MJ Palsson BO Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model Genome Res 2004, 14(7):1298-309 442145 15197165 10.1101/ gr.2250904
    • (2004) Genome Res , vol.14 , Issue.7 , pp. 1298-1309
    • Duarte, N.C.1    Herrgard, M.J.2    Palsson, B.O.3
  • 34
    • 17544366029 scopus 로고    scopus 로고
    • Expa: A program for calculating extreme pathways in biochemical reaction networks
    • 10.1093/bioinformatics/bti228 15613397
    • Bell SL Palsson BO expa: A program for calculating extreme pathways in biochemical reaction networks Bioinformatics 2005, 21(8):1739-1740 10.1093/bioinformatics/bti228 15613397
    • (2005) Bioinformatics , vol.21 , Issue.8 , pp. 1739-1740
    • Bell, S.L.1    Palsson, B.O.2
  • 35
    • 0033136109 scopus 로고    scopus 로고
    • Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post-genomic Era
    • 10.1021/bp990048k 10356246
    • Schilling C Schuster S Palsson B Heinrich R Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post-genomic Era Biotechnology Progress 1999, 15(3):296-303 10.1021/bp990048k 10356246
    • (1999) Biotechnology Progress , vol.15 , Issue.3 , pp. 296-303
    • Schilling, C.1    Schuster, S.2    Palsson, B.3    Heinrich, R.4
  • 36
    • 0036840340 scopus 로고    scopus 로고
    • Extreme Pathways and Kirchhoff's Second Law
    • 1302372 12425318 10.1016/S0006-3495(02)75297-1
    • Price ND Famili I Beard DA Palsson BO Extreme Pathways and Kirchhoff's Second Law Biophys J 2002, 83(5):2879-2882 1302372 12425318 10.1016/ S0006-3495(02)75297-1
    • (2002) Biophys J , vol.83 , Issue.5 , pp. 2879-2882
    • Price, N.D.1    Famili, I.2    Beard, D.A.3    Palsson, B.O.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.