메뉴 건너뛰기




Volumn 14, Issue 4, 2012, Pages 344-353

Integrating tracer-based metabolomics data and metabolic fluxes in a linear fashion via Elementary Carbon Modes

Author keywords

Constraints based modeling; Elementary Carbon Modes; Flux Variability Analysis; Isotope Labeling Experiments; Metabolic Flux Analysis

Indexed keywords

BIOSYNTHETIC CAPACITY; CARBON LEVEL; COMBINATORIAL EXPLOSION; ELEMENTARY CARBON MODES; EXPERIMENTAL DATA; FLUX VARIABILITY; GENOME-SCALE METABOLIC NETWORK; HIGH-THROUGHPUT; HUMAN METABOLISMS; ISOTOPE LABELING; METABOLIC FLUX; METABOLIC FLUX ANALYSIS; METABOLIC NETWORK; METABOLOMICS DATA; NOVEL METHODS; STATE OF THE ART; SYSTEMS BIOLOGY;

EID: 84862167873     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2012.03.011     Document Type: Article
Times cited : (9)

References (52)
  • 2
    • 33845679072 scopus 로고    scopus 로고
    • Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions
    • Antoniewicz M.R., Kelleher J.K., Stephanopoulos G. Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab. Eng. 2007, 9:68-86.
    • (2007) Metab. Eng. , vol.9 , pp. 68-86
    • Antoniewicz, M.R.1    Kelleher, J.K.2    Stephanopoulos, G.3
  • 3
    • 79952105018 scopus 로고    scopus 로고
    • A flexible state-space approach for the modeling of metabolic networks, I: development of mathematical methods
    • Baughman A.C., Sharfstein S.T., Martin L.L. A flexible state-space approach for the modeling of metabolic networks, I: development of mathematical methods. Metab. Eng. 2011, 13:125.
    • (2011) Metab. Eng. , vol.13 , pp. 125
    • Baughman, A.C.1    Sharfstein, S.T.2    Martin, L.L.3
  • 7
    • 84857994816 scopus 로고    scopus 로고
    • Selection of tracers for 13C-Metabolic Flux Analysis using Elementary Metabolite Units (EMU) basis vector methodology.
    • in press.
    • Crown, S.B., Antoniewicz, M.R. Selection of tracers for 13C-Metabolic Flux Analysis using Elementary Metabolite Units (EMU) basis vector methodology. Metab. Eng., in press. http://dx.doi.org/10.1016/j.ymben.2011.12.005.
    • Metab. Eng.
    • Crown, S.B.1    Antoniewicz, M.R.2
  • 8
    • 78049255973 scopus 로고    scopus 로고
    • Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
    • Chandrasekaran S., Price N.D. Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 2010, 107:17845-17850.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 17845-17850
    • Chandrasekaran, S.1    Price, N.D.2
  • 9
    • 76749151341 scopus 로고    scopus 로고
    • Improving NADPH availability for natural product biosynthesis in Escherichia coli by metabolic engineering
    • Chemler J.A., Fowler Z.L., McHugh K.P., Koffas M.A.G. Improving NADPH availability for natural product biosynthesis in Escherichia coli by metabolic engineering. Metab. Eng. 2010, 12:96.
    • (2010) Metab. Eng. , vol.12 , pp. 96
    • Chemler, J.A.1    Fowler, Z.L.2    McHugh, K.P.3    Koffas, M.A.G.4
  • 11
    • 0036007687 scopus 로고    scopus 로고
    • Metabolomics-the link between genotypes and phenotypes
    • Fiehn O. Metabolomics-the link between genotypes and phenotypes. Plant Mol. Biol. 2002, 48:155-171.
    • (2002) Plant Mol. Biol. , vol.48 , pp. 155-171
    • Fiehn, O.1
  • 12
    • 54949122903 scopus 로고    scopus 로고
    • The adaptive convexification algorithm: a feasible point method for semi-infinite programming
    • Floudas C.A., Stein O. The adaptive convexification algorithm: a feasible point method for semi-infinite programming. SIAM J. Optim. 2007, 18:1187-1208.
    • (2007) SIAM J. Optim. , vol.18 , pp. 1187-1208
    • Floudas, C.A.1    Stein, O.2
  • 14
    • 29044444888 scopus 로고    scopus 로고
    • Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyces cerevisiae strains
    • Grotkjaer T., Christakopoulos P., Nielsen J., Olsson L. Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyces cerevisiae strains. Metab. Eng. 2005, 7:437-444.
    • (2005) Metab. Eng. , vol.7 , pp. 437-444
    • Grotkjaer, T.1    Christakopoulos, P.2    Nielsen, J.3    Olsson, L.4
  • 15
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa M., Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28:27-30.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 17
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: a brief overview
    • Kitano H. Systems biology: a brief overview. Science 2002, 295:1662-1664.
    • (2002) Science , vol.295 , pp. 1662-1664
    • Kitano, H.1
  • 18
    • 25444435195 scopus 로고    scopus 로고
    • Global solution approach for a nonconvex MINLP problem in product portfolio optimization
    • Lin X., Floudas C.A., Kallrath J. Global solution approach for a nonconvex MINLP problem in product portfolio optimization. J. Global Optim. 2005, 32:417-431.
    • (2005) J. Global Optim. , vol.32 , pp. 417-431
    • Lin, X.1    Floudas, C.A.2    Kallrath, J.3
  • 20
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    • Mahadevan R., Schilling C.H. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 2003, 5:264-276.
    • (2003) Metab. Eng. , vol.5 , pp. 264-276
    • Mahadevan, R.1    Schilling, C.H.2
  • 21
    • 78149478671 scopus 로고    scopus 로고
    • Current status of 13C-metabolic flux analysis and future perspectives
    • Matsuoka Y., Shimizu K. Current status of 13C-metabolic flux analysis and future perspectives. Process. Biochem. 2010, 45:1873-1881.
    • (2010) Process. Biochem. , vol.45 , pp. 1873-1881
    • Matsuoka, Y.1    Shimizu, K.2
  • 22
    • 60849114730 scopus 로고    scopus 로고
    • Overexpression of isocitrate lyase-glyoxylate bypass influence on metabolism in Aspergillus niger
    • Meijer S., Otero J., Olivares R., Andersen M.R., Olsson L., Nielsen J. Overexpression of isocitrate lyase-glyoxylate bypass influence on metabolism in Aspergillus niger. Metab. Eng. 2009, 11:107-116.
    • (2009) Metab. Eng. , vol.11 , pp. 107-116
    • Meijer, S.1    Otero, J.2    Olivares, R.3    Andersen, M.R.4    Olsson, L.5    Nielsen, J.6
  • 24
    • 79960383412 scopus 로고    scopus 로고
    • Do elementary flux modes combine linearly at the "atomic" level? Integrating tracer-based metabolomics data and elementary flux modes
    • Pey J., Theodoropoulos C., Rezola A., Rubio A., Cascante M., Planes F.J. Do elementary flux modes combine linearly at the "atomic" level? Integrating tracer-based metabolomics data and elementary flux modes. Biosystems 2011, 105:140-146.
    • (2011) Biosystems , vol.105 , pp. 140-146
    • Pey, J.1    Theodoropoulos, C.2    Rezola, A.3    Rubio, A.4    Cascante, M.5    Planes, F.J.6
  • 25
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: evaluating the consequences of constraints
    • Price N.D., Reed J.L., Palsson B.O. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat. Rev. Microbiol. 2004, 2:886-897.
    • (2004) Nat. Rev. Microbiol. , vol.2 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, B.O.3
  • 26
    • 33846061120 scopus 로고    scopus 로고
    • Metabolic networks in motion: 13C-based flux analysis
    • Sauer U. Metabolic networks in motion: 13C-based flux analysis. Mol. Syst. Biol. 2006, 2:62.
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 62
    • Sauer, U.1
  • 27
    • 77951612556 scopus 로고    scopus 로고
    • BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
    • Schellenberger J., Park J.O., Conrad T.M., Palsson B.O. BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinf. 2010, 11:213.
    • (2010) BMC Bioinf. , vol.11 , pp. 213
    • Schellenberger, J.1    Park, J.O.2    Conrad, T.M.3    Palsson, B.O.4
  • 28
    • 0343471424 scopus 로고    scopus 로고
    • Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices
    • Schmidt K., Carlsen M., Nielsen J., Villadsen J. Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices. Biotechnol. Bioeng. 1997, 55:831-840.
    • (1997) Biotechnol. Bioeng. , vol.55 , pp. 831-840
    • Schmidt, K.1    Carlsen, M.2    Nielsen, J.3    Villadsen, J.4
  • 29
    • 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.A., Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 2000, 18:326-332.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 326-332
    • Schuster, S.1    Fell, D.A.2    Dandekar, T.3
  • 30
    • 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. Journal of Biological Systems 1994, 2:165.
    • (1994) Journal of Biological Systems , vol.2 , pp. 165
    • Schuster, S.1    Hilgetag, C.2
  • 31
    • 33750988804 scopus 로고    scopus 로고
    • Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis
    • Selivanov V.A., Marin S., Lee P.W., Cascante M. Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis. Bioinformatics 2006, 22:2806-2812.
    • (2006) Bioinformatics , vol.22 , pp. 2806-2812
    • Selivanov, V.A.1    Marin, S.2    Lee, P.W.3    Cascante, M.4
  • 34
    • 77957312267 scopus 로고    scopus 로고
    • Edelfosine-induced metabolic changes in cancer cells that precede the overproduction of reactive oxygen species and apoptosis
    • Selivanov V.A., Vizan P., Mollinedo F., Fan T.W., Lee P.W., Cascante M. Edelfosine-induced metabolic changes in cancer cells that precede the overproduction of reactive oxygen species and apoptosis. BMC Syst. Biol. 2010, 4:135.
    • (2010) BMC Syst. Biol. , vol.4 , pp. 135
    • Selivanov, V.A.1    Vizan, P.2    Mollinedo, F.3    Fan, T.W.4    Lee, P.W.5    Cascante, M.6
  • 35
    • 33746954260 scopus 로고    scopus 로고
    • A review on metabolic pathway analysis with emphasis on isotope labeling approach
    • Shimizu A. A review on metabolic pathway analysis with emphasis on isotope labeling approach. Biotechnol. Bioprocess. Eng. 2002, 7:237.
    • (2002) Biotechnol. Bioprocess. Eng. , vol.7 , pp. 237
    • Shimizu, A.1
  • 36
    • 84857845281 scopus 로고    scopus 로고
    • Influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labeling experiments
    • Sokol S., Millard P., Portais J.C. influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labeling experiments. Bioinformatics 2012, 28:687-693.
    • (2012) Bioinformatics , vol.28 , pp. 687-693
    • Sokol, S.1    Millard, P.2    Portais, J.C.3
  • 39
    • 76749140314 scopus 로고    scopus 로고
    • Improved computational performance of MFA using elementary metabolite units and flux coupling
    • Suthers P.F., Chang Y.J., Maranas C.D. Improved computational performance of MFA using elementary metabolite units and flux coupling. Metab. Eng. 2010, 12:123.
    • (2010) Metab. Eng. , vol.12 , pp. 123
    • Suthers, P.F.1    Chang, Y.J.2    Maranas, C.D.3
  • 41
    • 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, 24:2229-2235.
    • (2008) Bioinformatics , vol.24 , pp. 2229-2235
    • Terzer, M.1    Stelling, J.2
  • 42
    • 0028108519 scopus 로고
    • Metabolic flux balancing: basic concepts, scientific and practical use
    • Varma A., Palsson B. Metabolic flux balancing: basic concepts, scientific and practical use. Bio/Technology 1994, 12:994-998.
    • (1994) Bio/Technology , vol.12 , pp. 994-998
    • Varma, A.1    Palsson, B.2
  • 43
    • 33845250184 scopus 로고    scopus 로고
    • Isotopomer analysis of myocardial substrate metabolism: a systems biology approach
    • Vo T.D., Palsson B.O. Isotopomer analysis of myocardial substrate metabolism: a systems biology approach. Biotechnol. Bioeng. 2006, 95:972-983.
    • (2006) Biotechnol. Bioeng. , vol.95 , pp. 972-983
    • Vo, T.D.1    Palsson, B.O.2
  • 44
    • 84862777903 scopus 로고    scopus 로고
    • Optimization of 13C isotopic tracers for metabolic flux analysis in mammalian cells
    • Walther J.L., Metallo C.M., Zhang J., Stephanopoulos G. Optimization of 13C isotopic tracers for metabolic flux analysis in mammalian cells. Metab. Eng. 2012, 14:162-171.
    • (2012) Metab. Eng. , vol.14 , pp. 162-171
    • Walther, J.L.1    Metallo, C.M.2    Zhang, J.3    Stephanopoulos, G.4
  • 45
    • 0001221508 scopus 로고
    • On respiratory impairment in cancer cells
    • Warburg O. On respiratory impairment in cancer cells. Science 1956, 124:269-270.
    • (1956) Science , vol.124 , pp. 269-270
    • Warburg, O.1
  • 46
    • 0034741983 scopus 로고    scopus 로고
    • 13C metabolic flux analysis
    • Wiechert W. 13C metabolic flux analysis. Metab. Eng. 2001, 3:195-206.
    • (2001) Metab. Eng. , vol.3 , pp. 195-206
    • Wiechert, W.1
  • 47
    • 0343267841 scopus 로고    scopus 로고
    • Bidirectional reaction steps in metabolic networks, III: explicit solution and analysis of isotopomer labeling systems
    • Wiechert W., Mollney M., Isermann N., Wurzel M., de Graaf A.A. Bidirectional reaction steps in metabolic networks, III: explicit solution and analysis of isotopomer labeling systems. Biotechnol. Bioeng. 1999, 66:69-85.
    • (1999) Biotechnol. Bioeng. , vol.66 , pp. 69-85
    • Wiechert, W.1    Mollney, M.2    Isermann, N.3    Wurzel, M.4    de Graaf, A.A.5
  • 49
    • 80052021573 scopus 로고    scopus 로고
    • Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA
    • Xu P., Ranganathan S., Fowler Z.L., Maranas C.D., Koffas M.A. Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. Metab. Eng. 2011, 13:578-587.
    • (2011) Metab. Eng. , vol.13 , pp. 578-587
    • Xu, P.1    Ranganathan, S.2    Fowler, Z.L.3    Maranas, C.D.4    Koffas, M.A.5
  • 50
    • 33746875213 scopus 로고    scopus 로고
    • Metabolomic assays of the concentration and mass isotopomer distribution of gluconeogenic and citric acid cycle intermediates
    • Yang L., Kasumov T., Yu L., Jobbins K., David F., Previs S., Kelleher J., Brunengraber H. Metabolomic assays of the concentration and mass isotopomer distribution of gluconeogenic and citric acid cycle intermediates. Metabolomics 2006, 2:85-94.
    • (2006) Metabolomics , vol.2 , pp. 85-94
    • Yang, L.1    Kasumov, T.2    Yu, L.3    Jobbins, K.4    David, F.5    Previs, S.6    Kelleher, J.7    Brunengraber, H.8
  • 51
    • 77954197778 scopus 로고    scopus 로고
    • Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model
    • Yizhak K., Benyamini T., Liebermeister W., Ruppin E., Shlomi T. Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model. Bioinformatics 2010, 26:i255-i260.
    • (2010) Bioinformatics , vol.26
    • Yizhak, K.1    Benyamini, T.2    Liebermeister, W.3    Ruppin, E.4    Shlomi, T.5
  • 52
    • 0028036096 scopus 로고
    • Modeling of isotope distributions and intracellular fluxes in metabolic networks using atom mapping matrices
    • Zupke C., Stephanopoulos G. Modeling of isotope distributions and intracellular fluxes in metabolic networks using atom mapping matrices. Biotechnol. Prog. 1994, 10:489-498.
    • (1994) Biotechnol. Prog. , vol.10 , pp. 489-498
    • Zupke, C.1    Stephanopoulos, G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.