Article number: 62 REVIEW Metabolic networks in motion: 13 C-based flux analysis
暂无分享,去创建一个
[1] Barbara M. Bakker,et al. Unraveling the complexity of flux regulation: A new method demonstrated for nutrient starvation in Saccharomyces cerevisiae , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[2] Carbohydrate cycling in micro-organisms: what can (13)C-NMR tell us? , 2002, FEMS microbiology reviews.
[3] Juho Rousu,et al. Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes , 2006, Bioinform..
[4] Jens Nielsen,et al. Metabolic Network Analysis of Streptomyces tenebrarius, a Streptomyces Species with an Active Entner-Doudoroff Pathway , 2005, Applied and Environmental Microbiology.
[5] U. Alon,et al. Just-in-time transcription program in metabolic pathways , 2004, Nature Genetics.
[6] Barbara M. Bakker,et al. Hierarchical and metabolic regulation of glucose influx in starved Saccharomyces cerevisiae. , 2005, FEMS yeast research.
[7] Jens Nielsen,et al. CreA influences the metabolic fluxes of Aspergillus nidulans during growth on glucose and xylose. , 2005, Microbiology.
[8] A. Aristidou,et al. Metabolic Engineering in the -omics Era: Elucidating and Modulating Regulatory Networks , 2005, Microbiology and Molecular Biology Reviews.
[9] S. Previs,et al. Using isotope tracers to study metabolism: application in mouse models. , 2004, Metabolic engineering.
[10] Vipul Periwal,et al. Complexity and Robustness of Cellular Systems , 2006 .
[11] An-Ping Zeng,et al. The Connectivity Structure, Giant Strong Component and Centrality of Metabolic Networks , 2003, Bioinform..
[12] Markus J. Herrgård,et al. Integrating high-throughput and computational data elucidates bacterial networks , 2004, Nature.
[13] A. Barabasi,et al. Global organization of metabolic fluxes in the bacterium Escherichia coli , 2004, Nature.
[14] P. Verheijen,et al. Possible pitfalls of flux calculations based on (13)C-labeling. , 2001, Metabolic engineering.
[15] M. Vidal,et al. Interactome: gateway into systems biology. , 2005, Human molecular genetics.
[16] U. Sauer,et al. Metabolic Flux Responses to Pyruvate Kinase Knockout in Escherichia coli , 2002, Journal of bacteriology.
[17] U. Sauer,et al. A Novel Metabolic Cycle Catalyzes Glucose Oxidation and Anaplerosis in Hungry Escherichia coli* , 2003, Journal of Biological Chemistry.
[18] J. Doyle,et al. Bow Ties, Metabolism and Disease , 2022 .
[19] H Sahm,et al. Determination of the fluxes in the central metabolism of Corynebacterium glutamicum by nuclear magnetic resonance spectroscopy combined with metabolite balancing , 1996, Biotechnology and bioengineering.
[20] Stephanopoulos,et al. Metabolite and isotopomer balancing in the analysis of metabolic cycles: I. Theory. , 1999, Biotechnology and bioengineering.
[21] U. Sauer,et al. Metabolic Flux Ratio Analysis of Genetic and Environmental Modulations of Escherichia coli Central Carbon Metabolism , 1999, Journal of bacteriology.
[22] H Sahm,et al. Metabolic consequences of altered phosphoenolpyruvate carboxykinase activity in Corynebacterium glutamicum reveal anaplerotic regulation mechanisms in vivo. , 2001, Metabolic engineering.
[23] Jens Nielsen,et al. Identification of the Entner–Doudoroff pathway in an antibiotic‐producing actinomycete species , 2004, Molecular microbiology.
[24] U. Sauer,et al. Impact of Global Transcriptional Regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on Glucose Catabolism in Escherichia coli , 2005, Journal of bacteriology.
[25] W. Wiechert,et al. In Vivo Quantification of Parallel and Bidirectional Fluxes in the Anaplerosis of Corynebacterium glutamicum * , 2000, The Journal of Biological Chemistry.
[26] U. Sauer,et al. Experimental Identification and Quantification of Glucose Metabolism in Seven Bacterial Species , 2005, Journal of bacteriology.
[27] U. Sauer. High-throughput phenomics: experimental methods for mapping fluxomes. , 2004, Current opinion in biotechnology.
[28] W Wiechert,et al. Bidirectional reaction steps in metabolic networks: IV. Optimal design of isotopomer labeling experiments. , 1999, Biotechnology and bioengineering.
[29] Vipul Periwal,et al. Biological Data Acquisition for System Level Modeling—An Exercise in the Art of Compromise , 2006 .
[30] Ganesh Sriram,et al. Quantification of Compartmented Metabolic Fluxes in Developing Soybean Embryos by Employing Biosynthetically Directed Fractional 13C Labeling, Two-Dimensional [13C, 1H] Nuclear Magnetic Resonance, and Comprehensive Isotopomer Balancing1[w] , 2004, Plant Physiology.
[31] T. Ideker,et al. Supporting Online Material for A Systems Approach to Mapping DNA Damage Response Pathways , 2006 .
[32] J K Kelleher,et al. Flux estimation using isotopic tracers: common ground for metabolic physiology and metabolic engineering. , 2001, Metabolic engineering.
[33] U. Sauer,et al. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. , 2005, Genome research.
[34] Uwe Sauer,et al. TCA cycle activity in Saccharomyces cerevisiae is a function of the environmentally determined specific growth and glucose uptake rates. , 2004, Microbiology.
[35] Nicola Zamboni,et al. Model-independent fluxome profiling from 2H and 13C experiments for metabolic variant discrimination , 2004, Genome Biology.
[36] Christoph Wittmann,et al. Metabolic Fluxes in Corynebacterium glutamicum during Lysine Production with Sucrose as Carbon Source , 2004, Applied and Environmental Microbiology.
[37] A J Sinskey,et al. Metabolite and isotopomer balancing in the analysis of metabolic cycles: II. Applications. , 1999, Biotechnology and bioengineering.
[38] B. Palsson,et al. Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. , 2000, Journal of theoretical biology.
[39] U. Sauer,et al. Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast , 2005, Genome Biology.
[40] L. Hue,et al. Fructose 2,6‐bisphosphate and the control of glycolysis in bovine spermatozoa , 1986, FEBS letters.
[41] R. Mahadevan,et al. Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum , 2004, Biotechnology and bioengineering.
[42] G. Stephanopoulos,et al. Systematic quantification of complex metabolic flux networks using stable isotopes and mass spectrometry. , 2003, European journal of biochemistry.
[43] J. Nielsen,et al. From genomes to in silico cells via metabolic networks. , 2005, Current opinion in biotechnology.
[44] W. Eisenreich,et al. Elucidation of novel biosynthetic pathways and metabolite flux patterns by retrobiosynthetic NMR analysis , 1998 .
[45] W. Wiechert. 13C metabolic flux analysis. , 2001, Metabolic engineering.
[46] U. Sauer,et al. Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism , 2005, Nature Genetics.
[47] Jens Nielsen,et al. The next wave in metabolome analysis. , 2005, Trends in biotechnology.
[48] T Szyperski,et al. 13C-NMR, MS and metabolic flux balancing in biotechnology research , 1998, Quarterly Reviews of Biophysics.
[49] U. Sauer,et al. High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints. , 2004, Analytical biochemistry.
[50] J E Bailey,et al. Metabolic flux analysis with a comprehensive isotopomer model in Bacillus subtilis. , 2001, Biotechnology and bioengineering.
[51] B. Palsson,et al. Genome-scale models of microbial cells: evaluating the consequences of constraints , 2004, Nature Reviews Microbiology.
[52] D. Fell,et al. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. , 1999, Trends in biotechnology.
[53] Mark Stitt,et al. Flux an important, but neglected, component of functional genomics. , 2005, Current opinion in plant biology.
[54] J J Heijnen,et al. A priori analysis of metabolic flux identifiability from (13)C-labeling data. , 2001, Biotechnology and bioengineering.
[55] Gregory Stephanopoulos,et al. Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements. , 2006, Metabolic engineering.
[56] J. Nielsen,et al. Network Identification and Flux Quantification in the Central Metabolism of Saccharomyces cerevisiae under Different Conditions of Glucose Repression , 2001, Journal of bacteriology.
[57] T. Dandekar,et al. 13C isotopologue perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator PrfA , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[58] S. Panke,et al. Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data , 2006, Molecular systems biology.
[59] Christoph Wittmann,et al. Amplified Expression of Fructose 1,6-Bisphosphatase in Corynebacterium glutamicum Increases In Vivo Flux through the Pentose Phosphate Pathway and Lysine Production on Different Carbon Sources , 2005, Applied and Environmental Microbiology.
[60] Marc K Hellerstein,et al. Stable isotope-mass spectrometric measurements of molecular fluxes in vivo: emerging applications in drug development. , 2004, Current opinion in molecular therapeutics.
[61] J. Bailey,et al. Toward a science of metabolic engineering , 1991, Science.
[62] Gary D Bader,et al. Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.
[63] S. Aymerich,et al. CcpN (YqzB), a novel regulator for CcpA‐independent catabolite repression of Bacillus subtilis gluconeogenic genes , 2005, Molecular microbiology.
[64] T. Szyperski. Biosynthetically Directed Fractional 13C‐labeling of Proteinogenic Amino Acids , 1995 .
[65] Y. Shachar-Hill,et al. Measuring multiple fluxes through plant metabolic networks. , 2006, The Plant journal : for cell and molecular biology.
[66] Kazuyuki Shimizu,et al. An improved method for statistical analysis of metabolic flux analysis using isotopomer mapping matrices with analytical expressions. , 2003, Journal of biotechnology.
[67] U. Sauer,et al. Metabolic fluxes in riboflavin-producing Bacillus subtilis , 1997, Nature Biotechnology.
[68] Karl Sanford,et al. Genomics to fluxomics and physiomics - pathway engineering. , 2002, Current opinion in microbiology.
[69] H. Mori,et al. Responses of theCentral Metabolism in Escherichia coli to PhosphoglucoseIsomerase and Glucose-6-Phosphate DehydrogenaseKnockouts , 2003, Journal of bacteriology.
[70] Wolfgang Wiechert,et al. Experimental design principles for isotopically instationary 13C labeling experiments , 2006, Biotechnology and bioengineering.
[71] H. Westerhoff,et al. Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway , 2001, FEBS letters.
[72] Bernhard O. Palsson,et al. Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles , 2006, PLoS Comput. Biol..
[73] J. Schwender,et al. Understanding flux in plant metabolic networks. , 2004, Current opinion in plant biology.
[74] G. Stephanopoulos. Metabolic fluxes and metabolic engineering. , 1999, Metabolic engineering.
[75] G. Danuser,et al. Quantitative fluorescent speckle microscopy of cytoskeleton dynamics. , 2006, Annual review of biophysics and biomolecular structure.
[76] Martin Vingron,et al. A joint model of regulatory and metabolic networks , 2006, BMC Bioinformatics.
[77] Lucas Pelkmans,et al. Systems biology of virus entry in mammalian cells , 2006, Cellular microbiology.
[78] J. Stelling. Mathematical models in microbial systems biology. , 2004, Current opinion in microbiology.
[79] J. Heijnen,et al. Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113-7D based on mass isotopomer measurements of (13)C-labeled primary metabolites. , 2005, FEMS yeast research.
[80] Jens Nielsen,et al. Phenotypic characterization of glucose repression mutants of Saccharomyces cerevisiae using experiments with 13C‐labelled glucose , 2004, Yeast.
[81] Wolfgang Wiechert,et al. Metabolic isotopomer labeling systems. Part II: structural flux identifiability analysis. , 2003, Mathematical biosciences.
[82] Christoph Wittmann,et al. Comparative Metabolic Flux Analysis of Lysine-Producing Corynebacterium glutamicum Cultured on Glucose or Fructose , 2004, Applied and Environmental Microbiology.
[83] H. Mori,et al. Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout , 2003, Biotechnology and bioengineering.
[84] Bernhard O Palsson,et al. The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[85] Wolfgang Wiechert,et al. From stationary to instationary metabolic flux analysis. , 2005, Advances in biochemical engineering/biotechnology.
[86] Torsten Wittmann,et al. The spindle: a dynamic assembly of microtubules and motors , 2001, Nature Cell Biology.
[87] S. Billings,et al. Metabolic flux distribution analysis by 13C-tracer experiments using the Markov chain-Monte Carlo method. , 2005, Biochemical Society transactions.
[88] U. Sauer,et al. Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. , 2003, European journal of biochemistry.
[89] W Wiechert,et al. Metabolic isotopomer labeling systems. Part I: global dynamic behavior. , 2001, Mathematical biosciences.
[90] D. Fell. Understanding the Control of Metabolism , 1996 .
[91] Bernhard O Palsson,et al. Latent Pathway Activation and Increased Pathway Capacity Enable Escherichia coli Adaptation to Loss of Key Metabolic Enzymes* , 2006, Journal of Biological Chemistry.
[92] Craig R Malloy,et al. Analytical solutions for (13)C isotopomer analysis of complex metabolic conditions: substrate oxidation, multiple pyruvate cycles, and gluconeogenesis. , 2004, Metabolic engineering.
[93] Jens Nielsen,et al. Impact of transamination reactions and protein turnover on labeling dynamics in 13C‐labeling experiments , 2004, Biotechnology and bioengineering.
[94] G. Church,et al. Analysis of optimality in natural and perturbed metabolic networks , 2002 .
[95] J. Liao,et al. Pathway analysis, engineering, and physiological considerations for redirecting central metabolism. , 1996, Biotechnology and bioengineering.
[96] J. Varner,et al. Large-scale prediction of phenotype: concept. , 2000, Biotechnology and bioengineering.
[97] Shaoqun Zeng,et al. Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions , 2006, Molecular systems biology.
[98] T. Szyperski. Biosynthetically directed fractional 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism. , 1995, European journal of biochemistry.
[99] Wolfgang Wiechert,et al. Computational tools for isotopically instationary 13C labeling experiments under metabolic steady state conditions. , 2006, Metabolic engineering.
[100] A. Aderem. Systems Biology: Its Practice and Challenges , 2005, Cell.
[101] J. Schwender,et al. Rubisco without the Calvin cycle improves the carbon efficiency of developing green seeds , 2004, Nature.
[102] E. Ruppin,et al. Regulatory on/off minimization of metabolic flux changes after genetic perturbations. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[103] Markus J. Herrgård,et al. Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. , 2006, Genome research.
[104] Stephen S Fong,et al. Metabolic gene–deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes , 2004, Nature Genetics.
[105] Marc K Hellerstein,et al. In vivo measurement of fluxes through metabolic pathways: the missing link in functional genomics and pharmaceutical research. , 2003, Annual review of nutrition.