Computing the shortest elementary flux modes in genome-scale metabolic networks
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Angel Rubio | Francisco J. Planes | Christoph Kaleta | John E. Beasley | Stefan Schuster | Adam Podhorski | Luis F. de Figueiredo | S. Schuster | J. Beasley | C. Kaleta | Á. Rubio | A. Podhorski | L. F. D. Figueiredo | F. J. Planes
[1] J. Rabinowitz,et al. Kinetic flux profiling of nitrogen assimilation in Escherichia coli , 2006, Nature chemical biology.
[2] A. Goesmann,et al. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. , 2003, Journal of biotechnology.
[3] B. Palsson,et al. Genome-scale models of microbial cells: evaluating the consequences of constraints , 2004, Nature Reviews Microbiology.
[4] Francisco J. Planes,et al. Recovering metabolic pathways via optimization , 2007, Bioinform..
[5] Anders Blomberg,et al. Dihydroxyacetone Kinases in Saccharomyces cerevisiaeAre Involved in Detoxification of Dihydroxyacetone* , 2003, The Journal of Biological Chemistry.
[6] Chankyu Park,et al. Role of GldA in dihydroxyacetone and methylglyoxal metabolism of Escherichia coli K12. , 2008, FEMS microbiology letters.
[7] J. Liao,et al. Pathway analysis, engineering, and physiological considerations for redirecting central metabolism. , 1996, Biotechnology and bioengineering.
[8] N. W. Davis,et al. The complete genome sequence of Escherichia coli K-12. , 1997, Science.
[9] S Klamt,et al. Algorithmic approaches for computing elementary modes in large biochemical reaction networks. , 2005, Systems biology.
[10] J. Nielsen,et al. In silico genome‐scale reconstruction and validation of the Corynebacterium glutamicum metabolic network , 2009, Biotechnology and bioengineering.
[11] J. Stelling,et al. Combinatorial Complexity of Pathway Analysis in Metabolic Networks , 2004, Molecular Biology Reports.
[12] F. Srienc,et al. Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism , 2009, Applied Microbiology and Biotechnology.
[13] F. Montero,et al. Optimization of Metabolism: The Evolution of Metabolic Pathways Toward Simplicity Through the Game of the Pentose Phosphate Cycle , 1994 .
[14] Stefan Schuster,et al. A method for classifying metabolites in topological pathway analyses based on minimization of pathway number. , 2003, Bio Systems.
[15] Preben Krabben,et al. Metabolic flux and metabolic network analysis of Penicillium chrysogenum using 2D [13C, 1H] COSY NMR measurements and cumulative bondomer simulation. , 2003, Biotechnology and bioengineering.
[16] S. Schuster,et al. Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns. , 2009, Genome research.
[17] Francisco J. Planes,et al. Path finding approaches and metabolic pathways , 2009, Discret. Appl. Math..
[18] S. Bonhoeffer,et al. Evolution of Cross‐Feeding in Microbial Populations , 2004, The American Naturalist.
[19] Stefan Schuster,et al. Systems biology Metatool 5.0: fast and flexible elementary modes analysis , 2006 .
[20] R. V. Prasad,et al. A strategy for increasing an in vivo flux by genetic manipulations. The tryptophan system of yeast. , 1992, The Biochemical journal.
[21] M. Inui,et al. Metabolic Analysis of Corynebacterium glutamicum during Lactate and Succinate Productions under Oxygen Deprivation Conditions , 2004, Journal of Molecular Microbiology and Biotechnology.
[22] L. Eggeling,et al. Biology of L-lysine overproduction byCorynebacterium glutamicum , 1994, Amino Acids.
[23] L. Eggeling,et al. Handbook of Corynebacterium glutamicum , 2005 .
[24] G. Stephanopoulos,et al. Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction , 2000, Biotechnology and bioengineering.
[25] B. Palsson,et al. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. , 2000, Journal of theoretical biology.
[26] Bas Teusink,et al. Analysis of Growth of Lactobacillus plantarum WCFS1 on a Complex Medium Using a Genome-scale Metabolic Model* , 2006, Journal of Biological Chemistry.
[27] C. Wittmann,et al. The l -Lysine Story: From Metabolic Pathways to Industrial Production , 2007 .
[28] V. Wendisch,et al. Metabolic engineering of Escherichia coli and Corynebacterium glutamicum for biotechnological production of organic acids and amino acids. , 2006, Current opinion in microbiology.
[29] Steffen Klamt,et al. Structural and functional analysis of cellular networks with CellNetAnalyzer , 2007, BMC Systems Biology.
[30] Leen Stougie,et al. Modes and cuts in metabolic networks: Complexity and algorithms , 2009, Biosyst..
[31] V. Wendisch. Amino acid biosynthesis : pathways, regulation and metabolic engineering , 2007 .
[32] F. Neidhardt,et al. Escherichia Coli and Salmonella: Typhimurium Cellular and Molecular Biology , 1987 .
[33] D. Fell,et al. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks , 2000, Nature Biotechnology.
[34] 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.
[35] H. Kacser,et al. A universal method for achieving increases in metabolite production. , 1993, European journal of biochemistry.
[36] Albert A. de Graaf,et al. Metabolic Flux Analysis of Corynebacterium glutamicum , 2000 .
[37] Panos M. Pardalos,et al. Handbook of applied optimization , 2002 .
[38] Steffen Klamt,et al. Computation of elementary modes: a unifying framework and the new binary approach , 2004, BMC Bioinformatics.
[39] S. Schuster,et al. ON ELEMENTARY FLUX MODES IN BIOCHEMICAL REACTION SYSTEMS AT STEADY STATE , 1994 .
[40] Jörg Stelling,et al. Large-scale computation of elementary flux modes with bit pattern trees , 2008, Bioinform..
[41] U. Sauer,et al. A Novel Metabolic Cycle Catalyzes Glucose Oxidation and Anaplerosis in Hungry Escherichia coli* , 2003, Journal of Biological Chemistry.
[42] Wolfram Weckwerth,et al. Metabolomics : methods and protocols , 2007 .
[43] S. Schuster,et al. Understanding the roadmap of metabolism by pathway analysis. , 2007, Methods in molecular biology.
[44] D. Fell,et al. Reaction routes in biochemical reaction systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism , 2002, Journal of mathematical biology.
[45] D A Fell,et al. Physiological control of metabolic flux: the requirement for multisite modulation. , 1995, The Biochemical journal.
[46] G. Stephanopoulos,et al. Computer‐aided synthesis of biochemical pathways , 1990, Biotechnology and bioengineering.
[47] K. Sano,et al. Process for the production of L-lysine by fermentation , 1996 .
[48] Monika Heiner,et al. Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber , 2005, Bioinform..
[49] Adam M. Feist,et al. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information , 2007, Molecular systems biology.
[50] Michael Hecker,et al. Integrated network reconstruction, visualization and analysis using YANAsquare , 2007, BMC Bioinformatics.