Estimating biological elementary flux modes that decompose a flux distribution by the minimal branching property

Bioinformatics

Volumn 30, Issue 22, 2014, Pages 3232-3239

  Chan, Siu Hung Joshua ^a   Solem, Christian ^a   Jensen, Peter Ruhdal ^a   Ji, Ping ^b  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b HONG KONG POLYTECHNIC UNIVERSITY   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID DERIVATIVE; GLYOXYLIC ACID; GLYOXYLIC ACID DERIVATIVE;

ANIMAL; ESCHERICHIA COLI; GENETICS; HEART MUSCLE; LACTOCOCCUS LACTIS; METABOLIC FLUX ANALYSIS; METABOLISM; MOUSE; PROCEDURES;

ACETATES; ANIMALS; ESCHERICHIA COLI; GLYOXYLATES; LACTOCOCCUS LACTIS; METABOLIC FLUX ANALYSIS; METABOLIC NETWORKS AND PATHWAYS; MICE; MYOCARDIUM;

EID: 84911440614     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu529     Document Type: Article

References (36)

1. Almaas, E. et al. (2004) Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature, 427, 839-843.
2. Ayad, E.H.E. et al. (1999) Flavour forming abilities and amino acid requirements of Lactococcus lactis strains isolated from artisanal and non-dairy origin. Int. Dairy J., 9, 725-735.
3. Chan, S.H.J. and Ji, P. (2011) Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks. Bioinformatics, 27, 2256-2262.
4. de Figueiredo, L.F. et al. (2009) Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinformatics, 25, 3158-3165.
5. dos Santos, M.M. et al. (2003) Identification of in vivo enzyme activities in the cometabolism of glucose and acetate by Saccharomyces cerevisiae by using 13C-labeled substrates. Eukaryot. Cell, 2, 599-608.
6. Depre, C. et al. (1999) Glucose for the heart. Circulation, 99, 578-588.
7. Edwards, J.S. and Palsson, B.. (1999) Systems properties of the Haemophilus influenzae Rd metabolic genotype. J. Biol. Chem., 274, 17410-17416.
8. Feist, A.M. et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol., 3, 121.
9. Flahaut, N.A. et al. (2013) Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation. Appl. Microbiol. Biotechnol., 97, 8729-8739.
10. Ihmels, J. et al. (2004) Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat. Biotech., 22, 86-92.
11. Ip, K. et al. (2011) Analysis of complex metabolic behavior through pathway decomposition. BMC Syst. Biol., 5, 91.
12. Jensen, P.R. and Hammer, K. (1993) Minimal requirements for exponential growth of Lactococcus lactis. Appl. Environ. Microbiol., 59, 4263-4266.
13. Jol, S.J. et al. (2012) System-level insights into yeast metabolism by thermodynamic analysis of elementary flux modes. PLoS Comput. Biol., 8, e1002415.
14. Jungreuthmayer, C. et al. (2013) regEfmtool: speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic. Biosystems, 113, 37-39.
15. Klamt, S. and Stelling, J. (2002) Combinatorial complexity of pathway analysis in metabolic networks. Mol. Biol. Rep., 29, 233-236.
16. Lewis, N.E. et al. (2012) Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat. Rev. Micro., 10, 291-305.
17. Llaneras, F. and Pico, J. (2010) Which metabolic pathways generate and characterize the flux space? A comparison among elementary modes, extreme pathways and minimal generators. J. Biomed. Biotechnol, 2010, 753904.
18. Machado, D. et al. (2012) Random sampling of elementary flux modes in large-scale metabolic networks. Bioinformatics, 28, i515-i521.
19. Novichkov, P.S. et al. (2010) RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res., 38, D111-D118.
20. Oberhardt, M.A. et al. (2009) Applications of genome-scale metabolic reconstructions. Mol. Syst. Biol., 5, 320.
21. Orth, J.D. et al. (2010) Reconstruction and use of microbial metabolic networks: the core Escherichia coli metabolic model as an educational guide. In: Böck, A. et al. (eds) Escherichia coli and Salmonella: Cellular and Molecular Biology. 10.2.1. ASM Press, Washington DC.
22. Pey, J. and Planes, F.J. (2014) Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks. Bioinformatics, 30, 2197-2203.
23. Poolman, M.G. et al. (2004) A method for the determination of flux in elementary modes, and its application to Lactobacillus rhamnosus. Biotechnol. Bioeng., 88, 601-612.
24. Price, N.D. et al. (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat. Rev. Microbiol., 2, 886-897.
25. Ravcheev, D.A. et al. (2013) Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria. BMC Genomics, 14, 94.
26. Rezola, A. et al. (2011) Exploring metabolic pathways in genome-scale networks via generating flux modes. Bioinformatics, 27, 534-540.
27. Schuster, S. and Hilgetag, C. (1994) On the elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst, 2, 165-182.
28. Schwartz, J.M. and Kanehisa, M. (2005) A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. Bioinformatics, 21 (Suppl. 2), ii204-ii205.
29. Schwartz, J.M. and Kanehisa, M. (2006) Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinformatics, 7, 186.
30. Tabe-Bordbar, S. and Marashi, S.-A. (2013) Finding elementary flux modes in metabolic networks based on flux balance analysis and flux coupling analysis: application to the analysis of Escherichia coli metabolism. Biotechnol. Lett., 35, 2039-2044.
31. Terzer, M. and Stelling, J. (2008) Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics, 24, 2229-2235.
32. Thomas, T.D. et al. (1979) Change from homo- to heterolactic fermentation by Streptococcus lactis resulting from glucose limitation in anaerobic chemostat cultures. J. Bacteriol., 138, 109-117.
33. Trinh, C.T. et al. (2009) Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl. Microbiol. Biotechnol., 81, 813-826.
34. Vo, T.D. and Palsson, B.O. (2006) Isotopomer analysis of myocardial substrate metabolism: a systems biology approach. Biotechnol. Bioeng., 95, 972-983.
35. Wiback, S.J. et al. (2003) Reconstructing metabolic flux vectors from extreme pathways: defining the-spectrum. J. Theor. Biol., 224, 313-324.
36. Zanghellini, J. et al. (2013) Elementary flux modes in a nutshell: properties, calculation and applications. Biotechnol. J., 8, 1009-1016.