On flux coupling analysis of metabolic subsystems

Journal of Theoretical Biology

Volumn 302, Issue , 2012, Pages 62-69

  Marashi, Sayed Amir ^a,b   David, Laszlo ^a,c,d   Bockmayr, Alexander ^a,c  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^c Deutsche Forschungsgemeinschaft   (Germany)

^d Berlin Mathematical School   (Germany)

Author keywords

Boundary reactions; Exchange fluxes; Subnetworks; Subsystems; Uptake reactions

Indexed keywords

ALGORITHM; BOUNDARY CONDITION; EXPERIMENTAL STUDY; GENOME; METABOLISM; PLASTID; REACTION KINETICS;

ARTICLE; FLUX COUPLING ANALYSIS; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; METABOLISM; MITOCHONDRION; PLASTID; PRIORITY JOURNAL;

COMPUTATIONAL BIOLOGY; GENOME; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MITOCHONDRIA; MODELS, BIOLOGICAL; ORGANELLES; PLANTS; SYSTEMS BIOLOGY;

EID: 84858726254     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2012.02.023     Document Type: Article

References (32)

1. Burgard A.P., Nikolaev E.V., Schilling C.H., Maranas C.D. Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 2004, 14:301-312.
2. Chang R.L., Ghamsari L., Manichaikul A., Hom E.F.Y., Balaji S., Fu W., Shen Y., Hao T., Palsson B.O., Salehi-Ashtiani K., Papin J.A. Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol. Syst. Biol. 2011, 7:518.
3. Dandekar T., Moldenhauer F., Bulik S., Bertram H., Schuster S. A method for classifying metabolites in topological pathway analyses based on minimization of pathway number. BioSystems 2003, 70:255-270.
4. David L., Marashi S.-A., Larhlimi A., Mieth B., Bockmayr A. FFCA: a feasibility-based method for flux coupling analysis of metabolic networks. BMC Bioinf. 2011, 12:236.
5. de Oliveira Dal'Molin C.G., Quek L.-E., Palfreyman R.W., Brumbley S.M., Nielsen L.K. AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis. Plant Physiol. 2010, 152:579-589.
6. Duarte N.C., Becker S.A., Jamshidi N., Thiele I., Mo M.L., Vo T.D., Srivas R., Palsson B.O. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl. Acad. Sci. USA 2007, 104:1777-1782.
7. Duarte N.C., Herrgård M.J., Palsson B.O. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res. 2004, 14:1298-1309.
8. Grafahrend-Belau E., Schreiber F., Koschützki D., Junker B.H. Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol. 2009, 149:585-598.
9. Gross J., Bhattacharya D. Mitochondrial and plastid evolution in eukaryotes: an outsiders' perspective. Nat. Rev. Genet. 2009, 10:495-505.
10. Imielinski M., Belta C. Exploiting the pathway structure of metabolism to reveal high-order epistasis. BMC Syst. Biol. 2008, 2:40.
11. Jevremovic, D., Boley, D., Sosa, C.P., 2011. Divide-and-conquer approach to the parallel computation of elementary flux modes in metabolic networks. In: Proceedings of the IEEE International Symposium on Parallel and Distributed Processing Workshops and PhD Forum (IPDPSW). Shanghai, China. pp. 502-511.
12. Kaleta C., de Figueiredo L.F., Schuster S. Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns. Genome Res. 2009, 19:1872-1883.
13. Marashi S.-A., Bockmayr A. Flux coupling analysis of metabolic networks is sensitive to missing reactions. BioSystems 2011, 103:57-66.
14. Oberhardt M.A., Palsson B.O., Papin J.A. Applications of genome-scale metabolic reconstructions. Mol. Syst. Biol. 2009, 5:320.
15. Pfeiffer T., Sánchez-Valdenebro I., Nuño J.C., Montero F., Schuster S. METATOOL: for studying metabolic networks. Bioinformatics 1999, 15:251-257.
16. Poolman M.G., Fell D.A., Raines C.A. Elementary modes analysis of photosynthate metabolism in the chloroplast stroma. Eur. J. Biochem. 2003, 270:430-439.
17. Sagan L. On the origin of mitosing cells. J. Theor. Biol. 1967, 14:225-274.
18. Saha R., Suthers P.F., Maranas C.D. Zea mays i RS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism. PLoS One 2011, 6:e21784.
19. Schilling C.H., Covert M.W., Famili I., Church G.M., Edwards J.S., Palsson B.O. Genome-scale metabolic model of Helicobacter pylori26695. J. Bacteriol. 2002, 184:4582-4593.
20. Schilling C.H., Palsson B.O. Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J. Theor. Biol. 2000, 203:249-283.
21. 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.
22. Schuster S., Hilgetag C. On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst. 1994, 2:165-182.
23. Schuster S., Pfeiffer T., Moldenhauer F., Koch I., Dandekar T. Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 2002, 18:351-361.
24. Schwarz R., Musch P., von Kamp A., Engels B., Schirmer H., Schuster S., Dandekar T. YANA-a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinf. 2005, 6:135.
25. Terzer M., Stelling J. Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics 2008, 24:2229-2235.
26. Teusink B., Wiersma A., Jacobs L., Notebaart R.A., Smid E.J. Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation. PLoS Comput. Biol. 2009, 5:e1000410.
27. Urbanczik R. Enumerating constrained elementary flux vectors of metabolic networks. IET Syst. Biol. 2007, 1:274-279.
28. Verwoerd W.S. Dissecting metabolic networks into functional subnets. A Practical Guide to Bioinformatics Analysis 2010, 79-98. iConcept Press. G. Fung (Ed.).
29. Verwoerd W.S. A new computational method to split large biochemical networks into coherent subnets. BMC Syst. Biol. 2011, 5:25.
30. Vo T.D., Greenberg H.J., Palsson B.O. Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J. Biol. Chem. 2004, 279:39532-39540.
31. von Kamp A., Schuster S. Metatool 5.0: fast and flexible elementary modes analysis. Bioinformatics 2006, 22:1930-1931.
32. Wiback S.J., Palsson B.O. Extreme pathway analysis of human red blood cell metabolism. Biophys. J. 2002, 83:808-818.