A new constraint-based description of the steady-state flux cone of metabolic networks

Discrete Applied Mathematics

Volumn 157, Issue 10, 2009, Pages 2257-2266

  Larhlimi, Abdelhalim ^a   Bockmayr, Alexander ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

Metabolic network; Metabolic pathway analysis; Polyhedral cone; Steady state flux cone

Indexed keywords

COMPUTATIONAL BIOLOGIES; CONSTRAINT-BASED; FLUX DISTRIBUTIONS; IRREVERSIBLE REACTIONS; METABOLIC NETWORK; METABOLIC PATHWAY ANALYSIS; NON NEGATIVITIES; POLYHEDRAL CONE; SMALL NETWORKS; STEADY STATE; STEADY-STATE FLUX CONE;

BIOINFORMATICS;

METABOLISM;

EID: 50949094727     PISSN: 0166218X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dam.2008.06.039     Document Type: Article

References (22)

1. Avis D., Fukuda K., and Picozzi S. On canonical representations of convex polyhedra. In: Cohen A., Gao X.S., and Takayama N. (Eds). Mathematical Software, Proceedings of the First International Congress (2002), World Scientific 350-360
2. Clarke B.L. Stability of complex reaction networks. In: Prigogine I., and Rice S.A. (Eds). Advances in Chemical Physics vol. 43 (1980), John Wiley & Sons 1-216
3. Clarke B.L. Complete set of steady states for the general stoichiometric dynamical system. J. Chem. Phys. 75 10 (1981) 4970-4979
4. Dandekar T., Moldenhauer F., Bulik S., Bertram H., and Schuster S. A method for classifying metabolites in topological pathway analyses based on minimization of pathway number. BioSystems 70 3 (2003) 255-270
5. Fukuda K., and Prodon A. Double description method revisited. Combinatorics and Computer Science. LNCS vol. 1120 (1995), Springer 91-111
6. Gagneur J., and Klamt S. Computation of elementary modes: A unifying framework and the new binary approach. BMC Bioinformatics 5 175 (2004)
7. Heinrich R., and Schuster S. The Regulation of Cellular Systems (1996), Chapman and Hall, New York
8. Klamt S., and Stelling J. Combinatorial complexity of pathway analysis in metabolic networks. Mol. Biol. Rep. 29 1-2 (2002) 233-236
9. Klamt S., and Stelling J. Two approaches for metabolic pathway analysis?. Trends Biotechnol. 21 (2003) 64-69
10. Klamt S., and Stelling J. Stoichiometric and constraint-based modeling. In: Szallasi Z., Stelling J., and Periwal V. (Eds). System Modeling in Cellular Biology (2006), MIT Press 73-96 (chapter 5)
11. Larhlimi A., and Bockmayr A. A new approach to flux coupling analysis of metabolic networks. Computational Life Sciences II. CompLife'06, Cambridge, UK. LNBI vol. 4216 (2006), Springer 205-215
12. Palsson B. Systems Biology: Properties of Reconstructed Networks (2006), Cambridge Univ. Press
13. Papin J.A., Stelling J., Price N.D., Klamt S., Schuster S., and Palsson B.O. Comparison of network-based pathway analysis methods. Trends Biotechnol. 22 8 (2004) 400-405
14. Pfeiffer T., Sánchez-Valdenebro I., Nuno J.C., Montero F., and Schuster S. Metatool: for studying metabolic networks. Bioinformatics 15 3 (1999) 251-257
15. S. Picozzi, On canonical representation of convex polyhedra, Ph.D. Thesis, Ecole Polytechnique Fédérale de Lausanne, 2005
16. Schilling C.H., Letscher D., and Palsson B. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theoret. Biol. 203 (2000) 229-248
17. Schrijver A. Theory of Linear and Integer Programming (1986), Wiley
18. Schuster S. Metabolic pathway analysis in biotechnology. In: Khodolenko B.N., and Westerhoff H.V. (Eds). Metabolic Engineering in the Post Genomic Era (2004), MIT Press 181-208 (chapter 8)
19. Schuster S., and Hilgetag C. On elementary flux modes in biochemical systems at steady state. J. Biol. Syst. 2 (1994) 165-182
20. Schuster S., Hilgetag C., Woods J.H., and Fell D.A. Reaction routes in biochemical reaction systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism. J. Math. Biol. 45 (2002) 153-181
21. von Kamp A., and Schuster S. Metatool 5.0: fast and flexible elementary modes analysis. Bioinformatics 22 15 (2006) 1930-1931
22. Wagner C., and Urbanczik R. The geometry of the flux cone of a metabolic network. Biophys. J. 89 (2005) 3837-3845