Enumerating constrained elementary flux vectors of metabolic networks

IET Systems Biology

Volumn 1, Issue 5, 2007, Pages 274-279

  Urbanczik, R ^a  

^a UNIVERSITY OF BERN   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; METABOLITES; PHYSIOLOGY;

ELEMENTARY FLUX VECTORS; FLUX BALANCE ANALYSIS; METABOLIC NETWORKS;

METABOLISM;

ALGORITHM; COMPUTER ANALYSIS; CONFERENCE PAPER; CYTOSOL; HEART MITOCHONDRION; HUMAN; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; METABOLIC BALANCE; METABOLIC REGULATION; METABOLISM; MITOCHONDRIAL RESPIRATION; STEADY STATE; SYSTEMS BIOLOGY;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; ENERGY METABOLISM; HUMANS; MODELS, BIOLOGICAL; NUMERICAL ANALYSIS, COMPUTER-ASSISTED; PROTEOME; SIGNAL TRANSDUCTION;

EID: 34548406565     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb:20060073     Document Type: Conference Paper

References (20)

1. Price, N., Reed, J., and Palsson, B.: 'Genome-scale models of microbial cells: Evaluating the consequences of constraints', Nat. Rev. Microbiol., 2004, 2, p. 886-897
2. Schuster, S., Fell, D.A., and Dandekar, T.: 'A general definition of metabolic pathways useful for systematic organisation and analysis of complex metabolic pathways', Nat. Biotech., 2000, 18, p. 326-332
3. Urbanczik, R., and Wagner, C.: 'An improved algorithm for stoichiometric network analysis: Theory and applications', Bioinformatics, 2005, 21, p. 1203-1210
4. von Kamp,FA., and Schuster, S.: 'Metatool 5.0: fast and flexible elementary modes analysis', Bioinformatics, 2006, 22, p. 1930-1931
5. Klamt, S., Gagneur, J., and von Kamp, A.: 'Algorithmic approaches for computing elementary modes in large biochemical reaction networks', IEE Proc., Syst. Biol., 2005, 152, p. 249-255
6. Urbanczik, R., and Wagner, C.: 'Functional stoichiometric analysis of metabolic networks', Bioinformatics, 2005, 21, p. 4176-4180
7. Ibarra, R.U., Edwards, J.S., and Palsson, B.O.: 'Escherichia coli k-12 undergoes adaptive evolution to achieve in silico predicted optimal growth', Nature, 2002, 420, p. 186-189 0028-0836
8. Vo, T., Greenberg, H., and Palsson, B.: 'Reconstruction and functional characterization of the human mitrochondrial metabolic network based on proteomic and biochemical data', J. Biol. Chem., 2004, 279, p. 39532-39540
9. Rockafellar, R.T.: 'Convex analysis', (Princeton University Press, Princeton 1970)
10. 'Frequently asked questions in polyhedral computation', 2004 available at www.ifor.math.ethz.ch/~fukuda/polyfaq/
11. Schuster, S., Hilgetag, C., Woods, J.H.and, and Fell, D.A.: 'Reaction routes in biochemical reactions systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism', J. Math. Biol., 2002, 45, p. 153-181 0303-6812
12. Urbanczik, R.: 'SNA - a toolbox for the stoichiometric analysis of metabolic networks', BMC Bioinformatics, 2006, 7, p. 129
13. Avis, D.: 'lrs: a revised implementation of the reverse search vertex enumeration algorithm', Kalai, G., Ziegler, G., (Polytopes-combinatorics and computation', Birkhaüuser 2000), p. 177-198
14. Mahadevan, R., and Schilling, C.: 'The effects of alternate optimal solutions in constraint-based genome-scale metabolic models', Metabolic Eng., 2003, 5, p. 264-276
15. Burgard, A., Nikolaev, E.V., Schilling, C.H., and Maranas, C.D.: 'Flux coupling analysis of genome-scale metabolic network reconstructions', Genome Res., 2004, 14, p. 301-312
16. Lee, S., Palakornkule, C., Domach, M., and Grossmann, I.: 'Recursive MILP model for finding all the alternate optima in LP models for metabolic networks', Comp. Chem. Eng., 2000, 24, p. 711-716
17. Reed, J., and Palsson, B.: 'Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: Assessment of correlated reaction subsets that comprise network states', Genome Res., 2004, 14, p. 1797-1805
18. Pal, C., Papp, B., Lercher, M.J., Csermely, P., Oliver, S.G., and Hurst, L.D.: 'Chance and necessity in the evolution of minimal metabolic networks', Nature, 2006, 440, p. 667-670 0028-0836
19. Almaas, E., Kovács, B., Vicsek, T., Oltvai, Z.N., and Barabasi, A.-L.: 'Global organization of metabolic fluxes in the bacterium Escherichia coli', Nature, 2004, 427, p. 839-843 0028-0836
20. Price, N., Schellenberger, J., and Palsson, B.: 'Uniform sampling of steady-state flux spaces: Means to design experiments and to interpret enzymopathies', Biophys. J., 2004, 87, p. 2172-2186 0006-3495