Estimating the size of the solution space of metabolic networks

BMC Bioinformatics

Volumn 9, Issue 1, 2008, Pages

  Braunstein, Alfredo ^a,b   Mulet, Roberto ^c   Pagnani, Andrea ^b  

^a POLITECNICO DI TORINO   (Italy)

^b ISI FOUNDATION   (Italy)

^c UNIVERSITY OF HAVANA   (Cuba)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION ALGORITHMS; ESCHERICHIA COLI; GEOMETRY; INFORMATION THEORY; MESSAGE PASSING; METABOLISM; MONTE CARLO METHODS; PHYSIOLOGY; STATISTICAL PHYSICS; TOPOLOGY;

BIOLOGICAL CONDITIONS; BIOLOGICAL INTERACTIONS; DETERMINISTIC METHODS; FLUX BALANCE ANALYSIS; FUNCTIONAL BEHAVIORS; MESSAGE PASSING ALGORITHM; MONTE CARLO SAMPLING; STATISTICAL PROPERTIES;

BIOINFORMATICS;

BIOLOGY; BIOMASS; ERYTHROCYTE; EXPLOSION; HUMAN; IN-LAW; INFORMATION SCIENCE; KNOCKOUT GENE; METABOLISM; NUTRIENT; PHYSICS; PREDICTION; SAMPLING; ADAPTATION; ALGORITHM; ARTICLE; ARTIFICIAL NEURAL NETWORK; BIOLOGICAL MODEL; ESCHERICHIA COLI; GENE DELETION; GENETICS; METHODOLOGY; STATISTICAL MODEL; SYSTEMS BIOLOGY; THERMODYNAMICS;

ADAPTATION, PHYSIOLOGICAL; ALGORITHMS; COMPUTATIONAL BIOLOGY; ERYTHROCYTES; ESCHERICHIA COLI; GENE DELETION; INFORMATION THEORY; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; NEURAL NETWORKS (COMPUTER); SYSTEMS BIOLOGY; THERMODYNAMICS;

EID: 50649103751     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-240     Document Type: Article

References (34)

1. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL: The largescale organization of metabolic networks. Nature 2000, 407(6804):651-654.
2. Fell DA, Wagner A: The small world of metabolism. Nature Biotechnology 2000, 18:1121-1122.
3. Z D, Qin ZS: Structural comparison of metabolic networks in selected single cell organisms. BMC Bioinformatics 2005, 6(8):.
4. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita K, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M: From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, 34:D354-7.
5. Ibarra AU, Edwards J, Palsson B: Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 2002, 420:186-189.
6. Varma A, Palsson B: Metabolic Capabilities of Escherichia coli: I.Synthesis of biosynthetic precursors and cofactors. J theor Biol 1993, 165:477-502.
7. Segré D, Vitkup D, Church G: Analysis of optimality in natural and perturbed metabolic networks. PNAS 2002, 99:15112-15117.
8. LRS package [http://cgm.cs.mcgill.ca/~avis/C/lrs.html]
9. Avis D, Fukuda K: A pivoting algorithm for convex hulls and vertex enumeration of arrangements and polyhedra. Discrete Comput Geom 1992, 8(3):295-313.
10. Wiback S, Famili I, Greenberg HJ, Palsson B: Monte Carlo sampling can be used to determine the size and shape of the steadystate flux space. J Theor Biol 2004, 228:437-447.
11. Price N, Schellenberger J, Palsson B: Uniform Sampling of Steady-State Flux Spaces: Means to Design Experiments and to Interpret Enzymopathies. Biophysical Journal 2004, 87:2172-2186.
12. Thiele I, Price N, Vo T, Palsson B: Impact of diabetes, ischemia, and diet. J Biol Chem 2005, 280:11683-11695.
13. Price N, Thiele I, Palsson B: Candidate States of Helicobacter pylori's Genome-Scale Metabolic Network upon Application of "Loop Law" Thermodynamic Constraints. Biophysical Journal 2006, 90:3919-3928.
14. Almaas E, Kovacs B, Vicsek T, Oltval Z, Barabasi AL: Global organization of metabolic fluxes in the bacterium Escherichia col. Nature 2004, 427:839-843.
15. Simonovits M: How to compute the volume in high dimension? Math Progr 2003, 97(1-2):337-374.
16. Dyer M, Frieze A: On the complexity of computing the volume of a polyhedron. SIAM J Comput 1988, 17(5):967-97.
17. Khachiyan L: Complexity of volume computation. New trends in discrete and computational geometry, Springer-Verlag 1993:91-101.
18. Bëuler B, Enge A, Fukuda K: Exact volume computation for convex polytopes: A practical study. Polytopes-combinatorics and computation, Birkhauser 2000:131-154.
19. Yedidia J, Freeman W, Weiss Y: Generalized belief propagation. Advances in Neural Information Processing Systems (NIPS) 13, Denver, CO 2001:772-778.
20. Kschischang FR, Frey BJ, Loeliger HA: Factor graphs and the sumproduct algorithm. Information Theory, IEEE Transactions on 2001, 47(2):498-519.
21. Braunstein A, Mezard M, Zecchina R: Survey propagation: An algorithm for satisfiability. Random Struct Algorithms 2005, 27:201-226.
22. MacKay DJC: Information Theory, Inference, and Learning Algorithms Cambridge University Press; 2003.
23. Reed J, Vo T, Schilling C, Palsson B: An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biology 2003, 4(9):R54.
24. De Martino A, Martelli RMC, Castillo IP: Von Neumann expanding model on random graphs. Journal of Statistical Mechanics: Theory and Experiment 2007, 2007(05):P05012.
25. Bianconi G, Zecchina R: Viable flux distribution in metabolic networks. Technical report 2007 [http://aps.arxiv.org/pdf/ 0705.2816]. ArXiv:cond-mat/0705.2816
26. Beard D, Babson E, Curtis E, Qian H: Thermodynamic constraints for biochemical networks. J Theor Biol 2004, 228:327-333.
27. Baxter B: Exactly Solved Models in Statistical Mechanics London: Academic Press Inc; 1989.
28. Mezard M, Parisi G: The Bethe lattice spin glass revisited. The European Physical Journal B 2001, 20:217.
29. Mezard M, Parisi G: The cavity method at zero temperature. J Stat Phys 2003, 111:1.
30. Richardson T, Urbanke R: The capacity of low-density parity check codes under message passing decoding. IEEE, Trans Info Theory 2001, 47:599-618.
31. Weiss Y, Freeman WT: Correctness of Belief Propagation in Gaussian Graphical Models of Arbitrary Topology. Neural Comp 2001, 13(10):2173-2200.
32. Baldassi C, Braunstein A, Brunel N, Zecchina R: Efficient supervised learning in networks with binary synapses. PNAS 2007, 104:11079-11084 [http://aps.arxiv.org/pdf/0707.1295].
33. Mezard M, Parisi G, Zecchina R: Analytic and Algorithmic Solution of Random Satisfiability Problems. Science 2002, 297:812 [http://aps.arxiv.org/pdf/0707.1295].
34. Mulet R, Pagnani A, Weigt M, Zecchina R: Coloring random graphs. Phys Rev Lett 2002, 89:268701 [http://arxiv.org/abs/condmat/ 0208460].