Russian version English version
Volume 2   Issue 1   Year 2007
Nazipova N.N., Elkin Yu.E., Panjukov V.V., Drozdov-Tikhomirov L.N.

Rate Calculation for Metabolic Reactions in a Living and Growing Cell by the Method of Steady-State Stoichiometric Flux Balance

Mathematical Biology & Bioinformatics. 2007;2(1):98-119.

doi: 10.17537/2007.2.98.

References

  1. Holzhütter H-G. The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. Eur. J. Biochem. 2004;271:2905-2922. doi: 10.1111/j.1432-1033.2004.04213.x
  2. Papoutsakis ET. Equations and Calculations for Fermentations of Butyric Acid Bacteria. Biotechnology and Bioengineering. 1984;XXVI:174-187. doi: 10.1002/bit.260260210
  3. Desai RP, Nielsen LK, Papoutsakis ET. Stoichiometric modeling of Clostridium acetobutylicum fermentations with non-linear constraints. Journal of Biotechnology. 1999;71:191-205. doi: 10.1016/S0168-1656(99)00022-X
  4. Watson MR. A discrete model of bacterial metabolism. CABIOS. 1986;2(1): 23-27.
  5. Fell D, Small JR. Fat synthesis in adipose tissue. Biochem. J. 1986;238:781-786.
  6. Drozdov-Tikhomirov LN, Scurida GI, Serganova VV. Inner metabolic fluxes in multienzyme systems: Lysine syntesis on acetate by Corynebacterium glutamicum. Biotechnologia (Moscow). 1986;2(8):28-37.
  7. Drozdov-Tikhomirov LN, Scurida GI, Serganova VV. Flux Stoichiometric Models of Cell Metabolism. In: Reports of International Conference “Modeling and Computer Methods in Molecular Biology and Genetics. N.Y.: Nova Science Publisher; 1992. P. 329-334.
  8. Drozdov-Tikhomirov LN, Scurida GI, Davidov AV, Alexandrov AA, Zvyagilskaya RA. Mathematical modeling of living cell metabolism using the method of steady-state stoichiometric flux balance. Journal of Bioinformatics and Computational Biology. 2006;4(4):865-885. doi: 10.1142/S0219720006002247
  9. Schuster R,Schuster S. Refined algorithm and computer program for calculating all non-negative fluxes admissible in steady states of biochemical reaction systems with or without some flux rates fixed. Comput. Appl. Biosci. 1993;9:79-85.
  10. Savinell JM, Palsson BO. Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism. J. Theor. Biol. 1992;154(4)421-454. doi: 10.1016/S0022-5193(05)80161-4
  11. Varma A, Palsson B. Metabolic capabilities of Escherichia coli. II. Optimal growth patterns. J. Theor. Biol. 1993;165:503-522.
  12. Varma A, Palsson BO. Metabolic flux balancing: basic concepts, scientific and practical use. Bio/Technology. 1994;12:994-998. doi: 10.1038/nbt1094-994
  13. Edwards JS, Ramakrishna R, Schilling CH, Palsson BO. Metabolic flux balance analysis. In: Metabolic engineering. Ed. S.Y. Lee and E.T. Papoutsakis. N.Y.: Marcel Dekker; 1999. P. 13-57.
  14. Edwards JS, Covert M, Palsson BO. Metabolic modelling of microbes: the flux-balance approach. Environ. Microbiol. 2002;4:133-140.
  15. Foster J, Famili I, Fu PC, Palsson BO, Nielsen I. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 2003;13:244-253. doi: 10.1101/gr.234503
  16. Forster J, Famili I, Palsson BO, Nielsen J. Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS. 2003;7(2):193-202. doi: 10.1089/153623103322246584
  17. Famili I, Forster J, Nielsen J, Palsson BO. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc Natl Acad Sci USA. 2003;100(23):13134-13139. doi: 10.1073/pnas.2235812100
  18. Fong SS, Marciniak JY, Palsson BO. Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model. J. Bacteriol. 2003;185(21):6400-6408. doi: 10.1128/JB.185.21.6400-6408.2003
  19. Ibarra RU, Fu P, Palsson BO, DiTonno JR, Edwards JS. Quantitative analysis of Escherichia coli metabolic phenotypes within the context of phenotypic phase planes. J. Mol. Microbiol. Biotechnol. 2003;6(2):101-108.
  20. Allen TE, Herrgard MJ, Liu M, Qiu Y, Glasner JD, Blattner FR, Palsson BO. Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets. J Bacteriol. 2003;185(21):6392-6399. doi: 10.1128/JB.185.21.6392-6399.2003
  21. Duarte NC, Herrhard MJ, Palsson BO. Reconstruction and validation of Saccharomyces iND750, a fully ñompartmentalized genome-scale metabolic model. Genome Res. 2004;14(7):1298-1309. doi: 10.1101/gr.2250904
  22. Reed JL, Palsson BO. 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(9):1797-1805. doi: 10.1101/gr.2546004
  23. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004;429(6987):92-96. doi: 10.1038/nature02456
  24. Wiback SJ, Mahadevan R, Palsson BO. Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum. Biotechnol. Bioeng. 2004;86(3):317-331. doi: 10.1002/bit.20011
  25. Reed JL, Vo TD, Schilling CH, Palsson BO. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 2004;4(9):R54. doi: 10.1186/gb-2003-4-9-r54
  26. Famili I, Palsson BO. Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices. J Theor. Biol. 2004;224(1):87-96.
  27. Fong SS, Palsson BO. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat. Genet. 2004;36(10):1056-1058.
  28. Duarte NC, Palsson BO, Fu P. Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae. BMC Genomics. 2004;5(1):63. doi: 10.1186/1471-2164-5-63
  29. Duarte NC, Herrgard MJ, Palsson BO. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res. 2004;14(7):1298-1309. doi: 10.1101/gr.2250904
  30. Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BO. In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol. Bioeng. 2005;91(5):643-648. doi: 10.1002/bit.20542
  31. Mahadevan R, Palsson BO. Properties of metabolic networks: structure versus function. Biophys. J. 2005;88(1):L07-L09. doi: 10.1529/biophysj.104.055723
  32. Tempest DW, Neussell OM. Growth Yield and Energy Distribution In Escherichia Coli and Salmonella Typhimurium. In: Cellular and Molecular Biology. Ed. F.C.Neidhard. Washington: Am.Soc. for Microbiology; 1987. V. 1. 797 p.
  33. Stouthamer AN. The search for correlation between theoretical and experimental growth yield. Int .Rev. Biochem. 1979;21:1-47.
  34. Pirt SJ. Principles of Microbe and Cell Cultivation. Blackwell Scientific Publications; 1975.
  35. Vasil'ev FP, Ivanitskii AIu. Lineinoe programmirovanie (Linear programming). Moscow; 2003.
Table of Contents Original Article
Math. Biol. Bioinf.
2007;2(1):98-119
doi: 10.17537/2007.2.98
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

  Copyright IMPB RAS © 2005-2024