Stoichiometric synthesis of metabolic pathways

Minkevich I.G.
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List of references:

  1. R. Aris. Prolegomena to the rational analysis of systems of chemical reactions // Arch. Rational Mech. Anal. — 1965. — V. 19. — P. 81–98. — DOI: 10.1007/BF00282276. — ads: 1965ArRMA..19...81A.
  2. R. Aris. Prolegomena to the rational analysis of systems of chemical reactions. II. Some addenda // Arch. Rational Mech. Anal. — 1968. — V. 27. — P. 356–364. — DOI: 10.1007/BF00251438. — ads: 1968ArRMA..27..356A.
  3. A. Bordbar, H. Nagarajan, N. E. Lewis, H. Latif, E. Ebrahim, S. Federowicz, J. Schellenberger, B. O. Palsson. Minimal metabolic pathway structure is consistent with associated biomolecular interactions // Molecular Systems Biology. — 2014. — V. 10: 737, no. 7. — P. 1–16. — http://onlinelibrary.wiley.com/doi/10.15252/msb.20145243/epdf. — DOI: 10.15252/msb.20145243.
  4. KEGG: Kyoto Encyclopedia of Genes and Genomes. — http://www.genome.jp/kegg/.
  5. M. N. Kondrashova. Interaction of transamination and oxidation of carboxylic acids in different functional states of tissues // Biokhimiya (Biochemistry, Russian). — 1991. — V. 56, no. 3. — P. 388–405.
  6. S. Lee, C. Phalakornkule, M. M. Domach, E. Ignacio, I. E. Grossmann. Recursive MILP model for finding all the alternate optima in LP models for metabolic networks // Computers and Chemical Engineering. — 2000. — V. 24. — P. 711–716. — DOI: 10.1016/S0098-1354(00)00323-9.
  7. N. E. Lewis, H. Nagarajan, O. Bernhard, B. O. Palsson. Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods // Nature Reviews. Microbiology. — 2012. — V. 10. — P. 291–305. — DOI: 10.1038/nrmicro2737.
  8. I. G. Minkevich. Incomplete systems of linear equations with restrictions of variable values // Computer Research and Modeling. — 2014. — V. 6, no. 5. — P. 719–745. — in Russian. — DOI: 10.20537/2076-7633-2014-6-5-719-745
  9. J. A. Papin, J. Stelling, N. D. Price, S. Klamt, S. Schuster, B. O. Palsson. Comparison of network-based pathway analysis methods // Trends in Biotechnology. — 2004. — V. 22, no. 8. — P. 400–405. — DOI: 10.1016/j.tibtech.2004.06.010.
  10. I. Prigogine, R. Defay. Chemical Thermodynamics. — London–NY–Toronto: Longmans Green and Co, 1954.
  11. R. T. Rockafellar. Convex Analysis. — Princeton: Princeton University Press, 1970.
  12. C. H. Schilling, B. O. Palsson. The underlying pathway structure of biochemical reaction networks // Proceedings of National Academy of Sciences USA. — 1998. — V. 95. — P. 4193–4198. — DOI: 10.1073/pnas.95.8.4193. — ads: 1998PNAS...95.4193S.
  13. C. H. Schilling, S. Schuster, B. O. Palsson, R. Heinrich. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era // Biotechnology Progress. — 1999. — V. 15, no. 3. — P. 296–303. — DOI: 10.1021/bp990048k.
  14. S. Schuster, D. A. Fell, T. Dandekar. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks // Nature Biotechnology. — 2000. — V. 18. — P. 326–332. — DOI: 10.1038/73786.
  15. E. E. Sel’kov. Personal communication. — 2010.
  16. N. F. Stepanov, M. E. Erlykina, G. G. Filippov. Methods of Linear Algebra in Physical Chemistry. — Moscow: Moscow University Press, 1976. — 360 p. — in Russian.

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