Minkevich I.G.
Mathematical Problems of Metabolic Pathway Organization from Biochemical Reactions
Mathematical Biology & Bioinformatics. 2016;11(2):406-425.
doi: 10.17537/2016.11.406.
References
- BRENDA: The Comprehensive Enzyme Information System. http://www.brenda-enzymes.info/ (accessed 19 December 2016).
- ExPASy: the SIB Bioinformatics Resource Portal. http://www.expasy.org/ (accessed 19 December 2016).
- KEGG: Kyoto Encyclopedia of Genes and Genomes. http://www.genome.jp/kegg/ (accessed 19 December 2016).
- MetaCyc: MetaCyc Metabolic Pathway Database. https://metacyc.org/ (accessed 19 December 2016).
- Minkevich I.G. Material'no-energeticheskii balans i kinetika rosta mikroorganizmov (Material and energy balance and kinetics of microbial growth). Moscow-Izhevsk, 2005 (in Russ.).
- Bordbar A., Nagarajan H., Lewis N.E., Latif H., Ebrahim E., Federowicz S., Schellenberger J., Palsson B.O. Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Molecular Systems Biology. 2014;10.737(7):1-16.
- Lee S., Phalakornkule C., Domach M.M., Ignacio E., Grossmann I.E. Recursive MILP model for finding all the alternate optima in LP models for metabolic networks. Computers and Chemical Engineering. 2000;24:711-716. doi: 10.1016/S0098-1354(00)00323-9
- Lewis N.E., Nagarajan H., Bernhard O., Palsson B.O. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nature Reviews. Microbiology. 2012;10:291-305. doi: 10.1038/nrmicro2737
- Papin J.A., Stelling J., Price N.D., Klamt S., Schuster S., Palsson B.O. Comparison of network-based pathway analysis methods. Trends in Biotechnology. 2004;22(8):400-405. doi: 10.1016/j.tibtech.2004.06.010
- Schilling C.H., Palsson B.O. The underlying pathway structure of biochemical reaction networks. Proceedings of National Academy of Sciences USA. 1998;95:4193-4198. doi: 10.1073/pnas.95.8.4193
- Schilling C.H., Schuster S., Palsson B.O., Heinrich R. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnology Progress. 1999;15(3):296-303. doi: 10.1021/bp990048k
- Schuster S., Fell D.A., Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nature Biotechnology. 2000;18:326-332. doi: 10.1038/73786
- Stepanov N.F., Erlykina M.E., Filippov G.G. Metody lineinoi algebry v fizicheskoi khimii (Methods of linear algebra in physical chemistry). Moscow, 1976 (in Russ.).
- Prigogine I., Defay R. Khimicheskaia termodinamika. Novosibirsk, 1966. (Translation of Prigogine I., Defay R. Chemical Thermodynamics. Wiley, 1954. 543 p.
- Minkevich I.G. Incomplete systems of linear equations with restrictions of variable values. Computer Research and Modeling. 2014;6(5):719-745 (in Russ.).
- Chernikov S.N. Linear inequalities. In: Itogi Nauki. Ser. Mat. Algebra. Topol. Geom. 1966. Moscow: VINITI, 1968. P. 137-187 (in Russ.).
- Golikov A.I., Evtushenko Yu.G. A new method for solving systems of linear equalities and inequalities. Doklady Mathematics. 2001:64(3):370-373.
- Bastrakov S.I., Zolotykh N.Yu. Application of the Quickhull algorithm's principles to the double description method. Numerical Methods and Programming. 2011;12(2):232-237 (in Russ.).
- Bastrakov S.I., Zolotykh N.Yu. Fast method for verifying Chernikov rules in Fourier-Motzkin elimination. Computational Mathematics and Mathematical Physics. 2015;55(1):160-167. doi: 10.1134/S0965542515010042
- Minkevich I.G. Stoichiometric synthesis of metabolic pathways. Computer Research and Modeling. 2015;7(6):1241-1267.
|
|
|
