Graph models and mathematical programming in biochemical network analysis and metabolic engineering design

Computers and Mathematics with Applications

Volumn 55, Issue 5, 2008, Pages 970-983

  Lanzeni, Stefano ^a   Messina, Enza ^a   Archetti, Francesco ^a,b  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

^b CMR Consorzio Milano Ricerche   (Italy)

Author keywords

Biological networks; Linear programming; Metabolic networks; Petri nets

Indexed keywords

BIOCHEMISTRY; ESCHERICHIA COLI; LINEAR PROGRAMMING; METABOLISM; PETRI NETS; SENSITIVITY ANALYSIS;

BIOLOGICAL NETWORKS; METABOLIC NETWORKS; MOLECULAR UNITS;

BIOLOGICAL SYSTEMS;

EID: 38349120725     PISSN: 08981221     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.camwa.2006.12.101     Document Type: Article

References (28)

1. Evans G.A. Designer science and the "omics" revolution. Nat. Biotechnol. 18 (2000) 127
2. Kitano H. Foundations of Systems Biology (2001), The MIT Press. 0-262-11266-3
3. Strothman R.C. The coming kuhnian revolution in biology. Nat. Biotechnol. 15 (1997) 194-199
4. Palsson B.O. Systems Biology: Properties of Reconstructed Networks (2006), Cambridge Press
5. Palsson B.O. The challenges of in silico biology. Nat. Biotechnol. 18 (2000) 1147-1150
6. De Jong H. Modeling and simulation of genetic regulatory systems: A literature review. J. Comput. Biol. 9 (2002) 67-103
7. Kitano H. Cancer as a robust system: Implications for anticancer therapy. Nat. Rev. Cancer 4 (2004) 227-235
8. Palsson B.O. In silico biology through omics. Nat. Biotechnol. 20 (2002) 649
9. Ptashne G. Genes and Signals (2002), Cold Spring Harbor Press, New York
10. Gompets B.D., Kramer I.M., and Tatham P.E.R. Signal Transduction (2002), Academic Press, San Diego
11. Honisch C., Raghunathan A., Cantor C.R., Palsson B.O., and van den Boom D. High-throughput mutation detection underlying adaptive evolution of E. coli-K12. Genome Res. 14 (2004) 2495-2502
12. Karp P.D., Riley M., Saier M., Paulsen I.T., Collado-Vides J., Paley S.M., Pellegrini-Toole A., Bonavides C., and Gama-Castro S. The EcoCyc database. Nucleic. Acids Res. 30 (2002) 56-58
13. Yarmush M.L., and Banta S. Metabolic engineering: Advances in modeling and intervention in health and disease. Annu. Rev. Biomed. Eng. 5 (2003) 349-381
14. Zanzoni A., Montecchi-Palazzi L., Quondam M., Ausiello G., Helmer-Citterich M., and Cesareni G. MINT: A Molecular INTeraction database. FEBS Lett. 513 (2002) 135-140
15. A. Sheldon, Linear Algebra Done Right, Springer-Verlag
16. C.A. Petri, Ph.D. Thesis, Institut fur Instrumentelle Mathematik, Bonn, 1962
17. Peterson J.L. Petri Net Theory and the Modeling of Systems (1981), Prentice Hall, Englewood Cliffs, NY
18. Starke P.H. Analyse von Petri Netz Modellen (1990), B.G. TeubnerVerlag, Stuttgart
19. Schrijver A. Theory of Linear and Integer Programming (1999), John Wiley and Sons
20. Varma A. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild type E. coli W3110. Appl. Env. Microb. 60 (1994) 3724-3731
21. Varna A., and Palsson B.O. Metabolic flux balancing: Basic concept, scientific and practical use. Nat. Biotechnol. 12 (1994) 994-998
22. Edwards J.S., Covert M., and Palsson B.O. Metabolic modeling of microbes: The flux balance approach. Environ. Microbiol. 4 (2002) 133-140
23. Pramanik J., and Keasling J.D. Stoichiometric model of E. coli metabolism: Incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. Biotechnol. Bioeng. 56 (1997) 398-421
24. Lodish H., Berk A., Zipursky L., Matsudaira P., Baltimore D., and Darnell J. Molecular Cell Biology. fourth ed. (2000), Freeman
25. Varma A. Stoichiometric interpretation of E. coli glucose catabolism under various oxygenation rates. Appl. Env. Microb. 59 (1993) 2465-2473
26. Fong S.S., Marciniak J.Y., and Palsson B.O. Description and interpretation of adaptive evolution of E. coli K12 MG1655 using a genome-scale in silico metabolic model. J. Bacteriol. 185 (2003) 6400-6408
27. Ridley R.G. Medical need, scientific opportunity and the drive for antimalarian drugs. Nature 415 (2002) 686-693
28. Wallart T.E., Pras N., Beekman A.C., and Quax W.J. Seasonal variation of artemisin and its biosynthetic precursors in plants of Artemisa annua of different geographical origin: Proof for the existence of chemotypes. Planta Med. 66 (2000) 57-62