A metabolic network analysis & NMR experiment design tool with user interface-driven model construction for depth-first search analysis

Metabolic Engineering

Volumn 5, Issue 2, 2003, Pages 74-85

  Zhu, T ^a   Phalakornkule, C ^b   Ghosh, S ^c   Grossmann, I E ^c   Koepsel, R R ^a   Ataai, M M ^a   Domach, M M ^c  

^a University of Pittsburgh   (United States)

^b KING MONGKUT'S UNIVERSITY OF TECHNOLOGY NORTH BANGKOK   (Thailand)

^c CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0037810943     PISSN: 10967176     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1096-7176(03)00023-5     Document Type: Article

References (23)

1. Bailey, J.E., 1998. Mathematical modeling and analysis in biochemical engineering: past accomplishments and future opportunities. Biotechnol. Prog. 14, 8-20.
2. Bonarius, H.P.J., Schmid, G., Tramper, J., 1997. Flux analysis of underdetermined metabolic networks: the quest for the missing constraints. Trends Biotechnol. 15, 308-314.
3. Burgard, A.P., Vaidyaraman, S., Maranas, C.D., 2001. Minimal reaction sets for E. coli metabolism under different growth requirements and uptake environments. Biotechnol. Prog. 17, 791-797.
4. Fry, B., Zhu, T., Phalakornkule, C., Koepsel, R., Domach, M.M., Ataai, M.M., 2000. Characterization of cell growth, acid production in pyruvate kinase mutant of B subtilis. Appl. Environ. Microbiol. 66, 4045-4049.
5. Glaser, R., 1999. FCAL, Ver.2.3.0. ETH Zûrich, Zûrich.
6. Goel, A., Lee, J., Domach, M.M., Ataai, M.M., 1995. Suppressed acid formation by cofeeding glucose and citrate in Bacillus cultures: emergence of pyruvate kinase as a potential metabolic engineering site. Biotechnol. Prog. 11, 380-386.
7. Goryanin, I., Hodgman, C.T., Selkov, E., 1999. Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics 15, 749-758.
8. Lee, S., Phalakornkule, C., Ataai, M.M., Domach, M.M., Grossmann, I.E., 2000. Recursive MILP model for finding all the alternate optima in LP models for metabolic networks. Comput. Chem. Eng. 24, 711-716.
9. Liao, J.C., Oh, M.K., 1999. Toward predicting metabolic fluxes in metabolically engineered strains. Metab. Eng. 1, 214-223.
10. 13C NMR spectroscopy. J. Biol. Chem. 263, 6964-6971.
11. Mendes, P., 1997. Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22, 361-363.
12. Mollney, M., Weichert, W., Kownatzki, D., de Graaf, A.A., 1999. Bidirectional reaction steps in metabolic networks: IV. optimal design of isotopomer labeling experiments. Biotechnol. Bioeng. 66, 86-103.
13. Pfeiffer, T., Sánchez-Valdenebro, I., Nuňo, J.C., Montero, F., Schuster, S., 1999. METATOOL: for studying metabolic networks. Bioinformatics 15, 251-257.
14. 13C NMR evidence for pyruvate kinase flux attenuation underlying suppressed acid formation in B. subtilis cultures. Biotechnol. Prog. 16, 169-175.
15. Schaff, J., Fink, C.C., Slepchenko, B., Carson, J.H., Loew, L.M., 1997. A general computational framework for modeling cellular structure and function. Biophys. J. 73, 1135-1146.
16. Schmidt, K., Carlsen, M., Nielsen, J., Villadsen, J., 1997. Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices. Biotech. Bioeng. 55, 831-840.
17. Sedgewich, R., 2001. Algorithms in C Part 5: graph algorithms. Addison-Wesley, Reading, MA.
18. Stephanopoulos, G., Vallino, J.J., 1991. Network rigidity and metabolic engineering in metabolite overproduction. Science 252, 1675-1681.
19. Tempest, D.W., Meers, J.L., Brown, C.M., 1970. Influence of the environment on the content and composition of microbial free amino acid pools. J. Gen. Microbiol. 64, 171-185.
20. Tomita, M., 2001. Whole-cell simulation: a grand challenge of the 21st century. Trends Biotechnol. 19, 205-210.
21. Varma, A., Palsson, B.Ø., 1994. Metabolic flux balancing: basic concepts, scientific and practical use. Bio/Technology 12, 994-998.
22. Zhu, T., 2003. Convex analysis of metabolic network for optimal cell design & flux validation by GC-MS or NMR chemical engineering. Ph.D. Thesis, University of Pittsburgh, Pittsburgh, PA, USA.
23. Zhu, T., Phalakornkule, C., Koepsel, R.R., Domach, M.M., Ataai, M.M., 2001. Cell growth and by-product formation in a pyruvate kinase mutant of E coli. Biotechnol. Prog. 17, 624-628.