An algorithm for identifying dominant-edge metabolic pathways

IEEE/ACM International Conference on Computer-Aided Design, Digest of Technical Papers, ICCAD

Volumn , Issue , 2009, Pages 144-150

  Ullah, Ehsan ^a   Lee, Kyongbum ^a   Hassoun, Soha ^a  

^a Tufts University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GIBBS FREE ENERGY CHANGES; GRAPH-BASED; LIVING ORGANISMS; METABOLIC NETWORK; METABOLIC PATHWAY ANALYSIS; METABOLIC PATHWAYS; METABOLIC REACTIONS; REACTION ROUTES; RUNTIMES; SYNTHETIC BIOLOGY; TEST CASE;

COMPUTER AIDED DESIGN; STOICHIOMETRY;

METABOLISM;

EID: 76349099571     PISSN: 10923152     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (22)

1. Altintas, M.M., Eddy, C.K., Zhang, M., McMillan, J.D. and Kompala, D.S. 2006. Kinetic modeling to optimize pentose fermentation in Zymomonas mobilis. Biotechnol Bioeng 94, 273-295.
2. Atsumi, S., Hanai, T. and Liao, J.C. 2008. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451, 86-89.
3. Carlson, R., Fell, D. and Srienc, F. 2002. Metabolic pathway analysis of a recombinant yeast for rational strain development. Biotechnol Bioeng 79, 121-134.
4. Dijkstra, E.W. 1959. A Note on Two Problems in Connexion with Graphs. Numerische Mathematik 1, 269-271.
5. Forsythe, R.G., JR., Karp, P.D. and Mavrovouniotis, M.L. 1997. Estimation of equilibrium constants using automated group contribution methods. Comput Appl Biosci 13, 537-543.
6. Jankowski, M.D., Henery C.S., Broadbelt, L.J. and Hatzimanikatis, V. 2008. Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J 95, 1487-1499.
7. Klamt, S. and Stelling, J. 2002. Combinatorial complexity of pathway analysis in metabolic networks. Mol Biol Rep 29, 233-236.
8. Lee, S.K., Chou, H., Ham, T.S., Lee, T.S. and Keasling, J.D. 2008. Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels. Curr Opin Biotechnol 19, 556-563.
9. Nolan, R.P., Fenley, A.P. and Lee, K. 2006. Identification of distributed metabolic objectives in the hypermetabolic liver by flux and energy balance analysis. Metab Eng 8, 30-45.
10. Pollack, M. 1960. The Maximum Capacity through a Network. INFORMS 8, 733-736.
11. RO, D.K., Paradise, E.M., Ouellet, M., Fisher, K.J., Newman, K.L., Ndungu, J.M., HO, K.A., Eachus, R.A., Ham, T.S., Kirby, J., Chang, M.C., Withers, S.T., Shiba, Y., Sarpong, R. and Keasling, J.D. 2006. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440, 940-943.
12. Roca, C., Haack, M.B. and Olsson, L. 2004. Engineering of carbon catabolite repression in recombinant xylose fermenting Saccharomyces cerevisiae. Appl Microbiol Biotechnol 63, 578-583.
13. Rodriguez, J., Lema, J.M. and Kleerebezem, R. 2008. Energy-based models for environmental biotechnology. Trends Biotechnol 26, 366-374.
14. Schuster, S., Fell, D.A. and Dandekar, T. 2000. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol 18, 326-332.
15. Sonderegger, M., Schumperle, M. and Sauer, U. 2004. Metabolic engineering of a phosphoketolase pathway for pentose catabolism in Saccharomyces cerevisiae. Appl Environ Microbiol 70, 2892-2897.
16. Terzer, M. and Stelling, J. 2008. Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics 24, 2229-2235.
17. Trinh, C.T., Unrean, P. and Srienc, F. 2008. Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses. Appl Environ Microbiol 74, 3634-3643.
18. Vijayasankaran, N., Carlson, R. and Srienc, F. 2005. Metabolic pathway structures for recombinant protein synthesis in Escherichia coli. Appl Microbiol Biotechnol 68, 737-746.
19. Volker Kaibel, M.A.F.P. 2006. On the Bottleneck Shortest Path Problem. ZIB-Report 06-22.
20. Von Kamp, A. and Schuster, S. 2006. Metatool 5.0: fast and flexible elementary modes analysis. Bioinformatics 22, 1930-1931.
21. Wlaschin, A.P., Trinh, C.T., CARLSON, R. and Srienc, F. 2006. The fractional contributions of elementary modes to the metabolism of Escherichia coli and their estimation from reaction entropies. Metab Eng 8, 338-352.
22. Yeung, M., Thiele, I. and Palsson, B.O. 2007. Estimation of the number of extreme pathways for metabolic networks. BMC Bioinformatics 8, 363.