Modeling of in Silico Microbe System based on the Combination of a Hierarchical Regulatory Network with Metabolic Network
![]() |
Lee, Sung-Gun
(부산대학교 화학공학과)
Han, Sang-Il (부산대학교 화학공학과) Kim, Kyung-Hoon (부산대학교 화학공학과) Kim, Young-Han (동아대학교 화학공학과) Hwang, Kyu-Suk (부산대학교 화학공학과) |
1 | R. Mahadevan, J. S. Edwards, and J. D. Francis, 'Dynamic flux balance analysis of diauxic growth in Escherichia coli,' Biophys. J., vol. 83, pp. 1331-1340, 2002 DOI ScienceOn |
2 | P. Wong, S. Gladney, and J. D. Keasling, 'Mathematical model of the lac operon: Inducer exclusion, catabolite repression, and diauxic growth on glucose and lactose,' Biotechnol. Progr., vol13, pp132-143, 1997 DOI ScienceOn |
3 | A. Narang, A. Konopka, and D. Ramkrishna, 'New patterns of mixed-substrate utilization during batch growth of escherichia coli K12,' Biotechnol Bioeng., vol. 55, no 5, pp747-757, 1997 DOI ScienceOn |
4 | A. Kremling, K. Bettenbrock, B. Laube, J. W. Lengeler, and E. D. Gilles, 'The organization of metabolic reaction networks: Application for diauxic growth on glucose and lactose,' Meta. Eng., vol.3, pp.362-379, 2001 DOI ScienceOn |
5 | S. S. Shen-Orr, R. Milo, S. Mangan, and U. Alon, 'Network motifis in the transcriptional regulation network of Escherichia coli,' Nature Genetics, vol. 31, pp. 64-68, 2002 DOI ScienceOn |
6 | G. N. Stephanopoulos, A. A. Aristidou, and J. Nielsen, Metabolic Engineering: Principles and Methodologies, Academic press, London, UK, pp180-193, 1998 |
7 | K. B. Andersen and K. V. Meyenburg, 'Are growth rates of Escherichia coli in batch cultures limited by respiration?,' J. Bacteriol, vol. 144, no. 1, pp114-123, 1980 |
8 | C. H. Schilling, J. S. Edwards, Letsecher D., and B. O. Palsson, 'Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems,' Biotechnol. Bioeng., vol. 71, no.4, pp.286-306, 2000 DOI ScienceOn |
9 | P. A. Cotter and R. P. Gunsalus, 'Contribution of the fnr and arcA gene products in coordinate regulation of cytochrome o and d oxide (cyoABCDE and cydAB) gene in Escherichia coli,' FEMS Microbiol Lett, vol. 70, pp.31-36, 1992 DOI ScienceOn |
10 | A. M. Huerta, H. Salgado, D. Thieffiy, and J. Collado-Vides, 'RegulonDB: A database on transcriptional regulation in Escherichia coli,' Nucleic Acids Res., vol. 26, pp. 55-59, 1998 DOI |
11 | M. W. Covert, E. M Knight, J. L. Reed, M. J. Herrgard, and B. O. Palsson, 'Integrating high-throughput and computational data elucidates bacterial networks,' Nature, vol. 429, pp.92-96, 2004 DOI ScienceOn |
12 | S. G Lee, 'A study on in silico simulation of various carbon sources-grown Escherichia coli based on a hierarchical regulatory network and flux balance analysis,' Doctoral Thesis, Pusan National University, 2005 |
13 | S. G Lee, C. M. Kim, and K. S. Hwang, 'Development of a software tool for in silico simulation of Escherichia coli using a visual programming environment,' Journal of Biotechnology, vol. 119, pp. 87-92, 2005 DOI ScienceOn |
14 | S. G Lee, K. S. Hwang, and C. M. Kim, 'Dynamic behavior of regulatory elements in the hierarchical regulatory network of various carbon sources-grown Escherichia coli,' Journal of Microbiology and Biotechnology, vol. 15, pp. 551-559, 2005 과학기술학회마을 |
15 | W. C. Covert, C. H. Schilling, and B. O. Palsson, 'Regulation of gene expression in flux balance models of metabolism,' J. Theor. Biol. vol. 213, pp. 73-88, 2001 DOI ScienceOn |
16 | P. H. Winston, Artificial Intelligence, Addison Wesley, U.S.A, pp. 119-137, 1992 |
17 | A. Vanna and B. O. Palsson, 'Stoichiometric flux balance models quantitatively predict growth and metabolic by-product Secretion in wild type Escherichia coli W3110,' Appl. Environ. Microbol., vol. 60, pp.3724-3731, 1994a |
18 | A. Varma and B. O. Palsson, 'Metabolic flux balancing: basic concepts, scientific and practical use,' Bio/Technology, vol. 12, pp. 994-998, 1994b DOI |
19 | W. C. Covert and B. O. Palsson, 'Transcriptional regulation in constraints-based metabolic models of Escherichia coli,' J. Biol. Chem., vol. 277, pp.28058-28064, 2002 DOI ScienceOn |
20 | H. H. MacAdams, and L. Shapiro, 'Circuit simulation of genetic networks,' Science, vol. 269, pp. 650-656, 1995 DOI |
21 | S. Meyers, and P. Friedland, 'Knowledge-based simulation of genetic regulation in bacteriophage lambda,' Nucleic Acids Res., vol. 12, pp. 1-9, 1984 DOI ScienceOn |
22 | M. Tomita, K. Hashimoto, K. Takahashi, T. S. Shimizu, Y. Matsuzaki, F. Miyoshi, K. Saito, S. Tanida, K. Yugi, J. C. Venter, and C. A. Hutchison III, 'E-Cell: software environment for whole-cell simulation,' Bioinformatics, vol. 15, pp. 72-84, 1999 DOI ScienceOn |
23 | J. C. Liao and M. K. Oh, 'Toward predicting metabolic fluxes in metabolically engineered strains,' Metabolic Engineering., vol. 1, pp. 214-223, 1999 DOI ScienceOn |
24 | A. Varma, B. W. Boesch, and B. O. Palsson, 'Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates,' Appl. Environ. Microbiol., vol. 59, pp. 2465-2473, 1993 |
25 | S. Y. Lee and Papoutsakis, Metabolic flux balance analysis, Marcel Deker, New York, U.S.A, pp.13-57, 1999 |
![]() |