SSB@NUS:Publications

Peer reviewed journals

[2008]

• Yusufi, F. N. K., W. Park, M. M. Lee and D.-Y. Lee. 2008. An alpha-numeric code for representing N-linked glycan structures in secreted glycoproteins. Bioproc. Biosys. Eng., in press
• Ow, D. S.-W., D.-Y. Lee, M. G.-S. Yap and S. K.-W. Oh. 2008. Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis. Biotechnol. Prog., in press.
• Ahn, J. O., H. W. Lee, R. Saha, M. S. Park, J.-K. Jung and D.-Y. Lee. 2008. Exploring the effects of carbon sources on the metabolic capacity for shikimic acid production in Escherichia coli using in silico metabolic predictions. J. Microbiol. Biotechnol., in press.

[2007]

• Kim, P.-J.†, D.-Y. Lee†, T. Y. Kim, K. H. Lee, H. Jeong, S. Y. Lee and S. Park. 2007. Metabolite-essentiality elucidates robustness of Escherichia coli metabolism. Proc. Natl. Acad. Sci. USA, 104(34): 13638-13642. (†Equally contributed authors)

• Selvarasu, S., D.-Y. Lee and I. A. Karimi. 2007. Identifying synergistically switching pathways for multi-product strain improvement using multiobjective flux balance analysis. Computer-Aided Chemical Engineering, 24: 1007-1012.

• Choi, H. S., T. Y. Kim, D.-Y. Lee and S. Y. Lee. 2007. Incorporating metabolic flux ratios into constraint-based flux analysis by using artificial metabolites and converging ratio determinants. J. Biotechnol., 129: 696-705.

[2006]

• Lee, D.-Y., C. Yun, A. Cho, B. K. Hou, S. Park and S. Y. Lee. 2006. WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks. Bioinformatics, 22: 1150-1151.

• Lee, D.-Y., R. Zimmer, S. Y. Lee and S. Park. 2006. Colored Petri net modeling and simulation of signal transduction pathways. Metab. Eng., 8: 112-122.

[2005]

• Fan, L. T., S. Shafie, B. Bertók, F. Friedler, D.-Y. Lee, H. Seo, S. Park and S. Y. Lee. 2005. Graph-theoretic approach for identifying catalytic or metabolic pathways. J. Chin. Inst. Eng., 28: 1021-1037.

• Lee, S. J.†, D.-Y. Lee†, T. Y. Kim, B. H. Kim and S. Y. Lee. 2005. Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation. Appl. Environ. Microbiol., 71: 7880-7887. (†Equally contributed authors)

• Lee, S. Y., H. M. Woo, D.-Y. Lee, H. S. Choi, T. Y. Kim and H. Yun. 2005. Systems-level analysis of genome-scale in silico metabolic models using MetaFluxNet. Biotechnol. Bioproc. Eng., 10: 425-431.

• Yun, C., D.-Y. Lee, A. Cho, S. Y. Lee and S. Park. 2005. Quantitative analysis of biological models under the internet environment. J. Contr. Autom. Syst. Eng., 11(10): 837-842.

• Yun, C., Y. Kim, D.-Y. Lee, S. Y. Lee and S. Park. 2005. Development of an environment for dynamic simulation of biological systems. ICASE Magazine, 11(3): 38-43.

• Yun, H., D.-Y. Lee, J. Jeong, S. Lee and S. Y. Lee. 2005. MFAML: a standard data structure for representing and exchanging metabolic flux models. Bioinformatics, 21: 3329-3330.

• Lee, S. Y., D.-Y. Lee and T. Y. Kim. 2005. Systems biotechnology for strain improvement. Trends Biotechnol., 23: 349-358.

• Lee, D.-Y., L. T. Fan, S. Park, S. Y. Lee, S. Shafie, B. Bertók and F. Friedler. 2005. Complementary identification of multiple flux distributions and multiple metabolic pathways. Metab. Eng., 7: 182-200.

[2004]

• Lee, D.-Y., R. Zimmer, S. Y. Lee, D. Hanisch and S. Park. 2004. Knowledge representation model for systems-level analysis of signal transduction networks. Genome Informatics, 15(2): 234-243.

• Hou, B. K., J. S. Kim, J. H. Jun, D.-Y. Lee, Y. W. Kim, S. Chae, M. Roh, Y.-H. In and S. Y. Lee. 2004. BioSilico: an integrated metabolic database system. Bioinformatics, 20: 3270-3272.

• Oh, Y.-G., D.-Y. Lee, H. Yun, S. Y. Lee and S. Park. 2004. Multi-product trade-off analysis of E. coli by multiobjective flux balance analysis. Computer-Aided Chemical Engineering, 18: 1099-1104.

• Lee, D.-Y., S. W. Sung, S. Y. Lee and S. Park. 2004. Combined deterministic-stochastic approach for pharmacokinetic modeling. Ind. Eng. Chem. Res., 43: 1133-1143.

[2003]

• Lee, S. Y., D.-Y. Lee, S. H. Hong, T. Y. Kim, H. Yun, Y.-G. Oh and S. Park. 2003. MetaFluxNet, a program package for metabolic pathway construction and analysis, and its use in large-scale metabolic flux analysis of Escherichia coli. Genome Informatics, 14: 23-33.

• Lee, D.-Y., H. Yun, S. Park and S. Y. Lee. 2003. MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics, 19: 2144-2146.

• Lee, D.-Y., M. Lee, Y. Lee and S. Park. 2003. Mp criterion-based multiloop PID controllers tuning for desired closed loop responses. Korean J. Chem. Eng., 20: 8-13.

[2002]

• Lee, D.-Y., Y.-G. Oh, H. Yoon, S. Y. Lee and S. Park. 2002. Exploring flux distribution profiles for switching pathways using multiobjective flux balance analysis. Genome Informatics, 13: 363-364.

• Song, J., H. Park, D.-Y. Lee and S. Park. 2002. Scheduling of actual size refinery processes considering environmental impacts with multiobjective optimization. Ind. Eng. Chem. Res., 41: 4794-4806.

[2001]

• Song, J., H. Park, D.-Y. Lee and S. Park. 2001. Scheduling model for actual size refinery processes considering supply chain management. J. Korean Soc. SCM, 1: 73-80.

• Song, J., J.-K. Bok, H. Lee, H. Park, D.-Y. Lee and S. Park. 2001. Introduction and research status of supply chain management in chemical engineering and its applications to chemical industry. ICASE Magazine, 7(4): 7-18.

• Seo, H., D.-Y. Lee, S. Park, L. T. Fan, S. Shafie, B. Bertók and F. Friedler. 2001. Graph-theoretical identification of pathways for biochemical reactions. Biotechnol. Lett., 23: 1551-1557.

[2000]

• Lim, H., D.-Y. Lee and S. Park. 2000. Environmental analysis and improvement of PET production systems using life cycle assessment. Korean J. LCA, 2(1): 53-60.

[1999]

• Bok, J.-K., D.-Y. Lee and S. Park. 1999. Mixed-integer programming model for scheduling of steelmaking processes. J. Contr. Autom. Syst. Eng., 5(6): 714-723.

Patents

WO (World Intellectual Property Organization)

• Lee, S. Y., T. Y. Kim, D.-Y. Lee and S. J. Lee. Method for improving a strain based on in silico analysis. International application: PCT/KR2005/001501 (23 May 2005), Publication: WO 2006/107127 A1 (12 October 2006).

• Lee, S. Y., T. Y. Kim and D.-Y. Lee. Method of in-silico improvement of organisms using the flux sum of metabolites. International application: PCT/KR2005/003442 (14 October 2005), Publication: WO 2007/007933 A1 (18 January 2007).

US (United States of America)

• Lee, S. Y., H. S. Yun, D.-Y. Lee, S. Lee, J. Jeong and T. Y. Kim. Information system for metabolic flux anlaysis using eXtensible Markup Language and operating method thereof. US application: 11/148907 (9 June 2005), Publication: US 2006/0224371 A1 (5 October 2006).

KR (Republic of Korea)

• Lee, S. Y., H. S. Yun, D.-Y. Lee, S. Lee, J. Jeong and T. Y. Kim. Information system for metabolic flux anlaysis using eXtensible Markup Language and operating method thereof. KR application: 10-2005-0027215 (31 March 2005), Publication: 10-0616611 (21 August 2006).

• Lee, S. Y., T. Y. Kim, D.-Y. Lee and S. J. Lee. Method for improving a strain based on in silico analysis. KR application: 10-2005-0029568 (8 April 2005), Publication: 10-0630836 (26 September 2006).

• Lee, S. Y., T. Y. Kim and D.-Y. Lee. Method of in-silico improvement of organisms using the flux sum of metabolites. KR application: 10-2005-0062404 (11 July 2005), Publication: 10-0655495 (1 December 2006).

• Lee, S. Y., T. Y. Kim and D.-Y. Lee. Method of improvement of organisms using profiling the flux sum of metabolites. KR application: 10-2006-0040552 (4 May 2006), Publication: 10-0727053 (4 June 2007).