LEE, Dong-Yup

Assistant Professor

PhD (Chem. & Biomolecular Eng.) KAIST, 2004
MSc (Chem. & Biomeolecular Eng.) KAIST, 2000
BSc (Chem. Eng.) Yonsei Univ., 1998

Contact information
Blk E5, 4 Engineering Drive 4, #03-16, Singapore 117576
Tel: (65) 6516 6907   Fax: (65) 6779 1936
Email: cheld@nus.edu.sg

Research scientist (Joint appointment), Bioprocessing Technology Institute (BTI)
Research Group Home Page

RESEARCH

Systems Biology/Biotechnology

Special attention is recently being paid to Systems Biology and Biotechnology as promising research and development paradigms for elucidating the complex biological processes and for achieving efficient biotechnological processes. The central task of this area is to comprehensively collect the global cellular information such as omics-data, and to combine such data through complex biological processes, i.e., metabolic, signaling and regulatory networks, in order to generate predictive computational models of the biological system. Thus, better understanding the cellular physiology, regulation and metabolism at the systems level and designing strategies for metabolic and cellular engineering of organisms are a prime target of this research. My research subjects are part of this goal. More specifically, I would like to address some challenging topics as follows, but not limited to.

Identification and prioritization of antimicrobial drug targets

The large-scale organization principles and functional properties of the biological systems (like how these molecules are interacting with each other to maintain the robustness of cellular functions) can be elucidated by analyzing the topological and dynamic properties of biological networks. A graph-theoretic approach and constraints-based flux analysis for the identification of multiple biochemical pathways can be promising for the analysis of the genome-wide networks. This would facilitate the discovery of antimicrobial drug targets that are essential for the growth or survival of a pathogen satisfying the principle of selective toxicity.

Investigation of pharmacodynamic and mechanistic effects of drug candidates

To date, numerous drug targets for various diseases have been identified at different levels in the signaling pathways. A major challenge is to explore such identified drug effects on the pharmacological modulation within the reconstructed pathways in order to evaluate the efficacy, safety and cost-effectiveness of drug targets available. The detailed molecular mechanisms of the reconstructed cell-signaling network could provide useful information for developing a rational approach to the quantification of the mechanistic effects of drugs and prioritizing and verifying drug candidates at the system-level.

SELECTED PUBLICATIONS

D. S.-W. Ow, D.-Y. Lee, M. G.-S. Yap and S. K.-W. Oh, "Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis", Biotechnol. Prog., in press.
 

J. O. Ahn, H. W. Lee, R. Saha, M. S. Park, J.-K. Jung and D.-Y. Lee, "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.
 

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

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

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

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

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

S. J. Lee, D.-Y. Lee, T. Y. Kim, B. H. Kim and S. Y. Lee, "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 (2005).

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

S. Y. Lee, D.-Y. Lee and T. Y. Kim, “Systems biotechnology for strain improvement”, Trends Biotechnol., 23, 349 (2005).

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

D.-Y. Lee, S. W. Sung, S. Y. Lee and S. Park, “Combined deterministic-stochastic approach for pharmacokinetic modeling”, Ind. Eng. Chem. Res., 43, 1133 (2004).