Dr. LEE Dong-Yup
Research Scientist
(Group Leader since Aug 2005)
Assistant Professor, NUS
(Joint appointment since Aug 2005)
- PhD (2004) & MSc (2000) in Chem. & Biomolecular Eng. KAIST, Korea
- BSc in Chemical Engineering (1998) Yonsei Univ., Korea
lee_dong_yup
bti.a-star.edu.sg
DID:(65) 6407 0900
Research
- Computational Analysis and Engineering of Biological Systems
- Bioinformatics Analysis of Omics Data
- Bioinformatics Platform and Tool Development
Publications
2010
Lee, F. C., Rangaiah, G. P. and Lee, D.-Y. (2010) Modeling and optimization of a multi-product biosynthesis factory for multiple objectives. Metab. Eng., accepted.
Chin, J., Koh, G. and Lee, D.-Y. (2010) How necessary is a fast testkit for mitigation of pandemic flu? J. R. Soc. Interface, accepted.
Selvarasu, S., Karimi, I. A., Ghim, G.-H. and Lee, D.-Y. (2010) Genome-scale modeling and in silico analysis of mouse cell metabolic network. Mol. Biosyst., 6: 152-161. [Cover paper].
2009
Chung, B. K. S. and Lee, D.-Y. (2009) Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network. BMC Syst. Biol., 3: 117.
Chong, W. P. K., Goh, L. T., Reddy, S. G., Yusufi, F. N. K., Lee, D.-Y., Wong, N. S. C., Heng, C. K., Yap, M. G. S. and Ho, Y. S. (2009) Metabolomics profiling of extracellular metabolites in recombinant Chinese hamster ovary fed-batch culture. Rapid Commun. Mass Sp., 23: 3763-3771.
Kim, P.-J., Lee, D.-Y. and Jeong, H. (2009) Centralized modularity of N-linked glycosylation pathways in mammalian cells. PLoS ONE, 4(10): e7317.
Kharkwal, S., Karimi, I. A., Chang, M. W. and Lee, D.-Y. (2009) Strain improvement and process development for biobutanol production. Recent Pat. Biotechnol., 3: 202-210.
Jung, T.-S., Yeo, H. C., Reddy, S. G., Cho, W.-S. and Lee, D.-Y. (2009) WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E. coli model. Bioinformatics, 25(21): 2850-2852.
Ow, D. S. W., Lee, D.-Y., Tung, H. H. and Chao, S. L. (2009) Plasmid regulation and systems-level effects on Escherichia coli metabolism. In S. Y. Lee (ed), Systems Biology and Biotechnology of Escherichia coli. Springer, Germany, pp. 273-294.
Oh, Y.-G., Lee, D.-Y., Lee, S. Y. and Park, S. (2009). Multiobjective flux balancing using the NISE method for metabolic network analysis. Biotechnol. Prog., 25(4): 999-1008.
Selvarasu, S., Wong, V. V. T., Karimi, I. A. and Lee, D.-Y.
(2009) Elucidation of metabolism in hybridoma cells grown in fed-batch culture by genome-scale modeling. Biotechnol. Bioeng., 102(5): 1494-1504.
Selvarasu, S., Ow, D. S.-W., Lee, S. Y., Lee, M. M., Oh, S. K.-W., Karimi, I. A. and Lee, D.-Y.
(2009) Characterizing Escherichia coli DH5α growth and metabolism in a complex medium using
genome-scale flux analysis. Biotechnol. Bioeng., 102(3): 923-934.
Lee, D.-Y., Saha, R., Yusufi, F. N. K., Park, W. and Karimi, I. A.
(2009) Web-based applications for building, managing and analyzing
kinetic models of biological systems. Brief. Bioinform., 10: 65-74.
Yusufi F.N.K., Park W., Lee M.M., Lee D.-Y.
(2009) An alpha-numeric code for representing N-linked glycan
structures in secreted glycoproteins. Bioproc. Biosys. Eng., 32: 97-107.
Ow, D. S.-W.,Lee, D.-Y., Yap, M. G-S. and Oh, S. K.-W. (2009)
Identification of cellular objective for elucidating the
physiological state of plasmid-bearing Escherichia coli using
genome-scale in silico analysis. Biotechnol. Prog., 25(1): 61-67.
2008
Lee, F. C., Rangaiah, G. P. and Lee, D.-Y. (2008) Optimization of a
multi-product microbial cell factory for multiple objectives-a
paradigm for metabolic pathway recipe. In G. P. Rangaiah (ed),
Multi-objective Optimization: Techniques and Applications in
Chemical Engineering. World Scientific, Singapore.
Ahn, J. O., Lee, H. W., Saha, R., Park, M. S., Jung, J.-K. and
Lee, D.-Y. (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., 18(11): 1773-1784.
2007
Kim, P.-J.*,
Lee, D.-Y.*, Kim, T. Y., Jeong, H., Lee, S. Y. and Park, S.
(2007) Metabolite-essentiality elucidates robustness of
Escherichia coli metabolism. Proc. Natl. Acad. Sci. USA, 104(34):
13638-13642. (*Equally contributed authors)
Selvarasu, S.,
Lee, D.-Y. and Karimi, I. A. (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., Kim, T. Y.,
Lee, D.-Y. and Lee, S. Y. (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., Yun, C., Cho, A., Hou, B. K., Park, S. and Lee,
S. Y. (2006) WebCell: a web-based environment for kinetic modeling
and dynamic simulation of cellular networks. Bioinformatics, 22:
1150-1151.
Lee, D.-Y., Zimmer, R., Lee, S. Y. and Park, S. (2006)
Colored Petri net modeling and simulation of signal transduction
pathways. Metab. Eng., 8: 112-122.
2005
Fan, L. T., Shafie, S., Bertók, B., Friedler, F.,
Lee, D.-Y., Seo, H., Park, S. and Lee, S. Y. (2005)
Graph-theoretic approach for identifying catalytic or metabolic
pathways. J. Chin. Inst. Eng., 28: 1021-1037.
Lee, S. J.*,
Lee, D.-Y.*, Kim, T. Y., Kim, B. H. and Lee, S. Y. (2005)
Metabolic engineering of Escherichia coli for the enhanced
production of succinic acid based on genome comparison and in
silico gene knock-out simulation. Appl. Environ. Microbiol., 71:
7880-7887. (*Equally contributed authors)
Lee, S. Y., Woo, H. M.,
Lee, D.-Y., Choi, H. S., Kim, T. Y. and Yun, H. (2005)
Systems-level analysis of genome-scale in silico metabolic models
using MetaFluxNet. Biotechnol. Bioproc. Eng., 10: 425-431.
Yun, H.,
Lee, D.-Y., Jeong, J., Lee, S. and Lee, S. Y. (2005) MFAML:
a standard data structure for representing and exchanging
metabolic flux models. Bioinformatics, 21: 3329-3330.
Lee, S. Y.,
Lee, D.-Y. and Kim, T. Y. (2005) Systems biotechnology for
strain improvement. Trends Biotechnol., 23: 349-358.
Lee, D.-Y., Fan, L. T., Park, S., Lee, S. Y., Shafie, S.,
Bertók, B. and Friedler, F. (2005) Complementary identification of
multiple flux distributions and multiple metabolic pathways.
Metab. Eng., 7: 182-200.
2004
Lee, D.-Y., Zimmer, R., Lee, S. Y., Hanisch, D. and Park,
S. (2004) Knowledge representation model for systems-level
analysis of signal transduction networks. Genome Informatics,
15(2): 234-243.
Hou, B. K., Kim, J. S., Jun, J. H.,
Lee, D.-Y., Kim, Y. W., Chae, S., Roh, M., In, Y.-H. and
Lee, S. Y. (2004) BioSilico: an integrated metabolic database
system. Bioinformatics, 20: 3270-3272.
Oh, Y.-G.,
Lee, D.-Y., Yun, H., Lee, S. Y. and Park, S. (2004)
Multi-product trade-off analysis of E. coli by multiobjective flux
balance analysis. Computer-Aided Chemical Engineering, 18:
1099-1104.
Lee, D.-Y., Sung, S. W., Lee, S. Y. and Park, S. 2004.
Combined deterministic-stochastic approach for pharmacokinetic
modeling. Ind. Eng. Chem. Res., 43: 1133-1143.
2003
Lee, S. Y.,
Lee, D.-Y., Hong, S. H., Kim, T. Y., Yun, H., Oh, Y.-G. and
Park, S. (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., Yun, H., Park, S. and Lee, S. Y. (2003)
MetaFluxNet: the management of metabolic reaction information and
quantitative metabolic flux analysis. Bioinformatics, 19:
2144-2146.
Lee, D.-Y., Lee, M., Lee, Y. and Park, S. (2003) Mp
criterion-based multiloop PID controllers tuning for desired
closed loop responses. Korean J. Chem. Eng., 20: 8-13.
2002
Song, J., Park, H.,
Lee, D.-Y. and Park, S. (2002) Scheduling of actual size
refinery processes considering environmental impacts with
multiobjective optimization. Ind. Eng. Chem. Res., 41: 4794-4806.
2001
Seo, H.,
Lee, D.-Y., Park, S., Fan, L. T., Shafie, S., Bertók, B.
and Friedler, F. 2001. Graph-theoretical identification of
pathways for biochemical reactions. Biotechnol. Lett., 23:
1551-1557.
Posters
Yusufi F. N. K., Jacob N. M., Mulukutla B. C., Kantardjieff A., Johnson K., Loo B. L. W., Chuah S. H., Nissom P. M., Yap M., Lee D.-Y., Hu W. S.
Short-read sequencing reveals dynamic range of transcript abundance in CHO cells
ESACT 2009, Dublin, Ireland
pdf
Yusufi F.N.K., Reddy S.G., Lee M.M., Lee D.-Y. (Mar 2008) GlycoVault: An online storage and visualization system for glycan structures. RECOMB 2008, Singapore
pdf
Yusufi F.N.K., Park W., Lee M.M., Lee D.-Y. (Dec
2007) GlycoDigit: An alpha-numeric representation system to
visualize, store and compare glycan structure data. 18th
International Conference on Genome Informatics, GIW, Singapore
pdf
Yusufi F.N.K., Wong N.S.C., Wong D.C.F., Yap
M.G.S., Lee D.-Y. (Dec 2007) A multivariate approach to studying
glycosylation gene expression in CHO cells. 18th International
Conference on Genome Informatics, GIW, Singapore
pdf
Wong N.S.C., Wong D.C.F., Goh J.S.Y.,
Yusufi F.N.K., Lee D.-Y., Yap M.G.S. (July 2007)
An intracellular analysis of the glycosylation process in CHO
cells. Biochemical Engineering XIV, Harrison Hot Springs, BC,
Canada
pdf
