Publications


Publications

2015
Lakshmanan, M., S. -H. Lim, B. Mohanty, J. K. Kim, S. -H. Ha, and D.-Y. Lee. 2015. Unraveling the light-specific metabolic and regulatory signatures of rice through combined in silico modeling and multi-omics analysis. Plant Physiol., accepted.

Mohanty, B., A. Kitazumi, C. Y. M. Cheung, M. Lakshmanan, B. G. de los Reyes, I. -C. Jang, and D.-Y. Lee. 2015. Identification of candidate network hubs involved in metabolic adjustments of rice under drought stress by integrating transcriptome data and genome-scale metabolic network. Plant Sci. (Special Issue), accepted.

Kim, M., J. S. Yi, M. Lakshmanan, D.-Y. Lee and B.-G. Kim. 2015. Transcriptomics-based strain optimization tool for designing secondary metabolite overproducing strains of Streptomyces coelicolor. Biotechnol. Bioeng., accepted.

Lakshmanan, M., T. Y. Kim, B. K. S. Chung, S. Y. Lee and D.-Y. Lee. 2015. Flux-sum analysis identifies metabolite targets for strain improvement. BMC Syst. Biol., accepted.

Yeo, H. C., B. K.-S. Chung, W. Chong, J. X. Chin, K. S. Ang, M. Lakshmanan, Y. S. Ho and D.-Y. Lee. 2015. A genetic algorithm-based approach for pre-processing metabolomics and lipidomics LC-MS data. Metabolomics, accepted.

Liu, C., J. X. Chin, and D.-Y. Lee. 2015. SynLinker: an integrated system for designing linkers and synthetic fusion proteins. Bioinformatics, in press.

Lakshmanan, M., K. Yu, L. Koduru and D.-Y. Lee. 2015. In silico model-driven cofactor engineering strategies for improving the overall NADP(H) bioavailability in microbial cell factories. J. Ind. Microbiol. Biotechnol., in press.

Kwok, J. J. M. and D.-Y. Lee. 2015. Coopetitive supply chain relationship model: application to the smartphone manufacturing network. PLoS ONE, 10(7): e0132844.

Chen, B., D.-Y. Lee and M. W. Chang. 2015. Combinatorial metabolic engineering of Saccharomyces cerevisiae for terminal 2 alkene production. Metab. Eng., 31: 53-61.

Yu, N., L. T. J. Dieu, S. Harvey and D.-Y. Lee. 2015. Optimization of process configuration and strain selection for microalgae-based biodiesel production. Bioresour. Technol., 193: 25-34.

Pek, H. B., M. Klement, K. S. Ang, B. K. S. Chung, D. S.-W. Ow and D.-Y. Lee. 2015. Exploring codon context bias for designing a synthetic thermostable invertase gene in Escherichia coli. Enzyme Microb. Technol., 75-76: 57-63.

Klement, M., C. Liu, B. L. W. Loo, A. B.-H. Choo, D. S.-W. Ow and D.-Y. Lee. 2015. Effect of linker flexibility and length on the functionality of a cytotoxic engineered antibody fragment. J. Biotechnol., 199: 90-97.

de los Reyes, B. G., B. Mohanty, S.-J. Yun, M.-R. Park, and D.-Y. Lee. 2015. Upstream regulatory architecture of rice genes: Summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining. Rice, 8: 14. [Highly accessed].

Vishwanathan, N., A. Yongky, K. C. Johnson, H.-Y. Fu, N. M. Jacob, H. Le, F. N. K. Yusufi, D.-Y. Lee and W.-S. Hu. 2015. Global insights into the Chinese hamster and CHO cell transcriptomes. Biotechnol. Bioeng., 112(5): 965-976. [Spotlighted article]

Yu, K., C. Liu, B.-G Kim and D.-Y. Lee. 2015. Synthetic fusion protein design and applications. Biotechnol. Adv., 33: 155-164.

2014
Lee, D.-Y. and K. Yu. 2014. Synthetic biology in Singapore. Asia Pacific Biotech News, 18(5): 35-38.

Lakshmanan, M., B. Mohanty, S.-H. Lim, S.-H. Ha, and D.-Y. Lee. 2014. Metabolic and transcriptional regulatory mechanisms underlying the anoxic adaptation of rice coleoptile. AoB PLANTS, 6: plu026.

Loh, W. P., B. Loo, L. Zhou, P. Zhang, D.-Y. Lee, Y. Yang, K. P. Lam. 2014. Overexpression of microRNAs enhances recombinant protein production in Chinese hamster ovary cells. Biotechnol. J., 9(9): 1140-1151.

Lee, N.-R., M. Lakshmanan, S. Aggarwal, J.-W. Song, I. A. Karimi, D.-Y. Lee and J.-B. Park. 2014. Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus B27. Microb. Cell Fact., 13: 61.

Chin, J. X., B. K.-S. Chung and D.-Y. Lee. 2014. Codon Optimization On-Line (COOL): a web-based multi-objective optimization platform for synthetic gene design. Bioinformatics, 30(15): 2210-2212.

Park, S.-J., H. C. Yeo, N.-Y. Kang, H. Kim, J. Lin, H.-H. Ha, M. Vendrell, J.-S. Lee, Y. Chandran, D.-Y. Lee, S.-W. Yun and Y.-T. Chang. 2014. Mechanistic elements and critical factors of cellular reprogramming revealed by stepwise global gene expression analyses. Stem Cell Res., 12(3): 730-741.

Courtes, F. C., C. Gu, N. S. C. Wong, P. C. Dedon, M. G. S. Yap and D.-Y. Lee. 2014. 28S rRNA is inducibly pseudouridylated by the mTOR pathway in CHO cell cultures. J. Biotechnol., 174: 16-21.

Courtes, F. C., L. Vardy, N. S. C. Wong, M. Bardor, M. G. S. Yap and D.-Y. Lee. 2014. Understanding translational control mechanisms of the mTOR pathway in CHO cells by polysome profiling. New Biotechnol., 31(5): 514-523.

Lakshmanan, M., G. Koh, B. K. S. Chung and D.-Y. Lee. 2014. Software applications for flux balance analysis. Brief. Bioinform., 15(1): 108-122.

2013
Lakshmanan, M., B. K.-S. Chung, C. Liu, S.-W. Kim and D.-Y. Lee. 2013. Cofactor modification analysis: a computational framework to identify cofactor specificity engineering targets for strain improvement. J. Bioinform. Comput. Biol., 11(6): 1343006.

Lakshmanan, M., B. Mohanty and D.-Y. Lee. 2013. Identifying essential genes/reactions of the rice photorespiration by in silico model-based analysis. Rice, 6: 20.

Chung, B. K. S., F. N. K. Yusufi, Mariatia, Y. Yang and D.-Y. Lee. 2013. Enhanced expression of codon optimized interferon gamma in CHO cells. J. Biotechnol., 167(3): 326-333.

Courtes, F. C., J. Lin, H. L. Lim, S. W Ng, N. S. C. Wong, G. Koh, L. Vardy, M. G. S. Yap, B. Loo and D.-Y. Lee. 2013. Translatome analysis of CHO cells to identify key growth genes. J. Biotechnol., 167(3): 215-224.

Lakshmanan, M., Z. Zhang, B. Mohanty, J.-Y. Kwon, H.-Y. Choi, H.-J. Nam, D.-I. Kim and D.-Y. Lee. 2013. Elucidating the rice cells metabolism under flooding and drought stresses using flux-based modelling and analysis. Plant Physiol., 162(4): 2140-2150.

Chung, B. K. S., T. Dick and D.-Y. Lee. 2013. In silico analyses for the discovery of tuberculosis drug targets. J. Antimicrob. Chemoth., 68(12): 2701-2709.

Lee, T. S., Y. S. Ho, H. C. Yeo, J. P. Y. Lin and D.-Y. Lee. 2013. Precursor mass prediction by clustering ionization products in LC-MS-based metabolomics. Metabolomics, 9(6): 1301-1310.

Chung, B. K. S., M. Lakshmanan, M. Klement, C. B. Ching and D.-Y. Lee. 2013. Metabolic reconstruction and flux analysis in Pichia yeasts. Appl. Microbiol. Biotechnol., 97(5): 1865-1873. [Invited Min-Review]

Chung, B. K. S., M. Lakshmanan, M. Klement, B. Mohanty and D.-Y. Lee. 2013. Genome-scale in silico modeling and analysis for designing synthetic terpenoid-producing microbial cell factories. Chem. Eng. Sci., 103: 100-108. [Special Issue: Synthetic Biology, invited]

Kwok, J. J. M., N. Yu, I. A. Karimi and D.-Y. Lee. 2013. Microgrid scheduling for reliable, cost effective and environmentally friendly management. Ind. Eng. Chem. Res., 52(1): 142-151.

2012
Chung, B. K. S. and D.-Y. Lee. 2012. Computational codon optimization of synthetic gene for protein expression. BMC Syst. Biol., 6: 134. [Highly accessed].

Mohanty, B., V. Hearth, E. Wijaya, H. C. Yeo, B. G. de los Reyes and D.-Y. Lee. 2012. Patterns of cis-element enrichment reveal potential regulatory modules involved in the transcriptional regulation of anoxia response of japonica rice. Gene, 511(2): 235-242.

Kim, Y. J., H.-J. Eom, E.-Y. Seo, D.-Y. Lee, J. H. Kim and N. S. Han. 2012. Development of a chemically defined minimal medium for the exponential growth of Leuconostoc mesenteroides ATCC8293. J. Microbial. Biotechnol., 22(11): 1518-1522.

Aggarwal, S., I. A. Karimi, J. J. Kilbane II and D.-Y. Lee. 2012. Roles of sulfite oxidoreductase and fulfite reductase in improving desulfurization by Rhodococcus erythropolis. Mol. BioSyst., 8(10): 2724-2732.

Chong, W. P. K., S. H. Thng, A. P. Hui, D.-Y. Lee, E. C. Y. Chan and Y. S. Ho. 2012. LC-MS-based metabolic characterization of high monoclonal antibody-producing Chinese hamster ovary cells. Biotechnol. Bioeng., 109(12): 3103-3111.

Selvarasu, S., Y. S. Ho, W. P. K. Chong, N. S. C. Wong, F. N. K. Yusufi, Y. Y. Lee, M. G. S. Yap and D.-Y. Lee. 2012. Combined in silico modeling and metabolomics analysis to characterize fed-batch CHO cell culture. Biotechnol. Bioeng., 109(6): 1415-1429. [Special Issue: CHO Cell Genomics, invited] [Highlighted as Top 25 most accessed article from Jan-Dec 2012]

Wu, S. M., K. S. Tan, H. Chen, T. T. Beh, H. C. Yeo, S. K.-L. Ng, S. Wei, D.-Y. Lee, A. B.-H. Choo and K. K.-K. Chan. 2012. Enhanced production of neuroprogenitors, dopaminergic neurons and identification of target genes by overexpression of Sonic hedgehog in human embryonic stem cells. Stem Cells Dev., 21(5): 729-741.

Kang, J.-S., T.-Y. Lee and D.-Y. Lee. 2012. Robust optimization for engineering design. Eng. Optimiz., 44(2): 175-194.

2011
Yeo, H. C., T. T. Beh, J. Q. J. Ling, K. K.-K. Chan and D.-Y. Lee. 2011. Integrated transcriptome and in silico binding sites analysis reveals E2Fs as global coordinator of self-renewal in human pluripotent stems cells. PLoS ONE, 6(11): e27231.

Koh, G., A. Low, D. Poh, S. K. Ng, V. V. T. Wong, V. Vagenende, K.-P. Lam and D.-Y. Lee. 2011. Integrative analysis workflow for the structural and functional classification of C-type lectins. BMC Bioinformatics, 12(Suppl 14): S5.

Aggarwal, S., I. A. Karimi and D.-Y. Lee. 2011. Reconstruction of a genome-scale metabolic network of Rhodococcus erythropolis for desulfurization studies. Mol. BioSyst., 7(11): 3122-3131.

Ahn, J., B. K. S. Chung, D.-Y. Lee, M. Park, I. A. Karimi, J.-K. Jung and H. Lee. 2011. NADPH-dependent pgi-gene knockout Escherichia coli metabolism producing shikimate on different carbon sources. FEMS Microbiol. Lett., 324(1): 10-16.

Naraharisetti, P. K., I. A. Karimi, A. Anand and D.-Y. Lee. 2011. A linear diversity constraint – application to scheduling in microgrids. Energy, 36: 4235-4234.

Koh, G. and D.-Y. Lee. 2011. Mathematical modeling and sensitivity analysis of the integrated TNFa-mediated apoptotic pathway for identifying key regulators. Comput. Biol. Med., 41: 512-528.

Ding, V. M. Y., P. J. Boersema, L. Y. Foong, C. Preisinger, G. Koh, S. Natarajan, D.-Y. Lee, J. Boekhorst, B. Snel, S. Lemeer, A. J. R. Heck and A. Choo. 2011. Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells. PLoS ONE, 6(3): e17538.

Chong, W. P. K., F. N. K. Yusufi, D.-Y. Lee, S. G. Reddy, N. S. C. Wong, C. K. Heng, M. G. S. Yap and Y. S. Ho. 2011. Metabolomics-based identification of apoptosis-inducing metabolites in fed-batch CHO culture media. J. Biotechnol., 151: 218-224.

Aggarwal, S., I. A. Karimi and D.-Y. Lee. 2011. Flux-based analysis of sulfur metabolism in desulfurizing strains of Rhodococcus erythropolis. FEMS Microbiol. Lett., 315: 115-121.

Widiastuti, H., J. Y. Kim, S. Selvarasu, I. A. Karimi, H. Kim, J.-S. Seo and D.-Y. Lee. 2011. Genome-scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis. Biotechnol. Bioeng., 108: 655-665.

Lee, D.-Y., B. K. S. Chung, F. N. K. Yusufi and S. Selvarasu. 2011. In silico genome-scale modeling and analysis for identifying anti-tubercular drug targets. Drug Develop. Res., 72(2): 121-129. [Special Issue: In Silico Tools in Drug Design, invited]

2010
Selvarasu, S., D. Y. Kim, I. A. Karimi and D.-Y. Lee. 2010. Combined data preprocessing and multivariate statistical analysis characterizes fed-batch culture of mouse hybridoma cells for rational medium design, J. Biotechnol., 150: 94-100.

Chung, B. K. S., S. Selvarasu, C. Andrea, J. Ryu, H. Lee, J. Ahn, H. Lee and D.-Y. Lee. 2010. Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement. Microb. Cell Fact., 9: 50. [Highly accessed].

Chong, W. P. K., S. G. Reddy, F. N. K. Yusufi, D.-Y. Lee, N. S. C. Wong, C. K. Heng, M. G. S. Yap and Y. S. Ho. 2010. Metabolomics-driven approach for the improvement of Chinese hamster ovary cell growth: overexpression of malate dehydrogenase II. J. Biotechnol., 147: 116-121.

Lee, F. C., Rangaiah, G. P. and D.-Y. Lee. (2010) Modeling and optimization of a multi-product biosynthesis factory for multiple objectives. Metab. Eng., 12: 251-267.

Chin, J., Koh, G. and D.-Y. Lee (2010) How necessary is a fast testkit for mitigation of pandemic flu? J. R. Soc. Interface, 7: 1033-1047.

Selvarasu, S., Karimi, I. A., Ghim, G.-H. and D.-Y. Lee. (2010) Genome-scale modeling and in silico analysis of mouse cell metabolic network. Mol. Biosyst., 6: 152-161. [Cover paper][Highly accessed].

2009
Chung, B. K. S. and D.-Y. Lee. (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.

Kantardjieff A, Nissom PM, Chuah SH, Yusufi F, Jacob NM, Mulukutla BC, Yap M, Hu WS. (2009) Developing genomic platforms for Chinese hamster ovary cells. Biotechnol Adv., epub ahead of print.

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.

Vinsensius B. Vegaa, Xing Yi Woo, Habib Hamidib, Hock Chuan Yeo, Zhen Xuan Yeo, Guillaume Bourquea, and Neil D. Clarke (2009) Inferring direct regulatory targets of a transcription factor in the DREAM2 Challenge. NY Academy of Sciences. Volume 1158, Number 1, March 2009 , pp. 215-223.

Yeo ZX, Yeo HC, Yeo JK, Yeo AL, Li Y, Clarke ND (2009) Inferring transcription factor targets from gene expression changes and predicted promoter occupancy. J. Comput. Biol. 16(2):357-68.

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
Koh G., Tucker-Kellogg L., Hsu D., Thiagarajan P.S (2007) Composing Globally Consistent Pathway Parameter Estimates Through Belief Propagation, Workshop on Algorithms in Bioinformatics (WABI), 420-430

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
Koh G., Teong H.F., Clement M.V., Hsu D., Thiagarajan P.S. (2006) A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalk. Bioinformatics, 15(22), e271-280

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
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Koh G., Hsu D., Thiagarajan P.S. (Mar 2008) Composition of signaling pathway models and its application to parameter estimation, In ACM Int. Conf. on Computational Biology. RECOMB 2008, Singapore
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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
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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
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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
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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
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