MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis. - Dong-Yup Lee; Hongseok Yun; Sunwon Park; Sang Yup Lee (Bioinform., 2003)

BioSilico: an integrated metabolic database system. - Bo Kyeng Hou; Jin Sik Kim; Ji Hoon Jun; Dong-Yup Lee; Yong Wook Kim; Sujin Chae; Mira Roh; Yong-Ho In; Sang Yup Lee (Bioinform., 2004)

MFAML: a standard data structure for representing and exchanging metabolic flux models. - Hongseok Yun; Dong-Yup Lee; Joonwoo Jeong; Seunghyun Lee; Sang Yup Lee (Bioinform., 2005)

WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks. - Dong-Yup Lee; Choamun Yun; Ayoun Cho; Bo Kyeng Hou; Sunwon Park; Sang Yup Lee (Bioinform., 2006)

Web-based applications for building, managing and analysing kinetic models of biological systems. - Dong-Yup Lee; Rajib Saha; Faraaz Noor Khan Yusufi; Wonjun Park; Iftekhar A. Karimi (Briefings Bioinform., 2009)

WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model. - Tae-Sung Jung; Hock Chuan Yeo; Satty G. Reddy; Wan-Sup Cho; Dong-Yup Lee (Bioinform., 2009)

Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network. - Bevan Chung; Dong-Yup Lee (BMC Syst. Biol., 2009)

Integrative analysis workflow for the structural and functional classification of C-type lectins. - Geoffrey Koh; Ariana Low; Daren Poh; Yujian Yao; Say Ng; Victor Wong; Vincent Vagenende; Kong-Peng Lam; Dong-Yup Lee (BMC Bioinform., 2011)

Mathematical modeling and sensitivity analysis of the integrated TNFα-mediated apoptotic pathway for identifying key regulators. - Geoffrey Koh; Dong-Yup Lee (Comput. Biol. Medicine, 2011)

Computational codon optimization of synthetic gene for protein expression. - Bevan Chung; Dong-Yup Lee (BMC Syst. Biol., 2012)

Cofactor Modification Analysis: a Computational Framework to Identify cofactor specificity Engineering targets for strain Improvement. - Meiyappan Lakshmanan; Bevan Kai-Sheng Chung; Chengcheng Liu; Seon-Won Kim; Dong-Yup Lee (J. Bioinform. Comput. Biol., 2013)

Software applications for flux balance analysis. - Meiyappan Lakshmanan; Geoffrey Koh; Bevan Chung; Dong-Yup Lee (Briefings Bioinform., 2014)

Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design. - Ju Xin Chin; Bevan Kai-Sheng Chung; Dong-Yup Lee (Bioinform., 2014)

SynLinker: an integrated system for designing linkers and synthetic fusion proteins. - Chengcheng Liu; Ju Xin Chin; Dong-Yup Lee (Bioinform., 2015)

Flux-sum analysis identifies metabolite targets for strain improvement. - Meiyappan Lakshmanan; Tae Yong Kim; Bevan Kai-Sheng Chung; Sang Yup Lee; Dong-Yup Lee (BMC Syst. Biol., 2015)

BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemicals. - Minsuk Kim; Gwanggyu Sun; Dong-Yup Lee; Byung-Gee Kim (Bioinform., 2017)

Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica. - Pranjul Mishra; Na-Rae Lee; Meiyappan Lakshmanan; Minsuk Kim; Byung-Gee Kim; Dong-Yup Lee (BMC Syst. Biol., 2018)