List of works - Dong-Yup Lee

28S rRNA is inducibly pseudouridylated by the mTOR pathway translational control in CHO cell cultures

scientific article

An LC-MS-based lipidomics pre-processing framework underpins rapid hypothesis generation towards CHO systems biotechnology

scientific article published on 09 July 2018

Centralized modularity of N-linked glycosylation pathways in mammalian cells

scientific article

Characterizing Escherichia coli DH5alpha growth and metabolism in a complex medium using genome-scale flux analysis

scientific article

Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design

scientific article published on 10 April 2014

Cofactor modification analysis: a computational framework to identify cofactor specificity engineering targets for strain improvement.

scientific article published on 21 November 2013

Colored Petri net modeling and simulation of signal transduction pathways

scientific article published on 22 December 2005

Combinatorial metabolic engineering of Saccharomyces cerevisiae for terminal alkene production

scientific article published on 08 July 2015

Combined Deterministic−Stochastic Approach for Pharmacokinetic Modeling

Combined data preprocessing and multivariate statistical analysis characterizes fed-batch culture of mouse hybridoma cells for rational medium design.

scientific article

Combined multivariate statistical and flux balance analyses uncover media bottlenecks to the growth and productivity of Chinese hamster ovary cell cultures

scientific article published in 2022

Comparative phenotypic analysis of CHO clones and culture media for lactate shift

article

Complementary identification of multiple flux distributions and multiple metabolic pathways

scientific article published on May 2005

Computational codon optimization of synthetic gene for protein expression ⬇️

scientific article published on October 20, 2012

Coopetitive Supply Chain Relationship Model: Application to the Smartphone Manufacturing Network

scientific article

Development of a chemically defined minimal medium for the exponential growth of Leuconostoc mesenteroides ATCC8293

scientific article published on 01 November 2012

Effect of linker flexibility and length on the functionality of a cytotoxic engineered antibody fragment

scientific article published on 16 February 2015

Elucidating rice cell metabolism under flooding and drought stresses using flux-based modeling and analysis

scientific article published on 10 June 2013

Elucidation of metabolism in hybridoma cells grown in fed-batch culture by genome-scale modeling.

scientific article

Enhanced expression of codon optimized interferon gamma in CHO cells

scientific article published on 19 July 2013

Enhanced production of neuroprogenitors, dopaminergic neurons, and identification of target genes by overexpression of sonic hedgehog in human embryonic stem cells.

scientific article published on 08 August 2011

Exploring codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli.

scientific article published on May 2015

Flux-based analysis of sulfur metabolism in desulfurizing strains of Rhodococcus erythropolis

scientific article published on 23 December 2010

Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network

scientific article

Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing Megasphaera elsdenii

scientific article published on 09 April 2020

Genome-scale metabolic reconstruction and in silico analysis of the rice leaf blight pathogen, Xanthomonas oryzae

scientific article published on 18 February 2020

Genome-scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis.

scientific article

Genome-scale modeling and in silico analysis of mouse cell metabolic network

scientific article published on 02 September 2009

Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria.

scientific article published on 16 November 2017

Global insights into the Chinese hamster and CHO cell transcriptomes.

scientific article published on 16 March 2015

Identification of candidate network hubs involved in metabolic adjustments of rice under drought stress by integrating transcriptome data and genome-scale metabolic network.

scientific article

Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis.

scientific article

Identifying essential genes/reactions of the rice photorespiration by in silico model-based analysis

scientific article published on 13 August 2013

In silico model-based characterization of metabolic response to harsh sparging stress in fed-batch CHO cell cultures

scientific article published on 19 November 2019

In silico model-driven cofactor engineering strategies for improving the overall NADP(H) turnover in microbial cell factories.

scientific article published on 8 August 2015

In silico model-guided identification of transcriptional regulator targets for efficient strain design

scientific article published on 25 October 2018

Incorporating metabolic flux ratios into constraint-based flux analysis by using artificial metabolites and converging ratio determinants

scientific article published on 4 March 2007

Integrated transcriptome and binding sites analysis implicates E2F in the regulation of self-renewal in human pluripotent stem cells

scientific article

Integrative analysis workflow for the structural and functional classification of C-type lectins.

scientific article

LC-MS-based metabolic characterization of high monoclonal antibody-producing Chinese hamster ovary cells.

scientific article published on 4 July 2012

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

MFAML: a standard data structure for representing and exchanging metabolic flux models

scientific article

Mathematical modeling and sensitivity analysis of the integrated TNFα-mediated apoptotic pathway for identifying key regulators

scientific article published on 31 May 2011

Mechanistic elements and critical factors of cellular reprogramming revealed by stepwise global gene expression analyses.

scientific article published on 25 March 2014

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis ⬇️

scientific article published on November 1, 2003

Metabolic and transcriptional regulatory mechanisms underlying the anoxic adaptation of rice coleoptile.

scientific article

Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation

scientific article

Metabolic reconstruction and flux analysis of industrial Pichia yeasts.

scientific article published on 22 January 2013

Metabolite essentiality elucidates robustness of Escherichia coli metabolism

scholarly article

Metabolomics profiling of extracellular metabolites in recombinant Chinese Hamster Ovary fed-batch culture

scientific article published in December 2009

Metabolomics-based identification of apoptosis-inducing metabolites in recombinant fed-batch CHO culture media.

scientific article published on 16 December 2010

Metabolomics-driven approach for the improvement of Chinese hamster ovary cell growth: overexpression of malate dehydrogenase II.

scientific article published on 2 April 2010

Multi-omics data driven analysis establishes reference codon biases for synthetic gene design in microbial and mammalian cells

scientific article

Multi-omics profiling of CHO parental hosts reveals cell line-specific variations in bioprocessing traits

scientific article published on 20 May 2019

Multi-product trade-off analysis of E. coli by multiobjective flux balance analysis

Multiobjective flux balancing using the NISE method for metabolic network analysis

scientific article published in July 2009

Optimization of process configuration and strain selection for microalgae-based biodiesel production

scientific article published on 14 June 2015

Overexpression of microRNAs enhances recombinant protein production in Chinese hamster ovary cells

scientific article published on 23 June 2014

Patterns of cis-element enrichment reveal potential regulatory modules involved in the transcriptional regulation of anoxia response of japonica rice

scientific article published on 23 September 2012

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

Reconstruction of a genome-scale metabolic network of Rhodococcus erythropolis for desulfurization studies.

scientific article

Roles of sulfite oxidoreductase and sulfite reductase in improving desulfurization by Rhodococcus erythropolis

scientific article published on 01 October 2012

Strain improvement and process development for biobutanol production.

scientific article

Synthetic fusion protein design and applications

scientific article

Systems biotechnology for strain improvement

scientific article

Transcriptomics analysis of salt stress tolerance in the roots of the mangrove Avicennia officinalis.

scientific article published on 30 August 2017

Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells.

scientific article

Understanding translational control mechanisms of the mTOR pathway in CHO cells by polysome profiling

scientific article published on 22 October 2013

Unraveling the Light-Specific Metabolic and Regulatory Signatures of Rice through Combined in Silico Modeling and Multiomics Analysis.

scientific article

Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining

scientific article

WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model.

scientific article

WebCell-script: A web-based script for managing quantitative and qualitative information of cellular networks

WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks

scientific article published on 16 March 2006

List of works by Dong-Yup Lee

28S rRNA is inducibly pseudouridylated by the mTOR pathway translational control in CHO cell cultures

An LC-MS-based lipidomics pre-processing framework underpins rapid hypothesis generation towards CHO systems biotechnology

Centralized modularity of N-linked glycosylation pathways in mammalian cells

Characterizing Escherichia coli DH5alpha growth and metabolism in a complex medium using genome-scale flux analysis

Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design

Cofactor modification analysis: a computational framework to identify cofactor specificity engineering targets for strain improvement.

Colored Petri net modeling and simulation of signal transduction pathways

Combinatorial metabolic engineering of Saccharomyces cerevisiae for terminal alkene production

Combined Deterministic−Stochastic Approach for Pharmacokinetic Modeling

Combined data preprocessing and multivariate statistical analysis characterizes fed-batch culture of mouse hybridoma cells for rational medium design.

Combined multivariate statistical and flux balance analyses uncover media bottlenecks to the growth and productivity of Chinese hamster ovary cell cultures

Comparative phenotypic analysis of CHO clones and culture media for lactate shift

Complementary identification of multiple flux distributions and multiple metabolic pathways

Computational codon optimization of synthetic gene for protein expression ⬇️

Coopetitive Supply Chain Relationship Model: Application to the Smartphone Manufacturing Network

Development of a chemically defined minimal medium for the exponential growth of Leuconostoc mesenteroides ATCC8293

Effect of linker flexibility and length on the functionality of a cytotoxic engineered antibody fragment

Elucidating rice cell metabolism under flooding and drought stresses using flux-based modeling and analysis

Elucidation of metabolism in hybridoma cells grown in fed-batch culture by genome-scale modeling.

Enhanced expression of codon optimized interferon gamma in CHO cells

Enhanced production of neuroprogenitors, dopaminergic neurons, and identification of target genes by overexpression of sonic hedgehog in human embryonic stem cells.

Exploring codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli.

Flux-based analysis of sulfur metabolism in desulfurizing strains of Rhodococcus erythropolis

Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network

Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing Megasphaera elsdenii

Genome-scale metabolic reconstruction and in silico analysis of the rice leaf blight pathogen, Xanthomonas oryzae

Genome-scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis.

Genome-scale modeling and in silico analysis of mouse cell metabolic network

Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria.

Global insights into the Chinese hamster and CHO cell transcriptomes.

Identification of candidate network hubs involved in metabolic adjustments of rice under drought stress by integrating transcriptome data and genome-scale metabolic network.

Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis.

Identifying essential genes/reactions of the rice photorespiration by in silico model-based analysis

In silico model-based characterization of metabolic response to harsh sparging stress in fed-batch CHO cell cultures

In silico model-driven cofactor engineering strategies for improving the overall NADP(H) turnover in microbial cell factories.

In silico model-guided identification of transcriptional regulator targets for efficient strain design

Incorporating metabolic flux ratios into constraint-based flux analysis by using artificial metabolites and converging ratio determinants

Integrated transcriptome and binding sites analysis implicates E2F in the regulation of self-renewal in human pluripotent stem cells

Integrative analysis workflow for the structural and functional classification of C-type lectins.

LC-MS-based metabolic characterization of high monoclonal antibody-producing Chinese hamster ovary cells.

MEMOTE for standardized genome-scale metabolic model testing

MFAML: a standard data structure for representing and exchanging metabolic flux models

Mathematical modeling and sensitivity analysis of the integrated TNFα-mediated apoptotic pathway for identifying key regulators

Mechanistic elements and critical factors of cellular reprogramming revealed by stepwise global gene expression analyses.

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis ⬇️

Metabolic and transcriptional regulatory mechanisms underlying the anoxic adaptation of rice coleoptile.

Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation

Metabolic reconstruction and flux analysis of industrial Pichia yeasts.

Metabolite essentiality elucidates robustness of Escherichia coli metabolism

Metabolomics profiling of extracellular metabolites in recombinant Chinese Hamster Ovary fed-batch culture

Metabolomics-based identification of apoptosis-inducing metabolites in recombinant fed-batch CHO culture media.

Metabolomics-driven approach for the improvement of Chinese hamster ovary cell growth: overexpression of malate dehydrogenase II.

Multi-omics data driven analysis establishes reference codon biases for synthetic gene design in microbial and mammalian cells

Multi-omics profiling of CHO parental hosts reveals cell line-specific variations in bioprocessing traits

Multi-product trade-off analysis of E. coli by multiobjective flux balance analysis

Multiobjective flux balancing using the NISE method for metabolic network analysis

Optimization of process configuration and strain selection for microalgae-based biodiesel production

Overexpression of microRNAs enhances recombinant protein production in Chinese hamster ovary cells

Patterns of cis-element enrichment reveal potential regulatory modules involved in the transcriptional regulation of anoxia response of japonica rice

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

Reconstruction of a genome-scale metabolic network of Rhodococcus erythropolis for desulfurization studies.

Roles of sulfite oxidoreductase and sulfite reductase in improving desulfurization by Rhodococcus erythropolis

Strain improvement and process development for biobutanol production.

Synthetic fusion protein design and applications

Systems biotechnology for strain improvement

Transcriptomics analysis of salt stress tolerance in the roots of the mangrove Avicennia officinalis.

Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells.

Understanding translational control mechanisms of the mTOR pathway in CHO cells by polysome profiling

Unraveling the Light-Specific Metabolic and Regulatory Signatures of Rice through Combined in Silico Modeling and Multiomics Analysis.

Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining

WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model.

WebCell-script: A web-based script for managing quantitative and qualitative information of cellular networks

WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks