Gyu Min Lee
"Researcher contributing to industrial strain development with elucidating microbial adaptation mechanisms through multi-omics integrated analysis"
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Research Interests
Microbial adaptation to environmental and chemical stress
C1-based metabolism and methylotrophy
Multi-omics integration for metabolic engineering
Evolutionary approaches to microbial robustness
Systems and synthetic biology for strain optimization
Education
Ph.D. in Chemical Engineering (Expected Feb 2026)
Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
Thesis: Systems-level characterization of adaptive responses to methanol stress in Methylorubrum extorquens (In progress)
Advisor: Prof. Donghyuk Kim
B.S. in Genetic Engineering (2017)
Kyung Hee University, Yongin, Korea
Thesis: Isolation of Natural Substances to Inhibit Tumor-related Lymphangiogenesis
Advisor: Prof. In Sik Chung
Skills
Experimental Skills
Adaptive laboratory evolution (ALE)
Growth phenotype assays
Gene editing and allelic exchange (cre-loxP, sacB counterselection)
RNA extraction and rRNA-depleted RNA-seq library preparation
Bacteria handling
Computational & Bioinformatics
Whole-genome sequencing analysis
Pan-genome analysis
Transcriptome analysis
Functional enrichment analysis
Protein structure prediction and analysis (AlphaFold3, Foldseek, e.t.c.)
Metabolic analysis using genome-scale metabolic model (GEMs using COBRApy)
Programming & Visualization
Python
R
Custom figure generation for multi-omics data
Intergration
Genome-transcriptome integration
ALE-based adaptation analysis
Comparative genomics
Specialized fields
C1 metabolism, Stress adaptation mechanisms, Microbial systems biology
Experience
Research Assistant | Systems Biology Lab of Prof. Donghyuk Kim, UNIST | 2019
Researcher | Systems Biology Lab of Prof. Donghyuk Kim, School of Energy and Chemical Engineering, UNIST, Ulsan, Korea | Jul 2018 – Feb 2019
Graduate Student Researcher | Systems Biology Lab of Prof. Donghyuk Kim, School of Life Sciences, Kyung Hee University, Yongin, Korea | Mar 2017 – Jun 2018
Research Assistant | Systems Biology Lab of Prof. Donghyuk Kim, Kyung Hee University | 2017
Intern | Biotechnology Lab of Prof. In Sik Chung, Kyung Hee University | 2016
Presentations
Oral Presentation
Pan-genome analysis reveals comparative genomic features of central metabolic pathways in Methylorubrum extorquens, The Korean Society for Biotechnology and Bioengineering (KSBB), Sep 2022
Publications (#co-first author, *corresponding author )
8 peer-reviewed publications (including J. Virol, PNAS, Biotechnol Bioprocess Eng)
4 first-author papers (led experimental design, analysis, and manuscript preparation)
Co-first author (PNAS, 2020) - Clostridium drakei autotrophic growth study
International collaborations with researchers from multiple institutions
Papers in progress
Integrated Genomic and Transcriptomic Insights into Methanol Tolerance Mechanisms in Methylorubrum extorquens AM1 for C1-Based Bioproduction. Lee GM#, Pham KN, Bang I, Ko S*, Kim D*. Submitted.
Published
Characterization and therapeutic potential of newly isolated bacteriophages against Staphylococcus species in bovine mastitis. Cho JH#, Lee GM#, Ko S*, Kim Y*, Kim D*. J Virol. 2025 Feb 14. doi:10.1128/jvi.01901-24
Pan-genome analysis reveals comparative genomic features of central metabolic pathways in Methylorubrum extorquens. Lee GM, Scott-Nevros ZK, Lee SM, Kim D* . Biotechnol Bioprocess Eng. 2022 Sep 29. doi:10.1007/s12257-022-0154-1.
Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes. Lim J#, Park HT#, Ko S, Park HE, Lee GM, Kim S, Shin MK, Yoo HS*, Kim D*. Vet Res. 2021 Mar 18. doi:10.1186/s13567-021-00905-1.
on the media: BRIC 농림성과
Comparative Genome Analysis Reveals Natural Variations in the Genomes of Erwinia pyrifoliae, a Black Shoot Blight Pathogen in Apple and Pear. Lee GM, Ko S, Oh EJ, Song YR, Kim D*, Oh CS*. Plant Pathol J. 2020 Oct 1. doi:10.5423/PPJ.OA.06.2020.0097.
Functional cooperation of the glycine synthase-reductase and Wood-Ljungdahl pathways for autotrophic growth of Clostridium drakei. Song Y, Lee JS, Shin J, Lee GM, Jin S, Kang SG, Lee JK, Kim DR, Lee EY, Kim SC, Cho S, Kim D*, Cho BK*. Proc Natl Acad Sci U S A. 2020 Mar 13. doi:10.1073/pnas.1912289117.
on the media: 한국을 빛내는 사람들, 김동혁
Characterization of the Lytic Bacteriophage phiEaP-8 Effective against Both Erwinia amylovora and Erwinia pyrifoliae Causing Severe Diseases in Apple and Pear. Park J, Lee GM, Kim D, Park DH, Oh CS. Plant Pathol J. 2018 Oct 1. doi.org/10.5423/PPJ.NT.06.2018.0100.
Draft genome sequence of lytic bacteriophage SA7 infecting Staphylococcus aureus isolates. Kim Y, Lee GM, Taizhanova A, Han BK, Kim H, Ahn JK, Kim D. Korean J Microbiol. 2018 Apr 1. doi:10.7845/kjm.2018.7098.
Draft genome sequence of a bacterial plant pathogen Erwinia pyrifoliae strain EpK1/15 isolated from an apple twig showing black shoot blight. Lee GM, Oh EJ, Park J, Ko S, Park DH, Kim D*, Oh CS*. Korean J Microbiol. 2018 Apr 1. doi:10.7845/kjm.2018.7087.
References
Prof. Donghyuk Kim
Department of Chemical Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
E-mail: dkim@unist.ac.kr
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