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Gyu Min Lee (이규민)

Postdoctoral Researcher

Affiliation:
KRIBB (Korea Research Institute of Bioscience and Biotechnology), Center for Synthetic Biology
Principal Investigator:
Hyewon Lee, Ph.D.
Location:
Daejeon, South Korea

Biography

Postdoctoral researcher at KRIBB Center for Synthetic Biology, working on C1 microbe engineering with AI coding agents in the loop.

Research
Methanotroph and methylotroph engineering for C1 chemistry. Adaptive laboratory evolution (ALE) of Methylorubrum extorquens under methanol stress (700+ generations, PhD work at UNIST).
Methods
Whole-genome sequencing + RNA-seq + AlphaFold3 structural analysis to read mutations as a coherent stress-response network.
Tools
Custom dry-lab tooling on top of AI coding agents — primer design, NGS verification, lab notebook automation — so the wet-lab cycle never has to wait.

Education

  • 2019.03 – 2026.02
    Ph.D. (Integrated M.S./Ph.D.), Chemical Engineering
    Ulsan National Institute of Science and Technology (UNIST)
    Systems Biology and Machine Learning Lab, advisor: Donghyuk Kim, Ph.D.
    Dissertation: Systems-level characterization of adaptive responses to methanol stress in Methylorubrum extorquens.
  • 2011.03 – 2017.02
    B.S., Genetic Engineering
    Kyung Hee University

Experience

  • 2026.03 – present
    Postdoctoral Researcher
    KRIBB, Center for Synthetic Biology
    C1 team led by Hyewon Lee, Ph.D.
    Methanotroph strain engineering, multi-omics pipelines, agentic tooling for the C1 team.
  • 2019.03 – 2026.02
    Graduate Researcher
    UNIST, Department of Chemical Engineering
    Systems Biology and Machine Learning Lab (Donghyuk Kim)
    Methylotroph ALE, pan-genome and DEG analysis, bacteriophage and plant-pathogen comparative genomics.

Skills

Wet lab
  • Adaptive laboratory evolution (ALE)
  • Methylotroph and methanotroph cultivation
  • Allelic exchange and mutation reconstruction
  • Growth phenotyping
  • RNA-seq library prep
Omics and modeling
  • Whole-genome sequencing analysis
  • Pan-genome comparative analysis
  • RNA-seq and DEG analysis
  • AlphaFold3 structure-function interpretation
  • COBRApy genome-scale metabolic modeling
Engineering
  • Python and R omics pipelines
  • Visualization automation
  • Claude Code agent workflows for synthetic biology
  • GitHub Actions CI and cron jobs
  • TypeScript / Astro for research tooling

Selected Publications

  1. Systems-Level Dissection of Methanol Adaptation in Methylorubrum extorquens · Gyu Min Lee (2026). link.
  2. Characterization and therapeutic potential of newly isolated bacteriophages against Staphylococcus species in bovine mastitis · Jae-hyun Cho, Gyu Min Lee, Seyoung Ko, Youngju Kim et al. (2025, Journal of Virology). link.
  3. Integrated genomic and transcriptomic Insights into methanol tolerance mechanisms in Methylobacterium extorquens AM1, identifying key targets for strain engineering · Gyu Min Lee, Khoi Nhat Pham, Ina Bang, Seyoung Ko et al. (2025, Journal of Biological Engineering). link.
  4. Structural and Transcriptomic Signatures of Adaptive Optimization in Methylorubrum extorquens PA1 Δfdh234 under Methanol Stress · Gyu Min LEE, KIM Jaehyung, KIM Donghyuk (2025, 한국생물공학회 학술대회). link.
  5. Deciphering High-Methanol Adaptation in Methylorubrum extorquens AM1 through Genomic and Transcriptomic Analyses · Gyu Min LEE, PHAM Khoi, BANG Ina, KO Seyoung et al. (2025, 한국생물공학회 학술대회). link.
  6. Pan-genome Analysis Revealed Comparable Genomic Characteristics of Central Metabolic Pathways in Methylorubrum extorquens · Gyu Min LEE, Zoe SCOTT-NEVROS, LEE Sang-Mok, KIM Donghyuk (2025, 한국생물공학회 학술대회). link.
  7. Investigation of Evolutionary Strategies of M. extorquens AM1 for Enhanced Methanol Tolerance through Systems Biology Approaches · Gyu Min LEE, KO Seyoung, BANG Ina, KIM Donghyuk (2024, 한국생물공학회 학술대회). link.
  8. Pan-genome Analysis Reveals Comparative Genomic Features of Central Metabolic Pathways in Methylorubrum extorquens · Gyu Min Lee, Zoe K Scott-Nevros, Sang-Mok Lee, Donghyuk Kim (2023, Biotechnology and Bioprocess Engineering). link.

See full publication list →

Awards & Service

To be added