Curriculum Vitae

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Professional Experiences

• • • Postdoctoral Research Fellow, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, 2018.04. - present.

      • • Advisor: Prof. Nicholas Chia (Theoretical Biology Group) & Prof. Jaeyun Sung (Microbiome Systems Medicine Group)

    • Postdoctoral Researcher, Institute of Engineering Research, Seoul National University, Seoul, Korea, 2017.03. - 2018.02.

      • • Advisor: Prof. Byung-Gee Kim (Molecular Biotechnology & Biomaterials Lab)

Education

Ph.D. in Biological Engineering, 2012.03 - 2017.02

• • • School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea

    • Dissertation: "Computational design of microbial strains for nongrowth-associated production of antibiotics and oleochemicals"

    • Advisor: Prof. Byung-Gee Kim

B.S. in Biological Engineering, 2009.03 - 2012.02

• • • College of Liberal Studies, Seoul National University, Seoul, Korea

    • First to enter and graduate from College of Liberal Studies, Seoul National University (summa cum laude, early graduation)

    • First to design and complete 'student-designed major' in Korea

    • Advisor: Prof. Byung-Gee Kim and Prof. Kyung-Koo Han

Other Research Experiences

• • • Graduate Student Researcher, Molecular Biotechnology & Biomaterials Lab, School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea, 2012.03. - 2017.02.

    • Visiting Researcher, Systems Biology and Bioinformatics Group, Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 2014.06. - 2014.08.

      • • Funded by BK21+ Program in Chemical Engineering, Seoul National University

        • Advisor: Prof. Dong-Yup Lee (National University of Singapore)

    • Research Assistant, Molecular Biotechnology & Biomaterials Lab, School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea, 2011.08. - 2012.02.

    • Research Assistant, Biomolecular Engineering Lab, School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea, 2011.01. - 2011.02.

      • • Advisor: Prof. Ji-Sook Hahn

Teaching Experiences

• • • Invited Lecturer, "Applied Biochemistry", Seoul National University, Fall 2017.

    • Teaching Assistant, "Applied Biochemistry", Seoul National University, Fall 2013.

    • Teaching Assistant, "Chemical Reaction Engineering 1", Seoul National University, Spring 2013.

    • Teaching Assistant, "Chemical Reaction Engineering 1", Seoul National University, Spring 2012.

    • Teaching Assistant, "Basic Calculus 2", Seoul National University, Fall 2011.

    • Teaching Assistant, "Basic Physics 1", Seoul National University, Spring 2011.

    • Teaching Assistant, "Basic Calculus 2", Seoul National University, Fall 2010.

    • Teaching Assistant, "Basic Physics 1", Seoul National University, Spring 2010.

    • Teaching Assistant, "Basic Calculus 1", Seoul National University, Spring 2010.

International Exchanges

• • • Visiting Student, University of California, Los Angeles, California, USA, 2011.06.20 - 2011.07.29.

      • • Funded by College of Liberal Studies, Seoul National University.

Awards and Scholarships

• • • Global Ph.D. Fellowship, National Research Foundation of Korea, 2012 - 2016

    • The Best Poster Award, The 13th International Symposium on the Genetics of Industrial Microorganisms, 2016

    • Young Scientist Award, The Korean Society for Biomedical Laboratory Sciences, 2015

    • Best Paper Award, Institute of Molecular Biology and Genetics, Seoul National University, 2014

    • Summa Cum Laude, College of Liberal Studies, Seoul National University, 2012

    • National Scholarship for Science and Engineering, Korea Student Aid Foundation, 2009 - 2011

Publications

¶co-first author, *corresponding author

International Journals

• • 1. Minsuk Kim, Jaeyun Sung, Nicholas Chia*, "Resource-allocation constraint governs structure and function of microbial communities in metabolic modeling" Metabolic Engineering, 70:12-22 (2022).

    2. Vinod K. Gupta, Minsuk Kim, Utpal Bakshi, Kevin Y. Cunningham, John M. Davis III, Konstantinos N. Lazaridis, Heidi Nelson, Nicholas Chia, Jaeyun Sung, "A predictive index for health status using species-level gut microbiome profiling" Nature Communications, 11:4635 (2020).

    3. Minsuk Kim¶, Emily Vogtmann¶, David A. Ahlquist, Mary E. Devens, John B. Kisiel, William R. Taylor, Bryan A. White, Vanessa L. Hale, Jaeyun Sung, Nicholas Chia*, Rashmi Sinha*, Jun Chen, "Fecal metabolomic signatures in colorectal adenoma patients are associated with gut microbiota and early events of colorectal cancer pathogenesis" mBio, 11:e03186-19 (2020).

    4. Minsuk Kim¶, Beom Gi Park¶, Eun-Jung Kim, Joonwon Kim, Byung-Gee Kim*, "In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling" Biotechnology for Biofuels, 12:187 (2019).

    5. Pamela S. Tietz-Bogert¶, Minsuk Kim¶, Angela Cheung, James H. Tabibian, Julie K. Heimbach, Charles B. Rosen, Madhumitha Nandakumar, Konstantinos N. Lazaridis, Nicholas F. LaRusso, Jaeyun Sung*, Steven P. O'Hara*, "Metabolomic profiling of portal blood and bile reveals metabolic signatures of primary sclerosing cholangitis" International Journal of Molecular Sciences, 19(10):3188 (2018).

    6. Joonwon Kim, Hee-Wang Yoo, Minsuk Kim, Eun-Jung Kim, Changmin Sung, Pyung-Gang Lee, Beom Gi Park, Byung-Gee Kim*, "Rewiring FadR regulon for the selective production of ω-hydroxy palmitic acid from glucose in Escherichia coli" Metabolic Engineering, 47:414-422 (2018).

    7. Pranjul Mishra, Na-Rae Lee, Meiyappan Lakshmanan, Minsuk Kim, Byung-Gee Kim, Dong-Yup Lee*, "Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica" BMC Systems Biology, 12(Suppl 2):12 (2018).

    8. Jeong Sang Yi, Minsuk Kim, Eun-Jung Kim, Byung-Gee Kim*, "Production of pikromycin using branched chain amino acid catabolism in Streptomyces venezuelae ATCC 15439" Journal of Industrial Microbiology & Biotechnology, 45(5):293-303 (2018).

    9. Minsuk Kim, Beom Gi Park, Joonwon Kim, Jin Young Kim, Byung-Gee Kim*, "Exploiting transcriptomic data for metabolic engineering: toward a systematic strain design" Current Opinion in Biotechnology, 54:26-32 (2018).

    10. Jeong Sang Yi, Min Woo Kim, Minsuk Kim, Yujin Jeong, Eun-Jung Kim, Byung-Kwan Cho*, Byung-Gee Kim*, "A novel approach for gene expression optimization through native promoter and 5’ UTR combinations based on RNA-seq, Ribo-seq, and TSS-seq of Streptomyces coelicolor" ACS Synthetic Biology, 6(3):555-565 (2017).

    11. Beom Gi Park¶, Minsuk Kim¶, Joonwon Kim, Heewang Yoo, Byung-Gee Kim*, "Systems biology for understanding and engineering of heterotrophic oleaginous microorganisms" Biotechnology Journal, 12:1600104 (2017).

    12. Minsuk Kim, Gwanggyu Sun, Dong-Yup Lee, Byung-Gee Kim*, "BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemicals", Bioinformatics, 33(1):87-94 (2017).

    13. Minsuk Kim, Jeong Sang Yi, Meiyappan Lakshmanan, Dong-Yup Lee*, Byung-Gee Kim*, "Transcriptomics-based strain optimization tool for designing secondary metabolite overproducing strains of Streptomyces coelicolor", Biotechnology and Bioengineering, 113(3):651-660 (2016).

    14. Changmin Sung, Eunok Jung, Kwon-Young Choi, Jin-hyung Bae, Minsuk Kim, Joonwon Kim, Eun-Jung Kim, Pyoung Il Kim, Byung-Gee Kim*, "The production of ω-hydroxy palmitic acid using fatty acid metabolism and cofactor optimization in Escherichia coli", Applied Microbiology and Biotechnology, 99:6667-6676 (2015).

    15. Jeong Sang Yi, Minsuk Kim, Sung-Jin Kim, Byung-Gee Kim*, "Effects of sucrose, phosphate, and calcium carbonate on the productions of pikromycin from Streptomyces venezuelae", Journal of Microbiology and Biotechnology, 25(4):496-502 (2015).

    16. Minsuk Kim, Jeong Sang Yi, Joonwon Kim, Ji-Nu Kim, Min Woo Kim, Byung-Gee Kim*, "Reconstruction of a high-quality metabolic model enables the identification of gene overexpression targets for enhanced antibiotics production in Streptomyces coelicolor A3(2)", Biotechnology Journal, 9:1185-1194 (2014).

International Conferences (Talks)

• • 1. Minsuk Kim, Jaeyun Sung, Nicholas Chia, "Revisiting the definition of ecological interactions in community metabolic modeling studies: current approaches, limitations, and future directions", 3rd International Summer Symposium on Systems Biology (IS3B_2019), Mexico City, Mexico (2019).

    2. Minsuk Kim, Jeong Sang Yi, Byung-Gee Kim, "Advancing metabolic modeling of Streptomyces for enhancing antibiotic production", 18th International Symposium on the Biology of Actinomycetes (ISBA18), Jeju, Korea (2017).

International Conferences (Posters)

• • 1. Minsuk Kim, Emily Vogtmann, David A. Ahlquist, Mary E. Devens, John B. Kisiel, William R. Taylor, Bryan A. White, Vanessa L. Hale, Jaeyun Sung, Nicholas Chia, Rashmi Sinha, Jun Chen, "Gut metabolome of colorectal adenoma patients is associated with gut microbiome and early events of carcinogenesis", Cold Spring Harbor Laboratory Meetings - Microbiome, Cold Spring Harbor, NY, USA (2019).

    2. Minsuk Kim, Jaeyun Sung, Nicholas Chia, "Modeling pairwise microbial interactions in chemostats: can metabolic models answer ecological questions?", Gordon Research Conference - Microbial Population Biology, Andover, NH, USA (2019).

    3. Minsuk Kim, Jun Chen, Vanessa L. Hale, Emily Vogtmann, Rashmi Sinha, Jaeyun Sung, Nicholas Chia, "Linking microbial taxonomic and metabolomic profiles: a case study using stool samples from patients with colorectal adenomas", International Conference on Microbiome Engineering, Boston, MA, USA (2018).

    4. Minsuk Kim, Jeong Sang Yi, Beom Gi Park, Byung-Gee Kim, "Integrated model-based, data-driven design of microbial cell factories for production of antibiotics and oleochemicals", Data-driven Biotechnology - Bench, Bioreactor and Bedside - Copenhagen Bioscience Conferences, Copenhagen, Denmark (2017).

    5. Minsuk Kim, Byung-Gee Kim, "Next generation strain design algorithms using omics data for designing secondary metabolite overproducer", The 13th International Symposium on the Genetics of Industrial Microorganisms (GIM2016), Wuhan, China (2016).

    6. Minsuk Kim, Jeong Sang Yi, Byung-Gee Kim, "Identifying engineering targets from transcriptomic data using genome-scale metabolic model", 4th Conference on Constraint-Based Reconstruction and Analysis (COBRA), Heidelberg, Germany (2015).

    7. Minsuk Kim, Jeong Sang Yi, Byung-Gee Kim, "Integrative analysis of transcriptomic data into genome-scale model of metabolism results in identification of metabolic engineering targets", 23rd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 14th European Conference on Computational Biology (ECCB), Dublin, Ireland (2015).

    8. Minsuk Kim, Jeong Sang Yi, Byung-Gee Kim, "Designing antibiotic overproducing strain of Streptomyces coelicolor using the model of genome-scale metabolic network", Network Biology Special Interest Group Meeting - ISMB/ECCB 2015, Dublin, Ireland (2015).

Internal/Domestic Conferences (Talks)

• • 1. Minsuk Kim, Jaeyun Sung, Nicholas Chia, "Investigating the implications of resource-allocation constraints in metabolic modeling of gut microbiota", 26th Annual Balfour Surgery Research Symposium, Rochester, MN, USA (2020).

    2. Minsuk Kim, Byung-Gee Kim, "Computational identification of transcriptional regulator manipulation targets for microbial production of chemicals", 2016 Spring Meeting and International Symposium of The Korean Society for Biotechnology and Bioengineering (KSBB), Gyeongju, Korea (2016).

    3. Minsuk Kim, Jeong Sang Yi, Byung-Gee Kim, "Computational design of antibiotics overproducers using genome-scale model of metabolism", 2015 Fall Meeting and International Symposium of The Korean Society for Biomedical and Laboratory Sciences (KSBLS), Wonju, Korea (2015).

    4. Minsuk Kim, Jeong Sang Yi, Byung-Gee Kim, "Designing antibiotics overproducers through integrative analysis of transcriptomic data into metabolic model", 30th Anniversary Fall Meeting and International Symposium of The Korean Society for Biotechnology and Bioengineering (KSBB), Songdo Convensia, Korea (2015).

    5. Minsuk Kim, Jeong Sang Yi, Joonwon Kim, Byung-Gee Kim, "Genome-scale metabolic model-guided metabolic engineering of Streptomyces coelicolor for antibiotics overproduction", 2014 Fall Meeting and International Symposium of The Korean Society for Biotechnology and Bioengineering (KSBB), Changwon, Korea (2014).

Internal/Domestic Conferences (Posters)

• • 1. Minsuk Kim, Jaeyun Sung, Nicholas Chia, "Towards in silico gut microbiota model: modeling pairwise microbial interactions in chemostats", 25th Annual Balfour Surgery Research Symposium, Rochester, MN, USA (2019).

    2. Minsuk Kim, Jun Chen, Vanessa Hale, Emily Vogtmann, Rashmi Sinha, Jaeyun Sung, Nicholas Chia, "Fecal metabolomic signatures in colorectal adenomas patients are associated with gut microbiota and early events of colorectal cancer pathogenesis", 24th Annual Balfour Surgery Research Symposium, Rochester, MN, USA (2018).

    3. Minsuk Kim, Changmin Sung, Jeong Sang Yi, Byung-Gee Kim, "Characterizing an antibiotic overproducing AbsC deletion mutant of Streptomyces coelicolor using constraint-based modeling methods", 2015 Spring Meeting and International Symposium of The Korean Society for Biotechnology and Bioengineering (KSBB), Yeosu, Korea (2015).

    4. Minsuk Kim, Jeong Sang Yi, Joonwon Kim, Byung-Gee Kim, "Identifying genetic interventions for antibiotics overproduction using genome-scale metabolic model of Streptomyces coelicolor", 2014 Spring Meeting and International Symposium of The Korean Society for Biotechnology and Bioengineering (KSBB), Gyeongju, Korea (2014).

    5. Minsuk Kim, Joonwon Kim, Byung-Gee Kim, "High-quality reconstruction of genome-scale metabolic network for Streptomyces coelicolor", 2013 Fall Meeting and International Symposium of The Korean Society for Biotechnology and Bioengineering (KSBB), Busan, Korea (2013).

    6. Minsuk Kim, Byung-Gee Kim, "Transcriptional regulatory network inference for Streptomyces coelicolor using modular approach", 2013 Spring Meeting and International Symposium of The Korean Society for Biotechnology and Bioengineering (KSBB), Gwangju, Korea (2013).

Media Coverage (Domestic)

• • • "내 전공 내가 설계 3년만에..." 자유전공 1호 졸업생 나왔다, 동아일보, 2011.12.06.

    • "내 전공 내가 만든다"... 서울대생 2명의 도전, 조선일보, 2010.02.03.