Minsuk Kim, Ph.D.

E-mail: Kim.Minsuk at mayo.edu / kms1041 at gmail.com / kms1041 at hanmail.net

Links: Google Scholar, ORCID, ResearchGate, LinkedIn

Minsuk Kim is currently a Postdoctoral Research Fellow at Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota. He obtained his B.S. and Ph.D. degrees in Biological Engineering from Seoul National University, Korea. His research interests are in fields of systems biology, metabolic engineering and systems medicine. In particular, his previous works were focused on computational analysis and design of microbial metabolism for production of antibiotics and oleo-chemicals. He is now working on the development of computational methods for deciphering functions and assembly rules of human gut microbial community, and ultimately, designing probiotics with desired functions.

Curriculum Vitae

[Download CV]


Professional Experiences


Education

Ph.D. in Biological Engineering, 2012.03 - 2017.02

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

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)


Resources


Genome-scale Metabolic Models

Strain Design Algorithms