Curriculum Vitae

Last updated - Sep 4th, 2024

Research Interests

Microbiology, Pathonenicity, Antiomicrobial-resistance (AMR), Genomics, Systems Biology, Bioinformatics, Machine learning, Deep learning, Software development

Education

Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea, 2024

Degree    :    Integrated M.S. & Ph.D., Biomedical engineering

Thesis     :     Genomic investigation of bacterial pathogens with anti-microbial resistance genes and their lytic bacteriophage

Adviser   :    Dr. Donghyuk Kim

Department of Genetic Engineering, School of Life Science, Kyung Hee University, Yongin, Korea, 2017

Degree    :    B.S., Genetic Engineering

Thesis     :    Exploring miRNA based approaches in cancer diagnostics and therapeutics

Adviser   :    Dr. Sung Hee Bhoo

Professional Experience

• Graduate Student, Department of Biomedical Engineering, UNIST, Ulsan, Korea, Feb 2019 ~ present

• Researcher, Systems Biology Lab of Dr. Donghyuk Kim, School of Energy and Chemical Engineering, UNIST, Ulsan, Korea, July 2018 ~ Feb 2019

• Graduate Student Researcher, Systems Biology Lab of Dr. Donghyuk Kim, School of Life Sciences, Kyung Hee University, Yongin, Korea, Mar 2017 ~ June 2018

• Research Assistant, Systems Biology Lab of Dr. Donghyuk Kim, School of Life Sciences, Kyung Hee University, Yongin, Korea, Dec 2017 ~ Feb 2018

• Research Assistant, Microbial genetics lab of Dr. Eunjin Lee, college of life sciences, Kyung Hee University, Mar 2016 ~ Aug 2016

Awards 

• Poster Award, FKMS, Seoul, South Korea, Oct 2018-(link)

Webserver construction

• BOARDS web-based database: Antimicrobial-resistance gene DATABASE with structural informations-(link)

Publications (# First author, * Corresponding author)

• Developing the PIP-eco: An integrated genomic pipeline for identification and characterization of Escherichia coli pathotypes encompassing hybrid forms. Ko S, Nguyen HMT, Lee W, Kim D*. Comput Struct Biotechnol J. 2024 Jul 20. doi:10.1016/j.csbj.2024.07.017. 

• Blanket antimicrobial resistance gene database with structural information, BOARDS, provides insights on historical landscape of resistance prevalence and effects of mutations in enzyme structure. Ko S#, Kim J#, Lim J, Lee SM, Park JY, Woo J, Scott-Nevros ZK, Kim JR, Yoon H, Kim D*. mSystems. 2023 Dec 12. doi: 10.1128/msystems.00943-23. Editor's pick

• Delineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cell at early stage of infection via dual RNA-seq analysis. Park HT#, Lee SM#, Ko S, Kim S, Park HE, Shin MK, Kim D*, Yoo HS*. Vet Res. 2022 Sep 13. doi:10.1186/s13567-022-01089-y.

• Real-time PCR for Salmonella serotyping Rapid real-time PCR for Salmonella serotyping based on novel unique gene markers by pangenome analysis. Yang SM, Kim E, Kim D, Kim HB, Baek J, Ko S, Kim D, Yoon H, Kim HY. Front Microbiol. 2021 Sep 21. doi:10.3389/fmicb.2021.750379.

• 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. 

• Development of a genoserotyping method for Salmonella Infantis detection on the basis of pan-genome analysis. Yang SM, Baek J, Kim E, Kim HB, Ko S, Kim D, Yoon H*, Kim HY*. Microorganisms. 2020 Dec 29. doi:10.3390/microorganisms9010067. 

• Mechanism of tolerance improvement of Escherichia coli W against 3-hydroxypropionic acid by deletion of less-characterized transcription factor yieP. Nguyen-Vo TP#, Ko S#, Ryu H, Kim JR, Kim D*, Park S*. Sci Rep. 2020 Nov 04. doi:10.1038/s41598-020-76120-3. 

• Comparative genome analysis reveals an evolutionary trace 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. 

• Genomic and phenotypic characterization of a lytic bacteriophage CF1 infecting multi-drug resistant Citrobacter freundii . Kim Y#, Ko S#, Yeon YE, Kim H, Oh CS, Ahn JK*, Kim D*. Biotechnol Bioprocess Eng. 2020 Jun 29. doi:10.1007/s12257-019-0505-8. 

• Draft genome sequence of lytic bacteriophage CP3 infecting anaerobic bacterial pathogen Clostridium perfrigens. Kim Y#, Ko S#, Yeon YE, Le HT, Han BK, Kim H, Oh CS, Kim D. Korean J Microbiol. 2018 Jul 2. doi:10.7845/kjm.2018.54.2.149. 

• Draft genome sequence of lytic bacteriophage CF1 infecting Citrobacter freundii isolates. Kim Y, Ko S, Yeon YE, Lim J, Han BK, Kim H, Ahn JK, Kim D. Korean J Microbiol. 2018 Apr 1. doi:10.7845/kjm.2018.7099. 

• 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. 

Papers in progress or in preparation (# First author, * Corresponding author) 

• Characterization and therapeutic potential of newly isolated bacteriophages against Staphylococcus species in bovine mastitis. Cho JH#, Lee GM#, Ko S, Kim Y*, Kim D*. Submitted.

Other Experiences