Contact
jypark57@unist.ac.kr
jjypark56@gmail.com
Research Interests
Systems biology, Microbiology, Bioinformatics, Host-microbe interaction
Multi-omics experiment and analysis, Transcriptional regulatory network reconstruction
Automation of omics experiments
Genome-scale metabolic modeling
NGS data analysis pipeline construction
Education
Department of Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea, 2025
Degree: Ph.D. Chemical Engineering
Thesis: Deciphering bacterial transcriptional regulatory networks through an optimized ChIP-exo method and machine learning-based transcriptome analysis
Adviser: Prof. Donghyuk Kim
Department of Genetic Engineering, School of Life Science, Kyung Hee University, Yongin, Korea,
Degree: B.S. Genetic Engineering
Thesis: Comparative genomic analysis of the core genome in Methylomonas species.
Adviser: Prof. Donghyuk Kim
Awards
∘ Poster presentation
- 2020 KSBB Spring Meeting and International Symposium
- 2023 KSIEC Spring Meeting
- 2023 50th Anniversary KMB 2023 Annual Meeting & International Symposium
- 2023 KSBB Fall Meeting and International Symposium
- 2023 KSIEC Fall Meeting and International Symposium
- 2024 KSBB Spring Meeting and International Symposium
Experience
Intern | 2016, Systems biology lab of Prof. Donghyuk Kim, Kyung Hee University
Research Assistant | 2017, Systems biology lab of Prof. Donghyuk Kim, Kyung Hee University
Publications (#co-first author, *corresponding author )
Papers in progress: 3 papers, 1 first-author (co-first included), and 2 co-author papers.
Genome-wide regulon of NtrC reveals genetic regulation under nitrogen limitation in Methylomonas sp. DH-1. Han SJ#, Park JY#, Han YH#, Bang I, Lee OK, Hyung JS, Na JG*, Lee EY*, Kim D*, Seo SW*. iScience. In revision.
iTARGET: Genome-scale engineering targeting for strain improvement. Hwang J#, Han YH#, Bang I, Park JY, Kim D, Sung J, Seo SW*, Jang S*, Jung GY*. Submitted.
Published: 15 papers, 7 first-author (co-first included), and 8 co-author papers.
ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens. Park JY#, Jang M#, Choi E, Lee SM, Bang I, Woo J, Kim S, Lee EJ*, Kim D*. Nucleic Acids Res. 2025 Jan 27. doi:10.1093/nar/gkaf009
on the media: 한국을 빛낸 사람들, 김동혁, 박준영(interview), 장민창
Biosensor-guided evolution boosts itaconic acid production, unveiling unique insights into the stringent response. Moon JH#, Woo J#, Park JY, Noh MH*, Kim D*, Jung GY*. Bioresour Technol. Accepted.
Deep learning for NAD/NADP cofactor prediction and engineering using transformer attention analysis in enzymes. Kim J#, Woo J#, Park JY, Kim KJ, Kim D. Metab Eng. 2024 Nov 20. doi:10.1016/j.ymben.2024.11.007
An Optimized Method for Reconstruction of Transcriptional Regulatory Networks in Bacteria Using ChIP-exo and RNA-seq Datasets. Jang M#, Park JY#, Lee G, Kim D. J Microbiol. 2024 Nov 11. doi:10.1007/s12275-024-00181-6
Unveiling the novel regulatory roles of RpoD-family sigma factors in Salmonella Typhimurium heat shock response through systems biology approaches. Park JY#, Jang M#, Lee SM, Woo J, Lee EJ, Kim D. PLoS Genet. 2024 Oct 29. doi:10.1371/journal.pgen.1011464.
Use of acetate as substrate for sustainable production of homoserine and threonine by Escherichia coli W3110: A modular metabolic engineering approach. Vo TM, Park JY, Kim D, Park S. Metab Eng. 2024 May 22. doi:10.1016/j.ymben.2024.05.004 R.
Experimental promoter identification of a food-borne pathogen Salmonella Enterica Subsp. Enterica Serovar Typhimurium with near single base-pair resolution. Lee SM#, Le HT#, Taizhanova A, Nong LK, Park JY, Lee EJ, Palsson BO, Kim D. Front Microbiol. 2024 Jan 04. doi:10.3389/fmicb.2023.1271121.
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.
Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling. Bang I#, Lee SM#, Park S#, Park JY, Nong LK, Gao Y, Palsson BO, Kim D. Brief Bioinform. 2023 Jan 25. doi:10.1093/bib/bbad024.
Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli. Park JY, Lee SM, Ebrahim A, Scott-Nevros ZK, Kim J, Yang L, Sastry A, Seo SW*, Palsson BO*, Kim D*. NAR Genom Bioinform. 2023 Jan 20. doi:10.1093/nargab/lqad006.
ChEAP: ChIP-exo Analysis Pipeline and the investigation of Escherichia coli RpoN protein-DNA interactions. Bang I#, Nong LK#, Park JY, Le HT, Lee SM, Kim D. Comput Struct Biotechnol J. 2022 Dec 02. doi:10.1016/j.csbj.2022.11.053.
Genome-wide Identification of DNA-protein Interaction to Reconstruct Bacterial Transcription Regulatory Network. Park JY#, Rimal H#, Bang I, Nong LK, Kim D. Biotechnol Bioprocess Eng. 2020 Dec 29. doi:10.1007/s12257-020-0030-9.
Comprehensive Genome Analysis on the Novel Species Sphingomonas panacis DCY99T Reveals Insights into Iron Tolerance of Ginseng. Kim YJ#,*, Park JY#, Balusamy SR, Huo Y, Nong LK, Le HT, Yang DC, Kim D*. Int J Mol Sci. 2020 Mar 16. doi:10.3390/ijms21062019.
Genome-scale evaluation of core one-carbon metabolism in gammaproteobacterial methanotrophs grown on methane and methanol. Nguyen AD#, Park JY#, Hwang IY#, Hamilton R, Kalyuzhnaya MG, Kim D*, Lee EY*. Metab Eng. 2019 Oct 15. pii: S1096-7176(19)30307-6. doi: 10.1016/j.ymben.2019.10.004.
Draft genome sequence of lytic bacteriophage KP1 infecting bacterial pathogen Klebsiella pneumoniae. Kim Y#, Bang I#, Yeon YE, Park JY, Han BK, Kim H, Ahn JK, Kim D. Korean J Microbiol. 2018 Jul 2. doi.org/10.7845/kjm.2018.54.2.152.