Joon Young Park
Curriculum Vitae
M.S.-Ph.D. Student( 2018~ ), Chemical Engineering, UNIST
Systems Biology and Machine Learning Lab ( https://sites.google.com/view/systemskimlab )
Adviser - Dr. Donghyuk Kim
Education
Kyung Hee University, Yongin, South Korea, 2018
Degree : B.S., Genetic Engineering
Thesis : Comparative analysis of core genome from Methylomonas and Methylotroph species
Adviser : Dr. Donghyuk Kim
Experience
Intern | 2013, Biochemistry lab of Dr. Sunghee Bhoo, Kyung Hee University
Intern | 2014, Crop Biotech Institute, Kyung Hee University
Intern | 2016, Systems biology lab of Dr. Donghyuk Kim, Kyung Hee University
Research Assistant | 2017, Systems biology lab of Dr. Donghyuk Kim, Kyung Hee University
Awards
2020 | KSBB Fall Meeting and International Symposium ( Poster session ) - Site
2023 | KSIEC Spring Meeting and Symposium ( Poster session )
2023 | KMB 50th Annual Meeting & International Symposium ( Poster session )
2023 | KSBB Fall Meeting & International Symposium ( Poster session )
2023 | KSIEC Fall Meeting and Symposium ( Poster session )
2024 | KSBB Spring Meeting and International Symposium ( Poster session )
Papers in progress or in preparation (#co-first author, *co-corresponding author)
Elucidating DNA-binding protein dynamics in Salmonella Typhimurium under macrophages in vivo conditions using a breakthrough low-input ChIP-exo approach. Park JY#, Jang M#, Choi E, Lee SM, Bang I, Woo J, Kim S, Lee EJ*, Kim D*. In preparation.
Deciphering RpoD-family sigma factors transcriptional regulatory network highlights their multifaceted roles under heat shock conditions in Salmonella Typhimurium. Park JY#, Jang M#, Lee SM, Lee EJ, Kim D*. In preparation.
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 DK*, Seo SW*. Submitted.
Explanable deep learning for enzyme engineering with leveraging attention analysis of transformer-based model for NAD/NADP cofactor specificity. Kim J#, Woo J#, Park JY, Kim KJ, Kim D. In revision.
Next generation feasibility study model on H2 production process: Machine learning-based framework for feasibility prediction and parametric optimization in methanol steam reforming with membrane filters. Byun M#, Park S#, Lee A, Kim J, Scott-Nevros ZK, Park JY, Lim H*, Kim D*. Appl Energy. Resubmitted.
Publications (#co-first author, *co-corresponding author)
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. Accepted.
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.
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.
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 experimental methods to reconstruct and delineate 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 genomic 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, 21(6), 2019; https://doi.org/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 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.