Curriculum Vitae
Curriculum Vitae
Last updated - July 17th, 2025
Last updated - July 17th, 2025
E-mail: lsm920622@gmail.com / slee126@bwh.harvard.edu
Mobile: +82-10-7242-2382 (paused) / +1 (413) 345-9110
Microbiology, Host-Microbe Interaction, Immunometabolism, Gut metabolite profiling, Systems Biology, Multi-Omics Data Processing, Gut-Muscle Axis
Post-doctoral fellow, Microbiome Metabolomics Lab (co-PI: Sungwhan F. Oh & Jun R. Huh), Brigham and Women's Hospital, Boston, USA, June 2023 ~ Present
º Exploring the gut bacterial sphingolipid profile under various environmental change and its impact on host immunoregulation
Post-doctoral researcher, Systems Biology and Machine Learning lab (PI: Donghyuk Kim), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea, Oct 2021 ~ May 2023
º Leading the gut microbiota-based approach to develop microbiologic diagnostic strategy
º Characterizing the bacteriophage based on bioinformatics and 3D protein structure prediction
º Exploring the transcriptional regulation of bacteria in genome-scale level (Escherichia coli, Salmonella)
Post-doctoral researcher, Systems Biology and Machine Learning lab, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea, Mar 2021 ~ Oct 2021 (Served mandatory military service)
º Leading the gut microbiota-based approach to develop microbiologic diagnostic strategy
º Exploring the transcriptional regulation of bacteria in genome-scale level
Master, Material R&D Center of Insilico Co., Ltd., Ansan-City, Gyeonggi-Do, Republic of Korea, Oct 2018 ~ Feb 2021 (Served mandatory military service)
º Leading the research activities in R&BD
º Assisting in planning the R&BD strategy
Research Assistant, Animal Cell Biotechnology Lab (PI: Yun-Jaie Choi), Seoul National University, Seoul, Republic of Korea, Mar 2015 ~ Feb 2018
- In progress
Kim, S.#, Ju, D. B.#, Lee, S. M.#, Oh, S. H., Son, W. J., Park, M. G., Seok, Y. J., Han, S. H., Yun, C. H.*, Cho, C. S.*, Synbiotic Engineering via Internalized Curcumin-Loaded Pullulan Nanoparticles Enhances Mucosal Immunity and Microbiota Balance, Submitted.
- In preparation
Lee, Y.#, Goh, B.#, Park, J., Lee, S. M., Park, J., Kim, M., Shin, H., Kim, Y. K., Lee, C., Lee, N., Kim, E., Oh, S.*, Huh, J. R.*, Gut bacteria-derived metabolite drives sociability deficits through host genetic-driven intestinal permeability, Manuscript in preparation.
- 18 papers published: 8 first-author (co-first included) papers and 10 co-author papers.
18. Park JY, Jang M, Choi E, Lee SM, Bang I, Woo J, Kim S, Lee EJ, Kim D. (2025). ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens, Nucleic acids research, 53(3), gkaf009, https://doi.org/10.1093/nar/gkaf009.
17. Park JY, Jang M, Lee SM, Woo J, Lee EJ, Kim D. (2024). Unveiling the novel regulatory roles of RpoD-family sigma factors in Salmonella Typhimurium heat shock response through systems biology approaches, Plos Genetics, 20(10):e1011464.
$16. Lee SM#*, Le HT#, Taizhanova A, Nong LK, Park JY, Lee EJ, Palsson BO, Kim D*. (2024). Experimental promoter identification of a food-borne pathogen Salmonella Enterica Subsp. Enterica Serovar Typhimurium with near single base-pair resolution. Frontiers in Microbiology, 14, 1271121.
15. Ko S#, Kim J#, Lim J, Lee SM, Park JY, Woo JH, Scott-Nevros ZK, Kim JR, Yoon H, Kim D. (2023). Blanket antimicrobial resistance gene database with structural information, BOARDS, provides insights on historical landscape of resistance prevalence and effects of mutations in enzyme structure. Msystems, 9(1), pp.e00943-23.
$14. Bang I#, Lee SM#, Park S#, Park JY, Gao Y, Palsson BO, Kim D. (2023). Deep-learning optimized DEOCSU suite provides more accurate peak calling for ChIP-exo and iterable training pipeline, Briefings in bioinformatics, bbad024, https://doi.org/10.1093/bib/bbad024.
on the media: 대용량 염색질면역침전 데이터 분석의 실마리, 딥러닝에서 찾다! | UNIST News Center & BRIC 한빛사
13. Park JY, Lee SM, Ebrahim A, Scott-Nevros ZK, Kim J, Yang L, Sastry A, Seo SW*, Palsson BØ*, Kim D*. (2023). Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli. NAR genomics and bioinformatics, 5(1), lqad006, https://doi.org/10.1093/nargab/lqad006.
$12. Kim YJ#, Lee SM#, Nong LK#, Kim J, Kim SB, Kim D. (2023). Characterization of newly isolated lytic Klebsiella pneumoniae bacteriophages, KP1 and KP12 with deep learning-based structure prediction, Frontiers in Microbiology, 13, 5289.
$11. Lee SM#, Park HT#, Park S, Lee J, Kim D, Yoo HS*, Kim D*. (2023). A machine learning approach reveals microbiota signature for infection with Mycobacterium avium subspecies paratuberculosis in cattle, Microbiology Spectrum, 19:e0313422. doi:10.1128/spectrum.03134-22.
10. Bang I#, Nong LK#, Park JY, Le HT, Lee SM, Kim D. (2022). ChEAP: ChIP-exo Analysis Pipeline and the investigation of Escherichia coli RpoN protein-DNA interactions, Computational and Structural Biotechnology Journal, 21, 99-104.
9. Lee, G. M., Zoe, K. S., Lee, S. M., Kim, D. (2022). Pan-genome analysis reveals comparative genomic features of central metabolic pathways in Methylorubrum extorquens. Biotechnology and Bioprocess Engineering, doi: /10.1007/s12257-022-0154-1.
$8. Park, H. T.#, Lee, S. M.#, Ko, S., Kim, S., Park, H. E., Shin, M. K., Kim, D*., Yoo, H. S.* (2022). Delineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cells at the early stage of infection via dual RNA-seq analysis. Veterinary Research, 53:71. doi: 10.1186/s13567-022-01089-y
$7. Lee, S. M.#, Han, G. G.#, Choi, Y. J., Kim, E. B.*, Kang, S. K.* (2022). Evaluating sampling condition from farm animal for fecal microbiome study, Annals of Animal Resource Sciences, 31(1), 168-181.
$6. Lee, S. M., Kim, H. K., Lee, H. B., Kwon, O. D., Lee, E. B., ... & Kang, S. K. (2021). Effects of flaxseed supplementation on omega-6 to omega-3 fatty acid balance, lipid mediator profile, pro-inflammatory cytokines and stress indices in laying hens, Journal of Applied Animal Research, 49:1, 460-471, doi: 10.1080/09712119.2021.2000416
$5. Hong, L.#, Lee, S. M.#, Kim, W. S., Choi, Y. J., Oh, S. H., Li, Y. L., ... & Kang, S. K.*, Cho, C. S.* (2021). Synbiotics containing nanoprebiotics: A novel therapeutic strategy to restore gut dysbiosis, Frontiers in Microbiology, Front. Microbiol. 12:715241. doi: 10.3389/fmicb.2021.715241.
4. Oh, S. H., Kim Cho, Y. S., Lee, H. B., Lee, S. M., Kim, W. S., Hong, L., ... & Kang, S. K. (2019). Enhancement of antigen-specific humoral immune responses and protein solubility through conjugation of bacterial flagellin, Vibrio vulnificus FlaB, to the N-terminus of porcine epidemic diarrhea virus surface protein antigen S0. Journal of veterinary science, 20(6).
3. Hong, L., Kim, W. S., Lee, S. M., Kang, S. K., Choi, Y. J.*, & Cho, C. S.* (2019). Pullulan nanoparticles as prebiotics enhanced anti-bacterial properties of Lactobacillus plantarum through an induction of mild stress in probiotics. Frontiers in Microbiology, 10, 142.
2. Kim, W. S.#, Lee, J. Y.#, Singh, B., Maharjan, S., Hong, L., Lee, S. M., ... & Choi, Y. J.*, Kang, S. K.* (2018). A new way of producing pediocin in Pediococcus acidilactici through intracellular stimulation by internalized inulin nanoparticles. Scientific reports, 8(1), 1-14.
on the media: 유산균서 천연항균물질 대량 생산한다 | 한경닷컴 - 한국경제
1. Lee, J. Y., Han, G. G., Lee, H. B., Lee, S. M., Kang, S. K., Jin, G. D., ... & Choi, Y. J. (2017). Prohibition of antibiotic growth promoters has affected the genomic profiles of Lactobacillus salivarius inhabiting the swine intestine. PloS one, 12(10).
Seoul National University, Seoul, South Korea, Mar 2015 ~ Aug 2019
Degree : Integrated M.S. & Ph.D., Agricultural Biotechnology
Thesis : Research on physiological effects of omega-3 and omega-6 fatty acid balance on animal inflammation and stress
Adviser : Dr. Yun-Jaie Choi
Seoul National University, Seoul, South Korea, Mar 2011 ~ Feb 2015
Degree : B.S., Agriculture and Life Sciences, Animal Biotechnology Major
Thesis : 돼지 생산성 증진을 위한 항균활성이 증진된 유산균 생균제의 선발
(in English) Selection of lactic acid bacteria probiotics with enhanced antimicrobial activity to improve swine productivity
Adviser : Dr. Yun-Jaie Choi
1) Expertise
Bacterial handling technique
º Cultivation & lyophilisation of aerobes and facultative anaerobes
º General DNA/RNA/Protein works
º Antimicrobial assay (Co-culture assay, pathogen agar layer assay, paper disc assay etc.)
º Microscopic analysis (Confocal, TEM, SEM, FE-SEM)
Bioinformatic technique for data analysis
º 16S rRNA gene sequencing & downstream analysis (e.g. QIIME2 etc.)
º Pan-genomic approach for comparative genomics
º Genome & Transcriptome analysis for transcriptional network reconstruction (ChIP-exo, RNA-seq, etc.)
º Data analysis & visualization with computer programming language and web-based pipeline (Python, Perl, R, SAS etc.)
Metabolomic analysis
º Un-/targeted profiling of metabolites (mainly UPLC-MS/MS but also GC, NMR)
Biomaterial synthesis and drug delivery
º Synthesis of Polysaccharide-based nanoparticle and its characterization (DLS, 1H-NMR, SEM, FT-IR, MALDI-TOF etc.)
º Design drug delivery carrier - (core) probiotics, amino acid, and polyphenol
º Tablet press operation - probiotic tablet production
Mammalian cell handling technique
º In vitro proliferation & differentiation of cell: myoblast, fibroblast, enterocyte etc.
º Cell model construction: FFA-induced ectopic fat deposited skeletal muscle cell model
In vivo experimentation (chicken, pig, cattle, mouse, and guinea pig)
º Oral administration of feed additives (flaxseed, probiotics, and synbiotics)
º Dissection & sample harvest (serum, cecum, colon, feces etc.)
º Functional analysis - Viable cell count, cytokine analysis using ELISA, Gene expression in tissue
2) Note-worthy experiences
Basic molecular works - Gene cloning, transformation
Cell handling techniques
º Pilot scale fermenter operation (for LAB product) - 30L, 50L
º Cultivation of obligate anaerobes using anaerobic chamber
º Primary cell culture (mouse)
º Immunocytochemistry / immunohistochemistry
Lee, S. M., Chung, D. H., Jung, E., ... & Han, G. G., "Synbiotic composition for improving gut microbiota comprising polysaccharide nanoparticle" Korean patent: appl. 10-2020-0077942 (2020. 06. 25.)
1-1. Korean Patent: appl. 10-2020-0077942 (2020. 06. 25.)
1-2. PCT: appl. PCT/KR2020/008303 (2020. 06. 25.)
Choi, Y. J., Lee, S. M., Kim H. K., "Feed assifive for fowl comprising linseed and Lactobacillus plantarum sp, as an efficient component and preparation method of the same" Korean patent: 10-2392529 (2022. 04. 26.)
Awards
2 best poster awards, KMB 2022 49th Annual Meeting & International Symposium, Gyeongju, Jun 2022
1) Title: "Machine learning approach reveals microbiota signature for infection with Mycobacterium avium subspecies paratuberculosis in cattle"
2) Title: "DUCSU: Deeplearning model-based United ChIP-exo peak Selection Utility"
Best poster award, IBS&ACS publications & IBS forum: Nanomaterials for energy and life sciences, Seoul, Oct 2019
Grand prize for oral presentation, Korean Society of Animal Sciences and Technology, Jun 2019
Excellence prize for oral presentation, Korean Society of Animal Sciences and Technology, Jun 2018
Scholarships
Recipient, Research Scholarship, Brain Korea 21 Plus Program, Spring 2016 ~ Spring 2018
Recipient, Scholarship for the graduate study, iNtRON biotechnology, Inc. Seoul, South Korea, Spring 2015 ~ Spring 2019
Head teaching assistant, Domestic Animal Production and Lab, Fall 2017
Head teaching assistant, Domestic Animal Production and Lab, Fall 2016
Teaching assistant, Head Topics in Animal Cell Culture, Fall 2016
Teaching assistant, Topics in North Korea Agriculture, Spring 2015
1) Prof. Sungwhan F. Oh
co-Pricinpal Investigator during post-doc position in Brigham and Women's Hospital
Center for Experimental Therapeutics and Reperfusion Injury (CETRI), Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, United States
Tel: +1-617-525-5007 (Office) / E-mail: soh2@bwh.harvard.edu
2) Prof. Jun R. Huh
co-Pricinpal Investigator during post-doc position in Brigham and Women's Hospital
Department of Immunology, Blavatnik Institute, Harvard Medical School, United States
Tel: +1-617-525-5007 (Office) / E-mail: soh2@bwh.harvard.edu
3) Prof. Donghyuk Kim
Pricinpal Investigator during post-doc position in UNIST
Department of Chemical Engineering, School of Energy and Chemical Engineering, UNIST, Republic of Korea
Tel: +82-52-217-2945 (Office) / E-mail: dkim@unist.ac.kr
4) Prof. Yun-Jaie Choi (Retired)
Advisor for integrated M.S./Ph.D. dissertation
(Professor Emeritus, retired on Feb 2020) Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Republic of Korea
Tel: +82-2-3424-4800 (Office) / E-mail: cyjcow@snu.ac.kr
5) Prof. Chong-Su Cho
Research collaborator and Committee member for Ph.D. dissertation
Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Republic of Korea
Tel: +82-2-880-4868 (Office) / E-mail: chocs@snu.ac.kr
6) Prof. Sang-Kee Kang
Research collaborator and Committee member for Ph.D. dissertation
Institute of Green-Bio Science and Technology, Seoul National University, Republic of Korea
Tel: +82-33-339-5731 (Office) / E-mail: kangsk01@snu.ac.kr
7) Prof. Eun Bae Kim
Committee member for Ph.D. dissertation
Department of Animal Life Science, Kangwon National University, Republic of Korea
Tel: +82-33-250-8642 (Office) / E-mail: itanimal@kangwon.ac.kr