Experience
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Scientist, Lunit Inc.
Jun 2024 – Present- As the biomedical domain expert, architecting the scientific strategy for a large scale open-source biomedical foundation model by defining multimodal dataset curation pipelines to enable AI-driven scientific reasoning across multi-scale modalities.
- Collaborating with pharmaceutical partners to discover cancer drug targets via spatial AI analysis of the tumor microenvironment (TME).
- Developed and deployed a novel AI-powered morphology-guided analysis framework integrating H&E with spatial transcriptomics for biomarker and drug target discovery, identifying key mechanisms of therapeutic resistance.
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Graduate Student Researcher, Johns Hopkins University (Poster)
Sep 2018 – May 2024- Awarded the Mette Strand Young Investigator Award (Selected for outstanding research contributions at Johns Hopkins School of Medicine).
- Derived the mathematical formulation underlying gkm-align and implemented the core SIMD-accelerated computational kernel—a custom, high-performance C++ aligner for regulatory sequences.
- Decoded the complex functional logic of gene regulatory elements via advanced computational modeling, bridging the gap between genomic sequence and function.
- Deciphered the dynamics of regulatory evolution through the integration of sequence-based machine learning and comparative genomics, establishing a functional basis for sequence conservation.
Education
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Ph.D. in Biomedical Engineering, Johns Hopkins University (Thesis)
2018 – 2024 -
M.S. in Biomedical Engineering, Johns Hopkins University
2017 – 2018 -
B.S. Biomedical Engineering & Applied Mathematics and Statistics, Johns Hopkins University
2013 – 2017
Awards & Honors
- The Mette Strand Young Investigator Award, Johns Hopkins School of Medicine, 2024.
- Reviewer's Choice Top Abstract Award, American Society of Human Genetics, 2023.
- IGVF Consortium Poster Award, IGVF Consortium, 2022.
- ENCODE Consortium Team Science Award, ENCODE Consortium, 2022.
- David T. Yue Memorial Award for Teaching Excellence, Johns Hopkins University, 2017.
Highlights Gallery
Click a thumbnail to enlarge.
Morphology-guided Spatial AI (JITC 2025)
AI cell typing validated by Xenium ST markers.
Conserved Enhancer Detection (Nature Commun. 2024)
Orthologous enhancer mapping using gkm-align algorithm.
Algorithm Performance Optimization (Ph.D. Thesis 2024)
SIMD-accelerated computational kernel for gkm-align.
Skills
Programming & HPC Optimization
Python, C++ (Low-level Optimization, AVX2 SIMD Intrinsics, Multi-threading), R, Bash / Shell Scripting
Algorithm Design & Bioinformatics
Algorithm Design & Implementation (gkm-align)
(GitHub)
Bioinformatics tools (e.g., Bowtie, MACS2), Scalable Computational Genomics Pipeline Design
Bioinformatics tools (e.g., Bowtie, MACS2), Scalable Computational Genomics Pipeline Design
HPC & Systems
Slurm Workload Manager, Linux / Unix Utilities, Docker, High-Performance Computing (HPC) Environments
Leadership & Service
- Review Editor, Frontiers in Epigenetics and Epigenomics Nov 2024 – Present (Loop Profile)
- Teaching Assistant, Johns Hopkins University Sep 2016 – Dec 2022 — Instructed quantitative courses (Statistical Mechanics & Thermodynamics, Discrete Math, Sequence Analysis (Computational Genomics), Biomedical Data Science).
- President, Korean Graduate Student Association (KGSA), Johns Hopkins University Sep 2019 – Jun 2020 (Article)
Interviews
Publications
(* denotes co–first authors who contributed equally)
Johns Hopkins (2018–2024)
- Jin Woo Oh & Michael A Beer. "Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals." Nature Communications (2024)
- David Yao*, Josh Tycko*, Jin Woo Oh*, Lexi R Bounds*, Sager J Gosai*, Lazaros Lataniotis*, Ava Mackay-Smith, Benjamin R Doughty, Idan Gabdank, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D. White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly. "Multicenter integrated analysis of noncoding CRISPRi screens." Nature Methods (2024)
- Renhe Luo, Jielin Yan, Jin Woo Oh, Wang Xi, Dustin Shigaki, Wilfred Wong, Hyein S Cho, Dylan Murphy, Ronald Cutler, Bess P Rosen, Julian Pulecio, Dapeng Yang, Rachel A Glenn, Tingxu Chen, Qing V Li, Thomas Vierbuchen, Simone Sidoli, Effie Apostolou, Danwei Huangfu, Michael A Beer. "Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions." Nature Genetics (2023)
- IGVF Consortium. "Deciphering the impact of genomic variation on function." Nature (2024)
- Jin Woo Oh. "Enhanced Algorithms to detect and characterize conserved regulatory sequences." Johns Hopkins University (2024)
Lunit (2024–Present)
- Yeong Hak Bang*, Geun-Ho Park*, Jin Woo Oh*, Soohyun Hwang, Jun-Gi Jeong, Boram Lee, Cheol Yong Joe, Hyemin Kim, Jinyong Kim, Sehhoon Park, Hyun Ae Jung, Jong-Mu Sun, Jin Seok Ahn, Myung-Ju Ahn, Yoon-La Choi, Chang Ho Ahn, Siraj M. Ali, Chan-Young Ock, Se-Hoon Lee. "Artificial intelligence-powered spatial analysis of tumor microenvironment in patients with non-small cell lung cancer with acquired resistance to EGFR tyrosine kinase inhibitor." Journal for ImmunoTherapy of Cancer (2025)
- Hyunchul Kim, Jinhyung Heo, Soo Ick Cho, Beodeul Kang, Jung Sun Kim, Chan Kim, Chang Il Kwon, Min Je Sung, Seok-Pyo Shin, Seok Jeong Yang, Incheon Kang, Sung Hwan Lee, Chansik An, Seungeun Lee, Jin Woo Oh, Hee Yeon Kay, Jiwon Shin, Taebum Lee, Sanghoon Song, Sukjun Kim, Heon Song, Sergio Pereira, Gwangil Kim, Hong Jae Chon. "Pathologist-Artificial Intelligence Concordance in HER2 Interpretation for Advanced Biliary Tract Cancer: Intraobserver, Interobserver, and Human-Artificial Intelligence Variability." Laboratory Investigation (2025)
- Gwangil Kim, Beodeul Kang, Jung Yong Hong, Haeyoun Kang, Jung Sun Kim, Sohyun Hwang, Sung Hwan Lee, Sang Hoon Jung, Chansik An, Won Suk Lee, Chiyoon Oum, Gahee Park, Mingu Kang, Yoojoo Lim, Jin Woo Oh, Siraj M. Ali, Chan-Young Ock, Chan Kim, Ho Yeong Lim, Hong Jae Chon. "Differential implications of tumor endothelial cell and lymphocyte densities in advanced hepatocellular carcinoma patients treated with immunotherapy." npj Precision Oncology (2025)
Published Abstracts
- Jin Woo Oh, Sanghoon Song, Soohyun Hwang, Mingu Kang, Jinhee Lee, Sergio Pereira, Hyunsu Kim, Sehhoon Park, Junhun Cho, Se-Hoon Lee, Han-Sin Jeong, Chang Ho Ahn, Siraj M Ali, Chan-Young Ock, Myung-Ju Ahn. "A novel single-cell level approach integrating artificial intelligence (AI)–powered histomorphology labeling and spatial transcriptomics enables biomarker identification of treatment resistance in salivary gland cancer (SGC)." Proceedings of the AACR (2025)
- Hyunsu Kim, Sehhoon Park, Jin Woo Oh, Soohyun Hwang, Jinyoung Kim, Eun-hye Kim, Nayeon Choi, Junhun Cho, Hyun-Ae Jung, Dongryul Oh, Se-Hoon Lee, Yong Chan Ahn, Han-Sin Jeong, Chang Ho Ahn, Chan-Young Ock, Myung-Ju Ahn. "Exploratory analysis of tumor microenvironment using scRNA, scTCR, and spatial transcriptomics in salivary gland cancer with surgical sample after neoadjuvant immuno-chemotherapy." Proceedings of the AACR (2025)
- Seungeun Lee, Jin Woo Oh, Soohyun Hwang, Jeanne Shen, Sehhoon Park, Hyojin Kim, Young Kwang Chae, Se-Hoon Lee, Yoon-La Choi, Jin-haeng Chung, Jaewoong Shin, Heon Song, Aaron Valero Puche, Donggeun Yoo, Taebum Lee, Chiyoon Oum, Jeongmi Kim, Siraj M Ali, Chan-Young Ock. "Deep learning–powered H&E whole-slide image analysis of endothelial cells to characterize tumor vascular environment and correlate treatment outcome to immunotherapy." Journal of Clinical Oncology (2025)
Poster Presentations
Johns Hopkins (2018–2024)
- "Functional characterization of the mammalian genome." ASHG, 2023.
- "Gapped-kmer based machine learning and sequence alignment identify conserved regulatory vocabularies and enhancers in evolutionarily distant mammals." IGVF Consortium Meeting, 2022.
- "Identifying subsets of cell-specific regulatory sequence features from heterogeneous tissue-specific chromatin state data using predictive gapped k-mer features." Cold Spring Harbor Lab – Biology of Genomes, 2019.
- "Identifying subsets of cell-specific regulatory sequence features from heterogeneous tissue-specific chromatin state data using predictive gapped k-mer features." ENCODE Consortium Meeting, 2019.
Lunit (2024–Present)
- "A novel single-cell level approach integrating AI–powered histomorphology labeling and spatial transcriptomics enables biomarker identification of treatment resistance in salivary gland cancer (SGC)." AACR, 2025.
Invited Talks
- “Multi-center integrative analysis of non-coding CRISPR screens.” ENCODE Consortium Meeting, 2022.
- “Sequence alignment using gapped-kmer features identifies conserved orthologous mammalian enhancers with high precision.” ENCODE Consortium Meeting, 2021.