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Hyun-Hwan Jeong
Assistant Professor @ Baylor College of Medicine
Summary
Applied AI / Computational Biology Researcher
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Assistant Professor and applied scientist specializing in artificial intelligence, machine learning, and computational biology, with over a decade of experience leading high-impact research across academia, healthcare, and industry. Research focuses on scalable methods for electronic health record analysis, rare disease diagnosis, and multi-omics discovery. Developer of widely used platforms including CRISPRcloud, MARRVEL, AI-MARRVEL, LA-MARRVEL, and MARRVEL-MCP.
Professional Experience
Senior Scientist, Computational Biology & Bioinformatics
Boston, Massachusetts
2021 - 2024
Visiting Professor
Department of Artificial Intelligence, Ajou University
Suwon, South Korea
2021
Research Assistant Professor
School of Biomedical Informatics, The University of Texas Health Science Center at Houston
Houston, Texas
2020 - 2021
Postdoctoral Associate
Department of Molecular and Human Genetics, Baylor College of Medicine & Texas Children's Hospital
Houston, Texas
2015 - 2020
- Mentors: Zhandong Liu and Huda Y. Zoghbi
Research Support
VALIDATE ASD: Independent Multimodal Replication and Validation of Autism Data-Science Models
NIH / 1OT2OD040565 — Role: MPI (with Z. Liu, A. Annapragada, H.K. Harris, M. Bhagavatula)
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2025 - 2028
Constructing A Transcriptomic Atlas of Retrotransposon in Alzheimer's Disease
NIH / R03AG077191 — Role: PD/PI (Awarded; transferred to Zhongming Zhao upon position change)
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Education
Software
MARRVEL-MCP
A context-engineered natural-language query-to-response interface for Mendelian disease discovery using the Model Context Protocol.
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CB2
A R package which helps CRISPR pooled screen data analysis from the quantification to the hit gene selection.
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CRISPRCloud2
A user-friendly, cloud-based, one-stop analysis platform for the deconvolution of CRISPR pooled screen high-throughput sequencing data.
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SalmonTE
An ultra-fast and scalable quantification pipeline of transposable element abundances from next-generation sequencing data.
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MINA
A framework for integrative network analysis for gene-gene interactions associated with clinical outcome across multi-omics profiles.
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Preprints
LA-MARRVEL: A Knowledge-Grounded, Language-Aware LLM Framework for Clinically Robust Rare Disease Gene Prioritization
arXiv (under review at npj Digital Medicine)
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2026
Jaeyeon Lee, Lin Yao, Hyun-Hwan Jeong†, Zhandong Liu† (†co-corresponding)
CLINPREAI: An Agentic AI System for Early Postpartum Depression Risk Prediction from Multimodal EHR Data
medRxiv
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2026
Daniel Palacios, Sukru Aras, Yi Zhong, Jeff Zhao, Sasidhar Pasupuleti, Hyun-Hwan Jeong, Emily Miller, Terri Fletcher, Alison Goulding, Hu Chen, Zhandong Liu
MARRVEL-MCP: A Context-Engineered Natural-Language Query-to-Response Interface for Mendelian Disease Discovery
bioRxiv (under review at American Journal of Human Genetics)
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2025
Zachary Everton, Jorge Botas, Seon Young Kim, Zhandong Liu†, Hyun-Hwan Jeong† (†co-corresponding)
ConSol: Sequential Probability Ratio Testing to Find Consistent LLM Reasoning Paths Efficiently
arXiv
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2025
Jaeyeon Lee, Guantong Qi, Matthew Brady Neeley, Zhandong Liu†, Hyun-Hwan Jeong† (†co-corresponding)
Selected Peer-Reviewed Publications
Are HHV-6A and HHV-7 Really More Abundant in Alzheimer's Disease?
Neuron
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2019
Hyun-Hwan Jeong, Zhandong Liu
Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives
Genome Research
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2019
Hyun-Hwan Jeong, Seon Young Kim, Maxime W.C. Rousseaux, Huda Y. Zoghbi, Zhandong Liu
Tau Activates Transposable Elements in Alzheimer's Disease
Cell Reports
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2018
Caiwei Guo, Hyun-Hwan Jeong, Yi-Chen Hsieh, Hans-Ulrich Klein, David A. Bennett, Philip L. De Jager, Zhandong Liu, Joshua M. Shulman
An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data
Biocomputing 2018
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2018
Hyun-Hwan Jeong, Hari Krishna Yalamanchili, Caiwei Guo, Joshua M. Shulman, Zhandong Liu
CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution
Bioinformatics
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2017
Hyun-Hwan Jeong, Seon Young Kim, Maxime W C Rousseaux, Huda Y Zoghbi, Zhandong Liu
Oral & Poster Presentations
MARRVEL-MCP: A Context-Engineered Natural-Language Query-to-Response Interface for Mendelian Disease Discovery
TMC AI Summit 2026, Houston, Texas, USA
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2026
Zachary Everton, Jorge Botas, Seon Young Kim, Zhandong Liu, Hyun-Hwan Jeong
LA-MARRVEL: A Knowledge-Grounded, Language-Aware LLM Framework for Clinically Robust Rare Disease Gene Prioritization
TMC AI Summit 2026, Houston, Texas, USA
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2026
Jaeyeon Lee, Lin Yao, Hyun-Hwan Jeong, Zhandong Liu
MARRVEL-GPT: Advancing Rare Disease Genomics with Capable Semantic Exploration Tools
TMC AI Summit 2025, Houston, Texas, USA
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2025
Hyun-Hwan Jeong, Jaeyeon Lee, Zhandong Liu
A Novel Epigenomic Profiling Assay Reveals Disease Biology and Therapeutic Targets in Gastro-Esophageal Cancer from 1 Ml of Plasma (Poster)
Cancer Research, 84(6_Supplement):4643-4643
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2024
Jonathan Beagan, Aparna Gorthi, Anthony D'Ippolito, Hyun-Hwan Jeong, et al.
Comprehensive Epigenomic Profiling from Plasma to Inform Therapy Selection: A Proof-of-Concept Study in Cancer (Poster)
Cancer Research, 84(6_Supplement):963-963
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2024
Travis Clark, Ji-Heui Seo, Anthony D'Ippolito, Hyun-Hwan Jeong, et al.
Liquid Biopsy Determination of HER2 Status in Breast Cancer: Results from a Novel Epigenomic Platform (Poster)
Cancer Research, 84(9_Supplement):PS06-07
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2024
Heather Parsons, Sylvan Baca, Anthony D'Ippolito, Hyun-Hwan Jeong, et al.
Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives (Oral Presentation)
2019 Korean-American Biomedical Scientists Symposium (KABMS), Houston, Texas, USA
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2019
Hyun-Hwan Jeong, Seon Young Kim, Maxime W.C. Rousseaux, Huda Y. Zoghbi, Zhandong Liu
Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives (Oral Presentation)
Joint 27th Annual Meeting of ISMB/ECCB, Basel, Switzerland
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2019
Hyun-Hwan Jeong, Seon Young Kim, Maxime W.C. Rousseaux, Huda Y. Zoghbi, Zhandong Liu
An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data
Pacific Symposium on Biocomputing, The Big Island, Hawaii, USA
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2018
Hyun-Hwan Jeong, Hari Krishna Yalamanchili, Caiwei Guo, Joshua M. Shulman, Zhandong Liu
Integrative analysis for outcome-guided gene networks from multiple omics profiles (Oral Presentation)
Joint 23rd Annual Meeting of ISMB/ECCB, Dublin, Ireland
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2015
Hyun-Hwan Jeong, Garam Lee, Kyung-Ah Sohn
Invited Talks
From Technical Debt to Sustainable Workflows: The AI-MARRVEL Nextflow Journey
Nextflow Summit Boston 2025, Boston, Massachusetts, USA
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2025
Characterizing Retrotransposons in Alzheimer's Disease by Mining Large-Scale Human Brain Transcriptome Data
Seminar in Precision Medicine, UTHealth, Houston, Texas, USA (online)
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2021
CRISPR pooled screen data analysis using CB2
Biological Research Information Center (BRIC), South Korea (online)
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2019
Honors and Awards
Recognition Award
Precede Biosciences
Boston, Massachusetts
2023
Travel Fellowship
ISMB/ECCB (Intelligent Systems for Molecular Biology / European Conference on Computational Biology)
Basel, Switzerland
2019
TMC Biomedical Faculty Award (Winner)
2019 Korean-American Biomedical Scientists Symposium (KABMS), KSEA South Texas Chapter
Houston, Texas
2019
Travel Fellowship
The Summer School in Systems Medicine
Frauenchiemsee, Germany
2017
Best Paper Award
Korea National Institute of Health (KNIH) KARE
Seoul, South Korea
2014
First place (both years)
Java Algorithm Contest, SUN Microsystems
Seoul, South Korea
2008 - 2009
Sixth place
ACM International Collegiate Programming Contest (ACM-ICPC) Asia Regional
Taipei, Taiwan
2007
Bronze medal
ACM International Collegiate Programming Contest (ACM-ICPC) Asia Regional
Seoul, South Korea
2005