Everton Z, Botas J, Kim SY, Yao L, Liu Z†, Jeong H-H† (2026). MARRVEL-MCP: A Context-Engineered Natural-Language Query-to-Response Interface for Mendelian Disease Discovery American Journal of Human Genetics DOI: 10.1016/j.ajhg.2026.04.012

Lee J, Yao L, Jeong H-H†, Liu Z† (2026). LA-MARRVEL: A Knowledge-Grounded, Language-Aware LLM Framework for Clinically Robust Rare Disease Gene Prioritization arXiv (under review, npj Artificial Intelligence) DOI: 10.48550/arXiv.2511.02263

Ahn J, Fu S, Palacios D, Jeong H-H, Wang L, Swartz MC, Tosur M, Redondo MJ, Wu X, Yue Z, Kakadiaris A, Wang N, Li Z, Huang M, Wen A, Harris D, Wang Y, Kwak MJ, Liu Z, Liu H (2026). MedSDoH: A Rule-Based System for Extracting Social Determinants of Health from Multi-site EHRs Based on the OHNLP Framework medRxiv DOI: 10.64898/2026.04.27.26351699

Palacios D, Aras S, Zhong Y, Zhao J, Pasupuleti S, Jeong H-H, Miller ES, Fletcher TL, Goulding AN, Chen H, Liu Z (2026). CLINPREAI: An Agentic AI System for Early Postpartum Depression Risk Prediction from Multimodal EHR Data medRxiv DOI: 10.1101/2025.11.14.25340265

Lee J, Qi G, Neeley MB, Liu Z†, Jeong H-H† (2025). ConSol: Sequential Probability Ratio Testing to Find Consistent LLM Reasoning Paths Efficiently arXiv DOI: 10.48550/arXiv.2503.17587

Clark T, Seo J-H, D'Ippolito A, Gorthi A, Beagan J, Guess J, Donahue A, Greene M, Lau A, Ramirez F, Cibulskis K, Jeong H-H, et al. (2024). Comprehensive epigenomic profiling from plasma to inform therapy selection: A proof-of-concept study in cancer Cancer Research DOI: 10.1158/1538-7445.am2024-963

Guess J, Gorthi A, D'Ippolito A, Beagan J, Clark T, Coyne M, Tamakloe T, Tran B, Jeong H-H, Cibulskis K, et al. (2024). Novel liquid biopsy based determination of lung cancer histology using a comprehensive epigenomic platform reveals enhancer activity as a key determinant for accurate classification Cancer Research DOI: 10.1158/1538-7445.am2024-7558

Deisseroth CA, Lee W-S, Kim J, Jeong H-H, Dhindsa RS, Wang J, Zoghbi HY, Liu Z (2023). Literature-based predictions of Mendelian disease therapies The American Journal of Human Genetics DOI: 10.1016/j.ajhg.2023.08.018

Kim J, de Haro M, Al-Ramahi I, Garaicoechea LL, Jeong H-H, Sonn JY, Tadros B, Liu Z, et al. (2023). Evolutionarily conserved regulators of tau identify targets for new therapies Neuron DOI: 10.1016/j.neuron.2022.12.012

Olcum M, Fan S, Rouhi L, Cheedipudi S, Cathcart B, Jeong H-H, Zhao Z, Gurha P, et al. (2023). Genetic Inactivation of β-Catenin Attenuates and Its Activation Aggravates Desmoplakin Cardiomyopathy bioRxiv DOI: 10.1101/2023.03.02.530831

Olcum M, Rouhi L, Fan S, Gonzales MM, Jeong H-H, Zhao Z, Gurha P, Marian AJ (2023). PANoptosis is a prominent feature of desmoplakin cardiomyopathy Journal of Cardiovascular Aging DOI: 10.20517/jca.2022.34

Deisseroth CA, Lee W-S, Kim J-Y, Jeong H-H, Wang J, Zoghbi HY, Liu Z (2022). Literature-based predictions of treatments for genetic disease pathology bioRxiv DOI: 10.1101/2022.09.08.506253

Jeong H-H, Chandrakantan A, Adler AC (2021). Obstructive sleep apnea and dementia-common gene associations through network-based identification of common driver genes Genes DOI: 10.3390/genes12040542

Hu J, Jeong H-H, Al-Ouran R, Bado I, Zhang W, Zhang X, Liu Z (2021). A comprehensive evaluation of CRISPR lineage recorders using TraceQC bioRxiv DOI: 10.1101/2021.10.29.466515

Jeong H-H, Jia J, Dai Y, Simon LM, Zhao Z (2021). Investigating cellular trajectories in the severity of COVID-19 and their transcriptional programs using machine learning approaches Genes DOI: 10.3390/genes12050635

Zhang W, Bado IL, Hu J, Wan Y-W, Wu L, Wang H, Gao Y, Jeong H-H, et al. (2021). The bone microenvironment invigorates metastatic seeds for further dissemination Cell DOI: 10.1101/2020.11.16.383828

Bado IL, Wang H, Hu J, Sarkar P, Liu J, Gugala Z, Xu Z, Zhang W, et al. (2020). Phenotypic plasticity of ER+ breast cancer in the bone microenvironment bioRxiv DOI: 10.1101/2020.11.14.383000

Jeong H-H, Liu Z (2019). Are HHV-6A and HHV-7 Really More Abundant in Alzheimer's Disease? Neuron DOI: 10.1016/j.neuron.2019.11.009

Jeong H-H, Kim SY, Rousseaux MWC, Zoghbi HY, Liu Z (2019). Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives Genome Research DOI: 10.1101/gr.245571.118

Wang S, Jeong H-H, Sohn K-A (2019). ClearF: a supervised feature scoring method to find biomarkers using class-wise embedding and reconstruction BMC Medical Genomics DOI: 10.1186/s12920-019-0512-9

Kim TR, Jeong H-H, Sohn K-A (2019). Topological integration of RPPA proteomic data with multi-omics data for survival prediction in breast cancer via pathway activity inference BMC Medical Genomics DOI: 10.1186/s12920-019-0511-x

Kim SY, Jeong H-H, Kim J, Moon J-H, Sohn K-A (2019). Robust pathway-based multi-omics data integration using directed random walks for survival prediction in multiple cancer studies Biology Direct DOI: 10.1186/s13062-019-0239-8

Guo C, Jeong H-H, Hsieh Y-C, Klein H-U, Bennett DA, De Jager PL, Liu Z, Shulman JM (2018). Tau Activates Transposable Elements in Alzheimer's Disease Cell Reports DOI: 10.1016/j.celrep.2018.05.004

Jeong H-H, Yalamanchili HK, Guo C, Shulman JM, Liu Z (2018). An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data Biocomputing 2018 (Pacific Symposium on Biocomputing) DOI: 10.1142/9789813235533_0016

Kim SY, Kim TR, Jeong H-H, Sohn K-A (2018). Integrative pathway-based survival prediction utilizing the interaction between gene expression and DNA methylation in breast cancer BMC Medical Genomics DOI: 10.1186/s12920-018-0389-z

Yalamanchili HK, Jeong H-H, Liu Z (2018). Decoding TDP-43 Dependent Cryptic Splicing in Amyotrophic Lateral Sclerosis and Identifying Novel Disease-causing Genes Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics DOI: 10.1145/3233547.3233698

Jeong H-H, Kim SY, Rousseaux MWC, Zoghbi HY, Liu Z (2017). CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution Bioinformatics DOI: 10.1093/bioinformatics/btx335

Roh S-H, Hryc CF, Jeong H-H, Fei X, Jakana J, Lorimer GH, Chiu W (2017). Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1704725114

Wang S, Jeong H-H, Kim D, Wee K, Park H-S, Kim S-H, Sohn K-A (2017). Integrative information theoretic network analysis for genome-wide association study of aspirin exacerbated respiratory disease in Korean population BMC Medical Genomics DOI: 10.1186/s12920-017-0266-1

Sohn K-A, Ho JWK, Djordjevic D, Jeong H-H, Park PJ, Kim JH (2015). hiHMM: Bayesian non-parametric joint inference of chromatin state maps Bioinformatics DOI: 10.1093/bioinformatics/btv117

Leem S, Jeong H-H, Lee J, Wee K, Sohn K-A (2014). Fast detection of high-order epistatic interactions in genome-wide association studies using information theoretic measure Computational Biology and Chemistry DOI: 10.1016/j.compbiolchem.2014.01.005

Jeong H-H, Sohn K-A (2014). Relevance epistasis network of gastritis for intra-chromosomes in the Korea associated resource (KARE) cohort study Genomics & Informatics DOI: 10.5808/gi.2014.12.4.216

Jung W, Jeong H-H, Lee K (2012). Protein interactome and its application to protein function prediction Protein-Protein Interactions-Computational and Experimental Tools DOI: 10.5772/38413

Kim S-H, Jeong H-H, Cho B-Y, Kim M, Lee H-Y, Lee J, Wee K, Park H-S (2008). Association of four-locus gene interaction with aspirin-intolerant asthma in Korean asthmatics Journal of Clinical Immunology DOI: 10.1007/s10875-008-9190-7