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 Intellegence) DOI: 10.48550/arXiv.2511.02263

Palacios D, Aras S, Zhong Y, Zhao J, Pasupupulati S, Jeong H-H, Miller E, et al. (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, Travis, Seo, Ji-Heui, D'Ippolito, Anthony, Gorthi, Aparna, Beagan, Jonathan, Guess, Jamey, Donahue, Amy, Greene, Mandy, 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, Jamey, Gorthi, Aparna, D'ippolity, Anthony, Beagan, Jonathan, Clark, Travis, Coyne, Michael, Tamakloe, Tyrone, Tran, Baovy, 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, Cole A, Lee, Won-Seok, Kim, Jiyoen, Jeong, Hyun-Hwan, Dhindsa, Ryan S, Wang, Julia, Zoghbi, Huda Y, Liu, Zhandong (2023). Literature-based predictions of Mendelian disease therapies The American Journal of Human Genetics DOI: 10.1016/j.ajhg.2023.08.018

Kim, Jiyoen, de Haro, Maria, Al-Ramahi, Ismael, Garaicoechea, Lorena Laura, Jeong, Hyun-Hwan, Sonn, Jun Young, Tadros, Bakhos, Liu, Zhandong, et al. (2023). Evolutionarily conserved regulators of tau identify targets for new therapies Neuron DOI: 10.1016/j.neuron.2022.12.012

Olcum, Melis, Fan, Siyang, Rouhi, Leila, Cheedipudi, Sirisha, Cathcart, Benjamin, Jeong, Hyun-Hwan, Zhao, Zhongming, Gurha, Priyatansh, et al. (2023). Genetic Inactivation of $\beta$-Catenin Attenuates and Its Activation Aggravates Desmoplakin Cardiomyopathy bioRxiv DOI: 10.1101/2023.03.02.530831

Olcum, Melis, Rouhi, Leila, Fan, Siyang, Gonzales, Maya M, Jeong, Hyun-Hwan, Zhao, Zhongming, Gurha, Priyatansh, Marian, Ali J (2023). PANoptosis is a prominent feature of desmoplakin cardiomyopathy The journal of cardiovascular aging DOI: 10.20517/jca.2022.34

Deisseroth, Cole A, Lee, Won-Seok, Kim, Ji-Yoen, Jeong, Hyun-Hwan, Wang, Julia, Zoghbi, Huda Y, Liu, Zhandong (2022). Literature-based predictions of treatments for genetic disease pathology bioRxiv DOI: 10.1101/2022.09.08.506253

Jeong, Hyun-Hwan, Chandrakantan, Arvind, Adler, Adam C (2021). Obstructive sleep apnea and dementia-common gene associations through network-based identification of common driver genes Genes DOI: 10.3390/genes12040542

Hu, Jingyuan, Jeong, Hyun-Hwan, Al-Ouran, Rami, Bado, Igor, Zhang, Weijie, Zhang, Xiang, Liu, Zhandong (2021). A comprehensive evaluation of CRISPR lineage recorders using TraceQC bioRxiv DOI: 10.1101/2021.10.29.466515

Jeong, Hyun-Hwan, Jia, Johnathan, Dai, Yulin, Simon, Lukas M, Zhao, Zhongming (2021). Investigating cellular trajectories in the severity of COVID-19 and their transcriptional programs using machine learning approaches Genes DOI: 10.3390/genes12050635

Zhang, Weijie, Bado, Igor L, Hu, Jingyuan, Wan, Ying-Wooi, Wu, Ling, Wang, Hai, Gao, Yang, Jeong, Hyun-Hwan, et al. (2021). The bone microenvironment invigorates metastatic seeds for further dissemination Cell DOI: 10.1101/2020.11.16.383828

Bado, Igor L, Wang, Hai, Hu, Jingyuan, Sarkar, Poonam, Liu, Jun, Gugala, Zbigniew, Xu, Zhan, Zhang, Weijie, 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, Sehee, Jeong, Hyun-Hwan, Sohn, Kyung-Ah (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, Tae Rim, Jeong, Hyun-Hwan, Sohn, Kyung-Ah (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, So Yeon, Jeong, Hyun-Hwan, Kim, Jaesik, Moon, Jeong-Hyeon, Sohn, Kyung-Ah (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

Guo, Caiwei, Jeong, Hyun-Hwan, Hsieh, Yi-Chen, Klein, Hans-Ulrich, Bennett, David A, De Jager, Philip L, Liu, Zhandong, Shulman, Joshua M (2018). Tau activates transposable elements in Alzheimer’s disease Cell reports DOI: 10.1016/j.celrep.2018.05.004

Kim, So Yeon, Kim, Tae Rim, Jeong, Hyun-Hwan, Sohn, Kyung-Ah (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, Hari Krishna, Jeong, Hyun-Hwan, Liu, Zhandong (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, Soung-Hun, Hryc, Corey F, Jeong, Hyun-Hwan, Fei, Xue, Jakana, Joanita, Lorimer, George H, Chiu, Wah (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, Sehee, Jeong, Hyun-hwan, Kim, Dokyoon, Wee, Kyubum, Park, Hae-Sim, Kim, Seung-Hyun, Sohn, Kyung-Ah (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, Kyung-Ah, Ho, Joshua WK, Djordjevic, Djordje, Jeong, Hyun-hwan, Park, Peter J, Kim, Ju Han (2015). hiHMM: Bayesian non-parametric joint inference of chromatin state maps Bioinformatics DOI: 10.1093/bioinformatics/btv117

Leem, Sangseob, Jeong, Hyun-hwan, Lee, Jungseob, Wee, Kyubum, Sohn, Kyung-Ah (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, Hyun-hwan, Sohn, Kyung-Ah (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, Woojin, Jeong, Hyun-Hwan, Lee, KiYoung (2012). Protein interactome and its application to protein function prediction Protein-Protein Interactions-Computational and Experimental Tools DOI: 10.5772/38413

Kim, Seung-Hyun, Jeong, Hyun-Hwan, Cho, Bo-Young, Kim, MyoungKi, Lee, Hyun-Young, Lee, Jungseob, Wee, Kyubum, Park, Hae-Sim (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