Publications

Submitted

1. Zhe He, Balu Bhasuran, Mia Liza A. Lustria, Karim Hanna, Michael Killian, Cindy Shavor, Mandy Dailey, Sai Sidharth Manikandan, Xiao Luo. Generating Question Prompt Lists from EHR Data Using Large Language Models: An Iterative Evaluation Study. Journal of Medical Internet Research. Under review. 

2. Balu Bhasuran, Qiao Jin, Angelique Deville, Yonghui Wu, Karim Hanna, Zhiyong Lu, Zhe He. LabQAR: A Curated Dataset for Question Answering on Laboratory Test Reference Ranges and Interpretation. Scientific Data. Scientific Data. Under review.

3. Mia Liza A. Lustria, Lovinta Atrinawati, Obianuju Aliche, Kyunghye Kim, Zhe He. From Access to Activation: A Systematic Review of Patient Experiences with Online Lab Test Presentations. Journal of Medical Internet Research. Under review.

Published / In Press

1. Qiao Jin, Nicholas Wan, Robert Leaman, Shubo Tian, Zhizheng Wang, Yifan Yang, Zifeng Wang, Guangzhi Xiong, Po-Ting Lai, Qingqing Zhu, Benjamin Hou  Maame Sarfo-Gyamfi, Gongbo Zhang, Aidan Gilson, Balu Bhasuran, Zhe He, Aidong Zhang, Jimeng Sun, Chunhua Weng, Ronald Summers, Qingyu Chen, Yifan Peng, Zhiyong Lu. Entry-level guide to the use of large language models for medical research. Nature Protocols. 2026. In press.

2. Balu Bhasuran, Mattia Prosperi, Karim Hanna, John Petrilli, Caretia JeLayne Washington, Zhe He. Evaluation of Causal Reasoning for Large Language Models in Contextualized Clinical Scenarios of Laboratory Test Interpretation. npj Digital Medicine. 2026. DOI: https://doi.org/10.1038/s41746-026-02632-3. [Link]

3. Hanshu Rao, Weisi Liu, Haohan Wang, I-Chan Huang, Zhe He, Xiaolei Huang. A Scoping Review of Synthetic Data Generation by Language Models in Biomedical Research and Application: Data Utility and Quality Perspectives. Journal of Healthcare Informatics Research. 2026. DOI: https://doi.org/10.1007/s41666-026-00229-9. 

4. Qiao Jin, Zhizheng Wang, Yifan Yang, Qingqing Zhu, Donald Wright, Thomas Huang, Nikhil Khandekar, Nicholas Wan, Xuguang Ai, W John Wilbur, Zhe He, Andrew Taylor,  Qingyu Chen, and Zhiyong Lu. AgentMD: Empowering language agents for risk prediction with large-scale clinical tool learning. Nature Communications. 16: 9377. 2025. doi: 10.1038/s41467-025-64430-x  [Link]

5. Navya Martin Kollapally, James Geller, Vipina Kuttichi Keloth, Zhe He, Julia Xu. Ontology Enrichment using a Large Language Model: Applying Lexical, Semantic, and Knowledge Network-Based Similarity for Concept Replacement. Journal of Biomedical Informatics. 2025. 168: 104865. [Link]

6. Mahshad Koohi Habibi Dehkordi, Yehoshua Perl, Fadi Deek, Zhe He, Vipina Keloth, Hao Liu, Gai Elhanan, Andrew J. Einstein. Improving Large Language Models' Summarization Accuracy by Adding Highlights to Discharge Notes: Comparative Evaluation. JMIR Medical Informatics. 2025. 13:e66476. [Link]

7. Balu Bhasuran, Qiao Jin, Yuzhang Xie, Carl Yang, Karim Hanna, Jennifer Costa, Cindy Shavor, Zhiyong Lu, Zhe He. Preliminary analysis of the impact of lab results on large language model generated differential diagnoses. npj Digital Medicine (A Nature partner journal). 8, 166 (2025). [Link]

8. Xiaoyu Wang, Haoyong Ouyang, Balu Bhasuran, Xiao Luo, Karim Hanna, Mia Liza A. Lustria, Carl Yang, and Zhe He. Lab-AI - Using Retrieval-Augmented Generation to Enhance Personalized Lab Test Interpretation in Clinical Medicine. The 13th IEEE International Conference on Healthcare Informatics (ICHI 2025), Calabria, Italy, June 18-21, 2025.

9. Mia Liza A. Lustria, Obianuju Aliche, Michael Killian, Zhe He. Enhancing Patient Engagement and Understanding: Is Providing Direct Access to Laboratory Results through Patient Portals Adequate? JAMIA Open. 2025; 8(2) [Link]

10. Weisi Liu, Zhe He, Xiaolei Huang, Time Matters: Examine Temporal Effects on Biomedical Language Models. AMIA 2024 Annual Symposium. In press.

11. Wenshan Han, Balu Bhasuran, Victorine Muse, Søren Brunak, Lifeng Lin, Karim Hanna, Yu Huang, Jiang Bian, Zhe He.  Assessing the Seasonality of Lab Tests Among Patients with Alzheimer's Disease and Related Dementias in OneFlorida Data Trust. AMIA 2024 Annual Symposium. 2024: 483-492. 

12. Zhe He, Balu Bhasuran, Qiao Jin, Shubo Tian, Karim Hanna, Cindy Shavor, Lisbeth Garcia Arguello, Patrick Murray, Zhiyong Lu. Quality of Answers of Generative Large Language Models Versus Peer Users for Interpreting Laboratory Test Results for Lay Patients: Evaluation Study. Journal of Medical Internet Research. 2024;26:e56655. doi: 10.2196/56655. PMID: 38630520 [Link] 

13. Zhe He, Shubo Tian, Arslan Erdengsileng, Karim Hanna, Yang Gong, Xiao Luo, Zhan Zhang, Mia Liza A. Lustria. Annotation and Information Extraction of a Consumer-Friendly Health Website for Enhancing Laboratory Test Reporting in Patient Portals. AMIA 2023 Annual Symposium. 2024 Jan 11;2023:407-416. PMID: 38222337; PMCID: PMC10785897. [PubMed Central]

14. Yu Lu, Laura A. Barrett, Rebecca Lin, Muhammad Amith, Cui Tao, and Zhe He. Understanding Information Needs and Barriers to Accessing Health Information Across All Stages of Pregnancy: A Systematic Review. JMIR Pediatrics and Parenting. 2022;5(1):e32235. doi: 10.2196/32235.  PMID: 35188477 [JMIR]

15. Zhan Zhang, Lukas Kmoth, Xiao Luo, and Zhe He. User-Centered System Design for Communicating Clinical Laboratory Test Results: Design and Evaluation Study.  JMIR Human Factors. 2021; 8(4): e26017. (Acceptance rate: 25%) [JMIR]

16. Zhan Zhang, Daniel Citardi, Aiwen Xing, Xiao Luo, Yu Lu, and Zhe He. Patient Challenges and Needs in Comprehending Lab Test Results: A Mixed-Methods Study. Journal of Medical Internet Research. 2020; 22(12). e18725. [Link]

17. Yu Lu, Xiao Luo, Zhan Zhang, and Zhe He. Retrieving Lab Test Related Questions from Social QA Sites By Combining Shallow Features and Deep Representations. AMIA 2020 Annual Symposium.  November 14-18, 2020. Virtual. pp. 717-726. PMID: 33936453. PMCID: PMC8075538. [medRxiv] [PMC]

18. *Biyang Yu†, Zhe He†, Aiwen Xing, and Mia Liza Lustria.  An Informatics Framework to Assess Consumer Health Language Complexity Differences: Proof-of-Concept Study. Journal of Medical Internet Research. 2020;22(5):e16795. [Link]

19. Zhan Zhang, Caleb Wilson, and Zhe He. Contextualizing Consumer Health Information Seeking. AMIA 2019 Annual Symposium. In press. (Poster)

20. Zhan Zhang, Yu Lu, Yubo Kou, Danny Wu, Jina Huh-Yoo, and Zhe He. Understanding Patient Information Needs about their Clinical Laboratory Results: A Study of Social Q&A Site. MEDINFO 2019. August 26-30, 2019. Lyon, France. Studies in Health Technology and Informatics. In press. 

21. Jiang Bian, Yi Guo, Zhe He, and Xia Hu. Social Web and Health Research - Benefits, Limitations and Best Practice. Springer International Publishing AG. 2019. Print ISBN: 978-3-030-14713-6. Online ISBN: 978-3-030-14714-3. DOI: https://doi.org/10.1007/978-3-030-14714-3 [Link]

22. Zhe He. Understanding and Bridging the Language and Terminology Gap between Health Professionals and Consumers Using Social Media. Social Web and Health Research: Benefits, Limitations, and Best Practices. In: Bian J., Guo Y., He Z., Hu X. (eds) Social Web and Health Research. Springer, Cham. 2019. pp. 103-121. DOI: 10.1007/978-3-030-14714-3_6. [Link]

23. Zhe He*, Zhiwei Chen, Sanghee Oh, Jinghui Hou, and Jiang Bian. Enriching consumer health vocabulary through mining a social Q&A site: a similarity-based approach. Journal of Biomedical Informatics. 2017;69:75-85. PMID: 28359728  [PubMed] [ScienceDirect] 

24. Min Sook Park, Zhe He*, Zhiwei Chen, Sanghee Oh, and Jiang Bian. Consumer's Use of UMLS Concepts on Social Media: Diabetes-Related Textual Data Analysis in Blog and Social Q&A Sites. JMIR Medical Informatics. 2016; 4(4):e41. PMID: 27884812 (Park MS and He Z are equal-contribution first authors) [JMIR]

25. Zhe He, Min Sook Park, and Zhiwei Chen.  UMLS-Based Analysis of Medical Terminology Coverage for Tags in Diabetes-Related Blogs. Proceedings of iConference 2016.  March 20-23, 2016. Philadelphia, PA. (Preliminary results paper. Acceptance rate: 30%)  (Runner up of the Most Interesting Preliminary Results Paper Award) [Link]