| 2026 | PacificVis | OntoGrid: Supporting Analysis of Complex Associations in Biomedical Ontologies. | Ying Yang, Michael Wybrow, Yuan-Fang Li, Tobias Czauderna, Yongqun He |
| 2024 | ER | Enhancing Vaxign-DL for Vaccine Candidate Prediction with Added ESM-Generated Features. | Yichao Chen, Yuhan Zhang, Yongqun He |
| 2024 | ER | Integrative Ontology of Bipolar Disorder (OBD): Advancing Bipolar Disorder Research Through an Interoperable Ontological Framework. | Yujia Tian, Yongqun He, Rachel L. Richesson, Melvin G. McInnis |
| 2017 | AMIA | From Scoping Review to Metadata: An Evidence-Based Approach to Identifying Informed Consent Metadata for Biorepositories. | Marcelline R. Harris, Frank J. Manion, Hsing-yi Song, Yongqun He, Muhamamd F. Amith, Cui Tao |
| 2017 | AMIA | Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs. | Meiu Wong, Rebecca Racz, Edison Ong, Yongqun He |
| 2016 | AMIA | Ontology-Based Analysis of Adverse Drug Reactions Associated with Anti-infection Drugs in China. | Mei Li, Yuying Cao, Liwei Wang, Hongfang Liu, Yongqun He |
| 2016 | AMIA | Application of Ontobedia on Cell Line Ontology Development. | Edison Ong, Yongqun He |
| 2014 | AMIA | Analysis of Content Coverage for Informed Consent Concepts. | Frank J. Manion, Elizabeth Eisenhauer, Alla Karnovsky, Yongqun He, Yu Lin, Marcelline R. Harris |