| 2022 | AMIA | Reddit Caregiver Support Forums: NLP and Visualization for Digestion of Complex Themes. | Catherine C. Shoults, Michael W. Rutherford, Aaron S. Kemp, Merideth Addicott, Aliza Brown, Carolyn Greene, Corey J. Hayes, Jennifer Gan, Linda J. Larson-Prior, Jonathan P. Bona |
| 2019 | AMIA | Providing a User-oriented Interface to Enable Semantic Queries in PRISM. | Jonathan P. Bona, Joseph Utecht, Mathias Brochhausen |
| 2019 | AMIA | Using Semantic Representations for Urine Drug Tests in the Veterans Health Administration. | Corey J. Hayes, Jonathan P. Bona, Mathias Brochhausen |
| 2019 | AMIA | Semantic Representations of Multi-Modal Data, NeuroInformatic Processing Pipelines, and Derived Neuroimaging Results in the Arkansas Image Enterprise System (ARIES). | Aaron S. Kemp, Jonathan P. Bona, Tracy S. Nolan, Linda J. Larson-Prior, Tuhin Virmani, Lakshmi R. Pillai, Mathias Brochhausen, Lawrence Tarbox, Fred W. Prior |
| 2018 | AMIA | Ontologies Enabling Non-image Data Queries in The Cancer Imaging Archive. | Jonathan P. Bona, Tracy S. Nolan, Dillon Gibson, Mathias Brochhausen |
| 2017 | AMIA | Does Semantic Tag Usage in SNOMED CT Match its Concept Hierarchy? | Jonathan P. Bona |
| 2017 | AMIA | Creating RDF Data on Trauma Care Organizations from Questionnaires. | Joseph R. Utecht, Jonathan P. Bona, Mathias Brochhausen |
| 2016 | AMIA | Identifying Missing Finding Site Relations in SNOMED CT. | Jonathan P. Bona, Werner Ceusters |
| 2016 | AMIA | Analyzing SNOMED CT's Historical Data: Pitfalls and Possibilities. | Werner Ceusters, Jonathan P. Bona |
| 2016 | FOIS | Ontologies of Dynamical Systems and Verifiable Ontology-Based Computation: Towards a Haskell-Based Implementation of Referent Tracking. | Thomas Bittner, Jonathan P. Bona, Werner Ceusters |
| 2016 | FOIS | Representing SNOMED CT Concept Evolutions using Process Profiles. | Werner Ceusters, Jonathan P. Bona |
| 2015 | AMIA | An Ontology-Driven Patient History Questionnaire System. | Jonathan P. Bona |
| 2015 | VLDB | Comparing Small Graph Retrieval Performance for Ontology Concepts in Medical Texts. | Daniel R. Schlegel, Jonathan P. Bona, Peter L. Elkin |