| 2025 | FOIS | Towards Representing Change in the BFO. | Werner Ceusters, Alan Ruttenberg |
| 2024 | FOIS | Fiat Surfaces in the Basic Formal Ontology. | Michael Rabenberg, Werner Ceusters |
| 2023 | FOIS | Axiomatizing SNOMED CT Disorders: Should There Be Room for Interpretation? | Werner Ceusters, Anuwat Pengput |
| 2018 | AMIA | Enhancing the Representational Power of i2b2 through Referent Tracking. | Jonathan C. Blaisure, Werner Ceusters |
| 2017 | AMIA | Improving the 'Fitness for Purpose' of Common Data Models through Realism Based Ontology. | Jonathan C. Blaisure, Werner Ceusters |
| 2017 | AMIA | The Problems of Realism-Based Ontology Design: a Case Study in Creating Definitions for an Application Ontology for Diabetes Camps. | James C. Schuler, Werner Ceusters |
| 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 |
| 2014 | FOIS | Applying the Realism-Based Ontology-Versioning Method for Tracking Changes in the Basic Formal Ontology. | Selja Seppl, Barry Smith, Werner Ceusters |
| 2012 | AMIA | Domain and Application Ontologies for Medically Unexplained Syndromes. | Kristina Doing-Harris, Stphane M. Meystre, Matthew H. Samore, Werner Ceusters |
| 2008 | FOIS | Introducing Realist Ontology for the Representation of Adverse Events. | Werner Ceusters, Maria Capolupo, Georges De Moor, Jos Devlies |
| 2007 | AMIA | Would SNOMED CT benefit from Realism-Based Ontology Evolution? | Werner Ceusters, Kent A. Spackman, Barry Smith |
| 2007 | AMIA | A Middleware Approach to Integrate Referent Tracking in EHR Systems. | Shahid Manzoor, Werner Ceusters, Ron Rudnicki |
| 2007 | AMIA | What Particulars are Referred to in Electronic Health Record Data? A Case Study in Integrating Referent Tracking into an EHR Application. | Ron Rudnicki, Werner Ceusters, Shahid Manzoor, Barry Smith |
| 2006 | AMIA | A Realism-Based Approach to the Evolution of Biomedical Ontologies. | Werner Ceusters, Barry Smith |
| 2006 | FOIS | Towards A Realism-Based Metric for Quality Assurance in Ontology Matching. | Werner Ceusters |
| 2005 | AMIA | An Ontology-Based Methodology for the Migration of Biomedical Terminologies to Electronic Health Records. | Barry Smith, Werner Ceusters |
| 2004 | KR | Ontological Theory for Ontological Engineering: Biomedical Systems Information Integration. | James Matthew Fielding, Jonathan Simon, Werner Ceusters, Barry Smith |
| 2002 | EKAW | Some Ontology Engineering Processes and Their Supporting Technologies. | Alan Flett, Mariana Casella dos Santos, Werner Ceusters |
| 1998 | AMIA | A Comprehensive Approach to Developing and Integrating Multilingual Classifications: GALEN's Classification Workbench. | Alan L. Rector, Robert H. Baud, Werner Ceusters, A. M. W. Claassen, Jean Marie Rodrigues, Jeremy Rogers, Angelo Rossi Mori, Egbert J. van der Haring, W. D. Solomon, Pieter E. Zanstra |