| 2017 | AMIA | Cross-species Mapping of Human and Mouse Craniofacial Structures. | Jos L. V. Mejino Jr., Landon T. Detwiler, Timothy C. Cox, James F. Brinkley |
| 2015 | AMIA | Converting the Foundational Model of Anatomy to OWL2. | Landon T. Detwiler, Jos L. V. Mejino Jr., James F. Brinkley |
| 2012 | AMIA | Ontology-Based Federated Data Access to Human Studies Information. | Ida Sim, Simona Carini, Samson W. Tu, Landon Detwiler, James F. Brinkley, Shamin Mollah, Karl Burke, Harold P. Lehmann, Swati Chakraborty, Knut M. Wittkowski, Brad Pollock, Thomas Johnson, Vojtech Huser |
| 2012 | SSDBM | A Dataflow Graph Transformation Language and Query Rewriting System for RDF Ontologies. | Marianne Shaw, Landon Detwiler, James F. Brinkley, Dan Suciu |
| 2008 | AMIA | Regular Paths in SparQL: Querying the NCI Thesaurus. | Landon Detwiler, Dan Suciu, James F. Brinkley |
| 2008 | AMIA | FMA-RadLex: An Application Ontology of Radiological Anatomy derived from the Foundational Model of Anatomy Reference Ontology. | Jos L. V. Mejino Jr., Daniel L. Rubin, James F. Brinkley |
| 2008 | AMIA | Generating Application Ontologies from Reference Ontologies. | Marianne Shaw, Landon Detwiler, James F. Brinkley, Dan Suciu |
| 2007 | AMIA | XGI: A Graphical Interface for XQuery Creation. | Xiang Li, John H. Gennari, James F. Brinkley |
| 2007 | AMIA | A Model Browser for Biosimulation. | Gary Yngve, James F. Brinkley, Daniel L. Cook, Linda G. Shapiro |
| 2006 | AMIA | A framework for using reference ontologies as a foundation for the semantic web. | James F. Brinkley, Dan Suciu, Landon Detwiler, John H. Gennari, Cornelius Rosse |
| 2006 | AMIA | Custom Views of Reference Ontologies. | Landon Detwiler, James F. Brinkley |
| 2006 | AMIA | Customizable Electronic Laboratory Online (CELO): A Web-based Data Management System Builder for Biomedical Research Laboratories. | Christine Fong, James F. Brinkley |
| 2006 | AMIA | Model Driven Laboratory Information Management Systems. | Hao Li, John H. Gennari, James F. Brinkley |
| 2006 | AMIA | Intelligent Web-based Whole Body Visualization for Anatomy Education. | Wayne Warren, Augusto V. Agoncillo, Joshua D. Franklin, James F. Brinkley |
| 2005 | AMIA | A Pilot Bridging Data Integration and Analytics: BioMediator and R? | Sophia Jeng, Kelan Wang, Janos Barbero, James F. Brinkley, Peter Tarczy-Hornoch |
| 2005 | AMIA | Automatic XQuery Generation and Generalized Visualization for an XML Interface to a Relational Database. | E. Sally Lee, Dan Suciu, James F. Brinkley |
| 2005 | AMIA | BioMediator Data Integration: Beyond Genomics to Neuroscience Data. | Kelan Wang, Peter Tarczy-Hornoch, Ron Shaker, Peter Mork, James F. Brinkley |
| 2005 | AMIA | Knowledge-Based, Interactive, Custom Anatomical Scene Creation for Medical Education: The Biolucida System. | Wayne Warren, James F. Brinkley |
| 2003 | AMIA | Efficient Web-Based Navigation of the Foundational Model of Anatomy. | Landon T. Detwiler, Jos L. V. Mejino Jr., Cornelius Rosse, James F. Brinkley |
| 2003 | AMIA | A Prototype Natural Language Interface to a Large Complex Knowledge Base, the Foundational Model of Anatomy. | Gregory Distelhorst, Vishrut Srivastava, Cornelius Rosse, James F. Brinkley |
| 2003 | AMIA | The Evolving Neuroanatomical Component of the Foundational Model of Anatomy. | Richard F. Martin, Kurt L. Rickard, Jos L. V. Mejino Jr., Augusto V. Agoncillo, James F. Brinkley, Cornelius Rosse |
| 2003 | AMIA | Dynamic XML-Based Exchange of Relational Data: Application to the Human Brain Project. | Zhengming Tang, Yana Kadiyska, Hao Li, Dan Suciu, James F. Brinkley |
| 2002 | AMIA | An Online Image Management System for Anatomy Teaching. | James F. Brinkley, Rex M. Jakobovits, Cornelius Rosse |
| 2002 | AMIA | A Declarative Query Interface for Large Semantic Networks. | Peter Mork, Dan Suciu, James F. Brinkley, Cornelius Rosse |
| 2001 | AMIA | Enabling clinicians, researchers, and educators to build custom web-based biomedical information systems. | Rex M. Jakobovits, James F. Brinkley, Cornelius Rosse, Ed Weinberger |
| 2001 | AMIA | Foundational model of neuroanatomy: implications for the Human Brain Project. | Richard F. Martin, Jos L. V. Mejino Jr., Douglas M. Bowden, James F. Brinkley, Cornelius Rosse |
| 2001 | AMIA | Representation of Structural Relationships in the Foundational Model of Anatomy. | Jos L. V. Mejino Jr., Natalya Fridman Noy, Mark A. Musen, James F. Brinkley, Cornelius Rosse |
| 2001 | AMIA | Server-based approach to web visualization of integrated 3-D medical image data. | Andrew V. Poliakov, Evan Albright, David P. Corina, George A. Ojemann, Richard F. Martin, James F. Brinkley |
| 2000 | AMIA | Requirements of a Web-based experiment management system. | Rex M. Jakobovits, Stephen Soderland, Ricky K. Taira, James F. Brinkley |
| 2000 | AMIA | A Personal Annotated Image Server. | William B. Lober, James F. Brinkley |
| 1999 | AMIA | Representing the Digital Anatomist Foundational Model as a Protege Ontology. | Jin S. Hahn, Elizabeth S. Burnside, James F. Brinkley, Cornelius Rosse, Mark A. Musen |
| 1999 | AMIA | Anatomical information in radiation treatment planning. | Ira J. Kalet, Jonn Wu, Matthew Lease, Mary M. Austin-Seymour, James F. Brinkley, Cornelius Rosse |
| 1999 | AMIA | Design features of on-line anatomy information resources: a comparison with the Digital Anatomist. | Sara Kim, James F. Brinkley, Cornelius Rosse |
| 1999 | AMIA | A Portable Image Annotation Tool for Web-based Anatomy Atlases. | William B. Lober, James F. Brinkley |
| 1999 | AMIA | Integration and visualization of multimodality brain data for language mapping. | Andrew V. Poliakov, Kevin P. Hinshaw, Cornelius Rosse, James F. Brinkley |
| 1999 | AMIA | Semi-automatic scene generation using the Digital Anatomist Foundational Model. | Benjamin A. Wong, Cornelius Rosse, James F. Brinkley |
| 1998 | AMIA | Requirements for an on-line knowledge-based anatomy information system. | James F. Brinkley, Cornelius Rosse |
| 1998 | AMIA | Incorporating constraint-based shape models into an interactive system for functional brain mapping. | Kevin P. Hinshaw, James F. Brinkley |
| 1998 | AMIA | Query-by-Context: A Framework for Modeling and Navigating Multimedia Research. | Rex M. Jakobovits, James F. Brinkley |
| 1998 | AMIA | The digital anatomist foundational model: principles for defining and structuring its concept domain. | Cornelius Rosse, Linda G. Shapiro, James F. Brinkley |
| 1998 | AMIA | Dynamic 3-D Scene Navigation in Web-Based Anatomy Atlases. | Benjamin A. Wong, James F. Brinkley |
| 1997 | AMIA | Using 3-D shape models to guide segmentation of MR brain images. | Kevin P. Hinshaw, James F. Brinkley |
| 1997 | AMIA | Managing medical research data with a Web-Interfacing Repository Manager. | Rex M. Jakobovits, James F. Brinkley |
| 1997 | AMIA | Evaluation of a visualization-based approach to functional brain mapping. | Bharath R. Modayur, Rex M. Jakobovits, Kenneth Maravilla, George A. Ojemann, James F. Brinkley |
| 1986 | AAAI | PROTEAN: Deriving Protein Structure from Constraints. | Barbara Hayes-Roth, Bruce G. Buchanan, Olivier Lichtarge, Mike Hewitt, Russ B. Altman, James F. Brinkley, Craig Cornelius, Bruce S. Duncan, Oleg Jardetzky |