Knowledge-Driven Ultrasonic Three-Dimensional Organ Modeling. - James F. Brinkley (IEEE Trans. Pattern Anal. Mach. Intell., 1985)

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 (AAAI, 1986)

Heuristic refinement method for the derivation of protein solution structures: validation on cytochrome b562. - James F. Brinkley; Russ B. Altman; Bruce S. Duncan; Bruce G. Buchanan; Oleg Jardetzky (J. Chem. Inf. Comput. Sci., 1988)

A metric for quantifying response time in a browser application. - D. J. Dailey; James F. Brinkley (IEEE Trans. Syst. Man Cybern. Part A, 1996)

A Visual Database Environment for Scientific Research. - Rex M. Jakobovits; Lara M. Lewis; James P. Ahrens; Linda G. Shapiro; Steven L. Tanimoto; James F. Brinkley (J. Vis. Lang. Comput., 1996)

Using 3-D shape models to guide segmentation of MR brain images. - Kevin P. Hinshaw; James F. Brinkley (AMIA, 1997)

Managing medical research data with a Web-Interfacing Repository Manager. - Rex M. Jakobovits; James F. Brinkley (AMIA, 1997)

Evaluation of a visualization-based approach to functional brain mapping. - Bharath R. Modayur; Rex M. Jakobovits; Kenneth Maravilla; George A. Ojemann; James F. Brinkley (AMIA, 1997)

Synthesis of Research: The Digital Anatomist Distributed Framework and Its Applications to Knowledge-based Medical Imaging. - James F. Brinkley; Cornelius Rosse (J. Am. Medical Informatics Assoc., 1997)

Slisp: A Flexible Software Toolkit for Hybrid, Embedded and Distributed Applications. - James F. Brinkley; Jeffrey S. Prothero (Softw. Pract. Exp., 1997)

Requirements for an on-line knowledge-based anatomy information system. - James F. Brinkley; Cornelius Rosse (AMIA, 1998)

Incorporating constraint-based shape models into an interactive system for functional brain mapping. - Kevin P. Hinshaw; James F. Brinkley (AMIA, 1998)

Query-by-Context: A Framework for Modeling and Navigating Multimedia Research. - Rex M. Jakobovits; James F. Brinkley (AMIA, 1998)

The digital anatomist foundational model: principles for defining and structuring its concept domain. - Cornelius Rosse; Linda G. Shapiro; James F. Brinkley (AMIA, 1998)

Dynamic 3-D Scene Navigation in Web-Based Anatomy Atlases. - Benjamin A. Wong; James F. Brinkley (AMIA, 1998)

Research Paper: Motivation and Organizational Principles for Anatomical Knowledge Representation: The Digital Anatomist Symbolic Knowledge Base. - Cornelius Rosse; José L. V. Mejino Jr.; Bharath R. Modayur; Rex M. Jakobovits; Kevin P. Hinshaw; James F. Brinkley (J. Am. Medical Informatics Assoc., 1998)

Representing the Digital Anatomist Foundational Model as a Protege Ontology. - Jin S. Hahn; Elizabeth S. Burnside; James F. Brinkley; Cornelius Rosse; Mark A. Musen (AMIA, 1999)

Anatomical information in radiation treatment planning. - Ira J. Kalet; Jonn Wu; Matthew Lease; Mary M. Austin-Seymour; James F. Brinkley; Cornelius Rosse (AMIA, 1999)

Design features of on-line anatomy information resources: a comparison with the Digital Anatomist. - Sara Kim; James F. Brinkley; Cornelius Rosse (AMIA, 1999)

A Portable Image Annotation Tool for Web-based Anatomy Atlases. - William B. Lober; James F. Brinkley (AMIA, 1999)

Integration and visualization of multimodality brain data for language mapping. - Andrew V. Poliakov; Kevin P. Hinshaw; Cornelius Rosse; James F. Brinkley (AMIA, 1999)

Semi-automatic scene generation using the Digital Anatomist Foundational Model. - Benjamin A. Wong; Cornelius Rosse; James F. Brinkley (AMIA, 1999)

Design of an Anatomy Information System. - James F. Brinkley; Benjamin A. Wong; Kevin P. Hinshaw; Cornelius Rosse (IEEE Computer Graphics and Applications, 1999)

Requirements of a Web-based experiment management system. - Rex M. Jakobovits; Stephen Soderland; Ricky K. Taira; James F. Brinkley (AMIA, 2000)

A Personal Annotated Image Server. - William B. Lober; James F. Brinkley (AMIA, 2000)

Enabling clinicians, researchers, and educators to build custom web-based biomedical information systems. - Rex M. Jakobovits; James F. Brinkley; Cornelius Rosse; Ed Weinberger (AMIA, 2001)

Foundational model of neuroanatomy: implications for the Human Brain Project. - Richard F. Martin; José L. V. Mejino Jr.; Douglas M. Bowden; James F. Brinkley; Cornelius Rosse (AMIA, 2001)

Representation of Structural Relationships in the Foundational Model of Anatomy. - José L. V. Mejino Jr.; Natalya Fridman Noy; Mark A. Musen; James F. Brinkley; Cornelius Rosse (AMIA, 2001)

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 (AMIA, 2001)

An Online Image Management System for Anatomy Teaching. - James F. Brinkley; Rex M. Jakobovits; Cornelius Rosse (AMIA, 2002)

A Declarative Query Interface for Large Semantic Networks. - Peter Mork; Dan Suciu; James F. Brinkley; Cornelius Rosse (AMIA, 2002)

Application of Information Technology: WIRM: An Open Source Toolkit for Building Biomedical Web Applications. - Rex M. Jakobovits; Cornelius Rosse; James F. Brinkley (J. Am. Medical Informatics Assoc., 2002)

Shape-Based Cortical Surface Segmentation for Visualization Brain Mapping. - Kevin P. Hinshaw; Andrew V. Poliakov; Eider B. Moore; Richard F. Martin; Linda G. Shapiro; James F. Brinkley (NeuroImage, 2002)

Efficient Web-Based Navigation of the Foundational Model of Anatomy. - Landon T. Detwiler; José L. V. Mejino Jr.; Cornelius Rosse; James F. Brinkley (AMIA, 2003)

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 (AMIA, 2003)

The Evolving Neuroanatomical Component of the Foundational Model of Anatomy. - Richard F. Martin; Kurt L. Rickard; José L. V. Mejino Jr.; Augusto V. Agoncillo; James F. Brinkley; Cornelius Rosse (AMIA, 2003)

Dynamic XML-Based Exchange of Relational Data: Application to the Human Brain Project. - Zhengming Tang; Yana Kadiyska; Hao Li; Dan Suciu; James F. Brinkley (AMIA, 2003)

OQAFMA Querying Agent for the Foundational Model of Anatomy: a prototype for providing flexible and efficient access to large semantic networks. - Peter Mork; James F. Brinkley; Cornelius Rosse (J. Biomed. Informatics, 2003)

Towards effective and rewarding data sharing. - Daniel Gardner; Arthur W. Toga; Giorgio A. Ascoli; Jackson T. Beatty; James F. Brinkley; Anders M. Dale; Peter T. Fox; Esther P. Gardner; John S. George; Nigel H. Goddard; Kristen M. Harris; Edward Herskovits; et al. (Neuroinformatics, 2003)

A Relation-Centric Query Engine for the Foundational Model of Anatomy. - Landon T. Detwiler; Emily Chung; Ann Li; José L. V. Mejino Jr.; Augusto V. Agoncillo; James F. Brinkley; Cornelius Rosse; Linda G. Shapiro (MedInfo, 2004)

A Pilot Bridging Data Integration and Analytics: BioMediator and R? - Sophia Jeng; Kelan Wang; Janos Barbero; James F. Brinkley; Peter Tarczy-Hornoch (AMIA, 2005)

Automatic XQuery Generation and Generalized Visualization for an XML Interface to a Relational Database. - E. Sally Lee; Dan Suciu; James F. Brinkley (AMIA, 2005)

BioMediator Data Integration: Beyond Genomics to Neuroscience Data. - Kelan Wang; Peter Tarczy-Hornoch; Ron Shaker; Peter Mork; James F. Brinkley (AMIA, 2005)

Knowledge-Based, Interactive, Custom Anatomical Scene Creation for Medical Education: The Biolucida System. - Wayne Warren; James F. Brinkley (AMIA, 2005)

A Framework for XML-Based Integration of Data, Visualization and Analysis in a Biomedical Domain. - Nathan Bales; James F. Brinkley; E. Sally Lee; Shobhit Mathur; Christopher Ré; Dan Suciu (XSym, 2005)

Application of Information Technology: Server-based Approach to Web Visualization of Integrated Three-dimensional Brain Imaging Data. - Andrew V. Poliakov; Evan Albright; Kevin P. Hinshaw; David P. Corina; George A. Ojemann; Richard F. Martin; James F. Brinkley (J. Am. Medical Informatics Assoc., 2005)

Application of Information Technology: Processes and Problems in the Formative Evaluation of an Interface to the Foundational Model of Anatomy Knowledge Base. - Linda G. Shapiro; Emily Chung; Landon Detwiler; José L. V. Mejino Jr.; Augusto V. Agoncillo; James F. Brinkley; Cornelius Rosse (J. Am. Medical Informatics Assoc., 2005)

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 (AMIA, 2006)

Custom Views of Reference Ontologies. - Landon Detwiler; James F. Brinkley (AMIA, 2006)

Customizable Electronic Laboratory Online (CELO): A Web-based Data Management System Builder for Biomedical Research Laboratories. - Christine Fong; James F. Brinkley (AMIA, 2006)

Model Driven Laboratory Information Management Systems. - Hao Li; John H. Gennari; James F. Brinkley (AMIA, 2006)

Intelligent Web-based Whole Body Visualization for Anatomy Education. - Wayne Warren; Augusto V. Agoncillo; Joshua D. Franklin; James F. Brinkley (AMIA, 2006)

XGI: A Graphical Interface for XQuery Creation. - Xiang Li; John H. Gennari; James F. Brinkley (AMIA, 2007)

A Model Browser for Biosimulation. - Gary Yngve; James F. Brinkley; Daniel L. Cook; Linda G. Shapiro (AMIA, 2007)

MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data. - Eider B. Moore; Andrew V. Poliakov; Peter Lincoln; James F. Brinkley (BMC Bioinform., 2007)

Research Paper: Issues in Biomedical Research Data Management and Analysis: Needs and Barriers. - Nicholas R. Anderson 001; E. Sally Lee; J. Scott Brockenbrough; Mark E. Minie; Sherrilynne S. Fuller; James F. Brinkley; Peter Tarczy-Hornoch (J. Am. Medical Informatics Assoc., 2007)

Unobtrusive integration of data management with fMRI analysis. - Andrew V. Poliakov; Xenia Hertzenberg; Eider B. Moore; David P. Corina; George A. Ojemann; James F. Brinkley (Neuroinformatics, 2007)

Regular Paths in SparQL: Querying the NCI Thesaurus. - Landon Detwiler; Dan Suciu; James F. Brinkley (AMIA, 2008)

FMA-RadLex: An Application Ontology of Radiological Anatomy derived from the Foundational Model of Anatomy Reference Ontology. - José L. V. Mejino Jr.; Daniel L. Rubin; James F. Brinkley (AMIA, 2008)

Generating Application Ontologies from Reference Ontologies. - Marianne Shaw; Landon Detwiler; James F. Brinkley; Dan Suciu (AMIA, 2008)

An independent component analysis based tool for exploring functional connections in the brain. - S. M. Rolfe; L. Finney; Rosalia F. Tungaraza; J. Guan; Linda G. Shapiro; James F. Brinkley; Andrew V. Poliakov; Natalia M. Kleinhans; E. Alyward (Image Processing, 2009)

A similarity retrieval method for functional magnetic resonance imaging (fMRI) statistical maps. - Rosalia F. Tungaraza; J. Guan; S. M. Rolfe; Indriyati Atmosukarto; Andrew V. Poliakov; Natalia M. Kleinhans; Elizabeth H. Aylward; Jeffrey G. Ojemann; James F. Brinkley; Linda G. Shapiro (Image Processing, 2009)

Distributed XQuery-based integration and visualization of multimodality brain mapping data. - Landon T. Detwiler; Dan Suciu; Joshua D. Franklin; Eider B. Moore; Andrew V. Poliakov; Eunjung Lee; David P. Corina; George A. Ojemann; James F. Brinkley (Frontiers Neuroinformatics, 2009)

Content-specific auditing of a large scale anatomy ontology. - Ira J. Kalet; José L. V. Mejino Jr.; Vania Wang; Mark Whipple; James F. Brinkley (J. Biomed. Informatics, 2009)

Application of neuroanatomical ontologies for neuroimaging data annotation. - Jessica A. Turner; José L. V. Mejino Jr.; James F. Brinkley; Landon T. Detwiler; Hyo Jong Lee; Maryann E. Martone; Daniel L. Rubin (Frontiers Neuroinformatics, 2010)

The Foundational Model of Neuroanatomy Ontology: An Ontology Framework to Support Neuroanatomical Data Integration. - B. Nolan Nichols; José L. V. Mejino Jr.; James F. Brinkley (ICBO, 2011)

Ontological Labels for Automated Location of Left Ventricular Remodeling. - Shane Steinert-Threlkeld; Siamak Ardekani; José L. V. Mejino Jr.; Landon Detwiler; James F. Brinkley; Michael Halle; Ron Kikinis; Raimond L. Winslow; Michael I. Miller; J. Tilak Ratnanather (ICSC, 2011)

A partnership approach for Electronic Data Capture in small-scale clinical trials. - Joshua D. Franklin; Alicia F. Guidry; James F. Brinkley (J. Biomed. Informatics, 2011)

vSPARQL: A view definition language for the semantic web. - Marianne Shaw; Landon Fridman Detwiler; Natalya Fridman Noy; James F. Brinkley; Dan Suciu (J. Biomed. Informatics, 2011)

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; et al. (AMIA, 2012)

A Dataflow Graph Transformation Language and Query Rewriting System for RDF Ontologies. - Marianne Shaw; Landon Detwiler; James F. Brinkley; Dan Suciu (SSDBM, 2012)

A Query Integrator and Manager for the Query Web. - James F. Brinkley; Landon Detwiler (J. Biomed. Informatics, 2012)

Ontological labels for automated location of anatomical shape differences. - Shane Steinert-Threlkeld; Siamak Ardekani; José L. V. Mejino Jr.; Landon Detwiler; James F. Brinkley; Michael Halle; Ron Kikinis; Raimond L. Winslow; Michael I. Miller; J. Tilak Ratnanather (J. Biomed. Informatics, 2012)

Human Development Domain of the Ontology of Craniofacial Development and Malformation. - José L. V. Mejino Jr.; Ravensara S. Travillian; Timothy C. Cox; Linda G. Shapiro; James F. Brinkley (ICBO, 2013)

Neuroanatomical domain of the foundational model of anatomy ontology. - B. Nolan Nichols; José L. V. Mejino Jr.; Landon Detwiler; Trond T. Nilsen; Maryann E. Martone; Jessica A. Turner; Daniel L. Rubin; James F. Brinkley (J. Biomed. Semant., 2014)

Converting the Foundational Model of Anatomy to OWL2. - Landon T. Detwiler; José L. V. Mejino Jr.; James F. Brinkley (AMIA, 2015)

Multi-species Ontologies of the Craniofacial Musculoskeletal System. - José Leonardo Villaraza Mejino Jr.; James F. Brinkley; Timothy C. Cox; Landon Detwiler (ICBO/BioCreative, 2016)

From frames to OWL2: Converting the Foundational Model of Anatomy. - Landon T. Detwiler; José L. V. Mejino Jr.; James F. Brinkley (Artif. Intell. Medicine, 2016)

Cross-species Mapping of Human and Mouse Craniofacial Structures. - José L. V. Mejino Jr.; Landon T. Detwiler; Timothy C. Cox; James F. Brinkley (AMIA, 2017)