Items where Author is "Brinkley, James F"

Article

Brinkley, James F and Fisher, Shannon and Harris, Matthew P. and Holmes, Greg and Hooper, Joan E. and Wang Jabs, Ethylin and Jones, Kenneth L. and Kesselman, Carl and Klein, Ophir D. and Maas, Richard L. and Marazita, Mary L. and Selleri, Licia and Spritz, Richard A. and van Bakel, Harm and Visel, Axel and Williams, Trevor J. and Wysocka, Joanna and Chai, Yang (2016) The FaceBase Consortium: a comprehensive resource for craniofacial researchers. Development, 143 (14). pp. 2677-2688. ISSN 0950-1991

Detwiler, Landon T. and Mejino, Jose L.V. and Brinkley, James F (2016) From Frames to OWL2: Converting the Foundational Model of Anatomy. Artificial Intelligence in Medicine, 69. pp. 12-21. ISSN 09333657

Wang, Kenneth C. and Salunkhe, Aditya R. and Morrison, James J. and Lee, Pearlene P. and Mejino, José L. V. and Detwiler, Landon T. and Brinkley, James F and Siegel, Eliot L. and Rubin, Daniel L. and Carrino, John A. (2015) Ontology-based Image Navigation: Exploring 3.0-T MR Neurography of the Brachial Plexus Using AIM and RadLex. RadioGraphics, 35 (1). pp. 142-151. ISSN 0271-5333

Wang, Kathie H. and Heike, Carrie L. and Clarkson, Melissa D. and Mejino, Jose L. V. and Brinkley, James F and Tse, Raymond W. and Birgfeld, Craig B. and Fitzsimons, David A. and Cox, Timothy C. (2014) Evaluation and integration of disparate classification systems for clefts of the lip. Frontiers in Physiology, 5. ISSN 1664-042X

Nichols, B and Mejino, Jose LV and Detwiler, Landon T and Nilsen, Trond T and Martone, Maryann E and Turner, Jessica A and Rubin, Daniel L and Brinkley, James F (2014) Neuroanatomical domain of the foundational model of anatomy ontology. Journal of Biomedical Semantics, 5 (1). p. 1. ISSN 2041-1480

Tungaraza, Rosalia and Guan, Jinyan and Shapiro, Linda and Brinkley, James F and Ojemann, Jeffrey and Franklin, Joshua (2013) A Similarity Retrieval Tool for Functional Magnetic Resonance Imaging Statistical Maps. International Journal of Biomedical Data Mining, 2. pp. 1-12. ISSN 2090-4916

Brinkley, James F and Borromeo, C. and Clarkson, M. and Cox, T.C. and Cunningham, M.J. and Detwiler, L.T. and Heike, C.L. and Hochheiser, H. and Mejino, J.L.V. and Travillian, R.S. and Shapiro, L.G. (2013) The ontology of craniofacial development and malformation for translational craniofacial research. American Journal of Medical Genetics Part C: Seminars in Medical Genetics, 163 (4). pp. 232-245. ISSN 15524868

Steinert-Threlkeld, Shane and Ardekani, Siamak and Mejino, Jose L.V. and Detwiler, Landon Todd and Brinkley, James F and Halle, Michael and Kikinis, Ron and Winslow, Raimond L. and Miller, Michael I. and Ratnanather, J. Tilak (2012) Ontological labels for automated location of anatomical shape differences. Journal of Biomedical Informatics, 45 (3). pp. 522-527. ISSN 15320464

Brinkley, James F and Detwiler, Landon T. (2012) A Query Integrator and Manager for the Query Web. Journal of Biomedical Informatics, 45 (5). pp. 975-991. ISSN 15320464

Puget, A. and Mejino, J. L. V. and Detwiler, L. T. and Franklin, J. D. and Brinkley, James F (2012) Spatial-symbolic Query Engine in Anatomy. Methods of Information in Medicine, 51 (6). pp. 463-478. ISSN 0026-1270

Shaw, Marianne and Detwiler, Landon T and Noy, N. F. and Brinkley, James F and Suciu, Dan (2011) vSPARQL: A View Definition Language for the Semantic Web. Journal of Biomedical Informatics, 44 (1). pp. 102-117.

Franklin, Joshua D. and Guidry, Alicia and Brinkley, James F (2011) A partnership approach for Electronic Data Capture in small-scale clinical trials. Journal of Biomedical Informatics, 44. S103-S108. ISSN 15320464

Turner, Jessica A and Mejino, Jose L V and Brinkley, James F and Detwiler, Landon T and Lee, Hyo Jong and Martone, Maryann E and Rubin, Daniel L (2010) Application of neuroanatomical ontologies for neuroimaging data annotation. Frontiers in Neuroinformatics, 4 (10). pp. 1-12.

Corina, David P. and Loudermilk, Brandon C. and Detwiler, Landon and Martin, Richard F. and Brinkley, James F and Ojemann, George (2010) Analysis of naming errors during cortical stimulation mapping: Implications for models of language representation. Brain and Language, 115 (2). pp. 101-112. ISSN 0093934X

Kalet, Ira and Mejino, Jose L V and Wang, Vania and Whipple, Mark and Brinkley, James F (2009) Content-specific auditing of a large scale anatomy ontology. Journal of Biomedical Informatics, 42 (3). pp. 540-549.

Detwiler, Landon T and Suciu, Dan and Franklin, Joshua D and Moore, Eider B and Poliakov, Andrew W and Lee, E Sally and Corina, David P and Ojemann, George A and Brinkley, James F (2009) Distributed XQuery-based integration and visualization of multimodality data: Application to brain mapping. Frontiers in Neuroinformatics, 3 (2). pp. 1-13.

Poliakov, Andrew V and X., Hertzenberg and Moore, Eider B and Corina, David P and Ojemann, George A and Brinkley, James F (2008) Unobtrusive Integration of Data Management With fMRI Analysis. NeuroInformatics, 5 (1). pp. 3-10.

Yuen, Jenny and Li, Yi and Shapiro, Linda G. and Clark, John I. and Arnett, Ernest and Sage, E. Helene and Brinkley, James F (2008) Automated, computerized, feature-based phenotype analysis of slit lamp images of the mouse lens. Experimental Eye Research, 86 (4). pp. 562-575. ISSN 00144835

Altman, R. B. and Balling, R and Brinkley, James F and Coiera, E and Consorti, F and Dhansay, MA and Geissbuhler, A and Hersh, W and Kwankam, SY and Lorenzi, NM and Martin-Sanchez, F and Mihalas, GI and Shahar, Y and Takabayashi, K and Wiederhold, G (2008) Commentaries on “Informatics and Medicine: From Molecules to Populations”. Methods of Information in Medicine, 47 (4). pp. 296-317.

Anderson, Nicholas R and Lee, E. Sally and Brockenbrough, J Scott and Minie, Mark E and Fuller, Sherrilynne and Brinkley, James F and Tarczy-Hornoch, Peter (2007) Issues in biomedical research data management and analysis: needs and barriers. Journal of the American Medical Informatics Association, 14. pp. 478-488.

Moore, Eider B and Poliakov, Andrew V and Lincoln, Peter and Brinkley, James F (2007) MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data. BMC Bioinformatics, 8. p. 389.

Moore, Eider B and Poliakov, Andrew V and Lincoln, Peter and Brinkley, James F (2007) MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data. BMC Bioinformatics, 8 (1). p. 389. ISSN 1471-2105

Poliakov, Andrew V and Albright, Evan M and Hinshaw, Kevin P and Corina, David P and Martin, Richard F and Brinkley, James F (2005) Server-based Approach to Web Visualization of Integrated Three-dimensional Brain Imaging Data. Journal of the American Medical Informatics Association, 12 (2). pp. 140-151.

Shapiro, Linda G and Chung, Emily and Detwiler, Landon T and Mejino, Jose L V and Agoncillo, Augusto V and Brinkley, James F and Rosse, Cornelius (2005) Processes and Problems in the Formative Evaluation of an Interface to the Foundational Model of Anatomy Knowledge Base. Journal of the American Medical Informatics Association, 12 (1). pp. 35-46.

Corina, David P and Gibson, Erin K. and Martin, Richard F and Poliakov, Andrew V and Brinkley, James F and Ojemann, George A (2005) Dissociation of Action and Object Naming: Evidence From Cortical Stimulation Mapping. Human Brain Mapping, 24 (1). pp. 1-10.

Mork, Peter and Brinkley, James F and Rosse, Cornelius (2003) OQAFMA Querying Agent for the Foundational Model of Anatomy: a Prototype for Providing Flexible and Efficient Access to Large Semantic Networks. Journal of Biomedical Informatics, 36. pp. 501-517.

Kim, S. and Brinkley, James F and Rosse, Cornelius (2003) Profile of On-Line Anatomy Information Resources: Design and Instructional Implications. Clinical Anatomy, 16 (1). pp. 55-71.

Gardner, Daniel and W.Toga, Arthur and Ascoli, Giorgio A. and Beatty, ackson T. and Brinkley, James F and Dale, Anders M. and Fox, PT and Gardner, EP and George, JS and Goddard, N and Harris, KM and Herskovits, EH and Hines, ML and Jacobs, GA and Jones, EG and Kennedy, DN and Kimberg, DY and Mazziotta, JC and Miller, PL and Mori, S and Mountain, DC and Reiss, AL and Rosen, GD and Rottenberg, DA and Shepherd, GM and Smalheiser, NR and Smith, KP and Strachan, T and Van Essen, DC and Williams, RW and Wong, ST (2003) Towards Effective and Rewarding Data Sharing. Neuroinformatics, 1 (3). pp. 289-296. ISSN 1539-2791

Jakobovits, Rex M and Rosse, Cornelius and Brinkley, James F (2002) WIRM: an Open Source Toolkit for Building Biomedical Web Applications. Journal of the American Medical Informatics Association, 9 (6). pp. 557-570.

Hinshaw, Kevin P and Poliakov, Andrew V and Martin, Richard F and Moore, Eider B and Shapiro, Linda G and Brinkley, James F (2002) Shape-Based Cortical Surface Segmentation for Visualization Brain Mapping. Neuroimage, 16 (2). pp. 295-316.

Brinkley, James F and Rosse, Cornelius (2002) Imaging Informatics and the Human Brain Project: the Role of Structure, Review. Yearbook of Medical Informatics 2002. pp. 111-128.

Brinkley, James F and Rosse, Cornelius (2002) Imaging and the Human Brain Project: a Review. Methods of Information in Medicine, 41. pp. 245-260.

Corina, David P and McBurney, S. L. and Dodrill, C. and Hinshaw, Kevin P and Brinkley, James F and Ojemann, George A (1999) Functional Roles of Broca's Area and SMG: Evidence from Cortical Stimulation Mapping in a Deaf Signer. Neuroimage, 10 (5). pp. 570-581.

Brinkley, James F and Wong, B. A. and Hinshaw, Kevin P and Rosse, Cornelius (1999) Design of an Anatomy Information System. Computer Graphics and Applications, 19 (3). pp. 38-48.

Rosse, Cornelius and Mejino, Jose L V and Modayur, Bharath R and Jakobovits, Rex M and Hinshaw, Kevin P and Brinkley, James F (1998) Motivation and Organizational Principles for Anatomical Knowledge Representation: The Digital Anatomist Symbolic Knowledge Base. Journal of the American Medical Informatics Association, 5 (1). pp. 17-40.

Brinkley, James F and Rosse, Cornelius (1997) The Digital Anatomist Distributed Framework and Its Applications to Knowledge Based Medical Imaging. Journal of the American Medical Informatics Association, 4 (3). pp. 165-183.

Brinkley, James F and Bradley, S. W. and Sundsten, John W and Rosse, Cornelius (1997) The Digital Anatomist Information System and Its Use in the Generation and Delivery of Web-Based Anatomy Atlases. Computers and Biomedical Research, 30. pp. 472-503.

Brinkley, James F and Prothero, J. S. (1997) Slisp: A Flexible Software Toolkit for Hybrid, Embedded and Distributed Applications. Software -- Practice and Experience, 27 (1). pp. 33-48.

Modayur, Bharath R and Prothero, J. and Ojemann, George A and Maravilla, K. and Brinkley, James F (1997) Visualization-Based Mapping of Language Function in the Brain. Neuroimage, 6. pp. 245-258.

Jakobovits, Rex M and Lewis, L. M. and Ahrens, J. P. and Shapiro, Linda G and Tanimoto, S. L. and Brinkley, James F (1996) A Visual Database Environment for Scientific Research. Journal of Visual Languages and Computing, 7 (4). pp. 361-375.

Dailey, D. J. and Brinkley, James F (1996) A Metric for Quantifying Response Time in a Browser Application. IEEE Trans. Systems, Man and Cybernetics, Part A (Systems and Humans), 26 (2). pp. 271-275.

Brinkley, James F (1993) A Flexible, Generic Model for Anatomic Shape: Application to Interactive Two-Dimensional Medical Image Segmentation and Matching. Computers and Biomedical Research, 26. pp. 121-142.

Brinkley, James F and Eno, Kraig R and Sundsten, John W (1993) Knowledge-Based Client-Server Approach to Structural Information Retrieval: The Digital Anatomist Browser. Computer Methods and Programs in Biomedicine, 40. pp. 131-145.

Sundsten, JW and Brinkley, James F and Conley, DM and Eno, Kraig R and Kastella, KG and Rosse, Cornelius (1992) Three-dimensional computer graphics reconstructions of anatomy on videodisc. J. Audiovisual Media in Medicine, 15 (2). pp. 65-67.

Brinkley, James F (1991) Structural Informatics and Its Applications in Medicine and Biology. Academic Medicine, 66 (10). pp. 589-591.

Brinkley, James F and Altman, R. B. and Duncan, B. S. and Buchanan, B. G. and Jardetzky, O. (1988) Heuristic Refinement Method for the Derivation of Protein Solution Structures: Validation on Cytochrome B562. J. Chem. Inf. Comput. Sci., 28 (4). pp. 194-210.

Duncan, Bruce and Buchanan, Bruce G. and Hayes-Roth, Barbara and Lichtarge, Olivier and Altman, R. Peter and Brinkley, James F and Hewett, Micheal and Cornelius, Craig and Jardetzky, Oleg (1986) PROTEAN: A New Method for Deriving Solution Structures of Proteins. Bulletin of Magnetic Resonance, 8 (3/4). pp. 111-119.

Brinkley, James F (1985) Knowledge-driven ultrasonic three-dimensional organ modeling. IEEE transactions on pattern analysis and machine intelligence, 7 (4). pp. 431-41. ISSN 0162-8828

Brinkley, James F and McCallum, W D and Muramatsu, S K and Liu, D Y (1984) Fetal weight estimation from lengths and volumes found by three-dimensional ultrasonic measurements. Journal of ultrasound in medicine : official journal of the American Institute of Ultrasound in Medicine, 3 (4). pp. 163-8. ISSN 0278-4297

Eik-Nes, S.H. and Brinkley, James F (1983) Tredimensjonal framstilling av foster in utero ved hjelp av ultralyd og moderne datateknologi. Annual Meeting, Norwegian Society of Ultrasound Diagnosis. p. 40.

Brinkley, James F and McCallum, W.Desmond and Muramatsu, Saundra K. and Liu, Donna Yee (1982) Fetal weight estimation from ultrasonic three-dimensional head and trunk reconstructions: Evaluation in vitro. American Journal of Obstetrics and Gynecology, 144 (6). pp. 715-721. ISSN 00029378

Brinkley, James F and Muramatsu, SK and McCallum, WD and Popp, RL (1982) In vitro evaluation of an ultrasonic three-dimensional imaging and volume system. Ultrasonic Imaging, 4 (2). pp. 126-139. ISSN 01617346

Brinkley, James F and McCallum, W D and Popp, RL (1982) Ultrasonic three-dimensional imaging and volume: an in vitro evaluation. Am. J. Cardiol, 49. p. 897.

McCallum, W.D. and Brinkley, James F (1979) Estimation of fetal weight from ultrasonic measurements. American Journal of Obstetrics and Gynecology, 133 (2). pp. 195-200. ISSN 00029378

Brinkley, James F and Moritz, William E. and Baker, Donald W. (1978) Ultrasonic three-dimensional imaging and volume from a series of arbitrary sector scans. Ultrasound in Medicine & Biology, 4 (4). pp. 317-321. ISSN 03015629

Book Section

Mejino, Jose L V and Detwiler, Landon T and Cox, Timothy C and Brinkley, James F (2017) Cross-species Mapping of Human and Mouse Craniofacial Structures. In: Proceedings, Annual Symposium of the American Medical Informatics Association. p. 2105.

Mejino, Jose L V and Detwiler, Landon T and Cox, Timothy C and Brinkley, James F (2016) Multi-species Ontologies of the Craniofacial Musculoskeletal System. In: Proceedings of the Joint International Conference on Biological Ontology and BioCreative (ICBO). IP03.

Detwiler, Landon T and Mejino, Jose L V and Brinkley, James F (2015) Converting the Foundational Model of Anatomy to OWL2. In: Proceedings, Fall Symposium of the American Medical Informatics Association. p. 1452.

Mejino, Jose L V and Detwiler, Landon T and Brinkley, James F (2015) An ontology of the craniofacial musculoskeletal system. In: Proceedings of the AMIA Spring Summit on Clinical Research Informatics. p. 358.

Mejino, Jose Lv and Travillian, Ravensara S and Cox, Timothy C and Shapiro, Linda G and Brinkley, James F (2013) Human Development Domain of the Ontology of Craniofacial Development and Malformation. In: Proceedings, 4th International Conference on Biomedical Ontology (ICBO). pp. 74-77.

Detwiler, Landon T and Tu, Samson and Carini, Simona and Sim, Ida and Brinkley, James F (2013) Data schema from ontologies: An HSDB study. In: Proceedings of the AMIA Spring Summit on Clinical Research Informatics. San Francisco. p. 52.

Brinkley, James F and Mejino, Jose L V and Detwiler, Landon T and Travillian, Ravensara S and Clarkson, Melissa D. and Cox, Timothy C and Heike, C.L. and Cunningham, M.J. and Hochheiser, H. and Shapiro, Linda G (2013) Towards understanding craniofacial abnormalities: the ontology of craniofacial development and malformation. In: Proc AMIA Summit on Clinical Research Informatics. p. 20.

Mejino, Jose L V and Shapiro, Linda G and Brinkley, James F (2013) An ontology for human craniofacial development. In: Proceedings of the AMIA Spring Summit on Translational Bioinformatics. p. 108.

Shaw, Marianne and Detwiler, Landon T. and Brinkley, James F and Suciu, Dan (2012) A Dataflow Graph Transformation Language and Query Rewriting System for RDF Ontologies. In: SSDBM 12: Proceedings of the 24th International Conference on Scientific and Statistical Database Management. pp. 544-561.

Carini, Simona and Tu, Samson and Detwiler, Landon T and Burke, Karl and Brinkley, James F and Sim, Ida (2012) The Human Studies Database Project Uses the Ontology of Clinical Research to Federate Human Studies Information. In: Bio-Ontologies 2012. p. 366.

Shaker, Ronald and Hertzenberg, Xenia and Brinkley, James F (2012) Lightweight Data Integration Frameworks for Clinical Research. In: 2012 AMIA Summit on Clinical Research Informatics. p. 152.

Nichols, Nolan and Dougherty, RF and Detwiler, Landon T and Schaefer, G and Frank, RJ and Brinkley, James F and Wandell, BA and Grabowski, TJ (2012) NIQuery: neuroimaging informatics query framework for data sharing, discovery, and analysis. In: Proceedings Neuroinformatics 2012. p. 68.

Sim, Ida and Carini, Simona and Tu, Samson W and Detwiler, Landon T and Brinkley, James F and Mollah, Shamim A and Burke, Karl and Lehmann, Harold P and Chakraborty, Swati and Wittkowski, Knut M and Pollock, Brad H and Johnson, Thomas M and Huser, Vojtech (2012) Ontology-based federated data access to human studies information. In: Proceedings, Fall Symposium of the American Medical Informatics Association. pp. 856-865.

Hertzenberg, Xenia and Shaker, Ronald and Brinkley, James F (2012) RLab: A lightweight freezer management system for small laboratories. In: AMIA Spring Summit on Clinical Informatics. p. 164.

Nichols, Nolan and Dougherty, RF and Detwiler, Landon T and Schaefer, G and Frank, RJ and Brinkley, James F and Wandell, BA and Grabowski, TJ (2012) A framework for remote voxel-level access to distributed neuroimaging data. In: Abstracts, Annual Meeting of the Society for Neuroscience. 928.01/GGG7.

Nichols, Nolan and Detwiler, Landon T and Franklin, Joshua D and Brinkley, James F (2011) Distributed Queries for Quality Control Checks in Clinical Trials. In: Clinical Research Informatics Summit of the American Medical Informatics Association. p. 115.

Nichols, Nolan and Mejino, Jose L V and Brinkley, James F (2011) The Foundational Model of Neuroanatomy Ontology: Ontology framework to support neuroanatomical data integration. In: Proceedings, International Conference on Biomedical Ontology (ICBO). pp. 444-445.

Nichols, Nolan and Turner, Jessica A and Detwiler, Landon T and Mejino, Jose L V and Rubin, Daniel L and Brinkley, James F (2011) Integrating semantically annotated multi-modal imaging datasets. In: Proceedings, Annual Meeting of the Society for Neuroscience. 841.04/ZZ81.

Nichols, Nolan and Turner, Jessica A and Detwiler, Landon T and Mejino, Jose L V and Rubin, Daniel L and Brinkley, James F (2011) Integration of Semantically Annotated Neuroimaging Data via Chained Queries. In: Front. Neuroinform. Conference Abstract: 4th INCF Congress of Neuroinformatics.

Steinert-Threlkeld, Shane and Ardekani, Siamak and Mejino, Jose L V and Detwiler, Landon T and Brinkley, James F and Halle, Michael and Kikinis, Ron and Winslow, Raimond L. and Miller, Michael I. and Ratnanather, J. Tilak (2011) Ontological labels for automated location of left ventricular remodeling. In: IEEE International Conference on Semantic Computing. pp. 572-573.

Franklin, Joshua D and Guidry, Alicia F and Brinkley, James F (2011) A Partnership Approach for Electronic Data Capture in Small-Scale Clinical Trials. In: Clinical Research Informatics Summit of the American Medical Informatics Association. p. 10.

Detwiler, Landon T and Brinkley, James F (2011) Value Sets via Ontology Views. In: Clinical Research Informatics Summit of the American Medical Informatics Association. p. 100.

Wynden, Rob and Solbrig, Harold and Tu, Samson and Brinkley, James F (2011) The Value of Value Sets. In: Clinical Research Informatics Summit of the American Medical Informatics Association. pp. 162-163.

Mejino, Jose L V and Detwiler, Landon T and Turner, Jessica A and Martone, Maryann E and Rubin, Daniel L and Brinkley, James F (2010) Enabling RadLex with the Foundational Model of Anatomy Ontology to Organize and Integrate Neuro-imaging Data. In: Annual Symposium of the American Medical Informatics Association. p. 1171.

Brinkley, James F and Turner, Jessica A and Detwiler, Landon T and Mejino, Jose L V and Martone, Maryanne E and Rubin, Daniel L (2010) Intelligent Queries over BIRN Data using the Foundational Model of Anatomy and a Distributed Query-Based Data Integration System. In: Annual Symposium of the American Medical Informatics Association. p. 989.

Detwiler, Landon T and Shaw, Marianne and Brinkley, James F (2010) Ontology View Query Management. In: Annual Symposium of the American Medical Informatics Association. p. 1023.

Brinkley, James F and Detwiler, Landon T (2010) Query chains for dynamic generation of value sets. In: Proceedings, Fall Symposium of the American Medical Informatics Association. p. 1699.

Nichols, Nolan and Perlmutter, Aaron and Mejino, Jose L V and Brinkley, James F (2010) Representing Neural Connectivity in the Foundational Model of Anatomy Ontology. In: Annual Symposium of the American Medical Informatics Association. p. 1196.

Shaw, Marianne and Detwiler, Landon T and Brinkley, James F and Suciu, Dan (2010) An application for creating and debugging vSPARQL view definitions. In: Proceedings AMIA Fall Symposium. p. 1251.

Rolfe, S. M. and Finney, L. and Tungaraza, R. F. and Guan, J. and Shapiro, L. G. and Brinkley, James F and Poliakov, A. and Kleinhans, N. and Alyward, E. (2009) An independent component analysis based tool for exploring functional connections in the brain. In: Proc. SPIE 7259, Medical Imaging 2009: Image Processing. p. 725921.

Franklin, Joshua D and Detwiler, Landon T and Brinkley, James F (2009) Lightweight distributed XML-based integration of translational data. In: Annual Symposium of the American Medical Informatics Association. p. 847.

Detwiler, Landon T and Shaw, Marianne and Cook, Daniel L and Gennari, John H and Brinkley, James F (2009) Post-Coordinating Orthogonal Ontologies for Data Annotation. In: Annual Symposium of the American Medical Informatics Association. p. 815.

Yang, S. and Atmosukarto, I. and Franklin, J. and Brinkley, James F and Suciu, D. and Shapiro, L. G. (2009) A model of multimodal fusion for medical applications. In: Proc. SPIE 7255: Multimedia Content Access: Algorithms and Systems III. SPIE 72550H.

Tungaraza, R. F. and Guan, J. and Rolfe, S. and Atmosukarto, I. and Poliakov, A. and Kleinhans, N. M. and Aylward, E. and Ojemann, J. and Brinkley, James F and Shapiro, L. G. (2009) A similarity retrieval method for functional magnetic resonance imaging (fMRI) statistical maps. In: Proc. SPIE 7259, Medical Imaging 2009: Image Processing. 72590E.

Guidry, Alicia F and Brinkley, James F and Anderson, Nicholas R and Tarczy-Hornoch, Peter (2008) Concept Mapping to Develop a Framework for Characterizing Electronic Data Capture (EDC) Systems. In: American Medical Informatics Association Fall Symposium. p. 960.

Mejino, Jose L V and Rubin, Daniel L and Brinkley, James F (2008) FMA-RadLex: An Application Ontology of Radiological Anatomy derived from the Foundational Model of Anatomy Reference Ontology. In: American Medical Informatics Association Fall Symposium. pp. 465-469.

Shaw, Marianne and Detwiler, Landon T and Brinkley, James F and Suciu, Dan and Mejino, Jose L V (2008) Generating Application Ontologies from Reference Ontologies. In: American Medical Informatics Association Fall Symposium. pp. 672-676.

Detwiler, Landon T and Suciu, Dan and Brinkley, James F (2008) Regular Paths in SparQL: Querying the NCI Thesaurus. In: American Medical Informatics Association Fall Symposium. pp. 161-165.

Atmosukarto, I. and Travillian, Ravensara S and Franklin, Joshua D and Shapiro, Linda G and Brinkley, James F and Suciu, Dan and Clark, J. I. and Cunningham, M.J. (2008) A Unifying Framework for Combining Content-Based Image Retrieval with Relational Database Queries for Biomedical Applications. In: Society of Imaging Informatics in Medicine Annual Symposium.

Franklin, Joshua D and Mejino, Jose L V and Detwiler, Landon T and Rubin, Daniel L and Brinkley, James F (2008) Web Service Access to Semantic Web Ontologies for Data Annotation. In: American Medical Informatics Association Fall Symposium. p. 946.

Brinkley, James F (2007) Imaging Informatics. In: Frontiers in Biomedical Imaging Science. p. 56.

Mejino, Jose L V and Martin, Richard F and Detwiler, Landon T and Brinkley, James F (2007) Challenges in Reconciling Different Views of Neuroanatomy in a Reference Ontology of Anatomy. In: American Medical Informatics Association Fall Symposium. p. 1046.

Yngve, Gary and Brinkley, James F and Cook, Daniel L and Shapiro, Linda G (2007) A Model Browser for Biosimulation. In: American Medical Informatics Association Fall Symposium. pp. 836-840.

Detwiler, Landon T and Brinkley, James F (2007) Querying Non-Materialized Ontology Views. In: American Medical Informatics Association Fall Symposium. p. 934.

Brinkley, James F and Ach, Daniel and Franklin, Joshua D and Anderson, Nicholas R and Stevens, Anne and Tarczy-Hornoch, Peter (2007) Tools for Clinical Trials Management: Handling the Norm and the Outliers. In: American Medical Informatics Association Fall Symposium. p. 5.

Li, Xiang and Gennari, John H and Brinkley, James F (2007) XGI: A Graphical Interface for XQuery Creation. In: American Medical Informatics Association Fall Symposium. pp. 453-457.

Detwiler, Landon T and Brinkley, James F (2006) Custom Views of Reference Ontologies. In: American Medical Informatics Association Fall Symposium. p. 909.

Fong, Christine and Brinkley, James F (2006) Customizable Electronic Laboratory Online (CELO): A Web-based Data Management System Builder for Biomedical Research Laboratories. In: American Medical Informatics Association Fall Symposium. p. 922.

Greenes, R. G. and Brinkley, James F (2006) Imaging Systems in Radiology, Chapter 18. In: Biomedical Informatics: Computer Applications in Health Care and Biomedicine (3rd edition). pp. 626-659.

Brinkley, James F and Greenes, R. G. (2006) Imaging and Structural Informatics, Chapter 9. In: Biomedical Informatics: Computer Applications in Health Care and Biomedicine (3rd edition). pp. 344-378.

Warren, Wayne and Agoncillo, Augusto V and Franklin, Joshua D and Brinkley, James F (2006) Intelligent web-based whole body visualization for anatomy education. In: American Medical Informatics Association Fall Symposium. p. 1136.

Brinkley, James F and Poliakov, Andrew V and Moore, Eider B and Detwiler, Landon T and Franklin, Joshua D and Corina, David P and Ojemann, George A (2006) Lightweight XML-based query, integration and visualization of distributed, multimodality brain imaging data. In: Society for Neuroscience Annual Meeting. 100.13.

Li, Hao and Gennari, John H and Brinkley, James F (2006) Model Driven Laboratory Information Management Systems. In: American Medical Informatics Association Fall Symposium. pp. 484-488.

Poliakov, Andrew V and Moore, Eider B and Brinkley, James F (2006) Software tools for batch processing, management and visualization of functional MRI data. In: Proceedings, 14th Annual Meeting of the International Society for Magnetic Resonance in Medicine. p. 620.

Brinkley, James F and Suciu, Dan and Detwiler, Landon T and Gennari, John H and Rosse, Cornelius (2006) A framework for using reference ontologies as a foundation for the semantic web. In: American Medical Informatics Association Fall Symposium. pp. 96-100.

Wang, Kelan and Tarczy-Hornoch, Peter and Shaker, Ron and Mork, Peter and Brinkley, James F (2005) BioMediator data integration: beyond genomics to neuroscience data. In: American Medical Informatics Association Fall Symposium. pp. 779-783.

Smith, Veronica S and Shapiro, Linda G and Hanlon, D. and Martin, Richard F and Brinkley, James F and Poliakov, Andrew V and Ojemann, George A and Corina, David P (2005) Evaluating spatial normalization methods for the human brain. In: 27th Annual Conference of the IEEE Engineering and Biology Society (EMBS). pp. 5331-5334.

Bales, Nathan and Brinkley, James F and Lee, E. Sally and Mathur, Shobhit and Re, Chris and Suciu, Dan (2005) A Framework for XML-based Integration of Data, Visualization and Analysis in a Biomedical Domain. In: XSym 2005. pp. 207-221.

Fong, Christine and Arnett, Ernest and Brinkley, James F and Clark, J. I. (2005) Image Management System for Correlation of Temporal and Spatial Variation in Mouse Lens Phenotype. In: Invest. Ophthalmol. Vis. Sci. E-Abstract 2910.

Warren, Wayne and Brinkley, James F (2005) Knowledge-Based, Interactive, Custom Anatomical Scene Creation for Medical Education: The Biolucida System. In: American Medical Informatics Association Fall Symposium. pp. 789-793.

Cho, Hansang and Corina, David P and Brinkley, James F and Ojemann, George A and Shapiro, Linda G (2005) A New Template Matching Method using Variance Estimation for Spike Sorting. In: IEEE EMBS Second International Neural Conference on Engineering.

Moore, Eider B and Poliakov, Andrew V and Brinkley, James F (2005) Web-enabled 3D Multimodality Brain Visualization in Java. In: Society for Neuroscience Annual Meeting. 570.2.

Jeng, S and Wang, Kelan and Barbero, J and Brinkley, James F and Tarczy-Hornoch, Peter (2005) A pilot bridging data integration and analytics: BioMediator and R. In: Proceedings American Medical Informatics Fall Symposium. p. 995.

Ojemann, George A and Schoenfield-McNeill, J and Lettich, E. and Oskin, N and Zanos, S and Panagiotides, H and Zamora, L and Sengupta, X and Corina, David P and Poliakov, Andrew V and Martin, Richard F and Brinkley, James F (2005) The relationship between fMRI, single neuronal activity, and local field potentials in human association cortex. In: Abstracts, Society for Neuroscience Annual Meeting. 814.9.

Martin, Richard F and Brinkley, James F and Hertzenberg, X. and Poliakov, Andrew V and Corina, David P and Ojemann, George A (2004) Anatomical Parcellation of Cortical Language Sites. In: MedInfo 2004. p. 1742.

Moore, Eider B and Poliakov, Andrew V and Brinkley, James F (2004) Brain Visualization in Java3D. In: MedInfo 2004. p. 1761.

Re, Chris and Brinkley, James F and Hinshaw, Kevin P and Suciu, Dan (2004) Distributed XQuery. In: Workshop on Information Integration on the Web (IIWeb). pp. 116-121.

Distelhorst, G. M. and Hinshaw, Kevin P and Rosse, Cornelius and Brinkley, James F (2004) An Improved Natural Language Interface to a Complex Anatomical Knowledge Base. In: MedInfo 2004. p. 1575.

Brinkley, James F and Corina, David P and Suciu, Dan and Poliakov, Andrew V and Martin, Richard F and Hinshaw, Kevin P and Moore, Eider B and Li, Hao and Hertzenberg, X. and Smith, Veronica S and Gibson, Erin K. and Re, Chris and Lettich, E. and Cho, Hansang and Shapiro, Linda G and Ojemann, George A (2004) Neuroinformatics Tools for Language Mapping. In: A Decade of Neuroscience Informatics: Looking Ahead. p. 66.

Fong, Christine and Rosse, Cornelius and Clark, J. I. and Shapiro, Linda G and Brinkley, James F (2004) An Ontology-based Image Repository for a Biomedical Research Lab. In: MedInfo 2004. p. 1598.

Detwiler, Landon T and Chung, Emily and Li, A. and Mejino, Jose L V and Agoncillo, Augusto V and Brinkley, James F and Rosse, Cornelius and Shapiro, Linda G (2004) A Relation-Centric Query Engine for the Foundational Model of Anatomy. In: MedInfo 2004. pp. 341-345.

Tang, Z. and Kadiyska, Y. and Suciu, Dan and Brinkley, James F (2004) Results Visualization in the XBrain XML Interface to a Relational Database. In: MedInfo 2004. p. 1878.

Li, Hao and Brinkley, James F and Gennari, John H (2004) Semi-automatic Database Design for Neuroscience Experiment Management Systems. In: MedInfo 2004. p. 1717.

Hertzenberg, X. and Poliakov, Andrew V and Brinkley, James F (2004) Unobtrusive Integration of Data Management with fMRI Analysis. In: MedInfo 2004. p. 1639.

Poliakov, Andrew V and Moore, Eider B and Brinkley, James F (2004) Use of Remote Surface Based Tools for Visualizing Integrated Brain Imaging Data. In: MedInfo 2004. p. 1814.

Hertzenberg, X. and Poliakov, Andrew V and Corina, David P and Ojemann, George A and Brinkley, James F (2004) X-Batch: Embedded data management for fMRI analysis. In: Abstracts, Society for Neuroscience Annual Meeting. 694.21.

Brinkley, James F and Jakobovits, Rex M and Poliakov, Andrew V and Martin, Richard F and Gibson, E.R. and Corina, David P and Ojemann, George A (2004) An experiment management system for cortical stimulation mapping data. In: Society for Neuroscience Annual Meeting. 1032.12.

Tang, Z. and Kadiyska, Y. and Li, Hao and Suciu, Dan and Brinkley, James F (2003) Dynamic XML Based Exchange of Relational Data: Application to the Human Brain Project. In: American Medical Informatics Association Fall Symposium. pp. 649-653.

Detwiler, Landon T and Mejino, Jose L V and Rosse, Cornelius and Brinkley, James F (2003) Efficient Web-Based Navigation of the Foundational Model of Anatomy. In: American Medical Informatics Association Fall Symposium. p. 829.

Martin, Richard F and Rickard, K. and Mejino, Jose L V and Agoncillo, Augusto V and Brinkley, James F and Rosse, Cornelius (2003) The Evolving Neuroanatomical Component of the Foundational Model of Anatomy. In: American Medical Informatics Association Fall Symposium. p. 927.

Distelhorst, G. M. and Srivastava, V. and Rosse, Cornelius and Brinkley, James F (2003) A Prototype Natural Language Interface to a Large Complex Knowledge Base, the Foundational Model of Anatomy. In: American Medical Informatics Association Fall Symposium. pp. 200-204.

Poliakov, Andrew V and Moore, Eider B and Corina, David P and Brinkley, James F (2003) Software tools for visualization of multimodality brain data for language mapping. In: Proceedings, Society for Neuroscience Annual Meeting. 428.16.

Mork, Peter and Suciu, Dan and Brinkley, James F and Rosse, Cornelius (2002) A Declarative Query Interface for Large Semantic Networks. In: American Medical Informatics Association Fall Symposium. p. 1110.

Brinkley, James F and Jakobovits, Rex M and Rosse, Cornelius (2002) An Online Image Management System for Anatomy Teaching. In: American Medical Informatics Association Fall Symposium. p. 983.

Jakobovits, Rex M and Brinkley, James F and Rosse, Cornelius and Weinberger, E. (2001) Enabling Clinicians, Researchers, and Educators to Build Custom Web-Based Biomedical Information Systems. In: American Medical Informatics Association Fall Symposium. pp. 279-283.

Martin, Richard F and Mejino, Jose L V and Bowden, D. M. and Brinkley, James F and Rosse, Cornelius (2001) Foundational Model of Neuroanatomy: Implications for the Human Brain Project. In: American Medical Informatics Association Fall Symposium. pp. 438-442.

Lober, W. B. and Trigg, L. J. and Bliss, D. and Brinkley, James F (2001) IML: An Image Markup Language. In: American Medical Informatics Association Fall Symposium. pp. 403-407.

Kinbar, K. and Martin, Richard F and Hill, J. and Mulligan, K. and Poliakov, Andrew V and Brinkley, James F and Ojemann, George A and Corina, David P (2001) Naming Deficits During Cortical Stimulation Mapping: Functional Specificity Reconsidered. In: 8th Annual Meeting, Cognitive Neuroscience Society (CMS). p. 126.

Martin, Richard F and Mejino, Jose L V and Bowden, D. M. and Brinkley, James F and Mulligan, K. and Rosse, Cornelius (2001) A Next Generation Knowledge Source: Foundational Model of Neuroanatomy. In: Society for Neuroscience Annual Meeting. 23.48.

Mejino, Jose L V and Noy, N. F. and Musen, M. A. and Brinkley, James F and Rosse, Cornelius (2001) Representation of Structural Relationships in the Foundational Model of Anatomy. In: American Medical Informatics Association Fall Symposium. p. 973.

Poliakov, Andrew V and Albright, Evan M and Corina, David P and Ojemann, George A and Martin, Richard F and Brinkley, James F (2001) Server-Based Approach to Web Visualization of Integrated 3-D Brain Mapping Data. In: Thirty-First Annual Meeting, Society for Neuroscience. 529.1.

Poliakov, Andrew V and Albright, Evan M and Corina, David P and Ojemann, George A and Martin, Richard F and Brinkley, James F (2001) Server-Based Approach to Web Visualization of Integrated 3-D Medical Image Data. In: American Medical Informatics Association Fall Symposium. pp. 533-537.

Campbell, B. and Brinkley, James F and Rosse, Cornelius (2001) The Virtual Anatomy Lab: a Hands-On Anatomy Learning Environment. In: MedVR 2001. pp. 85-87.

Campbell, B and Rosse, Cornelius and Brinkley, James F (2001) The Virtual Anatomy Lab: a hands-on anatomy learning environment. In: Proceedings, Medicine Meets Virtual Reality 2001. IOS Press, Amsterdam pp. 85-87.

Corina, David P and Poliakov, Andrew V and Steury, K. and Martin, Richard F and Brinkley, James F and Mulligan, K. A. and Ojemann, George A (2000) Correspondences between Language Cortex Identified by Cortical Stimulation Mapping and FMRI. In: Neuroimage, Human Brain Mapping Annual Meeting. S295.

Martin, Richard F and Poliakov, Andrew V and Mulligan, K. A. and Kinbar, K. and Corina, David P and Maravilla, K. and Lettich, E. and Ojemann, George A and Brinkley, James F (2000) Multi-Patient Mapping of Language Sites on 3-D Brain Models. In: Abstracts, 30th Annual Meeting, Society for Neuroscience. 464.20.

Martin, Richard F and Poliakov, Andrew V and Mulligan, K. A. and Corina, David P and Ojemann, George A and Brinkley, James F (2000) Multi-Patient Mapping of Language Sites on 3-D Brain Models. In: Neuroimage, Human Brain Mapping Annual Meeting. S534.

Lober, W. B. and Brinkley, James F (2000) A Personal Annotated Image Server. In: JAMIA Supplement, Fall 2000 Annual Symposium. p. 1068.

Jakobovits, Rex M and Soderland, S. and Taira, R. K. and Brinkley, James F (2000) Requirements of a Web-Based Experiment Management System. In: American Medical Informatics Association Fall Symposium. pp. 374-378.

Poliakov, Andrew V and Jakobovits, Rex M and Martin, Richard F and Corina, David P and Brinkley, James F (2000) Software Tools for Visualization and Analysis of Human Brain Data for Language Mapping. In: Neuroimage, Human Brain Mapping Annual Meeting. S907.

Brinkley, James F and Albright, Evan M and Kim, S. and Mejino, Jose L V and Shapiro, Linda G and Rosse, Cornelius (2000) Visible Human, Construct Thyself: The Digital Anatomist Dynamic Scene Generator. In: Visible Human Project Conference 2000. National Library of Medicine pp. 27-28.

Rosse, Cornelius and Mejino, Jose L V and Shapiro, Linda G and Brinkley, James F (2000) Visible Human, Know Thyself: The Digital Anatomist Structural Abstraction. In: Visible Human Project Conference 2000. National Library of Medicine pp. 85-86.

Jakobovits, Rex M and Soderland, S. G. and Tiara, R. K. and Brinkley, James F (2000) The Web-Interfacing Repository Manager: A Framework for Developing Web-Based Multimedia Applications for Medical Research. In: International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences. pp. 527-533.

Lober, W. B. and Brinkley, James F (2000) XML-Based Image Annotation: PAIS - a Personal Annotated Image Server. In: Slice of Life 2000.

Bowden, D. M. and Robertson, J. E. and Martin, Richard F and Dubach, M. F. and Wu, J. S. and McLean, M. R. and Brinkley, James F (1999) BrainInfo: A primate brain atlas & neuroanatomic resource based on geographic information systems (GIS) software. In: Abstracts, Society for Neuroscience Annual Meeting. 47.23.

Kalet, Ira J and Wu, J. and Lease, M. and Austin-Seymour, M. M. and Brinkley, James F and Rosse, Cornelius (1999) Anatomical Information in Radiation Treatment Planning. In: American Medical Informatics Association Fall Symposium. pp. 291-295.

Corina, David P and Steury, K. R. and Mulligan, K. A. and Hinshaw, Kevin P and Poliakov, Andrew V and Brinkley, James F and Maravilla, K. R. and Ojemann, George A (1999) A Comparison of Language Cortex Indentified by Cortical Stimulation Mapping and FMRI Techniques. In: Abstracts, Society for Neuroscience Annual Meeting. 654.2.

Kim, S. and Brinkley, James F and Rosse, Cornelius (1999) Design Features of on-Line Anatomy Information Resources: A Comparison with the Digital Anatomist. In: American Medical Informatics Association Fall Symposium. pp. 560-564.

Stalder, D. S. and Brinkley, James F (1999) The Digital Anatomist Foundational Model Server. In: Perl Conference 3.0.

Poliakov, Andrew V and Hinshaw, Kevin P and Corina, David P and Steury, K. R. and Maravilla, K. R. and Ojemann, George A and Mulligan, K. A. and Brinkley, James F (1999) Integration and Visualization of Multimodality Brain Data for Language Mapping. In: Abstracts, Society for Neuroscience Annual Meeting. 654.1.

Poliakov, Andrew V and Hinshaw, Kevin P and Rosse, Cornelius and Brinkley, James F (1999) Integration and Visualization of Multimodality Brain Data for Language Mapping. In: American Medical Informatics Association Fall Symposium. pp. 349-353.

Lober, W. B. and Brinkley, James F (1999) A Portable Image Annotation Tool for Web-Based Anatomy Atlases. In: American Medical Informatics Association Fall Symposium. p. 1108.

Hahn, J. S. and Burnside, E. and Brinkley, James F and Rosse, Cornelius and Musen, M. A. (1999) Representing the Digital Anatomist Foundational Model as a Protege Ontology. In: American Medical Informatics Association Fall Symposium. p. 1070.

Wong, B. A. and Rosse, Cornelius and Brinkley, James F (1999) Semi-Automatic Scene Generation Using the Digital Anatomist Foundational Model. In: American Medical Informatics Association Fall Symposium. pp. 637-641.

Bowden, D. M. and Robertson, J. E. and Martin, Richard F and Dubach, M. F. and Wu, J. S. and McLean, M. R. and Brinkley, James F (1999) Web-Tools for Neuroscience Based on Neuronames, a Template Brain Atlas, Edgewarp and Geographic Information Systems Software. In: Fifth International Conference on Functional Mapping of the Human Brain.

Rosse, Cornelius and Shapiro, Linda G and Brinkley, James F (1998) The Digital Anatomist Foundational Model: Principles for Defining and Structuring Its Concept Domain. In: American Medical Informatics Association Fall Symposium. pp. 820-824.

Wong, B. A. and Brinkley, James F (1998) Dynamic 3-D Scene Navigation in Web-Based Anatomy Atlases. In: Proceedings, American Medical Informatics Association Fall Symposium. p. 1100.

Hinshaw, Kevin P and Brinkley, James F (1998) Incorporating Constraint-Based Shape Models into an Interactive System for Functional Brain Mapping. In: American Medical Informatics Association Fall Symposium. American Medical Informatics Association pp. 921-925.

Corina, David P and McBurney, S. L. and Hinshaw, Kevin P and Brinkley, James F and Lettich, E. and Ojemann, George A (1998) Left Hemisphere Specialization for American Sign Language: A Cortical Stimulation Study. In: Abstracts, Society for Neuroscience Annual Meeting. 15.4.

Jakobovits, Rex M and Brinkley, James F (1998) Query-by-Context: A Framework for Modelling and Navigating Multimedia Research Data. In: American Medical Informatics Association Fall Symposium. p. 1021.

Brinkley, James F and Rosse, Cornelius (1998) Requirements for an on-Line Knowledge-Based Anatomy Information System. In: American Medical Informatics Association Fall Symposium. pp. 892-896.

Brinkley, James F (1998) The Use of Anatomical Knowledge in Medical Imaging: An Overview of the University of Washington Structural Informatics Group. In: Advances in Biomedical Image Databases. Kluwer Academic Press pp. 89-116.

Modayur, Bharath R and Jakobovits, Rex M and Maravilla, K. and Ojemann, George A and Brinkley, James F (1997) Evaluation of a Visualization-Based Approach to Functional Brain Mapping. In: American Medical Informatics Association Fall Symposium. pp. 429-433.

Modayur, Bharath R and Ojemann, George A and Lettich, E. and Jakobovits, Rex M and Sundsten, John W and Brinkley, James F (1997) Information System for Mapping and Studying Cortical Language Organization. In: Abstracts, Society for Neuroscience Annual Meeting. p. 2228.

Jakobovits, Rex M and Brinkley, James F (1997) Managing Medical Research Data with a Web-Interfacing Repository Manager. In: American Medical Informatics Association Fall Symposium. pp. 454-458.

Hinshaw, Kevin P and Brinkley, James F (1997) Shape-Based Interactive Three-Dimensional Medical Image Segmentation. In: SPIE Medical Imaging: Image Processing. pp. 236-242.

Brinkley, James F and Myers, L. M. and Prothero, J. S. and Heil, G. H. and Tsuruda, J. S. and Maravilla, K. R. and Ojemann, George A and Rosse, Cornelius (1997) A Structural Information Framework for Brain Mapping. In: Neuroinformatics: An Overview of the Human Brain Project. Lawrence Erlbaum pp. 309-334.

Hinshaw, Kevin P and Brinkley, James F (1997) Using 3-D Shape Models to Guide Segmentation of MR Brain Images. In: American Medical Informatics Association Fall Symposium. American Medical Informatics Association pp. 469-473.

Modayur, Bharath R and Prothero, J. and Rosse, Cornelius and Jakobovits, Rex M and Brinkley, James F (1996) Visualization and Mapping of Neurosurgical Functional Data onto a 3-D MR-Based Model of the Brain Surface. In: 1996 AMIA Fall Symposium. pp. 304-308.

Jakobovits, Rex M and Modayur, Bharath R and Brinkley, James F (1996) A Web-Based Repository Manager for Brain Mapping Data. In: American Medical Informatics Association Fall Symposium. pp. 309-313.

Graney, D. and Conley, D. and Sundsten, John W and Ratiu, P. and Rauschning, Wolfgang and Brinkley, James F and Rosse, Cornelius (1995) Digital Anatomist Interactive Atlases. In: Journal of Clinical Anatomy. p. 213.

Brinkley, James F and Eno, Kraig R and Sundsten, John W and Conley, D. M. and Rosse, Cornelius (1995) A Distributed Framework for Distance Learning in Anatomy: The Digital Anatomist Interactive Atlas. In: 19th Symposium on Computer Applications in Medical Care. p. 972.

Rosse, Cornelius and Said, M. Ben and Eno, Kraig R and Brinkley, James F (1995) Enhancements of Anatomical Information in UMLS Knowledge Sources. In: 19th Annual Symposium on Computer Applications in Medical Care. pp. 873-877.

Hinshaw, Kevin P and Altman, R. B. and Brinkley, James F (1995) Shape-Based Models for Interactive Segmentation of Medical Images. In: SPIE Medical Imaging 1995: Image Processing. pp. 771-780.

Myers, L. M. and Brinkley, James F (1995) Visualization of Brain Surface Features Using Registered Partially Segmented MRI Scans. In: SPIE Medical Imaging: Image Display. pp. 43-52.

Myers, L. M. and Prothero, J. S. and Brinkley, James F (1995) Volume Rendering of Multi-Spectral MR Data for Brain Language Site Mapping. In: Advanced Visual Systems User Conference. pp. 471-480.

Bradley, S. W. and Rosse, Cornelius and Brinkley, James F (1995) Web-Based Access to an Online Atlas of Anatomy: The Digital Anatomist Common Gateway Interface. In: 19th Symposium on Computer Applications in Medical Care. pp. 512-516.

Brinkley, James F (1994) The Digital Anatomist Project. In: American Association for the Advancement of Science, Annual Meeting. p. 6.

Brinkley, James F (1994) A Distributed, Object-Oriented Framework for Medical Image Management and Analysis: Application to Evaluation of Medical Image Segmentation Techniques. In: IEEE Workshop on Biomedical Image Analysis. IEEE Computer Society Press pp. 194-203.

Brinkley, James F (1994) Educational Systems:Synopsis. In: Yearbook of Medical Informatics. American Medical Informatics Association pp. 465-467.

Dailey, D. J. and Eno, Kraig R and Brinkley, James F (1994) Performance Evaluation of a Distance Learning Program. In: 18th Annual Symposium on Computer Applications in Medical Care. pp. 76-80.

Shapiro, Linda G and Tanimoto, S. L. and Brinkley, James F and Ahrens, J. P. and Jakobovits, Rex M and Lewis, L. M. (1994) A Visual Database System for Data and Experiment Management in Model-Based Computer Vision. In: Proceedings of the Second Cad-Based Vision Workshop. pp. 64-72.

Shapiro, Linda G and Tanimoto, S. L. and Brinkley, James F (1993) Design of a visual database system for computer vision research. In: Proc. Workshop on Advances in Data Management for the Scientist and Engineer.

Sundsten, John W and Brinkley, James F and Eno, Kraig R (1993) Digital Anatomist Browser: Teaching Neuroanatomy with the Use of Digital and Video-Disc Images Accessed by Computer. In: Annual Meeting of American Association of Anatomists.

Conley, D. M. and Brinkley, James F and Rauschning, Wolfgang and Rosse, Cornelius (1993) A Multimedia Approach to the Study of the Mediastinum Utilizing a Computer-Generated Three-Dimensional Model. In: Proceedings, Annual Meeting of the American Association of Anatomists.

Dailey, D. J. and Eno, Kraig R and Zick, G. L. and Brinkley, James F (1993) A Network Model for Wide Area Access to Structural Information. In: 17th Symposium on Computer Applications in Medical Care. pp. 497-501.

Brinkley, James F (1993) The Potential for Three-Dimensional Ultrasound. In: Ultrasound in Obstetrics and Gynecology. Little, Brown and Company

Altman, R. B. and Brinkley, James F (1993) Probabilistic Constraint Satisfaction with Structural Models: Application to Organ Modelling by Radial Contours. In: 17th Symposium on Computer Applications in Medical Care. pp. 492-497.

Brinkley, James F (1992) Hierarchical Geometric Constraint Networks as a Representation for Spatial Structural Knowledge. In: 16th Annual Symposium on Computer Applications in Medical Care. pp. 140-144.

Brinkley, James F (1991) Spatial anatomic knowledge for 2-D interactive medical image segmentation and matching. In: Proceedings, 15th Annual Symposium on Computer Applications in Medical Care. pp. 460-464.

Brinkley, James F (1991) Semiautomatic medical image segmentation using knowledge of anatomic shape. In: Medical Imaging V: Image Processing. pp. 78-87.

Sundsten, John W and Brinkley, James F and Eno, Kraig R and Harris, R. M. and Kastella, K. G. (1991) Interactive Use of Videodisc Animations of Computer-Reconstructed Human Brain. In: Abstracts, Annual Meeting, Society for Neuroscience.

Eno, Kraig R and Sundsten, John W and Brinkley, James F (1991) A Multimedia Anatomy Browser Incorporating a Knowledge Base and 3-D Images. In: Symposium on Computer Applications in Medical Care. pp. 727-731.

Brinkley, James F (1990) Towards a knowledge base of structural biology. In: Proceedings, 1990 Spring Symposium Series: Artificial Intelligence in Medicine. American Association for Artificial Intelligence, Stanford University, Stanford University pp. 24-25.

Duncan, B. S. and Brinkley, James F and Altman, R. B. and Buchanan, B. G. and Jardetzky, O. (1990) Artificial Intelligence Techniques and NMR Spectroscopy: Application to the Structure of Proteins in Solution. In: NMR: Principles and Applications to Biomedical Research. pp. 99-123.

Greenes, R. G. and Brinkley, James F (1990) Radiology Applications. In: Medical Informatics: Computer Applications in Health Care. Addison Wesley pp. 324-365.

Rosse, Cornelius and Brinkley, James F and Prothero, J. (1990) Structural Informatics: The Representation of Anatomical Knowledge in Computer Readable Form. In: First Annual Educational and Research Conference. pp. 37-38.

Wiederhold, G and Brinkley, James F and Samadini, R and Clauer, C (1989) Model-driven image analysis to augment databases. In: Visual Database Systems, Proceeedings of the IFIP TC 2/WG 2.6 Working Conference on Visual Database Systems. Elsevier Science Publishers, Tokyo, Japan pp. 159-180.

Brinkley, James F and Prothero, J. S. and Prothero, John W and Rosse, Cornelius (1989) A Framework for the Design of Knowledge-Based Systems in Structural Biology. In: 15th Annual Symposium on Computer Applications in Medical Care. pp. 61-65.

Brinkley, James F and Prothero, John W (1989) Towards a knowledge-based system of structural biology. In: Eng. Med. Biol. 11th Annual Conference. pp. 1841-1842.

Jardetzky, O. and Lichtarge, Olivier and Brinkley, James F and Madrid, M (1989) The structure of proteins and their binding sites: NMR and artificial intelligence. In: Computer-Assisted Modeling of Receptor-Ligand Interactions. Alan R. Liss, Inc pp. 145-156.

Altman, R. B. and Duncan, B. S. and Brinkley, James F and Buchanan, B. G. and Jardetzky, O. (1988) Determination of the spatial distribution of protein structure using solution data. In: Proceedings of Alfred Benzon Symposium 26: NMR Spectroscopy in Research,. pp. 209-232.

Hayes-Roth, Barbara and Buchanan, B. G. and Lichtarge, Olivier and Hewett, Micheal and Altman, R. B. and Brinkley, James F and Cornelius, Craig and Duncan, B. S. and Jardetzky, O. (1988) Elucidating protein structure from constraints in PROTEAN. In: Blackboard Systems. Addison-Wesley, Menlo Park, CA pp. 417-431.

Brinkley, James F (1988) Representing Biologic Objects as Geometric Constraint Networks. In: AAAI Spring Symposium Series: Artificial Intelligence in Medicine. pp. 7-8.

Brinkley, James F and Carrara, Enrico and Jardetzky, O. (1988) A flexible software framework for protein structure determination from constraints. In: International Council on Magnetic Resonance in Biological Systems XIII. P11-14.

Brinkley, James F (1987) Representing Biologic Objects as Geometric Constraint Networks. In: Artificial Intelligence in Medicine Workshop.

Hayes-Roth, Barbara and Buchanan, B. G. and Lichtarge, Olivier and Hewett, Micheal and Altman, R. B. and Brinkley, James F and Cornelius, Craig and Duncan, B. S. and Jardetzky, O. (1986) PROTEAN: Deriving protein structure from constraints. In: Proceedings of the Fifth National Conference on Artificial Intelligence. American Association for Artificial Intelligence, Philadelphia, Pennsylvania pp. 904-909.

Brinkley, James F (1983) Learned shape knowledge in ultrasonic three-dimensional organ modelling. In: Symposium on Computer Applications in Medical Care.

Brinkley, James F (1983) Artificial intelligence and ultrasonic imaging: the use of learned shape knowledge to analyze 3D data. In: Proceedings, 28th Annual Meeting, AIUM. p. 71.

Brinkley, James F and McCallum, W D (1982) Organ volume determination by ultrasonic three-dimensional reconstruction. In: Proceedings of the First AMIA Congress on Medical Informatics. American Medical Informatics Association, San Francisco pp. 178-182.

Brinkley, James F and McCallum, W D and Muramatsu, S K and Liu, D.K. (1982) The use of ultrasonic three-dimensional volume measurements in the estimation of fetal weight. In: Proceedings of the 29th Annual Meeting, Society for Gynecologic Investigation. p. 6.

Brinkley, James F and McCallum, W D and Muramatsu, S K (1980) Three-dimensional display of fetus, placenta and uterus using an ultrasonic computer modelling system. In: Proceedings of the 25th Annual Conference, AIUM. p. 98.

Brinkley, James F and McCallum, W D and Daigle, R.E. (1979) A distributed computer system for fetal weight determination. In: Proceedings of the 24th Annual Conference, AIUM. p. 113.

Brinkley, James F and Moritz, W. E. and Baker, D. W. (1978) A Technique for Imaging Three-Dimensional Structures and Computing their Volumes Using Non-Parallel Ultrasonic Sector Scans. In: Ultrasound in Medicine. Springer, Boston pp. 471-474.

McCallum, W D and Brinkley, James F (1977) Fetal weight estimation from single and multiple ultrasonic measurements. In: 22nd Annual Conference of the American Institute of Ultrasound in Medicine. p. 33.

Brinkley, James F and Moritz, W. E. and Baker, D. W. (1977) A technique for imaging three-dimensional structures and computing their volumes using non-parallel ultrasonic sector scans. In: Abstracts, 22nd Annual Conference of the American Institute of Ultrasound in Medicine, Dallas, October, 1977. p. 63.

Lee, E. Sally and Suciu, Dan and Brinkley, James F Automatic XQuery Generation and Generalized Visualization for an XML Interface to a Relational Database. In: Proceedings Fall AMIA Symposium. p. 1019.

Tarczy-Hornoch, Peter and Brinkley, James F and Shaker, R. and Mork, Peter and Donelson, L and Barrier, M and Gennari, John H and Rosse, Cornelius and Rossini, A and Suciu, Dan and Halevy, A. Bio-PDMS: A structural ontology driven peer data management system (PDMS) for biology. In: Biomedical Information Science and Technology Initiative (BISTI) Symposium.

Rubin, D.L. and Greenspan, H. and Brinkley, James F Biomedical Imaging Informatics, Chapter 9. In: Biomedical Informatics: Computer Applications in Health Care and Biomedicine (4th edition). pp. 285-327.

Smith, Veronica S and Hanlon, D. and Martin, Richard F and Poliakov, Andrew V and Brinkley, James F and Shapiro, Linda G and Van Essen, DC and Ojemann, George A and Corina, David P Evaluating anatomical normalization methods. In: Abstracts, Society for Neuroscience Annual Meeting. 12.11.

Greenes, R. G. and Brinkley, James F Imaging Systems, Chapter 14. In: Medical Informatics: Computer Applications in Health Care (2nd edition). pp. 485-538.

Monograph

Detwiler, Landon T and Mejino, Jose L V and Brinkley, James F (2015) From Frames to OWL2: Converting the Foundational Model of Anatomy and the Ontology of Craniofacial Development and Malformation. Technical Report. (Unpublished)

Re, Chris and Brinkley, James F and Suciu, Dan (2006) A performant XQuery to SQL translator. Technical Report. (Unpublished)

Brinkley, James F and Buchanan, B. G. and Altman, R. B. and Duncan, B. S. and Cornelius, Craig (1987) A heuristic refinement method for spatial constraint satisfaction problems. Technical Report.

Brinkley, James F and Cornelius, Craig and Altman, R. B. and Hayes-Roth, Barbara and Lichtarge, Olivier and Duncan, B. S. and Buchanan, B. G. and Jardetzky, O. (1986) Application of constraint satisfaction techniques to the determination of protein tertiary structure. Technical Report.

Buchanan, B. G. and Hayes-Roth, Barbara and Lichtarge, Olivier and Altman, R. B. and Brinkley, James F and Hewett, Micheal and Cornelius, Craig and Duncan, B. S. and Jardetzky, O. (1986) The heuristic refinement method for deriving solution structures of proteins. Technical Report.

Brinkley, James F (1984) Ultrasonic three-dimensional organ modelling. Technical Report.