|
|
|
Publications
Return to Publication Home
Publications by Daniel L. Rubin, M.D., M.S.
There are 54 publications that list Daniel L. Rubin as an author.
 - BMIR-2011-1441
- The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research.
- J. Tenenbaum, T. Whetzel, K. Anderson, C. D. Borromeo, I. D. Dinov, D. Gabriel, B. Kirschner, B. Mirel, T. Morris, N. F. Noy, C. I. Nyulas, D. Rubenson, P. R. Saxman, H. Singh, N. Whelan, Z. Wright, B. D. Athey, M. J. Becich, G. S. Ginsburg, M. A. Musen, K. A. Smith, A. F. Tarantal, D. L. Rubin, P. Lyster
- Journal of Biomedical Informatics, J Biomed Inform., 44, 1, 137-145. Published in 2011
- BMIR-2011-1363
- A Practical Method for Transforming Free-Text Eligibility Criteria into Computable Criteria
- S. W. Tu, M. Peleg, S. Carini, M. Bobak, J. Ross, D. L. Rubin, I. Sim
- Journal of Biomedical Informatics, JBI, 44, 2, 239-250. Published in 2011
- BMIR-2009-1437
- Computational neuroanatomy: ontology-based representation of neural components and connectivity
- D. L. Rubin, I. Talos, M. A. Musen, R. Kikinis, M. Halle
- The First Summit on Translational Bioinformatics 2008, San Francisco, CA, BMC Bioinformatics, 10(Suppl 2), S3. Published in 2009
- BMIR-2009-1408
- Annotation and Image Markup: Accessing and Interoperating with the Semantic Content in Medical Imaging
- D. L. Rubin, K. S. Supekar, P. Mongkolwat, V. Kleper, D. S. Channin
- IEEE Intelligent Systems, 24, 1, 57-65. Published in 2009
- BMIR-2009-1398
- Comparison of Concept Recognizers for building the Open Biomedical Annotator
- N. H. Shah, B. Nipun, C. Jonquet, A. P. Chiang, D. L. Rubin, M. A. Musen
- BMC Bioinformatics, 10, (Suppl 9):S14. Published in 2009
- BMIR-2009-1389
- The caBIG Annotation and Image Markup Project.
- D. S. Channin, P. Mongkolwat, V. Kleper, K. S. Supekar, D. L. Rubin
- Journal of Digial Imaging, March. Published in 2009
- BMIR-2009-1387
- BioPortal: ontologies and integrated data resources at the click of a mouse
- N. F. Noy, N. H. Shah, T. Whetzel, B. Dai, M. V. Dorf, N. B. Griffith, C. Jonquet, M. A. Storey, C. G. Chute, D. L. Rubin, M. A. Musen
- Nucleic Acids Research, 37, Web Server Issue. Published in 2009
 - BMIR-2009-1380
- Semantic Reasoning with Image Annotations for Tumor Assessment
- M. Levy, M. J. O'Connor, D. L. Rubin
- AMIA Annual Symposium, San Francisco, CA. Published in 2009
- BMIR-2008-1332
- Comparing Concept Recognizers for Ontology-Based Indexing: MGREP vs. MetaMap
- N. Bathia, N. H. Shah, A. P. Chiang, D. L. Rubin, M. A. Musen
- . Published in 2008
- BMIR-2008-1319
- Network Analysis of Intrinsic Functional Brain Connectivity in Alzheimer's Disease
- K. S. Supekar, V. Menon, M. A. Musen, D. L. Rubin, M. Greicius
- Public Library of Science-Computational Biology., PLoS Computational Biology, June 2008. Published in 2008
- BMIR-2008-1315
- Medical Imaging on the Semantic Web: Annotation and Image Markup
- D. L. Rubin, P. Mongkolwat, V. Kleper, K. S. Supekar, D. S. Channin
- AAAI Spring Symposium Series, Semantic Scientific Knowledge Integration, Stanford. Published in 2008
- BMIR-2008-1298
- BioPortal: A Web Portal to Biomedical Ontologies
- D. L. Rubin, D. de Abreu Moreira, P. P. Kanjamala, M. A. Musen
- AAAI Spring Symposium Series, Symbiotic Relationships between Semantic Web and Knowledge Engineering, Stanford University, (in press). Published in 2008
 - BMIR-2008-1288
- Biomedical ontologies: a functional perspective
- D. L. Rubin, N. H. Shah, N. F. Noy
- Briefings in Bioinformatics, 9, 1, 75-90. Published in 2008
- BMIR-2007-1314
- Knowledge Zone: a public repository of peer-reviewed biomedical ontologies.
- K. S. Supekar, D. L. Rubin, N. F. Noy, M. A. Musen
- MEDINFO, Brisbane, Australia, 812-6. Published in 2007
 - BMIR-2007-1291
- A prototype symbolic model of canonical functional neuroamatomy of the motor system
- I. Talos, D. L. Rubin, M. Halle, M. A. Musen, R. Kikinis
- Journal of Biomedical Informatics, doi:10.1016/j.jbi.2007.11.003, (in press). Published in 2007
- BMIR-2007-1263
- Use of microcalcification descriptors in BI-RADS 4th edition to stratify risk of malignancy
- E. S. Burnside, J. E. Ochsner, K. J. Fowler, J. P. Fine, L. R. Salkowski, D. L. Rubin, G. A. Sisney
- Radiology, 242, 2, 388-395. Published in 2007
- BMIR-2007-1262
- Using annotations from controlled vocabularies to find meaningful associations
- W. Lee, L. Raschid, P. Srinivasan, N. H. Shah, D. L. Rubin, N. F. Noy
- Lecture Notes in Bioinformatics, LNBI, 4544, 247-263. Published in 2007
- BMIR-2007-1261
- Protege: A Tool for Managing and Using Terminology in Radiology Applications
- D. L. Rubin, N. F. Noy, M. A. Musen
- Journal of Digital Imaging, J Digit Imaging. Published in 2007
 - BMIR-2007-1249
- Annotation and query of tissue microarray data using the NCI Thesaurus
- N. H. Shah, D. L. Rubin, I. Espinosa, K. Montgomery, M. A. Musen
- BMC Bioinformatics, 8, 296. Published in 2007
- BMIR-2007-1234
- Translating the Foundational Model of Anatomy into OWL
- N. F. Noy, D. L. Rubin
- Journal of Web Semantics, 6, 2. Published in 2007
- BMIR-2006-1266
- Bayesian Network to Predict Breast Cancer Risk of Mammographic Microcalcifications and Reduce Number of Benign Biopsy Results: Initial Experience
- E. S. Burnside, J. P. Fine, R. Shachter, G. A. Sisney, D. L. Rubin, W. K. Leung
- Radiology, 240, 3, 666-673. Published in 2006
- BMIR-2006-1265
- An Ontology for PACS Integration
- C. E. Kahn Jr., D. S. Channin, D. L. Rubin
- Journal of Digital Imaging, J Digit Imaging. Published in 2006
- BMIR-2006-1264
- Ontology-Based Representation of Simulation Models of Physiology
- D. L. Rubin, D. Grossman, M. Neal, D. L. Cook, J. B. Bassingthwaighte, M. A. Musen
- AMIA Annual Symposium, Proc AMIA Symp, 664-668. Published in 2006
- BMIR-2006-1233
- Ontology-based Annotation and Query of Tissue Microarray Data
- N. H. Shah, K. S. Supekar, D. L. Rubin, M. A. Musen
- AMIA Annual Symposium, Washington DC, AMIA, 709-713. Published in 2006
- BMIR-2006-1148
- A Bayesian Network to Assist Mammography Interpretation
- D. L. Rubin, E. S. Burnside, R. Shachter
- Handbook of Operations Research and Health Care: Methods and Applications, Sainfort, F., Brandeau, M.L., and W.P. Pierskalla, Eds., Kluwer Academic Publishers. Published in 2006
- BMIR-2006-1119
- Using ontologies linked with geometric models to reason about penetrating injuries.
- D. L. Rubin, O. Dameron, Y. Bashir, D. Grossman, P. Dev, M. A. Musen
- Artificial Intelligence in Medicine, AIIM, 37, 3, 167 - 176. Published in 2006
- BMIR-2006-1118
- The National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge.
- D. L. Rubin, N. F. Noy, J. D. Richter, B. Smith, M. A. Storey, H. Solbrig, C. G. Chute, I. Sim, M. Ashburner, M. Westerfield, S. Misra, C. J. Mungall, S. E. Lewis, M. A. Musen
- OMICS: A Journal of Integrative Biology, 10, 2, 185-198. Published in 2006
- BMIR-2005-1267
- Using Petri Net tools to study properties and dynamics of biological systems
- M. Peleg, D. L. Rubin, R. B. Altman
- J Am Med Inform Assoc., JAMIA, 12, 181–199. Published in 2005
- BMIR-2005-1115
- Using OWL and Description Logics based classification for reasoning in biomedical applications.
- D. L. Rubin, O. Dameron, M. A. Musen
- 8th International Protégé Conference, Madrid, Spain. Published in 2005
- BMIR-2005-1100
- Use of Description Logic Classification to Reason about Consequences of Penetrating Injuries
- D. L. Rubin, O. Dameron, M. A. Musen
- AMIA 2005 Symposium Proceedings, 649-653. Published in 2005
- BMIR-2005-1085
- A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge
- D. L. Rubin, C. F. Thorn, T. E. Klein, R. B. Altman
- J Am Med Inform Assoc, JAMIA, 12, 2, 121-129. Published in 2005
- BMIR-2005-1084
- Using an ontology of human anatomy to inform reasoning with geometric models
- D. L. Rubin, O. Dameron, Y. Bashir, D. Grossman, P. Dev, M. A. Musen
- Stud Health Technol Inform, 111, 429-35. Published in 2005
- BMIR-2005-1067
- Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study
- O. Dameron, D. L. Rubin, M. A. Musen
- AMIA Annual Symposium, Washington DC, 181-185. Published in 2005
- BMIR-2004-1268
- Linking ontologies with three-dimensional models of anatomy to predict the effects of penetrating injuries
- D. L. Rubin, Y. Bashir, D. Grossman, P. Dev, M. A. Musen
- IEEE EMBS, San Francisco. Published in 2004
- BMIR-2004-1149
- Using Bayesian Network to Predict the Probability and Type of Breast Cancer Represented by Microcalcifications on Mammography.
- E. S. Burnside, D. L. Rubin, R. Shachter
- Medinfo. Published in 2004
- BMIR-2004-1131
- Making Biomedical Ontologies and Ontology Repositories Work
- N. F. Noy, D. L. Rubin, M. A. Musen
- IEEE Intelligent Systems, 19, 6, 78-81. Published in 2004
- BMIR-2004-1108
- Improving a bayesian network's ability to predict the probability of malignancy of microcalcifications on mammography
- E. S. Burnside, R. Shachter, R. E. Sohlich, D. L. Rubin, E. A. Sickles
- Computer Assisted Radiology and Surgery, Chicago. Published in 2004
- BMIR-2004-1107
- A probabilistic expert system that provides automated mammographic-histologic correlation: initial experience
- E. S. Burnside, R. Shachter, R. E. Sohlich, D. L. Rubin, E. A. Sickles
- American Journal of Roentgenology, 182, 2, 481-8. Published in 2004
- BMIR-2004-1061
- A resource to acquire and summarize pharmacogenetics knowledge in the literature.
- D. L. Rubin, M. Carillo, M. Woon, J. F. Conroy, T. E. Klein, R. B. Altman
- Medinfo, Bried Bioinform, 11, 2, 793-7. Published in 2004
- BMIR-2003-0988
- Indexing pharmacogenetic knowledge on the World Wide Web
- R. B. Altman, D. A. Flockhart, S. T. Sherry, D. E. Oliver, D. L. Rubin, T. E. Klein
- Pharmacogenetics, 13, 1, 3-5. Published in 2003
- BMIR-2002-1066
- Ontology development for a pharmacogenetics knowledge base.
- D. E. Oliver, M. Hewett, T. E. Klein, D. L. Rubin, R. B. Altman
- Pac Symp Biocomput, 65-76. Published in 2002
- BMIR-2002-1065
- Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML
- D. L. Rubin, M. Hewett, D. E. Oliver, T. E. Klein, R. B. Altman
- Pac Symp Biocomput, 88-99. Published in 2002
- BMIR-2002-0991
- Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models
- D. L. Rubin, F. Shafa, D. E. Oliver, M. Hewett, R. B. Altman
- Bioinformatics, 18, Suppl 1, 207-15. Published in 2002
- BMIR-2002-0919
- Integrating Genotype and Phenotype Information: An
- T. E. Klein, J. T. Chang, M. K. Cho, K. L. Easton, R. Fergerson, M. Hewett, Z. Lin, I. Liu, S. Liu, D. E. Oliver, F. Shafa, J. M. Stuart, D. L. Rubin, R. B. Altman
- . Published in 2002
- BMIR-2002-0910
- PharmGKB: the Pharmacogenetics Knowledge Base
- M. Hewett, D. E. Oliver, K. L. Easton, J. M. Stuart, R. B. Altman, D. L. Rubin, T. E. Klein
- Nucleic Acids Res, 30, 1, 163-165. Published in 2002
- BMIR-2001-1269
- Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base.
- T. E. Klein, J. T. Chang, M. K. Cho, K. L. Easton, R. Fergerson, M. Hewett, Z. Lin, I. Liu, S. Liu, D. E. Oliver, F. Shafa, J. M. Stuart, D. L. Rubin, R. B. Altman
- The Pharmacogenomics Journal, Pharmacogenomics J, 1, 3, 167-170. Published in 2001
- BMIR-2001-0901
- Management of Data, Knowledge, and Metadata on the
- D. E. Oliver, M. Hewett, J. M. Stuart, T. E. Klein, D. L. Rubin, R. B. Altman
- Semantic Web Working Symposium, Stanford, CA, 74-75. Published in 2001
- BMIR-2001-0867
- A Bayesian Network for Mammography
- E. S. Burnside, D. L. Rubin, R. Shachter
- AMIA Annual Symposium, Proc AMIA Symp, 106-110. Published in 2001
- BMIR-2000-1152
- A Bayesian Network to Assist Mammography
- E. S. Burnside, D. L. Rubin, R. Shachter
- AMIA Annual Symposium, Proc AMIA Symp, 106-110. Published in 2000
- BMIR-2000-1106
- Designing a Knowledge Base for Pharmacogenomics: an Ontology for Genetic Information
- D. L. Rubin, R. B. Altman
- Biomedical Computation at Stanford, Stanford, CA. Published in 2000
- BMIR-2000-1105
- Automated Indexing of Mammography Reports Using Linear Least Squares Fit
- E. S. Burnside, D. L. Rubin, H. R. Strasberg
- International Conference on Computer Assisted Radiology and Surgery, San Francisco. Published in 2000
- BMIR-2000-0847
- Cost Benefit Analysis of Computer-based Patient Records
- E. V. Bernstam, H. R. Strasberg, D. L. Rubin
- APAMI-MIC2000, Hong Kong. Published in 2000
- BMIR-2000-0844
- Knowledge Representation and Tool Support for
Critiquing Clinical Trial Protocols
- D. L. Rubin, J. Gennari, M. A. Musen
- AMIA Annual Symposium, Los Angeles, CA. Published in 2000
- BMIR-1999-0779
- Tool Support for Authoring Eligibility Criteria for
- D. L. Rubin, J. Gennari, S. Srinivas, A. Yuen, H. Kaizer, J. S. Silva, M. A. Musen
- AMIA Annual Symposium, 369-373. Published in 1999
|