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Publications
Featured Publications
- BMIR-2011-1468
- The National Center for Biomedical Ontology
- M. A. Musen, N. F. Noy, C. G. Chute, M. A. Storey, B. Smith, N. H. Shah
- . Published in 2011
- BMIR-2009-1378
- Prototyping a Biomedical Ontology Recommender Service
- C. Jonquet, N. H. Shah, M. A. Musen
- Bio-Ontologies: Knowledge in Biology, SIG, ISMB ECCB 2009, Stockholm, Sweden. Published in 2009
 - BMIR-2009-1376
- Translational bioinformatics applications in genome medicine
- A. J. Butte
- Genome Medicine, 1, 6, 64. Published in 2009
 - BMIR-2009-1362
- Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and ‘‘antibodyome’’ measures
- L. Li, P. Wadia, M. Sarwal, N. Kambham, T. Sigdel, D. B. Miklos, R. Chen, M. Naesens, A. J. Butte
- PNAS, 106, 11, 4148-4153. Published in 2009
- BMIR-2009-1361
- Technology for Building Intelligent Systems: From Psychology to Engineering
- M. A. Musen
- Modeling Complex Systems, Bill Shuart, Will Spaulding and Jeffrey Poland, U Nebraska P, Lincoln, Nebraska, Vol 52 of the Nebraska Symposium on Motivation, 145-184. Published in 2009
 - BMIR-2009-1358
- Software-Engineering Challenges of Building and Deploying Reusable Problem Solvers
- M. J. O'Connor, C. I. Nyulas, A. Okhmatovskaia, D. Buckeridge, S. W. Tu, M. A. Musen
- Artificial Intelligence for Engineering Design, Analysis and Manufacturing, 24, 3. Published in 2009
- BMIR-2009-1355
- Data-Driven Methods to Discover Molecular Determinants of Serious Adverse Drug Events
- A. P. Chiang, A. J. Butte
- Clinical Pharmacology and Therapeutics, 28 January 2009, Advance online publication, doi:10.1038/clpt.2008.274. Published in 2009
 - BMIR-2009-1318
- Knowledge-Data Integration for Temporal Reasoning in a Clinical Trial System
- M. J. O'Connor, R. D. Shankar, D. B. Parrish, A. K. Das
- International Journal of Medical Informatics, 78, Suppl. 1, S77-S85. Published in 2009
- BMIR-2008-1353
- GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed
- R. Chen, R. Mallelwar, A. Thosar, S. Venkatasubrahmanyam, A. J. Butte
- BMC Bioinformatics, 9, 1, 548. (doi:10.1186/1471-2105-9-548). Published in 2008
 - BMIR-2008-1346
- FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease
- R. Chen, A. A. Morgan, J. Dudley, A. M. Deshpande, L. Li, K. Kodama, A. P. Chiang, A. J. Butte
- Genome Biology, 9, 12, R170 (doi:10.1186/gb-2008-9-12-r170). Published in 2008
 - BMIR-2008-1341
- Translational Bioinformatics: Coming of Age
- A. J. Butte
- Journal of the American Medical Informatics Association, JAMIA, 15, 6, 709-14. Published in 2008
 - BMIR-2008-1329
- An Ontology-Driven Framework for Deploying JADE Agent Systems
- C. I. Nyulas, M. J. O'Connor, S. W. Tu, A. Okhmatovskaia, D. Buckeridge, M. A. Musen
- IEEE/WIC/ACM International Conference on Intelligent Agent Technology, Sydney, Australia, 2, 573-577. Published in 2008
 - BMIR-2008-1322
- Understanding Detection Performance in Public Health Surveillance: Modeling Aberrancy-Detection Algorithms
- D. Buckeridge, A. Okhmatovskaia, S. W. Tu, C. I. Nyulas, M. J. O'Connor, M. A. Musen
- Journal of the American Medical Informatics Association, 15, 6, 760-769. 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-2008-1303
- The Ultimate Model Organism
- A. J. Butte
- Science, 320, 5874, 325-327. 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-2007-1295
- AILUN: reannotating gene expression data automatically
- R. Chen, L. Li, A. J. Butte
- Nature Methods, 4, 11, 879. Published in 2007
 - BMIR-2007-1281
- Evaluation and Integration of 49 Genome-wide Experiments and the Prediction of Previously Unknown Obesity-related Genes
- S. B. English, A. J. Butte
- Bioinformatics, Epub. 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-2007-1244
- Efficiently Querying Relational Databases using OWL and SWRL
- M. J. O'Connor, R. D. Shankar, S. W. Tu, C. I. Nyulas, A. K. Das, M. A. Musen
- The First International Conference on Web Reasoning and Rule Systems, Innsbruck, Austria, Springer, LNCS 4524, 361-363. Published in 2007
 - BMIR-2006-1090
- Creation and implications of a phenome-genome network
- A. J. Butte, I. S. Kohane
- Nature Biotechnology, 24, 1, 55 - 62. Published in 2006
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