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Publications

The work of BMIR researchers is published in peer-reviewed medical journals as well as in books, working papers, evidence reports and other formats. A selection of recently published work is listed below. Click on the labels at right to view publications by type.

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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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