2009
Annotation and Image Markup: Accessing and Interoperating with the Semantic Content in Medical Imaging,
b>Rubin, D. L. </b> <, Supekar K., Mongkolwat P., Kleper V., and Channin D. S.
, IEEE Intelligent Systems, Jan-Feb, Volume 24, Number 1, p.57-65, (2009)
The annotation and image mark-up project,
Channin, D. S., Mongkolwat P., Kleper V., and b>Rubin D. L. </b> <
, Radiology, Dec, Volume 253, Number 3, p.590-2, (2009)
Computational neuroanatomy: ontology-based representation of neural components and connectivity,
b>Rubin, D. L. </b> <, Talos I. F., Halle M., Musen M. A., and Kikinis R.
, BMC Bioinformatics, Volume 10 Suppl 2, p.S3, (2009)
Computing human image annotation,
Channin, D. S., Mongkolwat P., Kleper V., and b>Rubin D. L. </b> <
, Conf Proc IEEE Eng Med Biol Soc, Volume 1, p.7065-8, (2009)
Informatics methods to enable patient-centered radiology,
b>Rubin, D. L. </b> <
, Acad Radiol, May, Volume 16, Number 5, p.524-34, (2009)
The IR RadLex project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology,
Kundu, S., Itkin M., Gervais D. A., Krishnamurthy V. N., Wallace M. J., Cardella J. F., b>Rubin D. L. </b> <, and Langlotz C. P.
, J Vasc Interv Radiol, Apr, Volume 20, Number 4, p.433-5, (2009)
A Semantic Image Annotation Model to Enable Integrative Translational Research,
b>Rubin, D. L. </b> <, Mongkolwat P., and Channin D. S.
, AMIA Summit on Translational Bioinformatics, San Francisco, CA, (2009)
Toward best practices in radiology reporting,
Kahn, Jr., C. E., Langlotz C. P., Burnside E. S., Carrino J. A., Channin D. S., Hovsepian D. M., and b>Rubin D. L. </b> <
, Radiology, Sep, Volume 252, Number 3, p.852-6, (2009)
2008
Biomedical ontologies: a functional perspective,
b>Rubin, D. L. </b> <, Shah N. H., and Noy N. F.
, Brief Bioinform, Jan, Volume 9, Number 1, p.75-90, (2008)
BioPortal: A Web Portal to Biomedical Ontologies,
b>Rubin, D. L. </b> <, Moreira D. A., Kanjamala P. P., and Musen M. A.
, 2008 AAAI Spring Symposium Series, Symbiotic Relationships between Semantic Web and Knowledge Engineering, Stanford University, (2008)
BioPortal: Ontologies and Data Resources with the Click of a Mouse,
Musen, M., Shah N., Noy N., Dai B., Dorf M., Griffith N., Buntrock J. D., Jonquet C., Montegut M. J., and b>Rubin D. L. </b> <
, AMIA Annu Symp Proc, p.1223-4, (2008)
Creating and curating a terminology for radiology: ontology modeling and analysis,
b>Rubin, D. L. </b> <
, J Digit Imaging, Dec, Volume 21, Number 4, p.355-62, (2008)
A data warehouse for integrating radiologic and pathologic data,
b>Rubin, D. L. </b> <, and Desser T. S.
, J Am Coll Radiol, Mar, Volume 5, Number 3, p.210-7, (2008)
iPad: Semantic Annotation and Markup of Radiological Images,
b>Rubin, D. L. </b> <, Rodriguez C., Shah P., and Beaulieu C.
, AMIA Annu Symp Proc, p.626-30, (2008)
iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources,
Dinov, Ivo D., b>Rubin D. L. </b> <, Lorensen William, Dugan Jonathan, Ma Jeff, Murphy Shawn, Kirschner Beth, Bug William, Sherman Michael, Floratos Aris, et al.
, PLoS ONE, Volume 3, Number 5, p.e2265, (2008)
Medical Imaging on the Semantic Web: Annotation and Image Markup,
b>Rubin, D. L. </b> <, Mongkolwat P., Kleper V., Supekar K., and Channin D. S.
, 2008 AAAI Spring Symposium Series, Semantic Scientific Knowledge Integration, Stanford University, (2008)
Network Analysis of Intrinsic Functional Brain Connectivity in Alzheimer's Disease,
Supekar, K., Menon V., b>Rubin D. L. </b> <, Musen M. A., and Greicius M. D.
, PLoS Computational Biology, Volume 4, Number 6, p.e1000100, (2008)
The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience,
Bug, W. J., Ascoli G. A., Grethe J. S., Gupta A., Fennema-Notestine C., Laird A. R., Larson S. D., b>Rubin D. L. </b> <, Shepherd G. M., Turner J. A., et al.
, Neuroinformatics, Sep, Volume 6, Number 3, p.175-94, (2008)
A prototype symbolic model of canonical functional neuroanatomy of the motor system,
b>Rubin, D. L. </b> <, Talos I. F., Halle M., Musen M., and Kikinis R.
, J Biomed Inform, Apr, Volume 41, Number 2, p.251-63, (2008)
Tool support to enable evaluation of the clinical response to treatment,
Levy, M. A., and b>Rubin D. L. </b> <
, AMIA Annu Symp Proc, p.399-403, (2008)
Toward Computational Neuroanatomy: A Functional Representation of Neural Components and Connectivity,
b>Rubin, D. L. </b> <, Talos I. F., Halle M., Musen M. A., and Kikinis R.
, AMIA Summit on Translational Bioinformatics, San Francisco, CA, (2008)
Translating the Foundational Model of Anatomy into OWL,
Noy, N. F., and b>Rubin D. L. </b> <
, Web Semantics: Science, Services and Agents on the World Wide Web, Volume 6, Number 2, p.133-136, (2008)
2007
Annotation and query of tissue microarray data using the NCI Thesaurus,
Shah, N. H., b>Rubin D. L. </b> <, Espinosa I., Montgomery K., and Musen M. A.
, BMC Bioinformatics, Aug 8, Volume 8, Number 1, p.296, (2007)
Knowledge Zone: a public repository of peer-reviewed biomedical ontologies,
Supekar, K., b>Rubin D. L. </b> <, Noy N., and Musen M.
, Medinfo, Volume 12, Number Pt 1, p.812-6, (2007)
LesionViewer: A tool for tracking cancer lesions over time,
Levy, M. A., Garg A., Tam A., Garten Y., and b>Rubin D. L. </b> <
, Proc AMIA Symp, p.443-447, (2007)
Protege: A Tool for Managing and Using Terminology in Radiology Applications,
b>Rubin, D. L. </b> <, Noy N. F., and Musen M. A.
, J Digit Imaging, Aug 9, (2007)
Use of microcalcification descriptors in BI-RADS 4th edition to stratify risk of malignancy,
Burnside, E. S., Ochsner J. E., Fowler K. J., Fine J. P., Salkowski L. R., b>Rubin D. L. </b> <, and Sisney G. A.
, Radiology, Feb, Volume 242, Number 2, p.388-95, (2007)
2006
Bayesian Network to Predict Breast Cancer Risk of Mammographic Microcalcifications and Reduce Number of Benign Biopsy Results: Initial Experience,
Burnside, E. S., b>Rubin D. L. </b> <, Fine J. P., Shachter R. D., Sisney G. A., and Leung W. K.
, Radiology, Sep, Volume 240, Number 3, p.666-673, (2006)
Coverage of emergency after-hours ultrasound cases: survey of practices at U.S. Teaching hospitals,
Desser, T. S., b>Rubin D. L. </b> <, and Schraedley-Desmond P.
, Acad Radiol, Feb, Volume 13, Number 2, p.249-53, (2006)
National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge,
b>Rubin, D. L. </b> <, Lewis S. E., Mungall C. J., Misra S., Westerfield M., Ashburner M., Sim I., Chute C. G., Storey M. A., Smith B., et al.
, OMICS, Summer, Volume 10, Number 2, p.185-98, (2006)
An Ontology for PACS Integration,
Kahn, Jr., C. E., Channin D. S., and b>Rubin D. L. </b> <
, J Digit Imaging, Jun 14, (2006)
Ontology-based Annotation and Query of Tissue Microarray Data,
Shah, N., b>Rubin D. L. </b> <, Supekar K., and Musen M. A.
, Proc AMIA Symp, (2006)
Ontology-Based Representation of Simulation Models of Physiology (AMIA Distinguished Paper Award),
b>Rubin, D. L. </b> <, Grossman D., Neal M., Cook D. L., Bassingthwaighte J. B., and Musen M. A.
, Proc AMIA Symp, p.664-668, (2006)
Using ontologies linked with geometric models to reason about penetrating injuries,
b>Rubin, D. L. </b> <, Dameron O., Bashir Y., Grossman D., Dev P., and Musen M. A.
, Artif Intell Med, Jul, Volume 37, Number 3, p.167-76, (2006)
2005
A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge,
b>Rubin, D. L. </b> <, Thorn C. F., Klein T. E., and Altman R. B.
, J Am Med Inform Assoc, Mar-Apr, Volume 12, Number 2, p.121-9, (2005)
Use of description logic classification to reason about consequences of penetrating injuries,
b>Rubin, D. L. </b> <, Dameron O., and Musen M. A.
, AMIA Annu Symp Proc, p.649-53, (2005)
Using an ontology of human anatomy to inform reasoning with geometric models,
b>Rubin, D. L. </b> <, Bashir Y., Grossman D., Dev P., and Musen M. A.
, Stud Health Technol Inform, Volume 111, p.429-35, (2005)
Using Petri Net tools to study properties and dynamics of biological systems,
Peleg, M., b>Rubin D. L. </b> <, and Altman R. B.
, J Am Med Inform Assoc, Mar-Apr, Volume 12, Number 2, p.181-99, (2005)
2004
Linking ontologies with three-dimensional models of anatomy to predict the effects of penetrating injuries,
b>Rubin, D. L. </b> <, Bashir Y., Grossman D., Dev P., and Musen M. A.
, 26th Annual International Conference of the IEEE Engineering in Medicine and Biology, San Francisco, CA, (2004)
Making biomedical ontologies and ontology repositories work,
Noy, N. F., b>Rubin D. L. </b> <, and Musen M. A.
, IEEE Intelligent Systems, Volume 19, Number 6, p.2-5, (2004)
An "omics" view of drug development,
Altman, R. B., b>Rubin D. L. </b> <, and Klein T. E.
, Drug Development Research, Jun, Volume 62, Number 2, p.81-85, (2004)
PharmGKB: A resource to link genotype and phenotype in Pharmacogenetics,
b>Rubin, D. L. </b> <, Woon M., Carillo M., Lin S., Liu F., Conroy J., Gor W., Thorn C., Hewett M., Klein T. E., et al.
, Medinfo, San Francisco, CA, (2004)
A probabilistic expert system that provides automated mammographic-histologic correlation: initial experience,
Burnside, E. S., b>Rubin D. L. </b> <, Shachter R. D., Sohlich R. E., and Sickles E. A.
, AJR Am J Roentgenol, Feb, Volume 182, Number 2, p.481-8, (2004)
A resource to acquire and summarize pharmacogenetics knowledge in the literature,
b>Rubin, D. L. </b> <, Carrillo M., Woon M., Conroy J., Klein T. E., and Altman R. B.
, Medinfo, Volume 2004, p.793-7, (2004)
2002
Ontology development for a pharmacogenetics knowledge base,
Oliver, D. E., b>Rubin D. L. </b> <, Stuart J. M., Hewett M., Klein T. E., and Altman R. B.
, Pac Symp Biocomput, p.65-76, (2002)
PharmGKB: the Pharmacogenetics Knowledge Base,
Hewett, M., Oliver D. E., b>Rubin D. L. </b> <, Easton K. L., Stuart J. M., Altman R. B., and Klein T. E.
, Nucleic Acids Res, Jan 1, Volume 30, Number 1, p.163-5, (2002)
Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models,
b>Rubin, D. L. </b> <, Shafa F., Oliver D. E., Hewett M., and Altman R. B.
, Bioinformatics, Jul, Volume 18 Suppl 1, p.S207-15, (2002)
2001
Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base,
Klein, T. E., Chang J. T., Cho M. K., Easton K. L., Fergerson R., Hewett M., Lin Z., Liu Y., Liu S., Oliver D. E., et al.
, Pharmacogenomics J, Volume 1, Number 3, p.167-70, (2001)
Management of Data, Knowledge, and Metadata on the Semantic Web: Experience with a Pharmacogenetics Knowledge Base.,
Oliver, D. E., Hewett M., b>Rubin D. L. </b> <, Stuart J. M., Klein T. E., and Altman R. B.
, Semantic Web Working Symposium, Stanford, CA, p.Position Papers, 74-75., (2001)
Splenic imaging with ultrasmall superparamagnetic iron oxide ferumoxtran-10 (AMI-7227): preliminary observations,
Harisinghani, M. G., Saini S., Weissleder R., b>Rubin D. L. </b> <, deLange E., Harms S., Weinreb J., Small W., Sukerkar A., Brown J. J., et al.
, J Comput Assist Tomogr, Sep-Oct, Volume 25, Number 5, p.770-6, (2001)
2000
Automated Indexing of Mammography Reports Using Linear Least Squares Fit,
Burnside, B. E., b>Rubin D. L. </b> <, and Strasberg H. R.
, CARS 2000 International Conference on Computer Assisted Radiology and Surgery, San Francisco, CA, (2000)
A Bayesian network for mammography,
Burnside, E., b>Rubin D. L. </b> <, and Shachter R.
, Proc AMIA Symp, p.106-10, (2000)
Efficacy and safety of mangafodipir trisodium (MnDPDP) injection for hepatic MRI in adults: results of the U.S. Multicenter phase III clinical trials. Efficacy of early imaging,
Federle, M., Chezmar J., b>Rubin D. L. </b> <, Weinreb J., Freeny P., Schmiedl U. P., Brown J. J., Borrello J. A., Lee J. K., Semelka R. C., et al.
, J Magn Reson Imaging, Nov, Volume 12, Number 5, p.689-701, (2000)
Knowledge representation and tool support for critiquing clinical trial protocols,
b>Rubin, D. L. </b> <, Gennari J., and Musen M. A.
, Proc AMIA Symp, p.724-8, (2000)
Magnetic resonance imaging in patients with central nervous system pathology: a comparison of OptiMARK (Gd-DTPA-BMEA) and Magnevist (Gd-DTPA),
Grossman, R. I., b>Rubin D. L. </b> <, Hunter G., Haughton V. M., Lee D., Sze G., Kuhn M. J., Maravilla K., Tu R., Heindel W., et al.
, Invest Radiol, Jul, Volume 35, Number 7, p.412-9, (2000)
Safety and efficacy of mangafodipir trisodium (MnDPDP) injection for hepatic MRI in adults: results of the U.S. multicenter phase III clinical trials (safety),
Federle, M. P., Chezmar J. L., b>Rubin D. L. </b> <, Weinreb J. C., Freeny P. C., Semelka R. C., Brown J. J., Borello J. A., Lee J. K., Mattrey R., et al.
, J Magn Reson Imaging, Jul, Volume 12, Number 1, p.186-97, (2000)
1999
Blood pool and liver enhancement in CT with liposomal lodixanol: comparison with lohexol,
Desser, T. S., b>Rubin D. L. </b> <, Muller H., McIntire G. L., Bacon E. R., and Toner J. L.
, Acad Radiol, Mar, Volume 6, Number 3, p.176-83, (1999)
Interstitial MR and CT lymphography with Gd-dTPA-co-alpha, omega-diaminoPEG(1450) and Gd-dTPA-co-1,6-diaminohexane polymers: preliminary experience,
Desser, T. S., b>Rubin D. L. </b> <, Muller H., McIntire G. L., Bacon E. R., and Hollister K. R.
, Acad Radiol, Feb, Volume 6, Number 2, p.112-8, (1999)
A multicenter, randomized, double-blind study to evaluate the safety, tolerability, and efficacy of OptiMARK (gadoversetamide injection) compared with Magnevist (gadopentetate dimeglumine) in patients with liver pathology: results of a Phase III clinical ,
b>Rubin, D. L. </b> <, Desser T. S., Semelka R., Brown J., Nghiem H. V., Stevens W. R., Bluemke D., Nelson R., Fultz P., Reimer P., et al.
, J Magn Reson Imaging, Feb, Volume 9, Number 2, p.240-50, (1999)
A multisite phase III study of the safety and efficacy of a new manganese chloride-based gastrointestinal contrast agent for MRI of the abdomen and pelvis,
Small, W. C., DeSimone-Macchi D., Parker J. R., Sukerkar A., Hahn P. F., b>Rubin D. L. </b> <, Zelch J. V., Kuhlman J. E., Outwater E. K., Weinreb J. C., et al.
, J Magn Reson Imaging, Jul, Volume 10, Number 1, p.15-24, (1999)
Polymeric gadolinium chelate magnetic resonance imaging contrast agents: design, synthesis, and properties,
Ladd, D. L., Hollister R., Peng X., Wei D., Wu G., Delecki D., Snow R. A., Toner J. L., Kellar K., Eck J., et al.
, Bioconjug Chem, May-Jun, Volume 10, Number 3, p.361-70, (1999)
Safety and efficacy of a new oral contrast agent for sonography: a phase II trial,
Lev-Toaff, A. S., Langer J. E., b>Rubin D. L. </b> <, Zelch J. V., Chong W. K., Barone A. E., and Goldberg B. B.
, AJR Am J Roentgenol, Aug, Volume 173, Number 2, p.431-6, (1999)
Tool support for authoring eligibility criteria for cancer trials,
b>Rubin, D. L. </b> <, Gennari J. H., Srinivas S., Yuen A., Kaizer H., Musen M. A., and Silva J. S.
, Proc AMIA Symp, p.369-73, (1999)
1995
Adrenal gland enhancement at MR imaging with Mn-DPDP,
Mitchell, D. G., Outwater E. K., Matteucci T., b>Rubin D. L. </b> <, Chezmar J. L., and Saini S.
, Radiology, Mar, Volume 194, Number 3, p.783-7, (1995)
Gadolinium zeolite as an oral contrast agent for magnetic resonance imaging,
Young, S. W., Qing F., b>Rubin D. L. </b> <, Balkus, Jr. K. J., Engel J. S., Lang J., Dow W. C., Mutch J. D., and Miller R. A.
, J Magn Reson Imaging, Sep-Oct, Volume 5, Number 5, p.499-508, (1995)
Influence of viscosity on WIN 39996 as a contrast agent for gastrointestinal magnetic resonance imaging,
b>Rubin, D. L. </b> <, Muller H. H., Young S. W., Hunke W. A., Gorman W. G., and Lee K. C.
, Invest Radiol, Apr, Volume 30, Number 4, p.226-31, (1995)
1994
Dynamics of tumor imaging with Gd-DTPA-polyethylene glycol polymers: dependence on molecular weight,
Desser, T. S., b>Rubin D. L. </b> <, Muller H. H., Qing F., Khodor S., Zanazzi G., Young S. W., Ladd D. L., Wellons J. A., Kellar K. E., et al.
, J Magn Reson Imaging, May-Jun, Volume 4, Number 3, p.467-72, (1994)
Nanoparticulate contrast media. Blood-pool and liver-spleen imaging,
b>Rubin, D. L. </b> <, Desser T. S., Qing F., Muller H. H., Young S. W., McIntire G. L., Bacon E., Cooper E., and Toner J.
, Invest Radiol, Jun, Volume 29 Suppl 2, p.S280-3, (1994)
Optimization of an oral magnetic particle formulation as a gastrointestinal contrast agent for magnetic resonance imaging,
b>Rubin, D. L. </b> <, Muller H. H., Young S. W., Hunke W. A., and Gorman W. G.
, Invest Radiol, Jan, Volume 29, Number 1, p.81-6, (1994)
Quantitation of saturation effects versus dose in three-dimensional time-of-flight magnetic resonance angiography with blood-pool contrast agents,
Desser, T. S., b>Rubin D. L. </b> <, Fan Q., Muller H. H., Young S. W., Kellar K. E., Wellons J. A., Ladd D. L., Toner J. L., and Snow R. A.
, Invest Radiol, Jun, Volume 29 Suppl 2, p.S65-8, (1994)