Publications

PUBLICATIONS IN BIOMEDICAL AND IMAGING INFORMATICS

Rubin DL, Talos IF, Halle M, Musen MA and Kikinis R, Computational neuroanatomy: ontology-based representation of neural components and connectivity. BMC Bioinformatics 10 Suppl 2: S3, 2009.

Rubin DL, Supekar K, Mongkolwat P, Kleper V and Channin DS, Annotation and Image Markup: Accessing and Interoperating with the Semantic Content in Medical Imaging. Ieee Intelligent Systems 24(1): 57-65, 2009.

Rubin DL, Informatics methods to enable patient-centered radiology. Acad Radiol 16(5): 524-34, 2009.

Kundu S, Itkin M, Gervais DA, Krishnamurthy VN, Wallace MJ, Cardella JF, Rubin DL and Langlotz CP, The IR RadLex project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology. J Vasc Interv Radiol 20(4): 433-5, 2009.

Kahn CE, Jr. and Rubin DL, Automated Semantic Indexing of Figure Captions to Improve Radiology Image Retrieval. J Am Med Inform Assoc, 2009.

Channin DS, Mongkolwat P, Kleper V, Sepukar K and Rubin DL, The caBIG Annotation and Image Markup Project. J Digit Imaging, 2009.

Supekar K, Menon V, Rubin DL, Musen MA and Greicius MD, Network Analysis of Intrinsic Functional Brain Connectivity in Alzheimer's Disease. PLoS Computational Biology 4(6): e1000100, 2008.

Rubin DL, Talos IF, Halle M, Musen MA and Kikinis R, Toward Computational Neuroanatomy: A Functional Representation of Neural Components and Connectivity. In: AMIA Summit on Translational Bioinformatics, San Francisco, CA,2008.

Rubin DL, Talos IF, Halle M, Musen M and Kikinis R, A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform 41(2): 251-63, 2008.

Rubin DL, Shah NH and Noy NF, Biomedical ontologies: a functional perspective. Brief Bioinform 9(1): 75-90, 2008.

Rubin DL, Rodriguez C, Shah P and Beaulieu C, iPad: Semantic Annotation and Markup of Radiological Images. AMIA Annu Symp Proc: 626-30, 2008.

Rubin DL, Moreira DA, Kanjamala PP and Musen MA, BioPortal: A Web Portal to Biomedical Ontologies. In: 2008 AAAI Spring Symposium Series, Symbiotic Relationships between Semantic Web and Knowledge Engineering, Stanford University, 2008.

Rubin DL, Mongkolwat P, Kleper V, Supekar K and Channin DS, Medical Imaging on the Semantic Web: Annotation and Image Markup. In: 2008 AAAI Spring Symposium Series, Semantic Scientific Knowledge Integration, Stanford University, 2008.

Rubin DL and Desser TS, A data warehouse for integrating radiologic and pathologic data. J Am Coll Radiol 5(3): 210-7, 2008.

Rubin DL, Creating and curating a terminology for radiology: ontology modeling and analysis. J Digit Imaging 21(4): 355-62, 2008.

Poulter GL, Rubin DL, Altman RB and Seoighe C, MScanner: a classifier for retrieving Medline citations. BMC Bioinformatics 9, 2008.

Noy NF and Rubin DL, Translating the Foundational Model of Anatomy into OWL. Web Semantics: Science, Services and Agents on the World Wide Web 6(2): 133-136, 2008.

Musen M, Shah N, Noy N, Dai B, Dorf M, Griffith N, Buntrock JD, Jonquet C, Montegut MJ and Rubin DL, BioPortal: Ontologies and Data Resources with the Click of a Mouse. AMIA Annu Symp Proc: 1223-4, 2008.

Mejino JL, Rubin DL and Brinkley JF, FMA-RadLex: An Application Ontology of Radiological Anatomy derived from the Foundational Model of Anatomy Reference Ontology. AMIA Annu Symp Proc: 465-9, 2008.

Liu YI, Kamaya A, Desser TD and Rubin DL, A Bayesian Classifier for Differentiating Benign versus Malignant Thyroid Nodules using Sonographic Features. AMIA Annu Symp Proc: 419-23, 2008.

Levy MA and Rubin DL, Tool support to enable evaluation of the clinical response to treatment. AMIA Annu Symp Proc: 399-403, 2008.

Dinov ID, Rubin DL, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS and Toga AW, iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources. PLoS ONE 3(5): e2265, 2008.

Bug WJ, Ascoli GA, Grethe JS, Gupta A, Fennema-Notestine C, Laird AR, Larson SD, Rubin DL, Shepherd GM, Turner JA and Martone ME, The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. Neuroinformatics 6(3): 175-94, 2008.

Supekar K, Rubin DL, Noy N and Musen M, Knowledge Zone: a public repository of peer-reviewed biomedical ontologies. Medinfo 12(Pt 1): 812-6, 2007.

Shah NH, Rubin DL, Espinosa I, Montgomery K and Musen MA, Annotation and query of tissue microarray data using the NCI Thesaurus. BMC Bioinformatics 8(1): 296, 2007.

Rubin DL, Talos IF, Halle M, Musen M and Kikinis R, A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform, 2007.

Rubin DL, Noy NF and Musen MA, Protege: A Tool for Managing and Using Terminology in Radiology Applications. J Digit Imaging, 2007.

Levy MA, Garg A, Tam A, Garten Y and Rubin DL, LesionViewer: A tool for tracking cancer lesions over time. Proc AMIA Symp: 443-447, 2007.

Lee W, Raschid L, Srinivasan P, Shah N, Rubin DL and Noy NF, Using annotations from controlled vocabularies to find meaningful associations. Lecture Notes in Bioinformatics 4544: 247-263, 2007.

Burnside ES, Ochsner JE, Fowler KJ, Fine JP, Salkowski LR, Rubin DL and Sisney GA, Use of microcalcification descriptors in BI-RADS 4th edition to stratify risk of malignancy. Radiology 242(2): 388-95, 2007.

Shah N, Rubin DL, Supekar K and Musen MA, Ontology-based Annotation and Query of Tissue Microarray Data. Proc AMIA Symp, 2006.

Rubin DL, Lewis SE, Mungall CJ, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Storey MA, Smith B, Day-Richter J, Noy NF and Musen MA, National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge. Omics 10(2): 185-98, 2006.

Rubin DL, Grossman D, Neal M, Cook DL, Bassingthwaighte JB and Musen MA, Ontology-Based Representation of Simulation Models of Physiology (AMIA Distinguished Paper Award). Proc AMIA Symp: 664-668, 2006.

Rubin DL, Dameron O, Bashir Y, Grossman D, Dev P and Musen MA, Using ontologies linked with geometric models to reason about penetrating injuries. Artif Intell Med 37(3): 167-76, 2006.

Kahn CE, Jr., Channin DS and Rubin DL, An Ontology for PACS Integration. J Digit Imaging, 2006.

Burnside ES, Rubin DL, Fine JP, Shachter RD, Sisney GA and Leung WK, Bayesian Network to Predict Breast Cancer Risk of Mammographic Microcalcifications and Reduce Number of Benign Biopsy Results: Initial Experience. Radiology 240(3): 666-673, 2006.

Rubin DL, Thorn CF, Klein TE and Altman RB, A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge. J Am Med Inform Assoc 12(2): 121-9, 2005.

Rubin DL, Dameron O and Musen MA, Use of description logic classification to reason about consequences of penetrating injuries. AMIA Annu Symp Proc: 649-53, 2005.

Rubin DL, Bashir Y, Grossman D, Dev P and Musen MA, Using an ontology of human anatomy to inform reasoning with geometric models. Stud Health Technol Inform 111: 429-35, 2005.

Peleg M, Rubin DL and Altman RB, Using Petri Net tools to study properties and dynamics of biological systems. J Am Med Inform Assoc 12(2): 181-99, 2005.

Dameron O, Rubin DL and Musen MA, Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study. AMIA Annu Symp Proc: 181-5, 2005.

Rubin DL, Woon M, Carillo M, Lin S, Liu F, Conroy J, Gor W, Thorn C, Hewett M, Klein TE and Altman RB, PharmGKB: A resource to link genotype and phenotype in Pharmacogenetics. In: Medinfo, San Francisco, CA,2004.

Rubin DL, Carrillo M, Woon M, Conroy J, Klein TE and Altman RB, A resource to acquire and summarize pharmacogenetics knowledge in the literature. Medinfo 2004: 793-7, 2004.

Rubin DL, Bashir Y, Grossman D, Dev P and Musen MA, Linking ontologies with three-dimensional models of anatomy to predict the effects of penetrating injuries. In: 26th Annual International Conference of the IEEE Engineering in Medicine and Biology, San Francisco, CA,2004.

Noy NF, Rubin DL and Musen MA, Making biomedical ontologies and ontology repositories work. IEEE Intelligent Systems 19(6): 2-5, 2004.

Burnside ES, Rubin DL, Shachter RD, Sohlich RE and Sickles EA, A probabilistic expert system that provides automated mammographic-histologic correlation: initial experience. AJR Am J Roentgenol 182(2): 481-8, 2004.

Burnside ES, Rubin DL and Shachter RD, Using a bayesian network to predict the probability and type of breast cancer represented by microcalcifications on mammography. Medinfo 2004: 13-7, 2004.

Burnside ES, Rubin DL and Shachter RD, Improving a bayesian network's ability to predict the probability of malignancy of microcalcifications on mammography. In: Proc Computer Assisted Radiology and Surgery2004.

Altman RB, Rubin DL and Klein TE, An "omics" view of drug development. Drug Development Research 62(2): 81-85, 2004.

Altman RB, Flockhart DA, Sherry ST, Oliver DE, Rubin DL and Klein TE, Indexing pharmacogenetic knowledge on the World Wide Web. Pharmacogenetics 13(1): 3-5, 2003.

Rubin DL, Shafa F, Oliver DE, Hewett M and Altman RB, Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models. Bioinformatics 18 Suppl 1: S207-15, 2002.

Rubin DL, Hewett M, Oliver DE, Klein TE and Altman RB, Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML. Pac Symp Biocomput: 88-99, 2002.

Oliver DE, Rubin DL, Stuart JM, Hewett M, Klein TE and Altman RB, Ontology development for a pharmacogenetics knowledge base. Pac Symp Biocomput: 65-76, 2002.

Hewett M, Oliver DE, Rubin DL, Easton KL, Stuart JM, Altman RB and Klein TE, PharmGKB: the Pharmacogenetics Knowledge Base. Nucleic Acids Res 30(1): 163-5, 2002.

Oliver DE, Hewett M, Rubin DL, Stuart JM, Klein TE and Altman RB, Management of Data, Knowledge, and Metadata on the Semantic Web: Experience with a Pharmacogenetics Knowledge Base. In: Semantic Web Working Symposium, Stanford, CA,2001, pp. Position Papers, 74-75.

Klein TE, Chang JT, Cho MK, Easton KL, Fergerson R, Hewett M, Lin Z, Liu Y, Liu S, Oliver DE, Rubin DL, Shafa F, Stuart JM and Altman RB, Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base. Pharmacogenomics J 1(3): 167-70, 2001.

Rubin DL, Gennari J and Musen MA, Knowledge representation and tool support for critiquing clinical trial protocols. Proc AMIA Symp: 724-8, 2000.

Rubin DL and Altman RB, Designing a Knowledge Base for Pharmacogenomics: an Ontology for Genetic Information. In: Biomedical Computation at Stanford, Stanford, CA,2000.

Burnside E, Rubin DL and Shachter R, A Bayesian network for mammography. Proc AMIA Symp: 106-10, 2000.

Burnside BE, Rubin DL and Strasberg HR, Automated Indexing of Mammography Reports Using Linear Least Squares Fit. In: CARS 2000 International Conference on Computer Assisted Radiology and Surgery, San Francisco, CA,2000.

Bernstam EV, Strasberg HR and Rubin DL, Cost Benefit Analysis of Computer-based Patient Records with Regard to Their Use in Colon Cancer Screening. In: APAMI-MIC2000, Hong Kong,2000.

Rubin DL, Gennari JH, Srinivas S, Yuen A, Kaizer H, Musen MA and Silva JS, Tool support for authoring eligibility criteria for cancer trials. Proc AMIA Symp: 369-73, 1999.

PUBLICATIONS IN RADIOLOGY

Desser TS, Rubin DL and Schraedley-Desmond P, Coverage of emergency after-hours ultrasound cases: survey of practices at U.S. Teaching hospitals. Acad Radiol 13(2): 249-53, 2006.

Harisinghani MG, Saini S, Weissleder R, Rubin DL, deLange E, Harms S, Weinreb J, Small W, Sukerkar A, Brown JJ, Zelch J, Lucas M, Morris M and Hahn PF, Splenic imaging with ultrasmall superparamagnetic iron oxide ferumoxtran-10 (AMI-7227): preliminary observations. J Comput Assist Tomogr 25(5): 770-6, 2001.

Grossman RI, Rubin DL, Hunter G, Haughton VM, Lee D, Sze G, Kuhn MJ, Maravilla K, Tu R, Heindel W, Wippold FJ, 2nd, Leeds N, Zelch J, Jinkins JR, Grodd W, Truwit C, Kanal E, Provenzale JM, Ramsey R, Simon J, Brunberg JA, Stevens GR and Kristy RM, Magnetic resonance imaging in patients with central nervous system pathology: a comparison of OptiMARK (Gd-DTPA-BMEA) and Magnevist (Gd-DTPA). Invest Radiol 35(7): 412-9, 2000.

Federle MP, Chezmar JL, Rubin DL, Weinreb JC, Freeny PC, Semelka RC, Brown JJ, Borello JA, Lee JK, Mattrey R, Dachman AH, Saini S, Harmon B, Fenstermacher M, Pelsang RE, Harms SE, Mitchell DG, Halford HH, Anderson MW, Johnson CD, Francis IR, Bova JG, Kenney PJ, Klippenstein DL, Foster GS and Turner DA, Safety and efficacy of mangafodipir trisodium (MnDPDP) injection for hepatic MRI in adults: results of the U.S. multicenter phase III clinical trials (safety). J Magn Reson Imaging 12(1): 186-97, 2000.

Federle M, Chezmar J, Rubin DL, Weinreb J, Freeny P, Schmiedl UP, Brown JJ, Borrello JA, Lee JK, Semelka RC, Mattrey R, Dachman AH, Saini S, Harms SE, Mitchell DG, Anderson MW, Halford HH, 3rd, Bennett WF, Young SW, Rifkin M, Gay SB, Ballerini R, Sherwin PF and Robison RO, 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. J Magn Reson Imaging 12(5): 689-701, 2000.

Small WC, DeSimone-Macchi D, Parker JR, Sukerkar A, Hahn PF, Rubin DL, Zelch JV, Kuhlman JE, Outwater EK, Weinreb JC, Brown JJ, de Lange EE, Woodward PJ, Arildsen R, Foster GS, Runge VM, Aisen AM, Muroff LR, Thoeni RF, Parisky YR, Tanenbaum LN, Totterman S, Herfkens RJ, Knudsen J, Bernardino ME and et al., 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. J Magn Reson Imaging 10(1): 15-24, 1999.

Rubin DL, Desser TS, Semelka R, Brown J, Nghiem HV, Stevens WR, Bluemke D, Nelson R, Fultz P, Reimer P, Ho V, Kristy RM and Pierro JA, 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 trial. J Magn Reson Imaging 9(2): 240-50, 1999.

Lev-Toaff AS, Langer JE, Rubin DL, Zelch JV, Chong WK, Barone AE and Goldberg BB, Safety and efficacy of a new oral contrast agent for sonography: a phase II trial. AJR Am J Roentgenol 173(2): 431-6, 1999.

Ladd DL, Hollister R, Peng X, Wei D, Wu G, Delecki D, Snow RA, Toner JL, Kellar K, Eck J, Desai VC, Raymond G, Kinter LB, Desser TS and Rubin DL, Polymeric gadolinium chelate magnetic resonance imaging contrast agents: design, synthesis, and properties. Bioconjug Chem 10(3): 361-70, 1999.

Desser TS, Rubin DL, Muller H, McIntire GL, Bacon ER and Toner JL, Blood pool and liver enhancement in CT with liposomal lodixanol: comparison with lohexol. Acad Radiol 6(3): 176-83, 1999.

Desser TS, Rubin DL, Muller H, McIntire GL, Bacon ER and Hollister KR, Interstitial MR and CT lymphography with Gd-dTPA-co-alpha, omega-diaminoPEG(1450) and Gd-dTPA-co-1,6-diaminohexane polymers: preliminary experience. Acad Radiol 6(2): 112-8, 1999.

Rubin DL, Falk KL, Sperling MJ, Ross M, Saini S, Rothman B, Shellock F, Zerhouni E, Stark D, Outwater EK, Schmiedl U, Kirby LC, Chezmar J, Coates T, Chang M, Silverman JM, Rofsky N, Burnett K, Engel J and Young SW, A multicenter clinical trial of Gadolite Oral Suspension as a contrast agent for MRI. J Magn Reson Imaging 7(5): 865-72, 1997.

Harisinghani MG, Saini S, Weissleder R, Halpern EF, Schima W, Rubin DL, Stillman AE, Sica GT, Small WC and Hahn PF, Differentiation of liver hemangiomas from metastases and hepatocellular carcinoma at MR imaging enhanced with blood-pool contrast agent Code-7227. Radiology 202(3): 687-91, 1997.

Young SW, Qing F, Rubin DL, Balkus KJ, Jr., Engel JS, Lang J, Dow WC, Mutch JD and Miller RA, Gadolinium zeolite as an oral contrast agent for magnetic resonance imaging. J Magn Reson Imaging 5(5): 499-508, 1995.

Rubin DL, Muller HH, Young SW, Hunke WA, Gorman WG and Lee KC, Influence of viscosity on WIN 39996 as a contrast agent for gastrointestinal magnetic resonance imaging. Invest Radiol 30(4): 226-31, 1995.

Mitchell DG, Outwater EK, Matteucci T, Rubin DL, Chezmar JL and Saini S, Adrenal gland enhancement at MR imaging with Mn-DPDP. Radiology 194(3): 783-7, 1995.

Rubin DL, Muller HH, Young SW, Hunke WA and Gorman WG, Optimization of an oral magnetic particle formulation as a gastrointestinal contrast agent for magnetic resonance imaging. Invest Radiol 29(1): 81-6, 1994.

Rubin DL, Desser TS, Qing F, Muller HH, Young SW, McIntire GL, Bacon E, Cooper E and Toner J, Nanoparticulate contrast media. Blood-pool and liver-spleen imaging. Invest Radiol 29 Suppl 2: S280-3, 1994.

Desser TS, Rubin DL, Muller HH, Qing F, Khodor S, Zanazzi G, Young SW, Ladd DL, Wellons JA, Kellar KE and et al., Dynamics of tumor imaging with Gd-DTPA-polyethylene glycol polymers: dependence on molecular weight. J Magn Reson Imaging 4(3): 467-72, 1994.

Desser TS, Rubin DL, Fan Q, Muller HH, Young SW, Kellar KE, Wellons JA, Ladd DL, Toner JL and Snow RA, Quantitation of saturation effects versus dose in three-dimensional time-of-flight magnetic resonance angiography with blood-pool contrast agents. Invest Radiol 29 Suppl 2: S65-8, 1994.

Rubin DL, Muller HH, Sidhu MK, Young SW, Hunke WA and Gorman WG, Liquid oral magnetic particles as a gastrointestinal contrast agent for MR imaging: efficacy in vivo. J Magn Reson Imaging 3(1): 113-8, 1993.

Rubin DL, Muller HH and Young SW, Formulation of radiographically detectable gastrointestinal contrast agents for magnetic resonance imaging: effects of a barium sulfate additive on MR contrast agent effectiveness. Magn Reson Med 23(1): 154-65, 1992.

Rubin DL, Muller HH and Young SW, Methods for the systematic investigation of gastrointestinal contrast media for MRI: evaluation of intestinal distribution by radiographic monitoring. Magn Reson Imaging 9(3): 285-93, 1991.

Rubin DL, Muller HH, Nino-Murcia M, Sidhu M, Christy V and Young SW, Intraluminal contrast enhancement and MR visualization of the bowel wall: efficacy of PFOB. J Magn Reson Imaging 1(3): 371-80, 1991.

Young SW, Bradley B, Muller HH and Rubin DL, Detection of hepatic malignancies using Mn-DPDP (manganese dipyridoxal diphosphate) hepatobiliary MRI contrast agent. Magn Reson Imaging 8(3): 267-76, 1990.

Rubin DL, Ratner AV and Young SW, Magnetic susceptibility effects and their application in the development of new ferromagnetic catheters for magnetic resonance imaging. Invest Radiol 25(12): 1325-32, 1990.

Burke CM, Glanville AR, Morris AJ, Rubin DL, Harvey JA, Theodore J and Robin ED, Pulmonary function in advanced pulmonary hypertension. Thorax 42(2): 131-5, 1987.

Theodore J, Robin ED, Burke CM, Jamieson SW, Van Kessel A, Rubin DL, Stinson EB and Shumway NE, Impact of profound reductions of PaO2 on O2 transport and utilization in congenital heart disease. Chest 87(3): 293-302, 1985.

Rubin DL and Blank N, Rapid pulmonary dissemination in mycosis fungoides simulating pneumonia. A case report and review of the literature. Cancer 56(3): 649-51, 1985.

Rubin DL, Burbank FH, Bradley BR and Brody WR, An experimental evaluation of central vs. peripheral injection for intravenous digital subtraction angiography (IV-DSA). Invest Radiol 19(1): 30-5, 1984.

Rubin DL, Carroll BA and Snow HD, The harmful effects of aqueous contrast agents on the gastrointestinal tract: a study of mechanism and means of counteraction. Invest Radiol 16(1): 50-8, 1981.

BOOK CHAPTERS

Rubin DL, Burnside ES, Shachter R. "A Bayesian Network to Assist Mammography Interpretation" in: Brandeau ML, Sainfort F, Pierskalla WP, eds. Operations Research and Health Care. Boston, MA: Kluwer Academic Publishers, 695-720, 2004.

Rubin DL and Carroll BA: "Possible mechanisms of the harmful effects of aqueous contrast agents on the gastrointestinal tract" in: Contrast Media: Biologic Effects and Clinical Application. Parvez Z, Moncada R, and Sovak M, eds., Vol 1. CRC Press, Inc., Boca Raton, Florida, pp 163-181, 1987.