Daniel Rubin

Publications

• Automatic classification of mammography reports by BI-RADS breast tissue composition class. Percha B, Nassif H, Lipson J, Burnside E, Rubin D. J Am Med Inform Assoc. 2012 Sep-Oct; 19 (5): 913-6
• Informatics in radiology: improving clinical work flow through an AIM database: a sample web-based lesion tracking application. Abajian AC, Levy M, Rubin DL. Radiographics. 2012 Sep-Oct; 32 (5): 1543-52
• A comprehensive descriptor of shape: method and application to content-based retrieval of similar appearing lesions in medical images. Xu J, Faruque J, Beaulieu CF, Rubin D, Napel S. J Digit Imaging. 2012; 25 (1): 121-8
• Automatic annotation of radiological observations in liver CT images. Gimenez F, Xu J, Liu Y, Liu T, Beaulieu C, Rubin D, Napel S. AMIA Annu Symp Proc. 2012: 2012 257-63
• Modeling Perceptual Similarity Measures in CT Images of Focal Liver Lesions. Faruque J, Rubin DL, Beaulieu CF, Napel S. J Digit Imaging. 2012
• Non-small cell lung cancer: identifying prognostic imaging biomarkers by leveraging public gene expression microarray data--methods and preliminary results. Gevaert O, Xu J, Hoang CD, Leung AN, Xu Y, Quon A, Rubin DL, Napel S, Plevritis SK. Radiology. 2012; 264 (2): 387-96
• Prognostic PET 18F-FDG uptake imaging features are associated with major oncogenomic alterations in patients with resected non-small cell lung cancer. Nair VS, Gevaert O, Davidzon G, Napel S, Graves EE, Hoang CD, Shrager JB, Quon A, Rubin DL, Plevritis SK. Cancer Res. 2012; 72 (15): 3725-34
• Quantifying the margin sharpness of lesions on radiological images for content-based image retrieval. Xu J, Napel S, Greenspan H, Beaulieu CF, Agrawal N, Rubin D. Med Phys. 2012; 39 (9): 5405-18
• The role of informatics in health care reform. Liu YI, Rubin DL. Acad Radiol. 2012; 19 (9): 1094-9
• Current and future trends in imaging informatics for oncology. Levy MA, Rubin DL. Cancer J. 2011 Jul-Aug; 17 (4): 203-10
• A bayesian network for differentiating benign from malignant thyroid nodules using sonographic and demographic features. Liu YI, Kamaya A, Desser TS, Rubin DL. AJR Am J Roentgenol. 2011; 196 (5): W598-605
• A practical method for transforming free-text eligibility criteria into computable criteria. Tu SW, Peleg M, Carini S, Bobak M, Ross J, Rubin D, Sim I. J Biomed Inform. 2011; 44 (2): 239-50
• Automated temporal tracking and segmentation of lymphoma on serial CT examinations. Xu J, Greenspan H, Napel S, Rubin DL. Med Phys. 2011; 38 (11): 5879-86
• Evaluation of negation and uncertainty detection and its impact on precision and recall in search. Wu AS, Do BH, Kim J, Rubin DL. J Digit Imaging. 2011; 24 (2): 234-42
• Informatics in radiology: Measuring and improving quality in radiology: meeting the challenge with informatics. Rubin DL, Radiographics. 2011; 31 (6): 1511-27
• Managing biomedical image metadata for search and retrieval of similar images. Korenblum D, Rubin D, Napel S, Rodriguez C, Beaulieu C. J Digit Imaging. 2011; 24 (4): 739-48
• Ontology-assisted analysis of Web queries to determine the knowledge radiologists seek. Rubin DL, Flanders A, Kim W, Siddiqui KM, Kahn CE. J Digit Imaging. 2011; 24 (1): 160-4
• Automated retrieval of CT images of liver lesions on the basis of image similarity: method and preliminary results. Napel SA, Beaulieu CF, Rodriguez C, Cui J, Xu J, Gupta A, Korenblum D, Greenspan H, Ma Y, Rubin DL. Radiology. 2010; 256 (1): 243-52
• Imaging informatics: toward capturing and processing semantic information in radiology images. Rubin DL, Napel S. Yearb Med Inform. 2010: 34-42
• Informatics in radiology: RADTF: a semantic search-enabled, natural language processor-generated radiology teaching file. Do BH, Wu A, Biswal S, Kamaya A, Rubin DL. Radiographics. 2010; 30 (7): 2039-48
• The caBIG annotation and image Markup project. Channin DS, Mongkolwat P, Kleper V, Sepukar K, Rubin DL. J Digit Imaging. 2010; 23 (2): 217-25
• A Controlled Vocabulary to Represent Sonographic Features of the Thyroid and its application in a Bayesian Network to Predict Thyroid Nodule Malignancy. Liu YI, Kamaya A, Desser TS, Rubin DL. Summit on Translat Bioinforma. 2009: 2009 68-72
• BioPortal: ontologies and integrated data resources at the click of a mouse. Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA. Nucleic Acids Res. 2009; 37 (Web Server issue): W170-3
• Comparison of concept recognizers for building the Open Biomedical Annotator. Shah NH, Bhatia N, Jonquet C, Rubin D, Chiang AP, Musen MA. BMC Bioinformatics. 2009: 10 Suppl 9 S14
• Computational neuroanatomy: ontology-based representation of neural components and connectivity. Rubin DL, Talos IF, Halle M, Musen MA, Kikinis R. BMC Bioinformatics. 2009: 10 Suppl 2 S3
• Computing human image annotation. Channin DS, Mongkolwat P, Kleper V, Rubin DL. Conf Proc IEEE Eng Med Biol Soc. 2009: 2009 7065-8
• Informatics methods to enable patient-centered radiology. Rubin DL, Acad Radiol. 2009; 16 (5): 524-34
• Semantic reasoning with image annotations for tumor assessment. Levy MA, O'Connor MJ, Rubin DL. AMIA Annu Symp Proc. 2009: 2009 359-63
• The Annotation and Image Mark-up project. Channin DS, Mongkolwat P, Kleper V, Rubin DL. Radiology. 2009; 253 (3): 590-2
• A Bayesian classifier for differentiating benign versus malignant thyroid nodules using sonographic features. Liu YI, Kamaya A, Desser TS, Rubin DL. AMIA Annu Symp Proc. 2008: 419-23
• A data warehouse for integrating radiologic and pathologic data. Rubin DL, Desser TS. J Am Coll Radiol. 2008; 5 (3): 210-7
• BioPortal: ontologies and data resources with the click of a mouse. Musen MA, Musen M, Shah NH, Shah N, Noy NF, Noy N, Dai BY, Dai B, Dorf M, Dorf M, Griffith N, Griffith N, Buntrok J, Buntrock JD, Jonquet C, Jonquet C, Montegut MJ, Montegut MJ, Rubin DL, Rubin DL. AMIA Annu Symp Proc. 2008: 1223-4
• Biomedical ontologies: a functional perspective. Rubin DL, Shah NH, Noy NF. Brief Bioinform. 2008; 9 (1): 75-90
• Creating and curating a terminology for radiology: ontology modeling and analysis. Rubin DL, J Digit Imaging. 2008; 21 (4): 355-62
• Network analysis of intrinsic functional brain connectivity in Alzheimer's disease. Supekar K, Menon V, Rubin D, Musen M, Greicius MD. PLoS Comput Biol. 2008; 4 (6): e1000100
• Tool support to enable evaluation of the clinical response to treatment. Levy MA, Rubin DL. AMIA Annu Symp Proc. 2008: 399-403
• iPad: Semantic annotation and markup of radiological images. Rubin DL, Rodriguez C, Shah P, Beaulieu C. AMIA Annu Symp Proc. 2008: 626-30
• Annotation and query of tissue microarray data using the NCI Thesaurus. Shah NH, Rubin DL, Espinosa I, Montgomery K, Musen MA. BMC Bioinformatics. 2007: 8 296
• Knowledge Zone: a public repository of peer-reviewed biomedical ontologies. Supekar K, Rubin D, Noy N, Musen M. Stud Health Technol Inform. 2007; 129 (Pt 1): 812-6
• LesionViewer: a tool for tracking cancer lesions over time. Levy MA, Garg A, Tam A, Garten Y, Rubin DL. AMIA Annu Symp Proc. 2007: 443-7
• Protégé: a tool for managing and using terminology in radiology applications. Rubin DL, Noy NF, Musen MA. J Digit Imaging. 2007: 20 Suppl 1 34-46
• Coverage of emergency after-hours ultrasound cases: survey of practices at U.S. Teaching hospitals. Desser TS, Rubin DL, Schraedley-Desmond P. Acad Radiol. 2006; 13 (2): 249-53
• National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. Rubin DL, Lewis SE, Mungall CJ, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Solbrig H, Storey MA, Smith B, Day-Richter J, Noy NF, Musen MA. OMICS. 2006; 10 (2): 185-98
• Ontology-based annotation and query of tissue microarray data. Shah NH, Rubin DL, Supekar KS, Musen MA. AMIA Annu Symp Proc. 2006: 709-13
• Ontology-based representation of simulation models of physiology. Rubin DL, Grossman D, Neal M, Cook DL, Bassingthwaighte JB, Musen MA. AMIA Annu Symp Proc. 2006: 664-8
• Using ontologies linked with geometric models to reason about penetrating injuries. Rubin DL, Dameron O, Bashir Y, Grossman D, Dev P, Musen MA. Artif Intell Med. 2006; 37 (3): 167-76
• A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge. Rubin DL, Thorn CF, Klein TE, Altman RB. J Am Med Inform Assoc. 2005 Mar-Apr; 12 (2): 121-9
• Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study. Dameron O, Rubin DL, Musen MA. AMIA Annu Symp Proc. 2005: 181-5
• Use of description logic classification to reason about consequences of penetrating injuries. Rubin DL, Dameron O, Musen MA. AMIA Annu Symp Proc. 2005: 649-53
• Using an ontology of human anatomy to inform reasoning with geometric models. Rubin DL, Bashir Y, Grossman D, Dev P, Musen MA. Stud Health Technol Inform. 2005: 111 429-35
• A resource to acquire and summarize pharmacogenetics knowledge in the literature. Rubin DL, Carrillo M, Woon M, Conroy J, Klein TE, Altman RB. Stud Health Technol Inform. 2004; 107 (Pt 2): 793-7
• Linking ontologies with three-dimensional models of anatomy to predict the effects of penetrating injuries. Rubin DL, Bashir Y, Grossman D, Dev P, Musen MA. Conf Proc IEEE Eng Med Biol Soc. 2004: 5 3128-31
• Indexing pharmacogenetic knowledge on the World Wide Web. Altman RB, Flockhart DA, Sherry ST, Oliver DE, Rubin DL, Klein TE. Pharmacogenetics. 2003; 13 (1): 3-5
• Automating data acquisition into ontologies from pharmacogenetics relational data sources using declarative object definitions and XML. Rubin DL, Hewett M, Oliver DE, Klein TE, Altman RB. Pac Symp Biocomput. 2002: 88-99
• Ontology development for a pharmacogenetics knowledge base. Oliver DE, Rubin DL, Stuart JM, Hewett M, Klein TE, Altman RB. Pac Symp Biocomput. 2002: 65-76
• PharmGKB: the Pharmacogenetics Knowledge Base. Hewett M, Oliver DE, Rubin DL, Easton KL, Stuart JM, Altman RB, Klein TE. Nucleic Acids Res. 2002; 30 (1): 163-5
• Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational models. Rubin DL, Shafa F, Oliver DE, Hewett M, Altman RB. Bioinformatics. 2002: 18 Suppl 1 S207-15
• Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base. 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, Altman RB. Pharmacogenomics J. 2001; 1 (3): 167-70
• A Bayesian network for mammography. Burnside E, Rubin D, Shachter R. Proc AMIA Symp. 2000: 106-10
• Influence of viscosity on WIN 39996 as a contrast agent for gastrointestinal magnetic resonance imaging. Rubin DL, Muller HH, Young SW, Hunke WA, Gorman WG, Lee KC. Invest Radiol. 1995; 30 (4): 226-31
• Dynamics of tumor imaging with Gd-DTPA-polyethylene glycol polymers: dependence on molecular weight. Desser TS, Rubin DL, Muller HH, Qing F, Khodor S, Zanazzi G, Young SW, Ladd DL, Wellons JA, Kellar KE. J Magn Reson Imaging. 1994 May-Jun; 4 (3): 467-72
• Nanoparticulate contrast media. Blood-pool and liver-spleen imaging. Rubin DL, Desser TS, Qing F, Muller HH, Young SW, McIntire GL, Bacon E, Cooper E, Toner J. Invest Radiol. 1994: 29 Suppl 2 S280-3
• Optimization of an oral magnetic particle formulation as a gastrointestinal contrast agent for magnetic resonance imaging. Rubin DL, Muller HH, Young SW, Hunke WA, Gorman WG. Invest Radiol. 1994; 29 (1): 81-6
• Quantitation of saturation effects versus dose in three-dimensional time-of-flight magnetic resonance angiography with blood-pool contrast agents. Desser TS, Rubin DL, Fan Q, Muller HH, Young SW, Kellar KE, Wellons JA, Ladd DL, Toner JL, Snow RA. Invest Radiol. 1994: 29 Suppl 2 S65-8
• Liquid oral magnetic particles as a gastrointestinal contrast agent for MR imaging: efficacy in vivo. Rubin DL, Muller HH, Sidhu MK, Young SW, Hunke WA, Gorman WG. J Magn Reson Imaging. 1993 Jan-Feb; 3 (1): 113-8
• Formulation of radiographically detectable gastrointestinal contrast agents for magnetic resonance imaging: effects of a barium sulfate additive on MR contrast agent effectiveness. Rubin DL, Muller HH, Young SW. Magn Reson Med. 1992; 23 (1): 154-65
• Intraluminal contrast enhancement and MR visualization of the bowel wall: efficacy of PFOB. Rubin DL, Muller HH, Nino-Murcia M, Sidhu M, Christy V, Young SW. J Magn Reson Imaging. 1991 May-Jun; 1 (3): 371-80
• Methods for the systematic investigation of gastrointestinal contrast media for MRI: evaluation of intestinal distribution by radiographic monitoring. Rubin DL, Muller HH, Young SW. Magn Reson Imaging. 1991; 9 (3): 285-93
• Detection of hepatic malignancies using Mn-DPDP (manganese dipyridoxal diphosphate) hepatobiliary MRI contrast agent. Young SW, Bradley B, Muller HH, Rubin DL. Magn Reson Imaging. 1990; 8 (3): 267-76
• Magnetic susceptibility effects and their application in the development of new ferromagnetic catheters for magnetic resonance imaging. Rubin DL, Ratner AV, Young SW. Invest Radiol. 1990; 25 (12): 1325-32
• Infectious rotavirus enters cells by direct cell membrane penetration, not by endocytosis. Kaljot KT, Shaw RD, Rubin DH, Greenberg HB. J Virol. 1988; 62 (4): 1136-44
• Pulmonary function in advanced pulmonary hypertension. Burke CM, Glanville AR, Morris AJ, Rubin D, Harvey JA, Theodore J, Robin ED. Thorax. 1987; 42 (2): 131-5