Research Topics
| Daniel L RubinSummaryAffiliation: Stanford University Country: USA Publications
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Detail Information
Publications
Using an ontology of human anatomy to inform reasoning with geometric modelsDaniel L Rubin
Stanford Medical Informatics, Stanford, California 94305 5479, USA
Stud Health Technol Inform 111:429-35. 2005..To accomplish this, we needed to develop an architecture to combine geometric data with anatomic knowledge and reasoning services that use this information to predict the consequences of injuries...- Representing genetic sequence data for pharmacogenomics: an evolutionary approach using ontological and relational modelsDaniel L Rubin
Department of Genetics, Stanford Medical Informatics, MSOB X 215, Stanford, CA 94305 5479, USA
Bioinformatics 18:S207-15. 2002.... - National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledgeDaniel L Rubin
Stanford Medical Informatics, Stanford University, Stanford, California 94305, USA
OMICS 10:185-98. 2006.... - Using ontologies linked with geometric models to reason about penetrating injuriesDaniel L Rubin
Stanford Medical Informatics, MSOB X 215, Stanford University, Stanford, CA 94305, USA
Artif Intell Med 37:167-76. 2006..We are developing a methodology to automate reasoning about penetrating injuries using canonical knowledge combined with specific subject image data... 
A statistical approach to scanning the biomedical literature for pharmacogenetics knowledgeDaniel L Rubin
Section of Medical Informatics, MSOB X 215, Stanford, CA 94305, USA
J Am Med Inform Assoc 12:121-9. 2005..The goal of the authors was to develop an automated method to identify articles in Medline citations that contain pharmacogenetics data pertaining to gene-drug relationships...- Prognostic PET 18F-FDG uptake imaging features are associated with major oncogenomic alterations in patients with resected non-small cell lung cancerViswam S Nair
Division of Pulmonary and Critical Care Medicine, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
Cancer Res 72:3725-34. 2012..Together, our findings suggest that leveraging tumor genomics with an expanded collection of PET-FDG imaging features may enhance our understanding of FDG uptake as an imaging biomarker beyond its association with glycolysis... - Creating and curating a terminology for radiology: ontology modeling and analysisDaniel L Rubin
Section of Medical Informatics, Stanford University, MSOB X 215, 251 Campus Drive, Stanford, CA 94305, USA
J Digit Imaging 21:355-62. 2008..We believe that adopting an ontology representation of RadLex will permit more widespread use of the terminology and make it easier to collect feedback from the community that will ultimately lead to improving RadLex... - A resource to acquire and summarize pharmacogenetics knowledge in the literatureDaniel L Rubin
Department of Genetics, Stanford University, Stanford, CA 94305-5210, USA
Medinfo 11:793-7. 2004..This resource is growing, containing entries for 138 genes and 215 drugs of pharmacogenetics significance, and is a core component of PharmGKB, a pharmacogenetics knowledge base (http://www.pharmgkb.org)... - Biomedical ontologies: a functional perspectiveDaniel L Rubin
Stanford Center for Biomedical Informatics Research, Stanford, CA, USA
Brief Bioinform 9:75-90. 2008.... - PharmGKB: the Pharmacogenetics Knowledge BaseMicheal Hewett
Stanford Medical Informatics, 251 Campus Drive, MSOB X 215, Stanford, CA 94305 5479, USA
Nucleic Acids Res 30:163-5. 2002..The PharmGKB project was initiated in April 2000 and the first version of the knowledge base went online in February 2001... - Indexing pharmacogenetic knowledge on the World Wide WebRuss B Altman
Department of Genetics, Stanford Medical Informatics, Stanford University, Stanford, California, USA
Pharmacogenetics 13:3-5. 2003 - Annotation and query of tissue microarray data using the NCI ThesaurusNigam H Shah
Stanford Medical Informatics, School of Medicine, Stanford University, Stanford, CA 94305, USA
BMC Bioinformatics 8:296. 2007..These text annotations are not structured according to any ontology, making future integration of this resource with other biological and clinical data difficult... - Protégé: a tool for managing and using terminology in radiology applicationsDaniel L Rubin
Section of Medical Informatics, Stanford University, MSOB X 215, 251 Campus Drive, Stanford, CA 94305, USA
J Digit Imaging 20:34-46. 2007..In this report, we describe Protégé's features and its particular advantages in the radiology domain in the creation, maintenance, and use of radiology terminology... - Informatics in radiology: improving clinical work flow through an AIM database: a sample web-based lesion tracking applicationAaron C Abajian
Departments of Radiology and Medicine, Stanford University School of Medicine, Richard M Lucas Center, Stanford University, Stanford, CA 94305, USA
Radiographics 32:1543-52. 2012.... - The role of informatics in health care reformYueyi I Liu
Department of Radiology, Stanford University, Richard M Lucas Center, CA 94305 5488, USA
Acad Radiol 19:1094-9. 2012..We also discuss informatics related to the increasing imperatives of state and local regulations (such as radiation dose tracking) and quality initiatives... - Non-small cell lung cancer: identifying prognostic imaging biomarkers by leveraging public gene expression microarray data--methods and preliminary resultsOlivier Gevaert
Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
Radiology 264:387-96. 2012.... 
A bayesian network for differentiating benign from malignant thyroid nodules using sonographic and demographic featuresYueyi I Liu
Department of Radiology, Stanford University School of Medicine, Richard M Lucas Center, CA 94305, USA
AJR Am J Roentgenol 196:W598-605. 2011....- Informatics in radiology: RADTF: a semantic search-enabled, natural language processor-generated radiology teaching fileBao H Do
Department of Radiology, Stanford University Hospitals and Clinics, 300 Pasteur Dr, Room H1307, Stanford, CA 94305, USA
Radiographics 30:2039-48. 2010..RADTF combines a compact representation of the teaching-relevant content in radiology reports and a versatile search engine with the scale of the entire RIS-PACS collection of case material... - Semantic reasoning with image annotations for tumor assessmentMia A Levy
Stanford University, Stanford, CA, USA
AMIA Annu Symp Proc 2009:359-63. 2009..Our methods enable automated inference of semantic information about cancer lesions in images... - Computational neuroanatomy: ontology-based representation of neural components and connectivityDaniel L Rubin
Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
BMC Bioinformatics 10:S3. 2009.... - Informatics methods to enable patient-centered radiologyDaniel L Rubin
Department of Radiology and the Center for Biomedical Informatics Research, Stanford University, 251 Campus Drive, Stanford, CA 94305, USA
Acad Radiol 16:524-34. 2009.... - Automated temporal tracking and segmentation of lymphoma on serial CT examinationsJiajing Xu
Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
Med Phys 38:5879-86. 2011..In this paper, we show a method to automatically and reproducibly identify and segment abnormal lymph nodes in serial computed tomography (CT) exams... - Ontology-assisted analysis of Web queries to determine the knowledge radiologists seekDaniel L Rubin
Department of Radiology, Stanford University, Richard M Lucas Center, 1201 Welch Road, Office P285, Stanford, CA 94305 5488, USA
J Digit Imaging 24:160-4. 2011..0001). We conclude that RadLex can enable processing and categorization of user queries of Web resources and enable understanding the types of information users seek from radiology knowledge resources on the Web... - Informatics in radiology: Measuring and improving quality in radiology: meeting the challenge with informaticsDaniel L Rubin
Department of Radiology, Stanford University, Richard M Lucas Center, 1201 Welch Rd, Office P285, Stanford, CA 94305 5488, USA dlrubin stanford edu
Radiographics 31:1511-27. 2011..Institutions can tackle the challenges of assessing and improving quality in radiology by means of informatics... - Automated retrieval of CT images of liver lesions on the basis of image similarity: method and preliminary resultsSANDY A NAPEL
Department of Radiology, Stanford University School of Medicine, James H Clark Center S323, Stanford, CA 94305 5450, USA
Radiology 256:243-52. 2010.... - A data warehouse for integrating radiologic and pathologic dataDaniel L Rubin
Stanford Medical Informatics, Stanford, California 94305, USA
J Am Coll Radiol 5:210-7. 2008.... - A Controlled Vocabulary to Represent Sonographic Features of the Thyroid and its application in a Bayesian Network to Predict Thyroid Nodule MalignancyYueyi I Liu
Department of Radiology, Stanford University, Stanford, CA
Summit on Translat Bioinforma 2009:68-72. 2009..Controlled terminology for describing thyroid radiology findings could be useful to characterize thyroid nodules and could enable decision support applications... - MScanner: a classifier for retrieving Medline citationsGraham L Poulter
UCT NBN Node, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
BMC Bioinformatics 9:108. 2008.... - An ontology for PACS integrationCharles E Kahn
Division of Informatics, Department of Radiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
J Digit Imaging 19:316-27. 2006..Ontologies can represent radiological and clinical knowledge to integrate PACS with the clinical enterprise and to support the radiology interpretation process... - A probabilistic expert system that provides automated mammographic-histologic correlation: initial experienceElizabeth S Burnside
Department of Radiology, University of California School of Medicine, Box 1667, San Francisco, CA 94143 1667, USA
AJR Am J Roentgenol 182:481-8. 2004.... - Using a Bayesian network to predict the probability and type of breast cancer represented by microcalcifications on mammographyElizabeth S Burnside
Department of Radiology, University of Wisconsin Medical School, 600 Highland Avenue, Madison, WI 53792, USA
Stud Health Technol Inform 107:13-7. 2004.... - Bayesian network to predict breast cancer risk of mammographic microcalcifications and reduce number of benign biopsy results: initial experienceElizabeth S Burnside
Department of Radiology, University of Wisconsin Medical School, E3 311 Clinical Science Center, 600 Highland Ave, Madison, WI 53792 3252, USA
Radiology 240:666-73. 2006.... - A prototype symbolic model of canonical functional neuroanatomy of the motor systemIon Florin Talos
Department of Radiology, Brigham and Women s Hospital, Harvard Medical School, 75 Francis St, Boston, MA 02115, USA
J Biomed Inform 41:251-63. 2008..Although the scope of our current prototype ontology is limited to a particular functional system in the brain, it may be possible to adapt this approach for modeling other brain functional systems as well...