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    First name: Joshua C.
    Last name: Denny
    DBLP: 41/7339
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    Below you find the publications which have been written by this author.

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    Conference paper
    Yonghui Wu, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Lulu Wang, Carmelo Blanquicett, Ergin Soysal, Jun Xu 0007, Hua Xu.
    A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD).
    JAMIA 2017, Volume 24 (0) 2017
    Conference paper
    Laura K. Wiley, Jacob P. VanHouten, David Samuels, Melinda Aldrich, Dan M. Roden, Josh F. Peterson, Joshua C. Denny.
    Strategies for Equitable Pharmacogenomic-Guided Warfarin Dosing Among European and African American Individuals in a Clinical Population.
    Biocomputing 2017: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 3-7, 2017 2017 (0) 2017
    Conference paper
    Alexander A. Morgan, Dana C. Crawford, Joshua C. Denny, Sean D. Mooney, Bruce J. Aronow, Steven E. Brenner.
    Session Introduction.
    Biocomputing 2017: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 3-7, 2017 2017 (0) 2017
    Conference paper
    Yukun Chen, Thomas A. Lasko, Qiaozhu Mei, Qingxia Chen, Sungrim Moon, Jingqi Wang, Ky Nguyen, Tolulola Dawodu, Trevor Cohen, Joshua C. Denny, Hua Xu.
    An active learning-enabled annotation system for clinical named entity recognition.
    BMC Med. Inf. Decision Making 2017, Volume 17 (0) 2017
    Journal article
    Robert M. Cronin, Daniel Fabbri, Joshua C. Denny, S. Trent Rosenbloom, Gretchen Purcell Jackson.
    A comparison of rule-based and machine learning approaches for classifying patient portal messages.
    I. J. Medical Informatics 2017, Volume 105 (0) 2017
    Conference paper
    Jette Henderson, Joyce C. Ho, Abel N. Kho, Joshua C. Denny, Bradley Malin, Jimeng Sun, Joydeep Ghosh.
    Granite: Diversified, Sparse Tensor Factorization for Electronic Health Record-Based Phenotyping.
    2017 IEEE International Conference on Healthcare Informatics, ICHI 2017, Park City, UT, USA, August 23-26, 2017 2017 (0) 2017
    Journal article
    Rachel L. Richesson, Jimeng Sun, Jyotishman Pathak, Abel N. Kho, Joshua C. Denny.
    Clinical phenotyping in selected national networks: demonstrating the need for high-throughput, portable, and computational methods.
    Artificial Intelligence in Medicine 2016, Volume 71 (0) 2016
    Conference paper
    Laura K. Wiley, Peter Tarczy-Hornoch, Joshua C. Denny, Robert R. Freimuth, Casey Lynnette Overby, Nigam H. Shah, Ross D. Martin, Indra Neil Sarkar.
    Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting.
    JAMIA 2016, Volume 23 (0) 2016
    Conference paper
    Raymond Heatherly, Luke V. Rasmussen, Peggy L. Peissig, Jennifer A. Pacheco, Paul A. Harris, Joshua C. Denny, Bradley Malin.
    A multi-institution evaluation of clinical profile anonymization.
    JAMIA 2016, Volume 23 (0) 2016
    Conference paper
    Wei-Qi Wei, Pedro L. Teixeira, Huan Mo, Robert M. Cronin, Jeremy L. Warner, Joshua C. Denny.
    Combining billing codes, clinical notes, and medications from electronic health records provides superior phenotyping performance.
    JAMIA 2016, Volume 23 (0) 2016
    Conference paper
    Guoqian Jiang, Richard C. Kiefer, Luke V. Rasmussen, Harold R. Solbrig, Huan Mo, Jennifer A. Pacheco, Jie Xu, Enid N. H. Montague, William K. Thompson, Joshua C. Denny, Christopher G. Chute, Jyotishman Pathak.
    Developing a data element repository to support EHR-driven phenotype algorithm authoring and execution.
    Journal of Biomedical Informatics 2016, Volume 62 (0) 2016
    Conference paper
    Jessica D. Tenenbaum, Subha Madhavan, Robert R. Freimuth, Joshua C. Denny, Lewis J. Frey.
    Translational Bioinformatics 101.
    Biocomputing 2016: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 4-8, 2016 2016 (0) 2016
    Conference paper
    Lewis J. Frey, Elmer V. Bernstam, Joshua C. Denny.
    Precision medicine informatics.
    JAMIA 2016, Volume 23 (0) 2016
    Conference paper
    Sungrim Moon, Yukun Chen, Jingqi Wang, Joshua C. Denny, S. Trent Rosenbloom, Ky Nguyen, Tolulola Dawodu, Hua Xu.
    Applying Active Learning to Clinical Abbreviation Disambiguation in Real Time.
    AMIA 2016, American Medical Informatics Association Annual Symposium, Chicago, IL, USA, November 12-16, 2016 2016 (0) 2016
    Conference paper
    Rui Duan, Ming Cao, Yonghui Wu, Jing Huang, Joshua C. Denny, Hua Xu, Yong Chen.
    An Empirical Study for Impacts of Measurement Errors on EHR based Association Studies.
    AMIA 2016, American Medical Informatics Association Annual Symposium, Chicago, IL, USA, November 12-16, 2016 2016 (0) 2016
    Conference paper
    Yang Huang, Hua Xu, Joshua C. Denny.
    Building Successful Natural Language Processing Applications in Clinical Research and Healthcare Operations.
    AMIA 2016, American Medical Informatics Association Annual Symposium, Chicago, IL, USA, November 12-16, 2016 2016 (0) 2016
    Conference paper
    Guoqian Jiang, William K. Thompson, Luke V. Rasmussen, Richard C. Kiefer, Jennifer A. Pacheco, Huan Mo, Peter Speltz, Joshua C. Denny, Jyotishman Pathak.
    An NLP Extension to the Quality Data Model for EHR-Driven Phenotype Algorithm Authoring and Execution.
    AMIA 2016, American Medical Informatics Association Annual Symposium, Chicago, IL, USA, November 12-16, 2016 2016 (0) 2016
    Conference paper
    Jacqueline Kirby, Peter Speltz, Luke V. Rasmussen, Melissa A. Basford, Omri Gottesman, Peggy L. Peissig, Jennifer A. Pacheco, Gerard Tromp, Jyotishman Pathak, David Carrell, Stephen B. Ellis, Todd Lingren, William K. Thompson, Guergana K. Savova, Jonathan L. Haines, Dan M. Roden, Paul A. Harris, Joshua C. Denny.
    PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability.
    JAMIA 2016, Volume 23 (0) 2016
    Journal article
    You Chen, Joydeep Ghosh, Cosmin Adrian Bejan, Carl A. Gunter, Siddharth Gupta, Abel N. Kho, David M. Liebovitz, Jimeng Sun, Joshua C. Denny, Bradley Malin.
    Building bridges across electronic health record systems through inferred phenotypic topics.
    Journal of Biomedical Informatics 2015, Volume 55 (0) 2015
    Journal article
    Min Jiang, Yang Huang, Jung-Wei Fan, Buzhou Tang, Joshua C. Denny, Hua Xu.
    Parsing clinical text: how good are the state-of-the-art parsers?
    BMC Med. Inf. Decision Making 2015, Volume 15 (0) 2015
    Conference paper
    Jingchun Sun, Min Zhao, Peilin Jia, Lily Wang, Yonghui Wu, Carissa Iverson, Yubo Zhou, Erica A. Bowton, Dan M. Roden, Joshua C. Denny, Melinda Aldrich, Hua Xu, Zhongming Zhao.
    Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action.
    PLoS Computational Biology 2015, Volume 11 (0) 2015
    Conference paper
    Yichen Wang, Robert Chen, Joydeep Ghosh, Joshua C. Denny, Abel N. Kho, You Chen, Bradley Malin, Jimeng Sun.
    Rubik: Knowledge Guided Tensor Factorization and Completion for Health Data Analytics.
    Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Sydney, NSW, Australia, August 10-13, 2015 2015 (0) 2015
    Journal article
    Joshua C. Denny, Anderson Spickard III, Peter Speltz, Renee Porier, Donna E. Rosenstiel, James S. Powers.
    Using natural language processing to provide personalized learning opportunities from trainee clinical notes.
    Journal of Biomedical Informatics 2015, Volume 56 (0) 2015
    Conference paper
    Guoqian Jiang, Harold R. Solbrig, Richard C. Kiefer, Luke V. Rasmussen, Huan Mo, Peter Speltz, William K. Thompson, Joshua C. Denny, Christopher G. Chute, Jyotishman Pathak.
    A Standards-based Semantic Metadata Repository to Support EHR-driven Phenotype Authoring and Execution.
    MEDINFO 2015: eHealth-enabled Health - Proceedings of the 15th World Congress on Health and Biomedical Informatics, São Paulo, Brazil, 19-23 August 2015 2015 (0) 2015
    Conference paper
    Yukun Chen, Thomas A. Lasko, Qiaozhu Mei, Joshua C. Denny, Hua Xu.
    A study of active learning methods for named entity recognition in clinical text.
    Journal of Biomedical Informatics 2015, Volume 58 (0) 2015
    Conference paper
    Huan Mo, William K. Thompson, Luke V. Rasmussen, Jennifer A. Pacheco, Guoqian Jiang, Richard C. Kiefer, Qian Zhu, Jie Xu, Enid N. H. Montague, David Carrell, Todd Lingren, Frank D. Mentch, Yizhao Ni, Firas H. Wehbe, Peggy L. Peissig, Gerard Tromp, Eric B. Larson, Christopher G. Chute, Jyotishman Pathak, Joshua C. Denny, Peter Speltz, Abel N. Kho, Gail P. Jarvik, Cosmin Adrian Bejan, Marc S. Williams, Kenneth Borthwick, Terrie E. Kitchner, Dan M. Roden, Paul A. Harris.
    Desiderata for computable representations of electronic health records-driven phenotype algorithms.
    JAMIA 2015, Volume 22 (0) 2015
    Conference paper
    Cosmin Adrian Bejan, Wei-Qi Wei, Joshua C. Denny.
    Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text.
    JAMIA 2015, Volume 22 (0) 2015
    Conference paper
    Chen Lin, Elizabeth W. Karlson, Dmitriy Dligach, Monica P. Ramirez, Timothy A. Miller, Huan Mo, Natalie S. Braggs, Andrew Cagan, Vivian S. Gainer, Joshua C. Denny, Guergana K. Savova.
    Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record.
    JAMIA 2015, Volume 22 (0) 2015
    Conference paper
    Jeremy L. Warner, Joshua C. Denny, David A. Kreda, Gil Alterovitz.
    Seeing the forest through the trees: uncovering phenomic complexity through interactive network visualization.
    JAMIA 2015, Volume 22 (0) 2015
    Conference paper
    Jie Xu, Luke V. Rasmussen, Pamela L. Shaw, Guoqian Jiang, Richard C. Kiefer, Huan Mo, Jennifer A. Pacheco, Peter Speltz, Qian Zhu, Joshua C. Denny, Jyotishman Pathak, William K. Thompson, Enid N. H. Montague.
    Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research.
    JAMIA 2015, Volume 22 (0) 2015
    Conference paper
    Guoqian Jiang, Harold R. Solbrig, Richard C. Kiefer, Luke V. Rasmussen, Huan Mo, Jennifer A. Pacheco, Enid N. H. Montague, Jie Xu, Peter Speltz, William K. Thompson, Joshua C. Denny, Christopher G. Chute, Jyotishman Pathak.
    Harmonization of Quality Data Model with HL7 FHIR to Support EHR-driven Phenotype Authoring and Execution: A Pilot Study.
    AMIA 2015, American Medical Informatics Association Annual Symposium, San Francisco, CA, USA, November 14-18, 2015 2015 (0) 2015
    Conference paper
    Huan Mo, Jennifer A. Pacheco, Richard C. Kiefer, Luke V. Rasmussen, Jyotishman Pathak, Joshua C. Denny, William K. Thompson.
    Translating Electronic Clinical Quality Measures to Executable, Portable, and Customizable Workflows in KNIME.
    AMIA 2015, American Medical Informatics Association Annual Symposium, San Francisco, CA, USA, November 14-18, 2015 2015 (0) 2015
    Conference paper
    Jyotishman Pathak, Joshua C. Denny, William K. Thompson, Luke V. Rasmussen.
    PhEMA: Phenotype Modeling, Sharing and Execution Architecture.
    AMIA 2015, American Medical Informatics Association Annual Symposium, San Francisco, CA, USA, November 14-18, 2015 2015 (0) 2015
    Conference paper
    Jessica D. Tenenbaum, Joshua C. Denny, David Flannery, Douglas B. Fridsma, Marc S. Williams.
    Building the Computational Workforce for Precision Medicine.
    AMIA 2015, American Medical Informatics Association Annual Symposium, San Francisco, CA, USA, November 14-18, 2015 2015 (0) 2015
    Conference paper
    Guergana K. Savova, Rebecca S. Jacobson, Joshua C. Denny, Nicole L. Washington, Harry Hochheiser.
    Natural Language Processing for Phenotype Extraction: Challenges in Extraction and Representation.
    AMIA 2015, American Medical Informatics Association Annual Symposium, San Francisco, CA, USA, November 14-18, 2015 2015 (0) 2015
    Conference paper
    Yukun Chen, Sungrim Moon, Thomas A. Lasko, Qiaozhu Mei, Jingqi Wang, Trevor Cohen, Qingxia Chen, Joshua C. Denny, Hua Xu.
    Real Time Active Learning Study for Clinical Named Entity Recognition.
    AMIA 2015, American Medical Informatics Association Annual Symposium, San Francisco, CA, USA, November 14-18, 2015 2015 (0) 2015
    Conference paper
    Jennifer A. Pacheco, Abel N. Kho, Jyotishman Pathak, Joshua C. Denny, Shawn N. Murphy.
    (Authoring) Rules, (Distributed Query) Tools, and Drools: The challenging new world of high throughput phenotyping.
    AMIA 2015, American Medical Informatics Association Annual Symposium, San Francisco, CA, USA, November 14-18, 2015 2015 (0) 2015
    Conference paper
    Enid N. H. Montague, Jie Xu, Luke V. Rasmussen, Joshua C. Denny, Guoqian Jiang, Richard C. Kiefer, Jennifer A. Pacheco, Peter Speltz, William K. Thompson, Jyotishman Pathak.
    Usability of a phenotype builder prototype and lessons learned for the design of phenotyping tools.
    AMIA 2015, American Medical Informatics Association Annual Symposium, San Francisco, CA, USA, November 14-18, 2015 2015 (0) 2015
    Conference paper
    Travis Osterman, Wei-Qi Wei, Joshua C. Denny.
    Quantifying Tobacco Exposure Using Clinical Notes and Natural Language Processing to Enable Lung Cancer Screening.
    AMIA 2015, American Medical Informatics Association Annual Symposium, San Francisco, CA, USA, November 14-18, 2015 2015 (0) 2015
    Conference paper
    Alex C. Cheng, Marc Beller, Joshua C. Denny.
    Predicting Clinical Laboratory Turnaround Time.
    AMIA 2015, American Medical Informatics Association Annual Symposium, San Francisco, CA, USA, November 14-18, 2015 2015 (0) 2015
    Conference paper
    Yoonjung Y. Joo, Jennifer A. Pacheco, Loren L. Armstrong, William K. Thompson, Robert J. Carroll, Joshua C. Denny, Peggy L. Peissig, James G. Linneman, Jyotishman Pathak, Girish Nadkarni, Laura Rasmussen-Torvik, M. Geoffrey Hayes, Abel N. Kho.
    A Genome- and Phenome- Wide Study of Diverticulosis.
    AMIA 2015, American Medical Informatics Association Annual Symposium, San Francisco, CA, USA, November 14-18, 2015 2015 (0) 2015
    Conference paper
    Yaomin Xu, Todd L. Edwards, Lisa Bastarache, Rebecca N. Jerome, Shilin Zho, Eric Torstenson, Wei-Qi Wei, Jana Shirey-Rice, Erica A. Bowton, Shyr Yu, Jill M. Pulley, Joshua C. Denny.
    PheWAS Network Analysis and Visualization.
    AMIA 2015, American Medical Informatics Association Annual Symposium, San Francisco, CA, USA, November 14-18, 2015 2015 (0) 2015
    Conference paper
    Robert M. Cronin, Daniel Fabbri, Joshua C. Denny, Gretchen Purcell Jackson.
    Automated Classification of Consumer Health Information Needs in Patient Portal Messages.
    AMIA 2015, American Medical Informatics Association Annual Symposium, San Francisco, CA, USA, November 14-18, 2015 2015 (0) 2015
    Conference paper
    Hua Xu, Melinda Aldrich, Qingxia Chen, Hongfang Liu, Neeraja B. Peterson, Qi Dai, Mia A. Levy, Anushi Shah, Han Xue, Xiaoyang Ruan, Min Jiang, Ying Li, Jamii St Julien, Jeremy L. Warner, Carol Friedman, Dan M. Roden, Joshua C. Denny.
    Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality.
    JAMIA 2015, Volume 22 (0) 2015
    Conference paper
    Jimeng Sun, Candace D. McNaughton, Ping Zhang, Adam Perer, Aris Gkoulalas-Divanis, Joshua C. Denny, Jacqueline Kirby, Thomas A. Lasko, Alexander Saip, Bradley Malin.
    Predicting changes in hypertension control using electronic health records from a chronic disease management program.
    JAMIA 2014, Volume 21 (0) 2014
    Conference paper
    Robert J. Carroll, Lisa Bastarache, Joshua C. Denny.
    R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment.
    Bioinformatics 2014, Volume 30 (0) 2014
    Journal article
    Luke V. Rasmussen, William K. Thompson, Jennifer A. Pacheco, Abel N. Kho, David Carrell, Jyotishman Pathak, Peggy L. Peissig, Gerard Tromp, Joshua C. Denny, Justin Starren.
    Design patterns for the development of electronic health record-driven phenotype extraction algorithms.
    Journal of Biomedical Informatics 2014, Volume 51 (0) 2014
    Conference paper
    Min Jiang, Yang Huang, Jung-Wei Fan, Buzhou Tang, Joshua C. Denny, Hua Xu.
    Parsing Clinical Text: How Good are the State-of-the-Art Parsers?
    Proceedings of the ACM 8th International Workshop on Data and Text Mining in Bioinformatics, DTMBIO@CIKM 2014, Shanghai, China, November 7, 2014 2014 (0) 2014
    Conference paper
    Wei Xie, Murat Kantarcioglu, William S. Bush, Dana C. Crawford, Joshua C. Denny, Raymond Heatherly, Bradley Malin.
    SecureMA: protecting participant privacy in genetic association meta-analysis.
    Bioinformatics 2014, Volume 30 (0) 2014
    Conference paper
    Janina M. Jeff, Kristin Brown-Gentry, Robert J. Goodloe, Marylyn D. Ritchie, Joshua C. Denny, Abel N. Kho, Loren L. Armstrong, Bob McClellan Jr., Ping Mayo, Melissa Allen, Hailing Jin, Niloufar B. Gillani, Nathalie Schnetz-Boutaud, Holli H. Dilks, Melissa A. Basford, Jennifer A. Pacheco, Gail P. Jarvik, Rex L. Chisholm, Dan M. Roden, M. Geoffrey Hayes, Dana C. Crawford.
    Replication of SCN5A Associations with Electrocardiographic Traits in African Americans from Clinical and Epidemiologic Studies.
    Applications of Evolutionary Computation - 17th European Conference, EvoApplications 2014, Granada, Spain, April 23-25, 2014, Revised Selected Papers 2014 (0) 2014
    Journal article
    Joyce C. Ho, Joydeep Ghosh, Steven R. Steinhubl, Walter F. Stewart, Joshua C. Denny, Bradley Malin, Jimeng Sun.
    Limestone: High-throughput candidate phenotype generation via tensor factorization.
    Journal of Biomedical Informatics 2014, Volume 52 (0) 2014
    Journal article
    Raymond Heatherly, Joshua C. Denny, Jonathan L. Haines, Dan M. Roden, Bradley Malin.
    Size matters: How population size influences genotype-phenotype association studies in anonymized data.
    Journal of Biomedical Informatics 2014, Volume 52 (0) 2014
    Conference paper
    Cosmin Adrian Bejan, Joshua C. Denny.
    Learning to Identify Treatment Relations in Clinical Text.
    AMIA 2014, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 15-19, 2014 2014 (0) 2014
    Conference paper
    Casey Lynnette Overby, Luke V. Rasmussen, Andrea Hartzler, John J. Connolly, Josh F. Peterson, RoseMary Hedberg, Robert R. Freimuth, Brian H. Shirts, Joshua C. Denny, Eric B. Larson, Christopher G. Chute, Gail P. Jarvik, James D. Ralston, Alan R. Shuldiner, Iftikhar J. Kullo, Peter Tarczy-Hornoch, Marc S. Williams.
    A Template for Authoring and Adapting Genomic Medicine Content in the eMERGE Infobutton Project.
    AMIA 2014, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 15-19, 2014 2014 (0) 2014
    Conference paper
    Robert J. Carroll, Jeremy L. Warner, Anne E. Eyler, Charles Moore, Jayanth Doss, Katherine P. Liao, Robert M. Plenge, Joshua C. Denny.
    PheWAS and Genetics Define Subphenotypes in Drug Response.
    AMIA 2014, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 15-19, 2014 2014 (0) 2014
    Conference paper
    Hua Xu, Qingxia Chen, Jeremy L. Warner, Han Xue, Min Jiang, Anushi Shah, Melinda Aldrich, Qi Dai, Joshua C. Denny.
    Mining electronic health record data to detect drug-repurposing signals for cancers.
    AMIA 2014, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 15-19, 2014 2014 (0) 2014
    Conference paper
    Yukun Chen, Jesse O. Wrenn, Hua Xu, Anderson Spickard III, Ralf Habermann, James S. Powers, Joshua C. Denny.
    Automated Assessment of Medical Students' Clinical Exposures according to AAMC Geriatric Competencies.
    AMIA 2014, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 15-19, 2014 2014 (0) 2014
    Conference paper
    Yukun Chen, Yaoyun Zhang, Qiaozhu Mei, Dead Account, Joshua C. Denny, Hua Xu.
    A Preliminary Study of Coupling Transfer Learning with Active Learning for Clinical Named Entity Recognition between Two Institutions.
    AMIA 2014, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 15-19, 2014 2014 (0) 2014
    Conference paper
    Wei-Qi Wei, Pedro L. Teixeira, Huan Mo, Robert M. Cronin, Jeremy L. Warner, Joshua C. Denny.
    Evaluation of Diagnosis Codes, Clinical Notes, and Medications on Identifying Subjects with a Specific Disease Phenotype.
    AMIA 2014, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 15-19, 2014 2014 (0) 2014
    Conference paper
    Qian Zhu, Huan Mo, Luke V. Rasmussen, Andrew R. Post, Jennifer A. Pacheco, Jie Xu, Richard C. Kiefer, Peter Speltz, Enid N. H. Montague, William K. Thompson, Joshua C. Denny, Jyotishman Pathak.
    Qualitative evaluation of three phenotype information models to find methotrexate liver injury.
    AMIA 2014, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 15-19, 2014 2014 (0) 2014
    Conference paper
    Luke V. Rasmussen, Jie Xu, Ruijue Liu, Qian Zhu, Jennifer A. Pacheco, Jyotishman Pathak, William K. Thompson, Joshua C. Denny, Huan Mo, Richard C. Kiefer, Peter Speltz, Enid N. H. Montague.
    Evaluation of Existing Phenotype Authoring Tools for Clinical Research.
    AMIA 2014, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 15-19, 2014 2014 (0) 2014
    Conference paper
    Ergin Soysal, Jeremy L. Warner, Joshua C. Denny, Hua Xu.
    Identifying Metastases from Pathology Reports in Lung Cancer Patients.
    AMIA 2014, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 15-19, 2014 2014 (0) 2014
    Conference paper
    Sungrim Moon, Yukun Chen, Jingqi Wang, Joshua C. Denny, Hua Xu.
    Applying Active Learning to Word Sense Disambiguation in a Real-Time Setting.
    AMIA 2014, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 15-19, 2014 2014 (0) 2014
    Conference paper
    Pedro L. Teixeira, Robert J. Carroll, Lisa Bastarache, Peter Speltz, Joshua Smith, Joshua C. Denny.
    Phenome-Wide Association Studies Using NLP-Derived Concepts.
    AMIA 2014, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 15-19, 2014 2014 (0) 2014
    Conference paper
    Matthew Oetjens, William S. Bush, Kelly A. Birdwell, Holli H. Dilks, Erica A. Bowton, Joshua C. Denny, Russell A. Wilke, Dan M. Roden, Dana C. Crawford.
    Utilization of an EMR-Biorepository to Identify the Genetic Predictors of Calcineurin-Inhibitor Toxicity in Heart Transplant Recipients.
    Biocomputing 2014: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 3-7, 2014 2014 (0) 2014
    Conference paper
    Ruth M. Reeves, Ferdo R. Ong, Michael E. Matheny, Joshua C. Denny, Dominik Aronsky, Glenn T. Gobbel, Diane Montella, Theodore Speroff, Steven H. Brown.
    Detecting temporal expressions in medical narratives.
    I. J. Medical Informatics 2013, Volume 82 (0) 2013
    Conference paper
    Nicholas P. Tatonetti, Joshua C. Denny, Russ B. Altman.
    Correspondence: Response to 'Use of an algorithm for identifying hidden drug-drug interactions in adverse event reports' by Gooden
    JAMIA 2013, Volume 20 (0) 2013
    Conference paper
    Mei Liu, Eugenia R. McPeek Hinz, Michael E. Matheny, Joshua C. Denny, Jonathan S. Schildcrout, Randolph A. Miller, Hua Xu.
    Comparative analysis of pharmacovigilance methods in the detection of adverse drug reactions using electronic medical records.
    JAMIA 2013, Volume 20 (0) 2013
    Conference paper
    Si Sun, Xiaomu Zhou, Joshua C. Denny, S. Trent Rosenbloom, Hua Xu.
    Messaging to your doctors: understanding patient-provider communications via a portal system.
    2013 ACM SIGCHI Conference on Human Factors in Computing Systems, CHI '13, Paris, France, April 27 - May 2, 2013 2013 (0) 2013
    Conference paper
    Wei-Qi Wei, Robert M. Cronin, Hua Xu, Thomas A. Lasko, Lisa Bastarache, Joshua C. Denny.
    Development and evaluation of an ensemble resource linking medications to their indications.
    JAMIA 2013, Volume 20 (0) 2013
    Conference paper
    Buzhou Tang, Yonghui Wu, Min Jiang, Yukun Chen, Joshua C. Denny, Hua Xu.
    A hybrid system for temporal information extraction from clinical text.
    JAMIA 2013, Volume 20 (0) 2013
    Conference paper
    Richard H. Epstein, Paul St. Jacques, Michael Stockin, Brian Rothman, Jesse M. Ehrenfeld, Joshua C. Denny.
    Automated identification of drug and food allergies entered using non-standard terminology.
    JAMIA 2013, Volume 20 (0) 2013
    Conference paper
    Yonghui Wu, Jianbo Lei, Wei-Qi Wei, Buzhou Tang, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Kai Zheng, Hua Xu.
    Analyzing Differences between Chinese and English Clinical Text: A Cross-Institution Comparison of Discharge Summaries in Two Languages.
    MEDINFO 2013 - Proceedings of the 14th World Congress on Medical and Health Informatics, 20-13 August 2013, Copenhagen, Denmark 2013 (0) 2013
    Conference paper
    Jeremy L. Warner, Joshua C. Denny, David A. Kreda, Gil Alterovitz.
    Analytic Approaches to Phenotypic Complexity.
    MEDINFO 2013 - Proceedings of the 14th World Congress on Medical and Health Informatics, 20-13 August 2013, Copenhagen, Denmark 2013 (0) 2013
    Conference paper
    Jung-Wei Fan, Elly W. Yang, Min Jiang, Rashmi Prasad, Richard M. Loomis, Daniel Zisook, Joshua C. Denny, Hua Xu, Yang Huang.
    Research and applications: Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences.
    JAMIA 2013, Volume 20 (0) 2013
    Conference paper
    Yonghui Wu, Joshua C. Denny, S. Trent Rosenbloom, Randolph A. Miller, Dario A. Giuse, Min Song, Hua Xu.
    A prototype application for real-time recognition and disambiguation of clinical abbreviations.
    Proceeding of the 7rd International Workshop on Data and Text Mining in Bioinformatics, DTMBIO 2013, San Francisco, CA, USA, November 1, 2013 2013 (0) 2013
    Conference paper
    Lisa Bastarache, Wei-Qi Wei, Joshua C. Denny.
    Classifying ICD-9 codes into meaningful disease categories: A comparison between two coding systems.
    AMIA 2013, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 16-20, 2013 2013 (0) 2013
    Conference paper
    Richard H. Epstein, Jesse M. Ehrenfeld, Michael Stockin, Paul St. Jacques, Brian Rothman, Joshua C. Denny.
    Automated Identification of Drug and Food Allergies Entered in EHRs Using Non-Standard Terminology.
    AMIA 2013, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 16-20, 2013 2013 (0) 2013
    Conference paper
    Robert J. Carroll, Lisa Bastarache, Joshua C. Denny.
    Open Source R Implementation of the PheWAS Methodology.
    AMIA 2013, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 16-20, 2013 2013 (0) 2013
    Conference paper
    Christine M. McEvoy, Robert J. Carroll, Lisa Bastarache, Wei-Qi Wei, Joshua C. Denny.
    Using PheWAS and Natural Language Processing to Discover Clinical Associations for Congenital Chest Deformities.
    AMIA 2013, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 16-20, 2013 2013 (0) 2013
    Conference paper
    Wei-Qi Wei, Jonathan D. Mosley, Lisa Bastarache, Joshua C. Denny.
    Validation and Enhancement of a Computable Medication Indication Resource (MEDI) Using a Large Practice-based Dataset.
    AMIA 2013, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 16-20, 2013 2013 (0) 2013
    Conference paper
    Eugenia R. McPeek Hinz, Joshua C. Denny, Lisa Bastarache.
    A Natural Language Processing Algorithm to define a Venous Thromboembolism Phenotype.
    AMIA 2013, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 16-20, 2013 2013 (0) 2013
    Conference paper
    Yukun Chen, Thomas A. Lasko, Qiaozhu Mei, Joshua C. Denny, Hua Xu.
    A Study of Active Learning Methods for Clinical Entities Recognition.
    AMIA 2013, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 16-20, 2013 2013 (0) 2013
    Conference paper
    Jeremy L. Warner, Gil Alterovitz, Joshua C. Denny, Robert Fassett, Kevin S. Hughes.
    Sharing of Genomic Information: Perspectives from Stakeholders.
    AMIA 2013, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 16-20, 2013 2013 (0) 2013
    Conference paper
    Yonghui Wu, S. Trent Rosenbloom, Joshua C. Denny, Randolph A. Miller, Dario A. Giuse, Hua Xu.
    Building a Large Clinical Abbreviation Sense Inventory from Discharge Summaries.
    AMIA 2013, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 16-20, 2013 2013 (0) 2013
    Conference paper
    Jeremy L. Warner, Quan Ding, David A. Kreda, Zi'ou Zheng, Keshav Gupta, Joshua C. Denny, Gil Alterovitz.
    Phenometric analysis of electronic health records: a new approach to visualization of high dimensional biomedical information.
    AMIA 2013, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 16-20, 2013 2013 (0) 2013
    Conference paper
    Laura K. Wiley, Josh F. Peterson, Joshua C. Denny, William S. Bush.
    Establishing the Need for Personalized Medicine: Simvastatin Exposure Among a SLCO1B1 Variant Population.
    AMIA 2013, American Medical Informatics Association Annual Symposium, Washington, DC, USA, November 16-20, 2013 2013 (0) 2013
    Conference paper
    Yonghui Wu, Buzhou Tang, Min Jiang, Sungrim Moon, Joshua C. Denny, Hua Xu.
    Clinical Acronym/Abbreviation Normalization using a Hybrid Approach.
    Working Notes for CLEF 2013 Conference , Valencia, Spain, September 23-26, 2013. 2014 (0) 2013
    Conference paper
    Buzhou Tang, Yonghui Wu, Min Jiang, Joshua C. Denny, Hua Xu.
    Recognizing and Encoding Discorder Concepts in Clinical Text using Machine Learning and Vector Space Model.
    Working Notes for CLEF 2013 Conference , Valencia, Spain, September 23-26, 2013. 2014 (0) 2013
    Conference paper
    Peggy L. Peissig, Luke V. Rasmussen, Richard L. Berg, James G. Linneman, Catherine A. McCarty, Carol Waudby, Lin Chen, Joshua C. Denny, Russell A. Wilke, Jyotishman Pathak, David Carrell, Abel N. Kho, Justin B. Starren.
    Importance of multi-modal approaches to effectively identify cataract cases from electronic health records.
    JAMIA 2012, Volume 19 (0) 2012
    Conference paper
    Abel N. Kho, M. Geoffrey Hayes, Laura Rasmussen-Torvik, Jennifer A. Pacheco, William K. Thompson, Loren L. Armstrong, Joshua C. Denny, Peggy L. Peissig, Aaron W. Miller, Wei-Qi Wei, Suzette J. Bielinski, Christopher G. Chute, Cynthia L. Leibson, Gail P. Jarvik, David R. Crosslin, Christopher S. Carlson, Katherine M. Newton, Wendy A. Wolf, Rex L. Chisholm, William L. Lowe.
    Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study.
    JAMIA 2012, Volume 19 (0) 2012
    Conference paper
    Shane P. Stenner, Kevin B. Johnson, Joshua C. Denny.
    Focus on health information technology, electronic health records and their financial impact: PASTE: patient-centered SMS text tagging in a medication management system.
    JAMIA 2012, Volume 19 (0) 2012
    Conference paper
    Robert J. Carroll, William K. Thompson, Anne E. Eyler, Arthur M. Mandelin, Tianxi Cai, Raquel M. Zink, Jennifer A. Pacheco, Chad S. Boomershine, Thomas A. Lasko, Hua Xu, Elizabeth W. Karlson, Raul G. Perez, Vivian S. Gainer, Shawn N. Murphy, Eric M. Ruderman, Richard M. Pope, Robert M. Plenge, Abel N. Kho, Katherine P. Liao, Joshua C. Denny.
    Portability of an algorithm to identify rheumatoid arthritis in electronic health records.
    JAMIA 2012, Volume 19 (0) 2012
    Conference paper
    Yanxin Lu, Hua Xu, Neeraja B. Peterson, Qi Dai, Min Jiang, Joshua C. Denny, Mei Liu.
    Extracting epidemiologic exposure and outcome terms from literature using machine learning approaches.
    IJDMB 2012, Volume 6 (0) 2012
    Conference paper
    Mei Liu, Michael E. Matheny, Yonghui Wu, Eugenia R. McPeek Hinz, Joshua C. Denny, Jonathan S. Schildcrout, Randolph A. Miller, Hua Xu.
    Detecting Adverse Drug Reactions Using Inpatient Medication Orders and Laboratory Tests Data.
    2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012, La Jolla, CA, USA, September 27-28, 2012 2012 (0) 2012
    Conference paper
    Eugenia R. McPeek Hinz, Lisa Bastarache, Joshua C. Denny.
    A General Purpose Phenotype Algorithm for Venous Thromboembolism Using Billing Codes and Natural Language Processing.
    2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012, La Jolla, CA, USA, September 27-28, 2012 2012 (0) 2012
    Conference paper
    Lisa Bastarache, Wei-Qi Wei, Joshua C. Denny.
    Diabetes and Susceptibility to Infection: A Study of Lab Culture Results in the EMR.
    AMIA 2012, American Medical Informatics Association Annual Symposium, Chicago, Illinois, USA, November 3-7, 2012 2012 (0) 2012
    Conference paper
    Jyotishman Pathak, Aref Al-Kali, Jayant Talwalkar, Abel N. Kho, Joshua C. Denny, Sean P. Murphy, Kevin Bruce, Matthew J. Durski, Christopher G. Chute.
    Using Electronic Health Records to Identify Patient Cohorts for Drug-Induced Thrombocytopenia, Neutropenia and Liver Injury.
    AMIA 2012, American Medical Informatics Association Annual Symposium, Chicago, Illinois, USA, November 3-7, 2012 2012 (0) 2012
    Conference paper
    Si Sun, Xiaomu Zhou, Hua Xu, Joshua C. Denny.
    Understanding Patient-Provider Communication via a Patient Portal.
    AMIA 2012, American Medical Informatics Association Annual Symposium, Chicago, Illinois, USA, November 3-7, 2012 2012 (0) 2012
    Conference paper
    William K. Thompson, Luke V. Rasmussen, Jennifer A. Pacheco, Peggy L. Peissig, Joshua C. Denny, Abel N. Kho, Aaron W. Miller, Jyotishman Pathak.
    An Evaluation of the NQF Quality Data Model for Representing Electronic Health Record Driven Phenotyping Algorithms.
    AMIA 2012, American Medical Informatics Association Annual Symposium, Chicago, Illinois, USA, November 3-7, 2012 2012 (0) 2012
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