Joshua C. Denny
Orcid: 0000-0002-3049-7332
According to our database1,
Joshua C. Denny
authored at least 198 papers
between 2002 and 2023.
Collaborative distances:
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Bibliography
2023
Systematic replication of smoking disease associations using survey responses and EHR data in the <i>All of Us</i> Research Program.
J. Am. Medical Informatics Assoc., December, 2023
J. Am. Medical Informatics Assoc., February, 2023
npj Digit. Medicine, 2023
2022
Patterns, 2022
Inf. Serv. Use, 2022
Cox regression is robust to inaccurate EHR-extracted event time: an application to EHR-based GWAS.
Bioinform., 2022
2021
Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies.
npj Digit. Medicine, 2021
Meeting the challenge: Health information technology's essential role in achieving precision medicine.
J. Am. Medical Informatics Assoc., 2021
DDIWAS: High-throughput electronic health record-based screening of drug-drug interactions.
J. Am. Medical Informatics Assoc., 2021
Real-time clinical note monitoring to detect conditions for rapid follow-up: A case study of clinical trial enrollment in drug-induced torsades de pointes and Stevens-Johnson syndrome.
J. Am. Medical Informatics Assoc., 2021
PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS.
Bioinform., 2021
Systematic replication of smoking disease associations in the All of Us Research Program.
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021
Using Genomic Association Replication Rates as an EHR Quality Measure via the Phenotype-Genotype Reference Map (PGRM).
Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021
2020
PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records.
J. Am. Medical Informatics Assoc., 2020
medExtractR: A targeted, customizable approach to medication extraction from electronic health records.
J. Am. Medical Informatics Assoc., 2020
Proceedings of the AMIA 2020, 2020
Real-time Clinical Note Monitoring to Detect Conditions for Follow-up: a Case Study of Clinical Trial Enrollment in Drug-induced Torsades de Pointes and Stevens-Johnson Syndrome.
Proceedings of the AMIA 2020, 2020
2019
Detecting time-evolving phenotypic topics via tensor factorization on electronic health records: Cardiovascular disease case study.
J. Biomed. Informatics, 2019
J. Biomed. Informatics, 2019
Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network.
J. Biomed. Informatics, 2019
J. Biomed. Informatics, 2019
J. Am. Medical Informatics Assoc., 2019
Improving the phenotype risk score as a scalable approach to identifying patients with Mendelian disease.
J. Am. Medical Informatics Assoc., 2019
Proceedings of the 2019 SIAM International Conference on Data Mining, 2019
Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43, 870 individuals from the eMERGE network.
Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019
Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP.
Proceedings of the MEDINFO 2019: Health and Wellbeing e-Networks for All, 2019
Deep Learning Using Electronic Health Records and Genetic Data to Predict Cardiovascular Diseases.
Proceedings of the AMIA 2019, 2019
Proceedings of the AMIA 2019, 2019
medExtractR: A medication extraction algorithm for electronic health records using the R programming language.
Proceedings of the AMIA 2019, 2019
Extracting Drug Exposure Epochs and Drug Response Outcomes from Electronic Health Records.
Proceedings of the AMIA 2019, 2019
Proceedings of the AMIA 2019, 2019
2018
A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments.
J. Am. Medical Informatics Assoc., 2018
J. Am. Medical Informatics Assoc., 2018
Mining 100 million notes to find homelessness and adverse childhood experiences: 2 case studies of rare and severe social determinants of health in electronic health records.
J. Am. Medical Informatics Assoc., 2018
Evaluating statistical approaches to leverage large clinical datasets for uncovering therapeutic and adverse medication effects.
Bioinform., 2018
Evaluation of a Novel System to Enhance Clinicians' Recognition of Preadmission Adverse Drug Reactions.
Appl. Clin. Inform., 2018
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018
Using Topic Modeling to Identify Relationship between LPA Variant and Disease Phenotypes.
Proceedings of the AMIA 2018, 2018
Proceedings of the AMIA 2018, 2018
Proceedings of the AMIA 2018, 2018
2017
BMC Medical Informatics Decis. Mak., 2017
A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD).
J. Am. Medical Informatics Assoc., 2017
Evaluating electronic health record data sources and algorithmic approaches to identify hypertensive individuals.
J. Am. Medical Informatics Assoc., 2017
A comparison of rule-based and machine learning approaches for classifying patient portal messages.
Int. J. Medical Informatics, 2017
Strategies for Equitable Pharmacogenomic-Guided Warfarin Dosing Among European and African American Individuals in a Clinical Population.
Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017
Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017
Granite: Diversified, Sparse Tensor Factorization for Electronic Health Record-Based Phenotyping.
Proceedings of the 2017 IEEE International Conference on Healthcare Informatics, 2017
Identifying Metastases related Information from Pathology Reports of Lung Cancer Patients.
Proceedings of the Summit on Clinical Research Informatics, 2017
A comparative study of different methods for automatic identification of clopidogrel-induced bleedings in electronic health records.
Proceedings of the Summit on Clinical Research Informatics, 2017
Development and Testing of Participant Provided Information Modules for the Precision Medicine Initiative.
Proceedings of the Summit on Clinical Research Informatics, 2017
A Phenome-Wide Association Study (PheWAS) of Iron Deficiency in a Large Electronic Health Record Database.
Proceedings of the AMIA 2017, 2017
The Phenotype Execution and Modeling Architecture: A Roadmap Towards Next-generation Phenotyping Using EHRs.
Proceedings of the AMIA 2017, 2017
Association of BMI and Obesity Genetic Risk Score with Surgical Procedures Through a Procedure-wide Association Study.
Proceedings of the AMIA 2017, 2017
Proceedings of the AMIA 2017, 2017
The All of Us Research Program Researcher Portal: Innovative access to Unprecendented Data.
Proceedings of the AMIA 2017, 2017
HealthPro: An integrated web application for essential health data and biological specimen collection in the Precision Medicine Initiative.
Proceedings of the AMIA 2017, 2017
Leveraging Value Sets from the Value Set Authority Center (VSAC) in a Standards-Based Clinical Data Repository.
Proceedings of the AMIA 2017, 2017
The Data and Research Center of the All of Us Research Program: Framework for a National Cohort Program and Research Opportunities.
Proceedings of the AMIA 2017, 2017
A Simple and Efficient Method for the Management of Multiple Electronic Health Record-Driven Phenotype Projects.
Proceedings of the AMIA 2017, 2017
Large-Scale Text Mining of Social Determinants from Electronic Health Records: Case Studies of Homelessness and Adverse Childhood Experiences.
Proceedings of the AMIA 2017, 2017
2016
Developing a data element repository to support EHR-driven phenotype algorithm authoring and execution.
J. Biomed. Informatics, 2016
Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting.
J. Am. Medical Informatics Assoc., 2016
Combining billing codes, clinical notes, and medications from electronic health records provides superior phenotyping performance.
J. Am. Medical Informatics Assoc., 2016
PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability.
J. Am. Medical Informatics Assoc., 2016
J. Am. Medical Informatics Assoc., 2016
Clinical phenotyping in selected national networks: demonstrating the need for high-throughput, portable, and computational methods.
Artif. Intell. Medicine, 2016
Appl. Clin. Inform., 2016
Developing an Algorithm to Detect Early Childhood Obesity in Two Tertiary Pediatric Medical Centers.
Appl. Clin. Inform., 2016
Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016
Evaluating Physician Response to Pharmacogenomic-Guided Warfarin Dosing in an Hospitalized Population.
Proceedings of the Summit on Clinical Research Informatics, 2016
Proceedings of the Summit on Clinical Research Informatics, 2016
A Decompositional Approach to Executing Quality Data Model Algorithms on the i2b2 Platform.
Proceedings of the Summit on Clinical Research Informatics, 2016
Proceedings of the AMIA 2016, 2016
An NLP Extension to the Quality Data Model for EHR-Driven Phenotype Algorithm Authoring and Execution.
Proceedings of the AMIA 2016, 2016
Building Successful Natural Language Processing Applications in Clinical Research and Healthcare Operations.
Proceedings of the AMIA 2016, 2016
An Empirical Study for Impacts of Measurement Errors on EHR based Association Studies.
Proceedings of the AMIA 2016, 2016
2015
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action.
PLoS Comput. Biol., 2015
BMC Medical Informatics Decis. Mak., 2015
Using natural language processing to provide personalized learning opportunities from trainee clinical notes.
J. Biomed. Informatics, 2015
J. Biomed. Informatics, 2015
Building bridges across electronic health record systems through inferred phenotypic topics.
J. Biomed. Informatics, 2015
Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research.
J. Am. Medical Informatics Assoc., 2015
Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality.
J. Am. Medical Informatics Assoc., 2015
Seeing the forest through the trees: uncovering phenomic complexity through interactive network visualization.
J. Am. Medical Informatics Assoc., 2015
Desiderata for computable representations of electronic health records-driven phenotype algorithms.
J. Am. Medical Informatics Assoc., 2015
Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record.
J. Am. Medical Informatics Assoc., 2015
Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text.
J. Am. Medical Informatics Assoc., 2015
A Standards-based Semantic Metadata Repository to Support EHR-driven Phenotype Authoring and Execution.
Proceedings of the MEDINFO 2015: eHealth-enabled Health, 2015
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, 2015
Proceedings of the AMIA 2015, 2015
Natural Language Processing for Phenotype Extraction: Challenges in Extraction and Representation.
Proceedings of the AMIA 2015, 2015
Proceedings of the AMIA 2015, 2015
(Authoring) Rules, (Distributed Query) Tools, and Drools: The challenging new world of high throughput phenotyping.
Proceedings of the AMIA 2015, 2015
Quantifying Tobacco Exposure Using Clinical Notes and Natural Language Processing to Enable Lung Cancer Screening.
Proceedings of the AMIA 2015, 2015
Usability of a phenotype builder prototype and lessons learned for the design of phenotyping tools.
Proceedings of the AMIA 2015, 2015
Translating Electronic Clinical Quality Measures to Executable, Portable, and Customizable Workflows in KNIME.
Proceedings of the AMIA 2015, 2015
Proceedings of the AMIA 2015, 2015
Harmonization of Quality Data Model with HL7 FHIR to Support EHR-driven Phenotype Authoring and Execution: A Pilot Study.
Proceedings of the AMIA 2015, 2015
Automated Classification of Consumer Health Information Needs in Patient Portal Messages.
Proceedings of the AMIA 2015, 2015
Proceedings of the AMIA 2015, 2015
2014
Design patterns for the development of electronic health record-driven phenotype extraction algorithms.
J. Biomed. Informatics, 2014
J. Biomed. Informatics, 2014
Size matters: How population size influences genotype-phenotype association studies in anonymized data.
J. Biomed. Informatics, 2014
Predicting changes in hypertension control using electronic health records from a chronic disease management program.
J. Am. Medical Informatics Assoc., 2014
Bioinform., 2014
R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment.
Bioinform., 2014
Utilization of an EMR-Biorepository to Identify the Genetic Predictors of Calcineurin-Inhibitor Toxicity in Heart Transplant Recipients.
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014
Replication of SCN5A Associations with Electrocardiographic Traits in African Americans from Clinical and Epidemiologic Studies.
Proceedings of the Applications of Evolutionary Computation - 17th European Conference, 2014
Qualitative evaluation of three phenotype information models to find methotrexate liver injury.
Proceedings of the AMIA 2014, 2014
Proceedings of the AMIA 2014, 2014
Evaluation of Diagnosis Codes, Clinical Notes, and Medications on Identifying Subjects with a Specific Disease Phenotype.
Proceedings of the AMIA 2014, 2014
Proceedings of the AMIA 2014, 2014
Proceedings of the AMIA 2014, 2014
Proceedings of the AMIA 2014, 2014
A Template for Authoring and Adapting Genomic Medicine Content in the eMERGE Infobutton Project.
Proceedings of the AMIA 2014, 2014
Proceedings of the AMIA 2014, 2014
A Preliminary Study of Coupling Transfer Learning with Active Learning for Clinical Named Entity Recognition between Two Institutions.
Proceedings of the AMIA 2014, 2014
Automated Assessment of Medical Students' Clinical Exposures according to AAMC Geriatric Competencies.
Proceedings of the AMIA 2014, 2014
Proceedings of the AMIA 2014, 2014
Proceedings of the AMIA 2014, 2014
2013
Development and evaluation of an ensemble resource linking medications to their indications.
J. Am. Medical Informatics Assoc., 2013
Correspondence: Response to 'Use of an algorithm for identifying hidden drug-drug interactions in adverse event reports' by Gooden <i>et al</i>.
J. Am. Medical Informatics Assoc., 2013
J. Am. Medical Informatics Assoc., 2013
Comparative analysis of pharmacovigilance methods in the detection of adverse drug reactions using electronic medical records.
J. Am. Medical Informatics Assoc., 2013
Research and applications: Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences.
J. Am. Medical Informatics Assoc., 2013
Automated identification of drug and food allergies entered using non-standard terminology.
J. Am. Medical Informatics Assoc., 2013
Int. J. Medical Informatics, 2013
Analyzing Differences between Chinese and English Clinical Text: A Cross-Institution Comparison of Discharge Summaries in Two Languages.
Proceedings of the MEDINFO 2013, 2013
Analytic Approaches to Phenotypic Complexity.
Proceedings of the MEDINFO 2013, 2013
Proceedings of the Working Notes for CLEF 2013 Conference , 2013
Recognizing and Encoding Discorder Concepts in Clinical Text using Machine Learning and Vector Space Model.
Proceedings of the Working Notes for CLEF 2013 Conference , 2013
A prototype application for real-time recognition and disambiguation of clinical abbreviations.
Proceedings of the Proceeding of the 7rd International Workshop on Data and Text Mining in Bioinformatics, 2013
Messaging to your doctors: understanding patient-provider communications via a portal system.
Proceedings of the 2013 ACM SIGCHI Conference on Human Factors in Computing Systems, 2013
Proceedings of the AMIA 2013, 2013
Establishing the Need for Personalized Medicine: Simvastatin Exposure Among a SLCO1B1 Variant Population.
Proceedings of the AMIA 2013, 2013
Validation and Enhancement of a Computable Medication Indication Resource (MEDI) Using a Large Practice-based Dataset.
Proceedings of the AMIA 2013, 2013
Phenometric analysis of electronic health records: a new approach to visualization of high dimensional biomedical information.
Proceedings of the AMIA 2013, 2013
Proceedings of the AMIA 2013, 2013
Using PheWAS and Natural Language Processing to Discover Clinical Associations for Congenital Chest Deformities.
Proceedings of the AMIA 2013, 2013
A Natural Language Processing Algorithm to define a Venous Thromboembolism Phenotype.
Proceedings of the AMIA 2013, 2013
Automated Identification of Drug and Food Allergies Entered in EHRs Using Non-Standard Terminology.
Proceedings of the AMIA 2013, 2013
Proceedings of the AMIA 2013, 2013
Proceedings of the AMIA 2013, 2013
Classifying ICD-9 codes into meaningful disease categories: A comparison between two coding systems.
Proceedings of the AMIA 2013, 2013
2012
PLoS Comput. Biol., 2012
Focus on health information technology, electronic health records and their financial impact: PASTE: patient-centered SMS text tagging in a medication management system.
J. Am. Medical Informatics Assoc., 2012
Importance of multi-modal approaches to effectively identify cataract cases from electronic health records.
J. Am. Medical Informatics Assoc., 2012
Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study.
J. Am. Medical Informatics Assoc., 2012
Portability of an algorithm to identify rheumatoid arthritis in electronic health records.
J. Am. Medical Informatics Assoc., 2012
Extracting epidemiologic exposure and outcome terms from literature using machine learning approaches.
Int. J. Data Min. Bioinform., 2012
Detecting Adverse Drug Reactions Using Inpatient Medication Orders and Laboratory Tests Data.
Proceedings of the 2012 IEEE Second International Conference on Healthcare Informatics, 2012
A General Purpose Phenotype Algorithm for Venous Thromboembolism Using Billing Codes and Natural Language Processing.
Proceedings of the 2012 IEEE Second International Conference on Healthcare Informatics, 2012
Proceedings of the Information, Interaction, Innovation: Celebrating the Past, Constructing the Present and Creating the Future, 2012
Electronic health record data suggests metformin improves cancer survival: A new model for drug repurposing studies.
Proceedings of the AMIA 2012, 2012
A comparative study of current clinical natural language processing systems on handling abbreviations in discharge summaries.
Proceedings of the AMIA 2012, 2012
Proceedings of the AMIA 2012, 2012
An Evaluation of the NQF Quality Data Model for Representing Electronic Health Record Driven Phenotyping Algorithms.
Proceedings of the AMIA 2012, 2012
Proceedings of the AMIA 2012, 2012
MedEx-UIMA - An Open-Source System for Medication Information Extraction from Clinical Text.
Proceedings of the AMIA 2012, 2012
Proceedings of the AMIA 2012, 2012
Using Electronic Health Records to Identify Patient Cohorts for Drug-Induced Thrombocytopenia, Neutropenia and Liver Injury.
Proceedings of the AMIA 2012, 2012
Proceedings of the AMIA 2012, 2012
A Study of Transportability of an Existing Smoking Status Detection Module across Institutions.
Proceedings of the AMIA 2012, 2012
Extracting Semantic Lexicons from Discharge Summaries using Machine Learning and the C-Value Method.
Proceedings of the AMIA 2012, 2012
Proceedings of the AMIA 2012, 2012
Proceedings of the AMIA 2012, 2012
2011
Applying semantic-based probabilistic context-free grammar to medical language processing - A preliminary study on parsing medication sentences.
J. Biomed. Informatics, 2011
Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin.
J. Am. Medical Informatics Assoc., 2011
Data from clinical notes: a perspective on the tension between structure and flexible documentation.
J. Am. Medical Informatics Assoc., 2011
A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries.
J. Am. Medical Informatics Assoc., 2011
2010
An analytical approach to characterize morbidity profile dissimilarity between distinct cohorts using electronic medical records.
J. Biomed. Informatics, 2010
Application of information technology: MedEx: a medication information extraction system for clinical narratives.
J. Am. Medical Informatics Assoc., 2010
J. Am. Medical Informatics Assoc., 2010
Integrating existing natural language processing tools for medication extraction from discharge summaries.
J. Am. Medical Informatics Assoc., 2010
Extracting timing and status descriptors for colonoscopy testing from electronic medical records.
J. Am. Medical Informatics Assoc., 2010
Identifying potential drugs that induce QT prolongation using electronic medical records.
BMC Bioinform., 2010
PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations.
Bioinform., 2010
2009
J. Biomed. Informatics, 2009
Research Paper: Evaluation of a Method to Identify and Categorize Section Headers in Clinical Documents.
J. Am. Medical Informatics Assoc., 2009
Identifying QT prolongation from ECG impressions using a general-purpose Natural Language Processor.
Int. J. Medical Informatics, 2009
Development of a Natural Language Processing System to Identify Timing and Status of Colonoscopy Testing in Electronic Medical Records.
Proceedings of the AMIA 2009, 2009
2008
Proceedings of the AMIA 2008, 2008
2007
Identifying QT prolongation from ECG impressions using Natural Language Processing and Negation Detection.
Proceedings of the MEDINFO 2007 - Proceedings of the 12th World Congress on Health (Medical) Informatics, 2007
Analysis of a Computerized Sign-out Tool: Identification of Unanticipated Uses and Contradictory Content.
Proceedings of the AMIA 2007, 2007
2006
Analysis of Medical Student Content Searches that Resulted in Unidentified UMLS Concepts.
Proceedings of the AMIA 2006, 2006
2005
Can Users Estimate Their Usage of a Web-Based Application? Validating a Self-Report Usage Questionnaire.
Proceedings of the AMIA 2005, 2005
Proceedings of the AMIA 2005, 2005
2003
Research Paper: "Understanding" Medical School Curriculum Content Using KnowledgeMap.
J. Am. Medical Informatics Assoc., 2003
Formative Evaluation to Guide Early Deployment of an Online Content Management Tool for Medical Curriculum.
Proceedings of the AMIA 2003, 2003
The KnowledgeMap Project: Development of a Concept-Based Medical School Curriculum Database.
Proceedings of the AMIA 2003, 2003
2002
Proceedings of the AMIA 2002, 2002
A New Tool to Identify Key Biomedical Concepts in Text Documents, with Special Application to Curriculum Content.
Proceedings of the AMIA 2002, 2002