Joshua C. Denny

According to our database1, Joshua C. Denny authored at least 159 papers between 2002 and 2018.

Collaborative distances:

Timeline

Legend:

Book 
In proceedings 
Article 
PhD thesis 
Other 

Links

Homepage:

On csauthors.net:

Bibliography

2018
Uncovering exposures responsible for birth season - disease effects: a global study.
JAMIA, 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.
JAMIA, 2018

Evaluating statistical approaches to leverage large clinical datasets for uncovering therapeutic and adverse medication effects.
Bioinformatics, 2018

Huge Cohorts, Genomics, and Clinical Data to Personalize Medicine.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017
An active learning-enabled annotation system for clinical named entity recognition.
BMC Med. Inf. & Decision Making, 2017

A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD).
JAMIA, 2017

Evaluating electronic health record data sources and algorithmic approaches to identify hypertensive individuals.
JAMIA, 2017

A comparison of rule-based and machine learning approaches for classifying patient portal messages.
I. 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

Session Introduction.
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

Sub-Phenotyping of Crohn's Disease Using a Large Electronic Record Cohort.
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.
Journal of Biomedical Informatics, 2016

Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting.
JAMIA, 2016

Combining billing codes, clinical notes, and medications from electronic health records provides superior phenotyping performance.
JAMIA, 2016

PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability.
JAMIA, 2016

A multi-institution evaluation of clinical profile anonymization.
JAMIA, 2016

Precision medicine informatics.
JAMIA, 2016

Clinical phenotyping in selected national networks: demonstrating the need for high-throughput, portable, and computational methods.
Artificial Intelligence in Medicine, 2016

Translational Bioinformatics 101.
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

The Many Meanings of Precision Medicine.
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

Applying Active Learning to Clinical Abbreviation Disambiguation in Real Time.
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 Computational Biology, 2015

Parsing clinical text: how good are the state-of-the-art parsers?
BMC Med. Inf. & Decision Making, 2015

Using natural language processing to provide personalized learning opportunities from trainee clinical notes.
Journal of Biomedical Informatics, 2015

A study of active learning methods for named entity recognition in clinical text.
Journal of Biomedical Informatics, 2015

Building bridges across electronic health record systems through inferred phenotypic topics.
Journal of Biomedical Informatics, 2015

Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research.
JAMIA, 2015

Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality.
JAMIA, 2015

Seeing the forest through the trees: uncovering phenomic complexity through interactive network visualization.
JAMIA, 2015

Desiderata for computable representations of electronic health records-driven phenotype algorithms.
JAMIA, 2015

Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record.
JAMIA, 2015

Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text.
JAMIA, 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


Building the Computational Workforce for Precision Medicine.
Proceedings of the AMIA 2015, 2015

Natural Language Processing for Phenotype Extraction: Challenges in Extraction and Representation.
Proceedings of the AMIA 2015, 2015

PhEMA: Phenotype Modeling, Sharing and Execution Architecture.
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


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

Predicting Clinical Laboratory Turnaround Time.
Proceedings of the AMIA 2015, 2015

Real Time Active Learning Study for Clinical Named Entity Recognition.
Proceedings of the AMIA 2015, 2015

2014
Design patterns for the development of electronic health record-driven phenotype extraction algorithms.
Journal of Biomedical Informatics, 2014

Limestone: High-throughput candidate phenotype generation via tensor factorization.
Journal of Biomedical Informatics, 2014

Size matters: How population size influences genotype-phenotype association studies in anonymized data.
Journal of Biomedical Informatics, 2014

Predicting changes in hypertension control using electronic health records from a chronic disease management program.
JAMIA, 2014

SecureMA: protecting participant privacy in genetic association meta-analysis.
Bioinformatics, 2014

R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment.
Bioinformatics, 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

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, 2014

Qualitative evaluation of three phenotype information models to find methotrexate liver injury.
Proceedings of the AMIA 2014, 2014

Mining electronic health record data to detect drug-repurposing signals for cancers.
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

Phenome-Wide Association Studies Using NLP-Derived Concepts.
Proceedings of the AMIA 2014, 2014

Identifying Metastases from Pathology Reports in Lung Cancer Patients.
Proceedings of the AMIA 2014, 2014

Evaluation of Existing Phenotype Authoring Tools for Clinical Research.
Proceedings of the AMIA 2014, 2014


Applying Active Learning to Word Sense Disambiguation in a Real-Time Setting.
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

PheWAS and Genetics Define Subphenotypes in Drug Response.
Proceedings of the AMIA 2014, 2014

Learning to Identify Treatment Relations in Clinical Text.
Proceedings of the AMIA 2014, 2014

2013
Development and evaluation of an ensemble resource linking medications to their indications.
JAMIA, 2013

Correspondence: Response to 'Use of an algorithm for identifying hidden drug-drug interactions in adverse event reports' by Gooden et al.
JAMIA, 2013

A hybrid system for temporal information extraction from clinical text.
JAMIA, 2013

Comparative analysis of pharmacovigilance methods in the detection of adverse drug reactions using electronic medical records.
JAMIA, 2013

Research and applications: Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences.
JAMIA, 2013

Automated identification of drug and food allergies entered using non-standard terminology.
JAMIA, 2013

Detecting temporal expressions in medical narratives.
I. 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

Clinical Acronym/Abbreviation Normalization using a Hybrid Approach.
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

Building a Large Clinical Abbreviation Sense Inventory from Discharge Summaries.
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

Sharing of Genomic Information: Perspectives from Stakeholders.
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

A Study of Active Learning Methods for Clinical Entities Recognition.
Proceedings of the AMIA 2013, 2013

Open Source R Implementation of the PheWAS Methodology.
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
Chapter 13: Mining Electronic Health Records in the Genomics Era.
PLoS Computational Biology, 2012

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

Importance of multi-modal approaches to effectively identify cataract cases from electronic health records.
JAMIA, 2012

Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study.
JAMIA, 2012

Portability of an algorithm to identify rheumatoid arthritis in electronic health records.
JAMIA, 2012

Extracting epidemiologic exposure and outcome terms from literature using machine learning approaches.
IJDMB, 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

Understanding patient-provider communication entered via a patient portal system.
Proceedings of the Information, Interaction, Innovation: Celebrating the Past, Constructing the Present and Creating the Future, 2012

Understanding patient-provider communication entered via a patient portal system.
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

Comparing Diagnoses Recorded in Problem Lists vs. Administrative Codes.
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

Understanding Patient-Provider Communication via a Patient Portal.
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

PheKB.org: An Online Collaboration Tool for Phenotype Algorithm Research.
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

Type 2 Diabetes Risk Forecasting from EMR Data using Machine Learning.
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

Establishing Drug Treatment discovery rate of MedEx.
Proceedings of the AMIA 2012, 2012

Diabetes and Susceptibility to Infection: A Study of Lab Culture Results in the EMR.
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.
Journal of Biomedical Informatics, 2011

Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin.
JAMIA, 2011

Data from clinical notes: a perspective on the tension between structure and flexible documentation.
JAMIA, 2011

A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries.
JAMIA, 2011

2010
An analytical approach to characterize morbidity profile dissimilarity between distinct cohorts using electronic medical records.
Journal of Biomedical Informatics, 2010

Application of information technology: MedEx: a medication information extraction system for clinical narratives.
JAMIA, 2010

The disclosure of diagnosis codes can breach research participants' privacy.
JAMIA, 2010

Integrating existing natural language processing tools for medication extraction from discharge summaries.
JAMIA, 2010

Extracting timing and status descriptors for colonoscopy testing from electronic medical records.
JAMIA, 2010

Identifying potential drugs that induce QT prolongation using electronic medical records.
BMC Bioinformatics, 2010

PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations.
Bioinformatics, 2010

2009
Tracking medical students' clinical experiences using natural language processing.
Journal of Biomedical Informatics, 2009

Research Paper: Evaluation of a Method to Identify and Categorize Section Headers in Clinical Documents.
JAMIA, 2009

Identifying QT prolongation from ECG impressions using a general-purpose Natural Language Processor.
I. 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
Development and Evaluation of a Clinical Note Section Header Terminology.
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

Identifying UMLS concepts from ECG Impressions using Knowledge Map.
Proceedings of the AMIA 2005, 2005

2003
Research Paper: "Understanding" Medical School Curriculum Content Using KnowledgeMap.
JAMIA, 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
Using Concept Markers to Find Genetics Content in a Medical School Curriculum.
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


  Loading...