Joshua C. Denny

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Building a Large Clinical Abbreviation Sense Inventory from Discharge Summaries

Hua Xu, Randolph A. Miller, Yonghui Wu, 2013, AMIA.

A General Purpose Phenotype Algorithm for Venous Thromboembolism Using Billing Codes and Natural Language Processing

Joshua C. Denny, Eugenia R. McPeek Hinz, Lisa Bastarache, 2012, 2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology.

Analysis of Medical Student Content Searches that Resulted in Unidentified UMLS Concepts

Joshua C. Denny, Benjamin P. Rosenbaum, Anderson Spickard, 2006, AMIA.

Clinical phenotyping in selected national networks: demonstrating the need for high-throughput, portable, and computational methods

Jimeng Sun, Joshua C. Denny, Jyotishman Pathak, 2016, Artif. Intell. Medicine.

Identifying Metastases-related Information from Pathology Reports of Lung Cancer Patients

Ergin Soysal, Hua Xu, Joshua C. Denny, 2017, CRI.

Utilization of an EMR-Biorepository to Identify the Genetic Predictors of Calcineurin-Inhibitor Toxicity in Heart Transplant Recipients

Joshua C. Denny, Dana C. Crawford, William S. Bush, 2014, Pacific Symposium on Biocomputing.

Analysis of a Computerized Sign-out Tool: Identification of Unanticipated Uses and Contradictory Content

Joshua C. Denny, Nancy M. Lorenzi, Lemuel R. Waitman, 2007, AMIA.

A case study evaluating the portability of an executable computable phenotype algorithm across multiple institutions and electronic health record environments

Joshua C. Denny, Jyotishman Pathak, Abel N. Kho, 2018, J. Am. Medical Informatics Assoc..

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

Joshua C. Denny, Lisa Bastarache, Robert J. Carroll, 2014, Bioinform..

Phenotyping through Semi-Supervised Tensor Factorization (PSST)

Huan He, Joshua C. Denny, Joydeep Ghosh, 2018, AMIA.

An analytical approach to characterize morbidity profile dissimilarity between distinct cohorts using electronic medical records

Christopher G. Chute, Joshua C. Denny, Abel N. Kho, 2010, J. Biomed. Informatics.

A Standards-based Semantic Metadata Repository to Support EHR-driven Phenotype Authoring and Execution

Christopher G. Chute, Joshua C. Denny, Jyotishman Pathak, 2015, MedInfo.

Chapter 13: Mining Electronic Health Records in the Genomics Era

Joshua C. Denny, J. Denny, 2012, PLoS Comput. Biol..

A New Tool to Identify Key Biomedical Concepts in Text Documents, with Special Application to Curriculum Content

Randolph A. Miller, Joshua C. Denny, Anderson Spickard, 2002, AMIA.

Understanding patient-provider communication entered via a patient portal system

Hua Xu, Xiaomu Zhou, S. Trent Rosenbloom, 2012, ASIST.

SecureMA: protecting participant privacy in genetic association meta-analysis

Raymond Heatherly, Murat Kantarcioglu, Joshua C. Denny, 2014, Bioinform..

Size matters: How population size influences genotype-phenotype association studies in anonymized data

Raymond Heatherly, Joshua C. Denny, Bradley Malin, 2014, J. Biomed. Informatics.

Data from clinical notes: a perspective on the tension between structure and flexible documentation

Hua Xu, William W. Stead, S. Trent Rosenbloom, 2011, J. Am. Medical Informatics Assoc..

Applying semantic-based probabilistic context-free grammar to medical language processing - A preliminary study on parsing medication sentences

Son Doan, Hua Xu, Joshua C. Denny, 2011, J. Biomed. Informatics.

The All of Us Research Program Researcher Portal: Innovative access to Unprecendented Data

Paul A. Harris, Joshua C. Denny, Gonçalo R. Abecasis, 2017, AMIA.

Building Successful Natural Language Processing Applications in Clinical Research and Healthcare Operations

Hua Xu, Joshua C. Denny, Yang Huang, 2016, American Medical Informatics Association Annual Symposium.

Automated Identification of Drug and Food Allergies Entered in EHRs Using Non-Standard Terminology

Joshua C. Denny, Richard H. Epstein, Jesse M. Ehrenfeld, 2013, AMIA.

An NLP Extension to the Quality Data Model for EHR-Driven Phenotype Algorithm Authoring and Execution

Joshua C. Denny, Jyotishman Pathak, Guoqian Jiang, 2016, AMIA.

Large-Scale Text Mining of Social Determinants from Electronic Health Records: Case Studies of Homelessness and Adverse Childhood Experiences

Cosmin Adrian Bejan, Joshua C. Denny, Kevin B. Johnson, 2017, AMIA.

Seeing the forest through the trees: uncovering phenomic complexity through interactive network visualization

Gil Alterovitz, Joshua C. Denny, Jeremy L. Warner, 2015, J. Am. Medical Informatics Assoc..

Phenome-Wide Association Studies Using NLP-Derived Concepts

Joshua C. Denny, Lisa Bastarache, Peter Speltz, 2014, AMIA.

The Many Meanings of Precision Medicine

Russ B. Altman, Joshua C. Denny, Jessica D. Tenenbaum, 2016, CRI.

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

Cosmin Adrian Bejan, Joshua C. Denny, Kevin B. Johnson, 2018, J. Am. Medical Informatics Assoc..

Importance of multi-modal approaches to effectively identify cataract cases from electronic health records

Lin Chen, Joshua C. Denny, Jyotishman Pathak, 2012, J. Am. Medical Informatics Assoc..

Combining Publicly-Available and Electronic Health Record Data to Reposition Drugs

Joshua C. Denny, Wei-Qi Wei, Patrick Wu, 2019, AMIA.

Detecting time-evolving phenotypic topics via tensor factorization on electronic health records: Cardiovascular disease case study

Yun Zhang, S. Trent Rosenbloom, Joshua C. Denny, 2019, J. Biomed. Informatics.

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

Russ B. Altman, Joshua C. Denny, Nicholas P. Tatonetti, 2013, J. Am. Medical Informatics Assoc..

A Simple and Efficient Method for the Management of Multiple Electronic Health Record-Driven Phenotype Projects

Cosmin Adrian Bejan, Joshua C. Denny, 2017, AMIA.

Qualitative evaluation of three phenotype information models to find methotrexate liver injury

Jie Xu, Joshua C. Denny, Jyotishman Pathak, 2014, American Medical Informatics Association Annual Symposium.

Extracting Semantic Lexicons from Discharge Summaries using Machine Learning and the C-Value Method

Hua Xu, Joshua C. Denny, Min Jiang, 2012, AMIA.

The Phenotype Execution and Modeling Architecture: A Roadmap Towards Next-generation Phenotyping Using EHRs

Joshua C. Denny, Jyotishman Pathak, William Thompson, 2017, AMIA.

Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences.

Hua Xu, Joshua C. Denny, Min Jiang, 2013, Journal of the American Medical Informatics Association : JAMIA.

MedEx-UIMA - An Open-Source System for Medication Information Extraction from Clinical Text

Hua Xu, Yonghui Wu, Joshua C. Denny, 2012, AMIA.

A Decision-Theoretic Approach to Panel-Based, Preemptive Genotyping

Joshua C. Denny, Zilu Zhou, Frank E. Harrell, 2019, MDM policy & practice.

Using PheWAS and Natural Language Processing to Discover Clinical Associations for Congenital Chest Deformities

Joshua C. Denny, Lisa Bastarache, Wei-Qi Wei, 2013, AMIA.

Analyzing Differences between Chinese and English Clinical Text: A Cross-Institution Comparison of Discharge Summaries in Two Languages

Kai Zheng, Hua Xu, Randolph A. Miller, 2016, MedInfo.

A Study of Active Learning Methods for Clinical Entities Recognition

Hua Xu, Joshua C. Denny, Qiaozhu Mei, 2013, American Medical Informatics Association Annual Symposium.

Identifying Metastases from Pathology Reports in Lung Cancer Patients

Ergin Soysal, Hua Xu, Joshua C. Denny, 2014, American Medical Informatics Association Annual Symposium.

A Template for Authoring and Adapting Genomic Medicine Content in the eMERGE Infobutton Project

Christopher G. Chute, Joshua C. Denny, Marc S. Williams, 2014, AMIA.

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

Cosmin Adrian Bejan, Joshua C. Denny, Wei-Qi Wei, 2015, J. Am. Medical Informatics Assoc..

Automated Classification of Consumer Health Information Needs in Patient Portal Messages

Joshua C. Denny, Daniel Fabbri, Gretchen Purcell Jackson, 2015, AMIA.

Replication of SCN5A Associations with Electrocardiographic Traits in African Americans from Clinical and Epidemiologic Studies

Marylyn D. Ritchie, Joshua C. Denny, Dana C. Crawford, 2014, EvoApplications.

The KnowledgeMap Project: Development of a Concept-Based Medical School Curriculum Database

Joshua C. Denny, Anderson Spickard, Jeffrey D. Smithers, 2003, AMIA.

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

Hua Xu, Marylyn D. Ritchie, Joshua C. Denny, 2011, J. Am. Medical Informatics Assoc..

Recognizing and Encoding Discorder Concepts in Clinical Text using Machine Learning and Vector Space Model

Hua Xu, Yonghui Wu, Joshua C. Denny, 2013, CLEF.

Understanding Patient-Provider Communication via a Patient Portal

Hua Xu, Xiaomu Zhou, Joshua C. Denny, 2012, American Medical Informatics Association Annual Symposium.

A Modular Architecture for Electronic Health Record-Driven Phenotyping

Joshua C. Denny, Jyotishman Pathak, Guoqian Jiang, 2015, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

Natural Language Processing for Phenotype Extraction: Challenges in Extraction and Representation

Harry Hochheiser, Joshua C. Denny, Guergana K. Savova, 2015, AMIA.

Facilitating phenotype transfer using a common data model

George Hripcsak, Chunhua Weng, Joshua C. Denny, 2019, J. Biomed. Informatics.

A Prototype for Executable and Portable Electronic Clinical Quality Measures Using the KNIME Analytics Platform

Joshua C. Denny, Jyotishman Pathak, William K. Thompson, 2015, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

Granite: Diversified, Sparse Tensor Factorization for Electronic Health Record-Based Phenotyping

Jimeng Sun, Joshua C. Denny, Joydeep Ghosh, 2017, 2017 IEEE International Conference on Healthcare Informatics (ICHI).

Quality Analysis of the All of Us Research Program Health Surveys

Joshua C. Denny, Scott Sutherland, Mick P. Couper, 2019, American Medical Informatics Association Annual Symposium.

Comparative analysis of pharmacovigilance methods in the detection of adverse drug reactions using electronic medical records

Hua Xu, Randolph A. Miller, Mei Liu, 2013, J. Am. Medical Informatics Assoc..

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

Chen Lin, Joshua C. Denny, Guergana K. Savova, 2015, J. Am. Medical Informatics Assoc..

Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action

Hua Xu, Peilin Jia, Zhongming Zhao, 2015, PLoS Comput. Biol..

Quantifying Tobacco Exposure Using Clinical Notes and Natural Language Processing to Enable Lung Cancer Screening

Joshua C. Denny, Wei-Qi Wei, Travis Osterman, 2015, AMIA.

PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene–disease associations

Marylyn D. Ritchie, Joshua C. Denny, Dana C. Crawford, 2010, Bioinform..

Extracting Drug Exposure Epochs and Drug Response Outcomes from Electronic Health Records

Joshua C. Denny, Jonathan S. Schildcrout, Josh F. Peterson, 2019, AMIA.

Clinical Acronym/Abbreviation Normalization using a Hybrid Approach

Hua Xu, Yonghui Wu, Joshua C. Denny, 2013, CLEF.

Detecting Adverse Drug Reactions Using Inpatient Medication Orders and Laboratory Tests Data

Hua Xu, Randolph A. Miller, Mei Liu, 2012, 2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology.

Translational Bioinformatics 101

Subha Madhavan, Joshua C. Denny, Lewis J. Frey, 2016, PSB.

Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms

George Hripcsak, Christopher G. Chute, Yuan Luo, 2018, 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Using Concept Markers to Find Genetics Content in a Medical School Curriculum

Randolph A. Miller, Joshua C. Denny, Anderson Spickard, 2002, AMIA.

Building bridges across electronic health record systems through inferred phenotypic topics

Jimeng Sun, Cosmin Adrian Bejan, Joshua C. Denny, 2015, J. Biomed. Informatics.

Phenometric analysis of electronic health records: a new approach to visualization of high dimensional biomedical information

Gil Alterovitz, Joshua C. Denny, Jeremy L. Warner, 2013, AMIA.

Sub-Phenotyping of Crohn's Disease Using a Large Electronic Record Cohort

Joshua C. Denny, Lisa Bastarache, Robert J. Carroll, 2017, AMIA.

Formative Evaluation to Guide Early Deployment of an Online Content Management Tool for Medical Curriculum

Brian Armstrong, Joshua C. Denny, Anderson Spickard, 2003, AMIA.

Developing and Evaluating Mappings of ICD-10 and ICD-10-CM Codes to Phecodes

Joshua C. Denny, Xue Li, Wei-Qi Wei, 2018, bioRxiv.

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

Randolph A. Miller, Joshua C. Denny, Anderson Spickard, 2009, J. Am. Medical Informatics Assoc..

Tracking medical students' clinical experiences using natural language processing

Joshua C. Denny, Lisa Bastarache, Anderson Spickard, 2009, J. Biomed. Informatics.

An Empirical Study for Impacts of Measurement Errors on EHR based Association Studies

Jing Huang, Rui Duan, Yong Chen, 2016, AMIA.

Automated Assessment of Medical Students' Clinical Exposures according to AAMC Geriatric Competencies

Hua Xu, Joshua C. Denny, Anderson Spickard, 2014, AMIA.

A hybrid system for temporal information extraction from clinical text

Hua Xu, Yonghui Wu, Joshua C. Denny, 2013, J. Am. Medical Informatics Assoc..

Using Topic Modeling to Identify Relationship between LPA Variant and Disease Phenotypes

Joshua C. Denny, Wei-Qi Wei, Juan Zhao, 2018, AMIA.

A comparative study of different methods for automatic identification of clopidogrel-induced bleedings in electronic health records

Hua Xu, Yonghui Wu, Joshua C. Denny, 2017, CRI.

(Authoring) Rules, (Distributed Query) Tools, and Drools: The challenging new world of high throughput phenotyping

Joshua C. Denny, Jyotishman Pathak, Abel N. Kho, 2015, AMIA.

Design patterns for the development of electronic health record-driven phenotype extraction algorithms

Gerard Tromp, Joshua C. Denny, Jyotishman Pathak, 2014, J. Biomed. Informatics.

Identifying UMLS concepts from ECG Impressions using Knowledge Map

Randolph A. Miller, S. Trent Rosenbloom, Joshua C. Denny, 2005, AMIA.

The Data and Research Center of the All of Us Research Program: Framework for a National Cohort Program and Research Opportunities

Joshua C. Denny, Robert J. Carroll, Karthik Natarajan, 2017, AMIA.

Development of a Natural Language Processing System to Identify Timing and Status of Colonoscopy Testing in Electronic Medical Records

Hua Xu, Randolph A. Miller, Joshua C. Denny, 2009, AMIA.

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

Qingxia Chen, Hua Xu, Joshua C. Denny, 2014, AMIA.

Automated identification of drug and food allergies entered using non-standard terminology

Joshua C. Denny, Richard H. Epstein, Jesse M. Ehrenfeld, 2013, J. Am. Medical Informatics Assoc..

A prototype application for real-time recognition and disambiguation of clinical abbreviations

Min Song, Hua Xu, Randolph A. Miller, 2013, DTMBIO '13.

Development and Testing of Participant Provided Information Modules for the Precision Medicine Initiative

Joshua C. Denny, Michael R. Elliott, Peter Speltz, 2017, CRI.

Classifying ICD-9 codes into meaningful disease categories: A comparison between two coding systems

Joshua C. Denny, Lisa Bastarache, Wei-Qi Wei, 2013, AMIA.

Learning from Longitudinal Data in Electronic Health Record and Genetic Data to Improve Cardiovascular Event Prediction

Joshua C. Denny, Wei-Qi Wei, Juan Zhao, 2018 .

Desiderata for computable representations of electronic health records-driven phenotype algorithms

Paul A. Harris, Gerard Tromp, Jie Xu, 2015, J. Am. Medical Informatics Assoc..

Electronic health record data suggests metformin improves cancer survival: A new model for drug repurposing studies

Ying Li, Hongfang Liu, Carol Friedman, 2012, American Medical Informatics Association Annual Symposium.

PheWAS and Genetics Define Subphenotypes in Drug Response

Charles Moore, Joshua C. Denny, Jeremy L. Warner, 2014, AMIA.

Evaluation of Existing Phenotype Authoring Tools for Clinical Research

Jie Xu, Joshua C. Denny, Jyotishman Pathak, 2014, AMIA.

Huge Cohorts, Genomics, and Clinical Data to Personalize Medicine

Joshua C. Denny, 2018, BCB.

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

Joshua C. Denny, Peter Speltz, Melissa A. Basford, 2012, AMIA.

A comparative study of current clinical natural language processing systems on handling abbreviations in discharge summaries

Hua Xu, Randolph A. Miller, Yonghui Wu, 2012, AMIA.

Limestone: High-throughput candidate phenotype generation via tensor factorization

Jimeng Sun, Joshua C. Denny, Joydeep Ghosh, 2014, J. Biomed. Informatics.

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

Hua Xu, Joshua C. Denny, Qi Dai, 2012, Int. J. Data Min. Bioinform..

Establishing Drug Treatment discovery rate of MedEx

Joshua C. Denny, Eugenia R. McPeek Hinz, Haresh Bhatia, 2012, AMIA.

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

Joshua C. Denny, Jeremy L. Warner, Wei-Qi Wei, 2016, J. Am. Medical Informatics Assoc..

CP Tensor Decomposition with Cannot-Link Intermode Constraints

Bradley Malin, Joyce Ho, Joshua C. Denny, 2019, SDM.

Learning to Identify Treatment Relations in Clinical Text

Cosmin Adrian Bejan, Joshua C. Denny, 2014, AMIA.

An Evaluation of the NQF Quality Data Model for Representing Electronic Health Record Driven Phenotyping Algorithms

Joshua C. Denny, Jyotishman Pathak, Abel N. Kho, 2012, AMIA.

Validation and Enhancement of a Computable Medication Indication Resource (MEDI) Using a Large Practice-based Dataset

Joshua C. Denny, Lisa Bastarache, Wei-Qi Wei, 2013, AMIA.

An active learning-enabled annotation system for clinical named entity recognition

Qingxia Chen, Jingqi Wang, Hua Xu, 2017, BMC Medical Informatics and Decision Making.

PheWAS Network Analysis and Visualization

Joshua C. Denny, Shyr Yu, Eric Torstenson, 2015, AMIA.

Comparing Diagnoses Recorded in Problem Lists vs. Administrative Codes

Joshua C. Denny, Lisa Bastarache, Wei-Qi Wei, 2012, AMIA.

Challenges and strategies for implementing genomic services in diverse settings: experiences from the Implementing GeNomics In pracTicE (IGNITE) network

Joshua C. Denny, Russell A. Wilke, Michael E. Matheny, 2017, BMC Medical Genomics.

EHR Extraction of Longitudinal Exposure to Proton Pump Inhibitors

Joshua C. Denny, Jonathan S. Schildcrout, Josh F. Peterson, 2018, AMIA.

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

Hua Xu, Mei Liu, S. Trent Rosenbloom, 2011, J. Am. Medical Informatics Assoc..

Precision medicine informatics

Joshua C. Denny, Elmer V. Bernstam, Lewis J. Frey, 2016, J. Am. Medical Informatics Assoc..

HealthPro: An integrated web application for essential health data and biological specimen collection in the Precision Medicine Initiative

Paul A. Harris, Joshua C. Denny, Robert J. Carroll, 2017, AMIA.

Evaluating Physician Response to Pharmacogenomic-Guided Warfarin Dosing in an Hospitalized Population

Joshua C. Denny, Josh F. Peterson, Laura K. Wiley, 2016, CRI.

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

Ying Li, Hongfang Liu, Carol Friedman, 2014, J. Am. Medical Informatics Assoc..

Development and Evaluation of a Clinical Note Section Header Terminology

Randolph A. Miller, Joshua C. Denny, Anderson Spickard, 2008, AMIA.

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

Jingqi Wang, Hua Xu, Joshua C. Denny, 2014, American Medical Informatics Association Annual Symposium.

Deep Learning Using Electronic Health Records and Genetic Data to Predict Cardiovascular Diseases

Joshua C. Denny, Wei-Qi Wei, Patrick Wu, 2019, AMIA.

Qualitative study of system level factors related to genomic implementation

Joshua C. Denny, Mia A. Levy, Paul R. Dexter, 2018, Genetics in Medicine.

Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies

Joshua C. Denny, Wei Zhou, Rounak Dey, 2017 .

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

Suzette J. Bielinski, Christopher G. Chute, Joshua C. Denny, 2012, J. Am. Medical Informatics Assoc..

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

Jun Xu, Ergin Soysal, Hua Xu, 2017, J. Am. Medical Informatics Assoc..

Type 2 Diabetes Risk Forecasting from EMR Data using Machine Learning

Joshua C. Denny, Subramani Mani, Yukun Chen, 2012, AMIA.

PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS

Joshua C. Denny, Jill M. Pulley, Yu Shyr, 2019, Bioinform..

The disclosure of diagnosis codes can breach research participants' privacy

Joshua C. Denny, Bradley Malin, Grigorios Loukides, 2010, J. Am. Medical Informatics Assoc..

WikiMedMap: Expanding the Phenotyping Mapping Toolbox Using Wikipedia

Joshua C. Denny, Lina M. Sulieman, Patrick Wu, 2019, bioRxiv.

Predicting changes in hypertension control using electronic health records from a chronic disease management program

Jimeng Sun, Joshua C. Denny, Bradley Malin, 2014, J. Am. Medical Informatics Assoc..

Using natural language processing to provide personalized learning opportunities from trainee clinical notes

Joshua C. Denny, Anderson Spickard, Peter Speltz, 2015, J. Biomed. Informatics.

Identifying a Rare Mortal Risk Factor Using Full Text Search of an EMR

Joshua C. Denny, William D. Dupont, Frederick V. Arndt, 2007 .

Building the Computational Workforce for Precision Medicine

Joshua C. Denny, Marc S. Williams, Douglas B. Fridsma, 2015, AMIA.

Rubik: Knowledge Guided Tensor Factorization and Completion for Health Data Analytics

Jimeng Sun, Yichen Wang, Robert Chen, 2015, KDD.

Focus on health information technology, electronic health records and their financial impact: PASTE: patient-centered SMS text tagging in a medication management system

Joshua C. Denny, Kevin B. Johnson, Shane P. Stenner, 2012, J. Am. Medical Informatics Assoc..

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

S. Trent Rosenbloom, Joshua C. Denny, Daniel Fabbri, 2017, Int. J. Medical Informatics.

PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability

Paul A. Harris, Gerard Tromp, Joshua C. Denny, 2016, J. Am. Medical Informatics Assoc..

Messaging to your doctors: understanding patient-provider communications via a portal system

Hua Xu, Xiaomu Zhou, S. Trent Rosenbloom, 2013, CHI.

Developing a data element repository to support EHR-driven phenotype algorithm authoring and execution

Jie Xu, Christopher G. Chute, Joshua C. Denny, 2016, J. Biomed. Informatics.

Association of BMI and Obesity Genetic Risk Score with Surgical Procedures Through a Procedure-wide Association Study

Joshua C. Denny, Lisa Bastarache, Wei-Qi Wei, 2017, AMIA.

Open Source R Implementation of the PheWAS Methodology

Joshua C. Denny, Lisa Bastarache, Robert J. Carroll, 2013, AMIA.

Uncovering exposures responsible for birth season – disease effects: a global study

Li Li, Phung Anh Nguyen, Yu-Chuan Li, 2017, J. Am. Medical Informatics Assoc..

Can Users Estimate Their Usage of a Web-Based Application? Validating a Self-Report Usage Questionnaire

Joshua C. Denny, Anderson Spickard, Firas H. Wehbe, 2005, AMIA.

A Study of Transportability of an Existing Smoking Status Detection Module across Institutions

Hongfang Liu, Qingxia Chen, Hua Xu, 2012, AMIA.

Identifying QT prolongation from ECG impressions using a general-purpose Natural Language Processor

Randolph A. Miller, Joshua C. Denny, Lemuel R. Waitman, 2009, Int. J. Medical Informatics.

A Genome- and Phenome- Wide Study of Diverticulosis

Girish N. Nadkarni, Joshua C. Denny, Jyotishman Pathak, 2015, AMIA.

Evaluating statistical approaches to leverage large clinical datasets for uncovering therapeutic and adverse medication effects

Joshua C. Denny, Cole Beck, Leena Choi, 2018, Bioinform..

Identifying potential drugs that induce QT prolongation using electronic medical records

Yong Hu, Hua Xu, Mei Liu, 2010, BMC Bioinformatics.

A post-processing algorithm for building longitudinal medication dose data from extracted medication information using natural language processing from electronic health records

Cosmin Adrian Bejan, Joshua C. Denny, Elizabeth McNeer, 2019, bioRxiv.

Detecting temporal expressions in medical narratives

Joshua C. Denny, Steven H. Brown, Michael E. Matheny, 2013, Int. J. Medical Informatics.

Applying Active Learning to Clinical Abbreviation Disambiguation in Real Time

Jingqi Wang, Hua Xu, S. Trent Rosenbloom, 2016, American Medical Informatics Association Annual Symposium.

Research Directions in the Clinical Implementation of Pharmacogenomics: An Overview of US Programs and Projects

Marylyn D. Ritchie, Joshua C. Denny, Teri E. Klein, 2018, Clinical pharmacology and therapeutics.

Real Time Active Learning Study for Clinical Named Entity Recognition

Qingxia Chen, Jingqi Wang, Hua Xu, 2015, American Medical Informatics Association Annual Symposium.

Integrating existing natural language processing tools for medication extraction from discharge summaries

Son Doan, Hua Xu, Joshua C. Denny, 2010, J. Am. Medical Informatics Assoc..

Translating Electronic Clinical Quality Measures to Executable, Portable, and Customizable Workflows in KNIME

Joshua C. Denny, Jyotishman Pathak, William K. Thompson, 2015, AMIA.

Identifying QT prolongation from ECG impressions using Natural Language Processing and Negation Detection

Joshua C. Denny, Josh F. Peterson, J. Denny, 2007, MedInfo.

Extracting timing and status descriptors for colonoscopy testing from electronic medical records

Hua Xu, Randolph A. Miller, Joshua C. Denny, 2010, J. Am. Medical Informatics Assoc..

Leveraging Value Sets from the Value Set Authority Center (VSAC) in a Standards-Based Clinical Data Repository

Joshua C. Denny, Jyotishman Pathak, Guoqian Jiang, 2017, AMIA.

Evaluation of Diagnosis Codes, Clinical Notes, and Medications on Identifying Subjects with a Specific Disease Phenotype

Joshua C. Denny, Jeremy L. Warner, Wei-Qi Wei, 2014, AMIA.

Usability of a phenotype builder prototype and lessons learned for the design of phenotyping tools

Jie Xu, Joshua C. Denny, Jyotishman Pathak, 2015, AMIA.

Sharing of Genomic Information: Perspectives from Stakeholders

Gil Alterovitz, Joshua C. Denny, Jeremy L. Warner, 2013, AMIA.

PhEMA: Phenotype Modeling, Sharing and Execution Architecture

Joshua C. Denny, Jyotishman Pathak, William K. Thompson, 2015, AMIA.

A Phenome-Wide Association Study (PheWAS) of Iron Deficiency in a Large Electronic Health Record Database

Joshua C. Denny, Wei-Qi Wei, Patrick Wu, 2017, AMIA.

A Natural Language Processing Algorithm to define a Venous Thromboembolism Phenotype

Joshua C. Denny, Eugenia R. McPeek Hinz, Lisa Bastarache, 2013, AMIA.

medExtractR: A medication extraction algorithm for electronic health records using the R programming language

Joshua C. Denny, Hannah L Weeks, Cole Beck, 2019, AMIA.

Detecting potential pleiotropy across cardiovascular and neurological diseases using univariate, bivariate, and multivariate methods on 43,870 individuals from the eMERGE network

Xinyuan Zhang, Marylyn D. Ritchie, Chunhua Weng, 2018, PSB.

Using Electronic Health Records to Identify Patient Cohorts for Drug-Induced Thrombocytopenia, Neutropenia and Liver Injury

Christopher G. Chute, Joshua C. Denny, Jyotishman Pathak, 2012, AMIA.

Making work visible for electronic phenotype implementation: Lessons learned from the eMERGE network

Joshua C. Denny, Chunhua Weng, Wei-Qi Wei, 2019, J. Biomed. Informatics.

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

Joshua C. Denny, Nigam H. Shah, Robert R. Freimuth, 2016, J. Am. Medical Informatics Assoc..

Predicting Clinical Laboratory Turnaround Time

Joshua C. Denny, Alex C. Cheng, Marc Beller, 2015, AMIA.

Development and evaluation of an ensemble resource linking medications to their indications

Hua Xu, Joshua C. Denny, Lisa Bastarache, 2013, J. Am. Medical Informatics Assoc..

SecureMA: protecting participant privacy in genetic association

Murat Kantarcioglu, Joshua C. Denny, Dana C. Crawford, 2014 .

Strategies for Equitable Pharmacogenomic-Guided Warfarin Dosing Among European and African American Individuals in a Clinical Population

Joshua C. Denny, Dan M. Roden, David Samuels, 2017, PSB.

Parsing clinical text: how good are the state-of-the-art parsers?

Hua Xu, Joshua C. Denny, Min Jiang, 2014, DTMBIO '14.

Harmonization of Quality Data Model with HL7 FHIR to Support EHR-driven Phenotype Authoring and Execution: A Pilot Study

Jie Xu, Christopher G. Chute, Joshua C. Denny, 2015, AMIA.

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

Jie Xu, Joshua C. Denny, Jyotishman Pathak, 2015, J. Am. Medical Informatics Assoc..

A Decompositional Approach to Executing Quality Data Model Algorithms on the i2b2 Platform

Joshua C. Denny, Jyotishman Pathak, William Thompson, 2016, CRI.

A multi-institution evaluation of clinical profile anonymization

Paul A. Harris, Raymond Heatherly, Joshua C. Denny, 2016, J. Am. Medical Informatics Assoc..

Establishing the Need for Personalized Medicine: Simvastatin Exposure Among a SLCO1B1 Variant Population

Joshua C. Denny, William S. Bush, Josh F. Peterson, 2013, American Medical Informatics Association Annual Symposium.

A Preliminary Study of Coupling Transfer Learning with Active Learning for Clinical Named Entity Recognition between Two Institutions

Yaoyun Zhang, Hua Xu, Joshua C. Denny, 2014, AMIA.

Portability of an algorithm to identify rheumatoid arthritis in electronic health records

Hua Xu, Joshua C. Denny, Tianxi Cai, 2012, J. Am. Medical Informatics Assoc..

A study of active learning methods for named entity recognition in clinical text

Hua Xu, Joshua C. Denny, Qiaozhu Mei, 2015, J. Biomed. Informatics.

Crowdsourcing Clinical Chart Reviews

Yevgeniy Vorobeychik, Joshua C. Denny, Daniel Fabbri, 2018, AMIA.

Analytic Approaches to Phenotypic Complexity

Gil Alterovitz, Joshua C. Denny, Jeremy L. Warner, 2013, MedInfo.

Diabetes and Susceptibility to Infection: A Study of Lab Culture Results in the EMR

Joshua C. Denny, Lisa Bastarache, Wei-Qi Wei, 2012, AMIA.

Meeting the challenge: Health information technology's essential role in achieving precision medicine

Joshua C. Denny, Teresa Zayas-Cabán, Kevin J. Chaney, 2021, J. Am. Medical Informatics Assoc..

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

Joshua C. Denny, Dario A. Giuse, Dan M. Roden, 2020, J. Am. Medical Informatics Assoc..

Precision Medicine and Informatics

Joshua C. Denny, Jessica D. Tenenbaum, Matt Might, 2021 .

Phenotype risk scores identify patients with unrecognized Mendelian disease patterns

Joshua C. Denny, Lisa Bastarache, Wei-Qi Wei, 2018, Science.

Creation and Validation of an EMR-based Algorithm for Identifying Major Adverse Cardiac Events while on Statins

Joshua C. Denny, Wei-Qi Wei, Russell A. Wilke, 2014, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

The IGNITE network: a model for genomic medicine implementation and research

Diane Hauser, Joshua C. Denny, Alan R. Shuldiner, 2015, BMC Medical Genomics.

LPA Variants Are Associated With Residual Cardiovascular Risk in Patients Receiving Statins

George Hripcsak, Joshua C. Denny, Peggy L. Peissig, 2018, Circulation.

Identifying lupus patients in electronic health records: Development and validation of machine learning algorithms and application of rule-based algorithms.

Joshua C. Denny, Tianxi Cai, Katherine P. Liao, 2019, Seminars in arthritis and rheumatism.

The Vanderbilt Experience with Electronic Health Records

Joshua C. Denny, Dario A. Giuse, J. Denny, 2005 .

The phenotypic legacy of admixture between modern humans and Neandertals

Gerard Tromp, Marylyn D. Ritchie, Joshua C. Denny, 2016, Science.

Genetic Variants Associated with Serum Thyroid Stimulating Hormone (TSH) Levels in European Americans and African Americans from the eMERGE Network

Suzette J. Bielinski, Christopher G. Chute, Marylyn D. Ritchie, 2014, PloS one.

Design and Anticipated Outcomes of the eMERGE-PGx Project: A Multi-Center Pilot for Pre-Emptive Pharmacogenomics in Electronic Health Record Systems

Suzette J. Bielinski, Christopher G. Chute, Marylyn D. Ritchie, 2014, Clinical pharmacology and therapeutics.

A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects

Christopher G. Chute, Marylyn D. Ritchie, Joshua C. Denny, 2013, Human Genetics.

Phenotyping Adverse Drug Reactions: Statin-Related Myotoxicity

Joshua C. Denny, William S. Bush, Josh F. Peterson, 2015, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

Abstract 19509: Identifying Genotype-Phenotype Relations in Electronic Medical Record Systems: Application to Warfarin Pharmacogenomics.

Marylyn D. Ritchie, Joshua C. Denny, Dana C. Crawford, 2010 .

Attitudes of Clinicians Following Large-Scale Pharmacogenomics Implementation

Joshua C. Denny, Dan M. Roden, Jonathan S. Schildcrout, 2015, The Pharmacogenomics Journal.

Automatic Capture of Student Notes to Augment Mentor Feedback and Student Performance on Patient Write-Ups

Joshua C. Denny, Joseph Gigante, J. Denny, 2008, Journal of General Internal Medicine.

Genome-wide Association Studies Identify Genetic Loci Associated With Albuminuria in Diabetes

Sylvia Stracke, Christian Gieger, Joshua C. Denny, 2015, Diabetes.

Electronic medical records and genomics (eMERGE) network exploration in cataract: Several new potential susceptibility loci

Marylyn D. Ritchie, Joshua C. Denny, Shefali S. Verma, 2014, Molecular vision.

Extracting and standardizing medication information in clinical text – the MedEx-UIMA system

Joshua C. Denny, Hua Xu, Min Jiang, 2014, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

Genome-and Phenome-Wide Analysis of Cardiac Conduction Identifies Markers of Arrhythmia Risk Running title : Ritchie et al . ; QRS GWAS and PheWAS in electronic records

Christopher G. Chute, Marylyn D. Ritchie, Joshua C. Denny, 2013 .

Phenome-wide association study (PheWAS) in EMR-linked pediatric cohorts, genetically links PLCL1 to speech language development and IL5-IL13 to Eosinophilic Esophagitis

Keith Marsolo, Marylyn D. Ritchie, Aleksey A. Porollo, 2014, Front. Genet..

Enabling Genomic-Phenomic Association Discovery without Sacrificing Anonymity

Joshua C. Denny, Grigorios Loukides, Dan M. Roden, 2013, PloS one.

Integration of Sequence Data from a Consanguineous Family with Genetic Data from an Outbred Population Identifies PLB1 as a Candidate Rheumatoid Arthritis Risk Gene

Joshua C. Denny, Jing Cui, Elaine R. Mardis, 2014, PloS one.

Analyses of longitudinal, hospital clinical laboratory data with application to blood glucose concentrations.

Joshua C. Denny, Lemuel R. Waitman, Michael E. Matheny, 2011, Statistics in medicine.

eMERGE Phenome-Wide Association Study (PheWAS) identifies clinical associations and pleiotropy for stop-gain variants

Suzette J. Bielinski, Gerard Tromp, Marylyn D. Ritchie, 2016, BMC Medical Genomics.

Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins

Matti Pirinen, David M. Herrington, Alex Doney, 2014, Nature Communications.

Practical considerations in genomic decision support: The eMERGE experience

Keith Marsolo, Suzette J. Bielinski, Gerard Tromp, 2015, Journal of pathology informatics.

An Automated Approach to Calculating the Daily Dose of Tacrolimus in Electronic Health Records

Son Doan, Joshua C. Denny, David W. Haas, 2010, Summit on translational bioinformatics.

Mapping the incidentalome: estimating incidental findings generated through clinical pharmacogenomics testing

Joshua C. Denny, Ellen Wright Clayton, Sara L. Van Driest, 2012, Genetics in Medicine.

Knowledge-Driven Multi-Locus Analysis Reveals Gene-Gene Interactions Influencing HDL Cholesterol Level in Two Independent EMR-Linked Biobanks

Marylyn D. Ritchie, Joshua C. Denny, Dana C. Crawford, 2011, PloS one.

Autoantibodies, autoimmune risk alleles and clinical associations in rheumatoid arthritis cases and non-RA controls in the electronic medical records

Peter Szolovits, Joshua C. Denny, Tianxi Cai, 2013 .

Linking Genomic and Clinical Data for Discovery and Personalized Care

Joshua C. Denny, Hua Xu, J. Denny, 2014 .

TYK2 Protein-Coding Variants Protect against Rheumatoid Arthritis and Autoimmunity, with No Evidence of Major Pleiotropic Effects on Non-Autoimmune Complex Traits

Joshua C. Denny, Lisa Bastarache, Jing Cui, 2015, PloS one.

Disease Heritability Studies Harness the Healthcare System to Achieve Massive Scale

Joshua C. Denny, Jonathan D. Mosley, J. Denny, 2018, Cell.

Trans-ethnic association study of blood pressure determinants in over 750,000 individuals

Laura J. Scott, Yu Wang, Joshua C. Denny, 2018, Nature Genetics.

Correction: Computational Phenotype Discovery Using Unsupervised Feature Learning over Noisy, Sparse, and Irregular Clinical Data

Joshua C. Denny, Thomas A. Lasko, Mia A. Levy, 2013, PLoS ONE.

Mining phenotypic keywords from a large collection of clinical narratives

Joshua C. Denny, Kevin B. Johnson, Erica A. Bowton, 2014 .

Return of individual research results from genome-wide association studies: experience of the Electronic Medical Records and Genomics (eMERGE) Network

Marylyn D. Ritchie, Joshua C. Denny, Eugenia R. McPeek Hinz, 2012, Genetics in Medicine.

Identification of Genomic Predictors of Atrioventricular ConductionClinical Perspective

Marylyn D. Ritchie, Joshua C. Denny, Dana C. Crawford, 2010 .

Phenome-wide association studies demonstrating pleiotropy of genetic variants within FTO with and without adjustment for body mass index

Suzette J. Bielinski, Gerard Tromp, Christopher G. Chute, 2014, Front. Genet..

Cox regression increases power to detect genotype-phenotype associations in genomic studies using the electronic health record

Qingxia Chen, Joshua C. Denny, Lisa Bastarache, 2019, BMC Genomics.