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List of works by Joshua C. Denny

"Understanding" medical school curriculum content using KnowledgeMap

scientific article

"Where do we teach what?" Finding broad concepts in the medical school curriculum.

scientific article published on October 2005

A Crowdsourcing Framework for Medical Data Sets.

scientific article

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

scientific article published on 01 July 2019

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

scientific article

A Modular Architecture for Electronic Health Record-Driven Phenotyping

scientific article

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

A Phenome-Wide Association Study Identifies a Novel Asthma Risk Locus Near TERC.

scientific article published in January 2016

A Phenome-Wide Association Study Uncovers a Role for Autoimmunity in the Development of Chronic Obstructive Pulmonary Disease.

scientific article published in June 2018

A Phenome-wide Mendelian Randomisation study on genetically determined serum urate levels in UK Biobank cohort

scientific article published on 10 May 2019

A Polygenic and Phenotypic Risk Prediction for Polycystic Ovary Syndrome Evaluated by Phenome-Wide Association Studies

scientific article published on 9 January 2020

A Preliminary Study of Clinical Abbreviation Disambiguation in Real Time.

scientific article published on 3 June 2015

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

scientific article published on 25 March 2015

A Robust e-Epidemiology Tool in Phenotyping Heart Failure with Differentiation for Preserved and Reduced Ejection Fraction: the Electronic Medical Records and Genomics (eMERGE) Network

scientific article

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

scientific article published on January 2015

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

scientific article published on 14 November 2014

A Trans-Ethnic Genome-Wide Association Study of Uterine Fibroids.

scientific article published on 12 June 2019

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

scientific article published on 01 November 2018

A common deletion in the haptoglobin gene associated with blood cholesterol levels among Chinese women

scientific article published on 29 June 2017

A common variant on chromosome 4q25 is associated with prolonged PR interval in subjects with and without atrial fibrillation.

scientific article published on 03 October 2013

A comparative study of current Clinical Natural Language Processing systems on handling abbreviations in discharge summaries

scientific article published on 3 November 2012

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

scientific article published on 23 June 2017

A conceptual model for translating omic data into clinical action

scientific article

A gene-based association method for mapping traits using reference transcriptome data

scientific article

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

scientific article published on 12 September 2013

A genome-wide association study identifies variants in KCNIP4 associated with ACE inhibitor-induced cough

scientific article

A genome-wide association study of heparin-induced thrombocytopenia using an electronic medical record

scientific article

A hybrid system for temporal information extraction from clinical text

scientific article published on 09 April 2013

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

scientific article published on 18 August 2016

A missense variant in Mitochondrial Amidoxime Reducing Component 1 gene and protection against liver disease

scientific article published on 13 April 2020

A multi-institution evaluation of clinical profile anonymization

scientific article

A multi-stage genome-wide association study of uterine fibroids in African Americans

scientific article

A natural language processing algorithm to define a venous thromboembolism phenotype

scientific article published on 16 November 2013

A phenome-wide association study to discover pleiotropic effects of , , and

A polymorphism in HLA-G modifies statin benefit in asthma

scientific article

A prognostic model based on readily available clinical data enriched a pre-emptive pharmacogenetic testing program.

scientific article

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

A stepwise approach to implementing pharmacogenetic testing in the primary care setting

scientific article published on 01 October 2019

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

scientific article published on 15 September 2015

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

scientific article

A study of transportability of an existing smoking status detection module across institutions.

scientific article published on 3 November 2012

A study paradigm integrating prospective epidemiologic cohorts and electronic health records to identify disease biomarkers

scientific article published in Nature Communications

Accelerating Precision Drug Development and Drug Repurposing by Leveraging Human Genetics

scientific article published on 5 April 2017

Admixture mapping and subsequent fine-mapping suggests a biologically relevant and novel association on chromosome 11 for type 2 diabetes in African Americans

scientific article

An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease

scientific article published on 01 August 2018

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

scientific article

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

scientific article

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

scientific article

An automated approach to calculating the daily dose of tacrolimus in electronic health records.

scientific article published on March 2010

An evaluation of the NQF Quality Data Model for representing Electronic Health Record driven phenotyping algorithms

scientific article

An integrative functional genomics framework for effective identification of novel regulatory variants in genome-phenome studies.

scientific article published on 29 January 2018

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

scientific article

Analysis of a computerized sign-out tool: identification of unanticipated uses and contradictory content.

scientific article published on 11 October 2007

Analysis of medical student content searches that resulted in unidentified UMLS concepts.

scientific article published on January 2006

Analysis of predicted loss-of-function variants in UK Biobank identifies variants protective for disease

scientific article published on 24 April 2018

Analyzing differences between chinese and english clinical text: a cross-institution comparison of discharge summaries in two languages

scientific article published on January 2013

Analyzing the heterogeneity and complexity of Electronic Health Record oriented phenotyping algorithms.

scientific article published on 22 October 2011

Anonymization of administrative billing codes with repeated diagnoses through censoring

scientific article (publication date: 13 November 2010)

Apolipoprotein L1 Variants and Blood Pressure Traits in African Americans

scientific article published on March 2017

Applying active learning to high-throughput phenotyping algorithms for electronic health records data

scientific article

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

scientific article published on 12 August 2011

Assessing the accuracy of observer-reported ancestry in a biorepository linked to electronic medical records

scientific article

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

scientific article published on 21 October 2014

Assessment of a pharmacogenomic marker panel in a polypharmacy population identified from electronic medical records

scientific article published on May 2013

Association of Arrhythmia-Related Genetic Variants With Phenotypes Documented in Electronic Medical Records

scientific article published on January 2016

Association of Genetic Risk of Obesity with Postoperative Complications Using Mendelian Randomization

scientific article published on 01 January 2020

Association of ST2 polymorphisms with atopy, asthma, and leukemia

scientific article published on 19 May 2018

Association of Thyroid Function Genetic Predictors With Atrial Fibrillation: A Phenome-Wide Association Study and Inverse-Variance Weighted Average Meta-analysis

scientific article published on 01 February 2019

Association of genetic variation with cirrhosis: a multi-trait genome-wide association and gene-environment interaction study

scientific article published on 10 December 2020

Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls

scientific article published on March 2013

Attitudes of clinicians following large-scale pharmacogenomics implementation

scientific article published on 11 August 2015

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

scientific article published on 14 November 2014

Automated Classification of Consumer Health Information Needs in Patient Portal Messages

scientific article published on 5 November 2015

Automated capture and assessment of medical student clinical experience.

scientific article

Automated extraction of clinical traits of multiple sclerosis in electronic medical records

scientific article published on 22 October 2013

Automated grouping of medical codes via multiview banded spectral clustering

scientific article published on 28 October 2019

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

scientific article published on 07 June 2013

Automatic capture of student notes to augment mentor feedback and student performance on patient write-ups.

scientific article published on July 2008

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

scientific article published on 25 October 2014

Automatic scoring of medical students' clinical notes to monitor learning in the workplace.

scientific article published on 7 November 2013

Benefit of pre-emptive pharmacogenetic information on clinical outcome

scientific article published on 29 January 2018

Biobanks and electronic medical records: enabling cost-effective research

scientific article

Building bridges across electronic health record systems through inferred phenotypic topics

scientific article

CMTR1 is associated with increased asthma exacerbations in patients taking inhaled corticosteroids

scientific article

CP Tensor Decomposition with Cannot-Link Intermode Constraints

scientific article published on 01 May 2019

CTNNA3 and SEMA3D: Promising loci for asthma exacerbation identified through multiple genome-wide association studies

scientific article

CYP2C19 Loss-of-Function is Associated with Increased Risk of Ischemic Stroke after Transient Ischemic Attack in Intracranial Atherosclerotic Disease

scientific article published on 24 November 2020

CYP2C19 and CES1 polymorphisms and efficacy of clopidogrel and aspirin dual antiplatelet therapy in patients with symptomatic intracranial atherosclerotic disease

scientific article

Calcium Channel Blockers as Drug Repurposing Candidates for Gestational Diabetes: Mining large scale genomic and electronic health records data to repurpose medications

scientific article published on 12 February 2018

Can users estimate their usage of a web-based application? Validating a self-report usage questionnaire.

scientific article published on January 2005

Case 40-2018: A Woman with Recurrent Sinusitis, Cough, and Bronchiectasis

scientific article published on 01 April 2019

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

scientific article

Chapter 13: Mining Electronic Health Records in the Genomics Era ⬇️

scientific article published on December 27, 2012

Characteristics and treatment of African-American and European-American patients with resistant hypertension identified using the electronic health record in an academic health centre: a case-control study.

scientific article

Characterization of statin dose response in electronic medical records

scientific article published on 04 October 2013

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

scientific article

Clinically actionable genotypes among 10,000 patients with preemptive pharmacogenomic testing

scientific article

Coding Variation in ANGPTL4, LPL, and SVEP1 and the Risk of Coronary Disease

scientific article published on 2 March 2016

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

scientific article published on 02 September 2015

Common variation near IRF6 is associated with IFN-β-induced liver injury in multiple sclerosis

scientific article published on 16 July 2018

Comorbidity Characterization Among eMERGE Institutions: A Pilot Evaluation with the Johns Hopkins Adjusted Clinical Groups® System.

scientific article published on 6 May 2019

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

scientific article published on 17 November 2012

Comparing content coverage in medical curriculum to trainee-authored clinical notes

scientific article

Comparison of HLA allelic imputation programs.

scientific article

Complement receptor 1 gene variants are associated with erythrocyte sedimentation rate

scientific article

Computational phenotype discovery using unsupervised feature learning over noisy, sparse, and irregular clinical data

scientific article

Correction: Enabling Genomic-Phenomic Association Discovery without Sacrificing Anonymity

scientific article published on 18 June 2013

Correction: Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations.

scientific article

Cost-aware active learning for named entity recognition in clinical text

scientific article published on 01 November 2019

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

scientific article published on 04 November 2019

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

scientific article published on 07 April 2014

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

scientific article

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

scientific article (publication date: June 2015)

Defining a Contemporary Ischemic Heart Disease Genetic Risk Profile Using Historical Data

scientific article

Defining the complex phenotype of severe systemic loxoscelism using a large electronic health record cohort

scientific article

Defining the role of common variation in the genomic and biological architecture of adult human height

scientific article

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

scientific article

Design and anticipated outcomes of the eMERGE-PGx project: a multicenter pilot for preemptive pharmacogenomics in electronic health record systems

scientific article

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

scientific article

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

Detecting abbreviations in discharge summaries using machine learning methods.

scientific article published on 22 October 2011

Detecting drug interactions from adverse-event reports: interaction between paroxetine and pravastatin increases blood glucose levels.

scientific article published on 25 May 2011

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

Detecting temporal expressions in medical narratives

scientific article published on 16 May 2012

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

scientific article published on 22 August 2019

Developing Electronic Health Record Algorithms That Accurately Identify Patients With Systemic Lupus Erythematosus

scientific article

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

scientific article

Developing an Algorithm to Detect Early Childhood Obesity in Two Tertiary Pediatric Medical Centers

scientific article published on 20 July 2016

Development and evaluation of a clinical note section header terminology

scientific article

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

scientific article (publication date: 2013)

Development of a System for Postmarketing Population Pharmacokinetic and Pharmacodynamic Studies Using Real-World Data From Electronic Health Records

scientific article published on 11 February 2020

Development of a natural language processing system to identify timing and status of colonoscopy testing in electronic medical records

scientific article

Development of an ensemble resource linking MEDications to their Indications (MEDI).

scientific article published on 18 March 2013

Development of inpatient risk stratification models of acute kidney injury for use in electronic health records.

scientific article published on 30 March 2010

Development of the Initial Surveys for the All of Us Research Program

scientific article published on 01 July 2019

Discovery of Noncancer Drug Effects on Survival in Electronic Health Records of Patients With Cancer: A New Paradigm for Drug Repurposing

scientific article published on 01 May 2019

Diversity and inclusion for the All of Us research program: A scoping review

scientific article published on 01 July 2020

Effect of CYP4F2, VKORC1, and CYP2C9 in Influencing Coumarin Dose: A Single-Patient Data Meta-Analysis in More Than 15,000 Individuals

scientific article published on 17 February 2019

Effects of G6pc2 deletion on body weight and cholesterol in mice

scientific article published on 25 January 2017

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

scientific article published on 13 August 2018

Electronic Health Record Based Algorithm to Identify Patients with Autism Spectrum Disorder

scientific article published on 29 July 2016

Electronic Medical Records as a Tool in Clinical Pharmacology: Opportunities and Challenges ⬇️

scientific article published on June 1, 2012

Electronic health record design and implementation for pharmacogenomics: a local perspective

scientific article published on 05 September 2013

Electronic health records-driven phenotyping: challenges, recent advances, and perspectives

scientific article published on December 2013

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

scientific article

Electronic medical records for genetic research: results of the eMERGE consortium

scientific article published on April 2011

Enabling genomic-phenomic association discovery without sacrificing anonymity

scientific article

Enhancing the power of genetic association studies through the use of silver standard cases derived from electronic medical records

scientific article

Erratum to: A multi-stage genome-wide association study of uterine fibroids in African Americans

scientific article published on 4 October 2017

Erratum: Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation

scientific article published in July 2017

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

scientific article

Evaluating phecodes, clinical classification software, and ICD-9-CM codes for phenome-wide association studies in the electronic health record

scientific article

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

scientific article published on 01 September 2018

Evaluating the Utility of Polygenic Risk Scores in Identifying High-Risk Individuals for Eight Common Cancers

scientific article published on 12 March 2020

Evaluation of a Novel System to Enhance Clinicians' Recognition of Preadmission Adverse Drug Reactions

scientific article published on 01 April 2018

Evaluation of a Prediction Model for the Development of Atrial Fibrillation in a Repository of Electronic Medical Records

scientific article published on 12 October 2016

Evaluation of a method to identify and categorize section headers in clinical documents

scientific article

Evaluation of a novel terminology to categorize clinical document section headers and a related clinical note section tagger ⬇️

master's thesis

Evaluation of the F2R IVS-14A/T PAR1 polymorphism with subsequent cardiovascular events and bleeding in patients who have undergone percutaneous coronary intervention

scientific article

Evaluation of the MC4R gene across eMERGE network identifies many unreported obesity-associated variants

scientific article published on 20 September 2020

Evidence for extensive pleiotropy among pharmacogenes

scientific article published on June 2016

Examining rare and low-frequency genetic variants previously associated with lone or familial forms of atrial fibrillation in an electronic medical record system: a cautionary note.

scientific article

Exome-wide association study of plasma lipids in >300,000 individuals

scientific article published on 30 October 2017

Extracting and integrating data from entire electronic health records for detecting colorectal cancer cases ⬇️

scientific article published on October 22, 2011

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

scientific article published on 7 April 2014

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

scientific article published in January 2012

Extracting research-quality phenotypes from electronic health records to support precision medicine

scientific article

Extracting semantic lexicons from discharge summaries using machine learning and the C-Value method ⬇️

scientific article published on November 3, 2012

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

scientific article

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

scientific article published on July 2011

Facilitating phenotype transfer using a common data model

scientific article published on 17 July 2019

Finding a Needle in a QT Interval Big Data Haystack

scientific article

Formative evaluation to guide early deployment of an online content management tool for medical curriculum.

scientific article published on January 2003

Four Susceptibility Loci for Gallstone Disease Identified in a Meta-analysis of Genome-Wide Association Studies

scientific article

GRIK5 Genetically Regulated Expression Associated with Eye and Vascular Phenomes: Discovery through Iteration among Biobanks, Electronic Health Records, and Zebrafish

article

Generalization of variants identified by genome-wide association studies for electrocardiographic traits in African Americans

scientific article published on 28 March 2013

Generating Clinical Notes for Electronic Health Record Systems

scientific article

Genetic Interactions with Age, Sex, Body Mass Index, and Hypertension in Relation to Atrial Fibrillation: The AFGen Consortium

scientific article published on 12 September 2017

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization

scientific article

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function

scientific article

Genetic determinants of variability in warfarin response after the dose-titration phase.

scientific article published on 14 September 2016

Genetic variants associated with serum thyroid stimulating hormone (TSH) levels in European Americans and African Americans from the eMERGE Network

scientific article

Genetic variants related to antihypertensive targets inform drug efficacy and side effects

Genetic variants that confer resistance to malaria are associated with red blood cell traits in African-Americans: an electronic medical record-based genome-wide association study

scientific article published on 08 July 2013

Genetic variation in the UGT1A locus is associated with simvastatin efficacy in a clinical practice setting

scientific article

Genetically determined serum urate levels and cardiovascular and other diseases in UK Biobank cohort: A phenome-wide mendelian randomization study

scientific article published on 18 October 2019

Genetics of glucocorticoid-associated osteonecrosis in children with acute lymphoblastic leukemia

scientific article

Genetics of rheumatoid arthritis contributes to biology and drug discovery

scientific article

Genome- and phenome-wide analyses of cardiac conduction identifies markers of arrhythmia risk

scientific article published on 05 March 2013

Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy

scientific article published on June 2015

Genome-Wide Association and Functional Studies Reveal Novel Pharmacological Mechanisms for Allopurinol

scientific article published on 23 May 2019

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

scientific article

Genome-wide and Phenome-wide Approaches to Understand Variable Drug Actions in Electronic Health Records

scientific article published on 17 November 2017

Genome-wide association and pathway analysis of left ventricular function after anthracycline exposure in adults.

scientific article published on 24 May 2017

Genome-wide association meta-analysis of PR interval identifies 47 novel loci associated with atrial and atrioventricular electrical activity

Genome-wide study of resistant hypertension identified from electronic health records

scientific article

Genotype and risk of major bleeding during warfarin treatment

scientific article

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

scientific article

High density GWAS for LDL cholesterol in African Americans using electronic medical records reveals a strong protective variant in APOE

scientific article

Hypertension is a modifiable risk factor for osteonecrosis in acute lymphoblastic leukemia

scientific article published on 13 August 2019

Identification of genomic predictors of atrioventricular conduction: using electronic medical records as a tool for genome science

scientific article

Identification of unique venous thromboembolism-susceptibility variants in African-Americans.

scientific article

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

scientific article

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

scientific article published on 19 October 2008

Identifying QT prolongation from ECG impressions using natural language processing and negation detection

scientific article published on January 2007

Identifying UMLS concepts from ECG Impressions using KnowledgeMap.

scientific article

Identifying genetically driven clinical phenotypes using linear mixed models

scientific article published on 25 April 2016

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

scientific article published on 04 January 2019

Identifying potential drugs that induce QT prolongation using electronic medical records

scientific article published on 23 July 2010

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

scientific article published on March 2012

Improving the phenotype risk score as a scalable approach to identifying patients with Mendelian disease

scientific article published on 01 December 2019

Inactivating mutations in NPC1L1 and protection from coronary heart disease

scientific article

Increased monocyte count as a cellular biomarker for poor outcomes in fibrotic diseases: a retrospective, multicentre cohort study

scientific article published on 29 March 2019

Influence of human leukocyte antigen (HLA) alleles and killer cell immunoglobulin-like receptors (KIR) types on heparin-induced thrombocytopenia (HIT).

scientific article

Integrating EMR-linked and in vivo functional genetic data to identify new genotype-phenotype associations

scientific article (publication date: 2014)

Integrating electronic health record genotype and phenotype datasets to transform patient care

scientific article published on 14 December 2015

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

scientific article

Integration of sequence data from a Consanguineous family with genetic data from an outbred population identifies PLB1 as a candidate rheumatoid arthritis risk gene

scientific article

Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions

scientific article published on 27 April 2016

Intelligent use and clinical benefits of electronic health records in rheumatoid arthritis

scientific article published on 8 February 2015

Investigating the Genetic Architecture of the PR Interval Using Clinical Phenotypes

scientific article published on April 2017

Joint mouse-human phenome-wide association to test gene function and disease risk

scientific article

Knowledge-driven multi-locus analysis reveals gene-gene interactions influencing HDL cholesterol level in two independent EMR-linked biobanks

scientific article

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

LabWAS: Novel findings and study design recommendations from a meta-analysis of clinical labs in two independent biobanks

scientific article published on 11 November 2020

Large-Scale Exome-wide Association Analysis Identifies Loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases

scientific article

Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation.

scientific article

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

scientific article published in Scientific Reports

Learning to identify treatment relations in clinical text

scientific article

Lessons learned from developing a drug evidence base to support pharmacovigilance

scientific article (publication date: 2013)

Letter by Mosley Regarding Article, "Iron Homeostasis and Pulmonary Hypertension: Iron Deficiency Leads to Pulmonary Vascular Remodeling in the Rat".

scientific article published in August 2015

Leveraging Human Genetics to Identify Safety Signals Prior to Drug Marketing Approval and Clinical Use

scientific article published on 28 February 2020

Limestone: high-throughput candidate phenotype generation via tensor factorization.

scientific article published on 16 July 2014

MR-PheWAS: exploring the causal effect of SUA level on multiple disease outcomes by using genetic instruments in UK Biobank.

scientific article published on 6 February 2018

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

scientific article published on 19 September 2019

Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial Evaluation

scientific article published on 29 November 2019

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

scientific article published on 29 November 2012

Mechanistic phenotypes: an aggregative phenotyping strategy to identify disease mechanisms using GWAS data

scientific article

MedEx: a medication information extraction system for clinical narratives.

scientific article

Mendelian Randomization of Circulating Polyunsaturated Fatty Acids and Colorectal Cancer Risk

scientific article published on 12 February 2020

Meta-analysis of genome-wide association studies of HDL cholesterol response to statins

scientific article

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

scientific article

Mining Biomedical Literature for Terms related to Epidemiologic Exposures

scientific article

Modeling drug exposure data in electronic medical records: an application to warfarin.

scientific article

Modulators of normal electrocardiographic intervals identified in a large electronic medical record

scientific article

Multi-ethnic genome-wide association study for atrial fibrillation

article

Multisite Investigation of Outcomes With Implementation of CYP2C19 Genotype-Guided Antiplatelet Therapy After Percutaneous Coronary Intervention

scientific article

Natural language processing improves identification of colorectal cancer testing in the electronic medical record

scientific article published on 10 March 2011

Naïve Electronic Health Record phenotype identification for Rheumatoid arthritis

scientific article published on 22 October 2011

New data and an old puzzle: the negative association between schizophrenia and rheumatoid arthritis

scientific article

On the Potential of Preemptive Genotyping Towards Preventing Medication-Related Adverse Events: Results from the South Korean National Health Insurance Database.

scientific article

Operational implementation of prospective genotyping for personalized medicine: the design of the Vanderbilt PREDICT project.

scientific article published on 16 May 2012

Opportunities and Challenges in Cardiovascular Pharmacogenomics: From Discovery to Implementation

scientific article published on 01 April 2018

Opportunities for genomic clinical decision support interventions

scientific article published on 19 September 2013

PASTE: patient-centered SMS text tagging in a medication management system

scientific article published on 8 October 2011

PCSK9 genetic variants and risk of type 2 diabetes: a mendelian randomisation study

scientific article published on 28 November 2016

PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity

scientific article published in Nature Communications

PRECISION MEDICINE: FROM DIPLOTYPES TO DISPARITIES TOWARDS IMPROVED HEALTH AND THERAPIES.

scientific article published in January 2018

PROTEIN-CODING VARIANTS IMPLICATE NOVEL GENES RELATED TO LIPID HOMEOSTASIS CONTRIBUTING TO BODY FAT DISTRIBUTION

article

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

scientific article published on 20 May 2015

Penetrance of Hemochromatosis in HFE Genotypes Resulting in p.Cys282Tyr and p.[Cys282Tyr];[His63Asp] in the eMERGE Network

scientific article

Performance of an electronic health record-based phenotype algorithm to identify community associated methicillin-resistant Staphylococcus aureus cases and controls for genetic association studies

scientific article

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

scientific article

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

scientific article

PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records

scientific article published on 24 September 2020

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

scientific article published on 14 October 2020

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

scientific article

Phenome-Wide Association Studies as a Tool to Advance Precision Medicine

scientific article

Phenome-Wide Association Study of Rheumatoid Arthritis Subgroups Identifies Association Between Seronegative Disease and Fibromyalgia

scientific article

Phenome-wide Mendelian-randomization study of genetically determined vitamin D on multiple health outcomes using the UK Biobank study

scientific article published on 01 October 2019

Phenome-wide association analysis of LDL-cholesterol lowering genetic variants in PCSK9

scientific article published on 29 October 2019

Phenome-wide association analysis suggests the APOL1 linked disease spectrum primarily drives kidney-specific pathways

scientific article published on 17 February 2020

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

scientific article

Phenome-wide association studies uncover a novel association of increased atrial fibrillation in males with systemic lupus erythematosus

scientific article published on 26 February 2018

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

scientific article

Phenome-wide association study identifies marked increased in burden of comorbidities in African Americans with systemic lupus erythematosus.

scientific article published on 10 April 2018

Phenome-wide scanning identifies multiple diseases and disease severity phenotypes associated with HLA variants.

scientific article published on May 2017

Phenotype risk scores identify patients with unrecognized Mendelian disease patterns

scientific article published in Science

Phenotyping Adverse Drug Reactions: Statin-Related Myotoxicity

scientific article published on 25 March 2015

Phenotyping through Semi-Supervised Tensor Factorization (PSST)

scientific article published on 05 December 2018

Physician response to implementation of genotype-tailored antiplatelet therapy

scientific article published on 22 December 2015

Platelet Inhibitors Reduce Rupture in a Mouse Model of Established Abdominal Aortic Aneurysm

scientific article

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

scientific article

Practical considerations for implementing genomic information resources. Experiences from eMERGE and CSER.

scientific article published on 21 September 2016

Practical considerations in genomic decision support: The eMERGE experience

scientific article

Precision medicine informatics

scientific article

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

scientific article published on 17 September 2013

Predicting clopidogrel response using DNA samples linked to an electronic health record.

scientific article published on 21 December 2011

Predicting warfarin dosage in European-Americans and African-Americans using DNA samples linked to an electronic health record

scientific article

PregOMICS-Leveraging systems biology and bioinformatics for drug repurposing in maternal-child health.

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Proceedings from the 9th annual conference on the science of dissemination and implementation: Washington, DC, USA. 14-15 December 2016.

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Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity

scientific article published on 22 December 2017

Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution

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Prototype Development: Context-Driven Dynamic XML Ophthalmologic Data Capture Application.

scientific article published on 13 September 2017

Publisher Correction: Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity

scientific article published on 16 March 2018

Publisher Correction: Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity

scientific article

Publisher Correction: Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity

scientific article published on 01 July 2019

Pulling the covers in electronic health records for an association study with self-reported sleep behaviors

scientific article published on 05 September 2018

Qualitative study of system-level factors related to genomic implementation

scientific article published on 23 November 2018

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

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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

scientific article published on 29 October 2020

Relationship between very low low-density lipoprotein cholesterol concentrations not due to statin therapy and risk of type 2 diabetes: A US-based cross-sectional observational study using electronic health records

scientific article published on 28 August 2018

Replication of Associations with Electrocardio-graphic Traits in African Americans from Clinical and Epidemiologic Studies

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Reply

Reply to Ward and Colleagues' Comment on "Using Human Experiments of Nature to Predict Drug Safety Issues: An Example with PCSK9 Inhibitors"

scientific article published on 01 November 2018

Research Directions in Genetic Predispositions to Stevens-Johnson Syndrome / Toxic Epidermal Necrolysis.

scientific article published on 6 November 2017

Research directions in the clinical implementation of pharmacogenomics - An Overview of US programs and projects

scientific article published on 20 February 2018

Response to “Doubt About the Feasibility of Preemptive Genotyping”

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

scientific article (publication date: April 2012)

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

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Robust Replication of Genotype-Phenotype Associations across Multiple Diseases in an Electronic Medical Record

Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record

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Rubik

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SJS/TEN 2017: Building Multidisciplinary Networks to Drive Science and Translation

scientific article published in January 2018

SOS2 and ACP1 Loci Identified through Large-Scale Exome Chip Analysis Regulate Kidney Development and Function

scientific article published on 5 December 2016

STRATEGIES FOR EQUITABLE PHARMACOGENOMIC-GUIDED WARFARIN DOSING AMONG EUROPEAN AND AFRICAN AMERICAN INDIVIDUALS IN A CLINICAL POPULATION

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Scalable Data-driven Phenotypes via Unsupervised Feature Learning

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SecureMA: protecting participant privacy in genetic association meta-analysis

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

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Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations.

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

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

scientific article published on August 2013

Systematic Evaluation of Pleiotropy Identifies 6 Further Loci Associated With Coronary Artery Disease ⬇️

scientific article published on February 2017

Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data

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TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits

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Teaching evidence-based medicine: Impact on students' literature use and inpatient clinical documentation

scientific article published in January 2011

The "All of Us" Research Program

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The All of Us Research Program: Data quality, utility, and diversity

scientific article published in 2022

The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future

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The Gain-of-Function Integrin β3 Pro33 Variant Alters the Serotonin System in the Mouse Brain.

scientific article published on 16 October 2017

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

scientific article published on 5 January 2016

The KnowledgeMap project: development of a concept-based medical school curriculum database

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The Pharmacogenomics Research Network Translational Pharmacogenetics Program: overcoming challenges of real-world implementation

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The Vanderbilt Experience with Electronic Health Records

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The disclosure of diagnosis codes can breach research participants' privacy

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The effect of reducing maximum shift lengths to 16 hours on internal medicine interns' educational opportunities

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The influence of big (clinical) data and genomics on precision medicine and drug development.

scientific article published on 24 November 2017

The phenotypic legacy of admixture between modern humans and Neandertals

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The polygenic architecture of left ventricular mass mirrors the clinical epidemiology

scientific article published on 05 May 2020

The use of a DNA biobank linked to electronic medical records to characterize pharmacogenomic predictors of tacrolimus dose requirement in kidney transplant recipients

scientific article published on January 2012

Tracking medical students' clinical experiences using natural language processing

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

scientific article published on 21 December 2018

Transcription factor ETV1 is essential for rapid conduction in the heart

scientific article published on 24 October 2016

Type 2 diabetes risk forecasting from EMR data using machine learning ⬇️

scientific article published on November 3, 2012

Unfolding of hidden white blood cell count phenotypes for gene discovery using latent class mixed modeling

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Use of Genetic Variants Related to Antihypertensive Drugs to Inform on Efficacy and Side Effects

scientific article published on 25 June 2019

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

scientific article published on 19 November 2011

Using Human 'Experiments of Nature' to Predict Drug Safety Issues: An Example with PCSK9 Inhibitors

scientific article published on 28 November 2017

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

scientific article published on 10 June 2015

Using systems approaches to address challenges for clinical implementation of pharmacogenomics

Using systems approaches to address challenges for clinical implementation of pharmacogenomics.

scientific article published on 06 December 2013

Using topic modeling via non-negative matrix factorization to identify relationships between genetic variants and disease phenotypes: A case study of Lipoprotein(a) (LPA)

scientific article published on 13 February 2019

Utilization of an EMR-biorepository to identify the genetic predictors of calcineurin-inhibitor toxicity in heart transplant recipients

scientific article published on January 2014

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

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Validation and enhancement of a computable medication indication resource (MEDI) using a large practice-based dataset

scientific article (publication date: 2013)

Validation of electronic medical record-based phenotyping algorithms: results and lessons learned from the eMERGE network

scientific article published on 26 March 2013

Variants near FOXE1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome- and phenome-wide studies

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

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eMERGEing progress in genomics-the first seven years

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ePhenotyping for Abdominal Aortic Aneurysm in the Electronic Medical Records and Genomics (eMERGE) Network: Algorithm Development and Konstanz Information Miner Workflow

scientific article published on 30 July 2015

medExtractR: A targeted, customizable approach to medication extraction from electronic health records

scientific article published on 01 March 2020

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