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List of works by Jyotishman Pathak

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 NOVEL GENOMIC SUSCEPTIBILITY LOCUS FOR PERIPHERAL ARTERIAL DISEASE ON CHROMOSOME 12

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 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 collaborative approach to developing an electronic health record phenotyping algorithm for drug-induced liver injury

scientific article published on 09 July 2013

A conceptual model for translating omic data into clinical action

scientific article

A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data

scientific article

Adopting Graph Traversal Techniques for Context-Driven Value Sets Extraction from Biomedical Knowledge Sources ⬇️

scientific article (publication date: 12 August 2008)

An OWL meta-ontology for representing the Clinical Element Model ⬇️

scientific article published on October 22, 2011

An electronic health record driven algorithm to identify incident antidepressant medication users

scientific article

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

scientific article

Analysis of online information searching for cardiovascular diseases on a consumer health information portal

scientific article published on 14 November 2014

Analyzing categorical information in two publicly available drug terminologies: RxNorm and NDF-RT

scientific article

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

scientific article published on 22 October 2011

Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank

scientific article (publication date: 17 December 2012)

Approaching patient engagement in research: what do patients with cardiovascular disease think?

scientific article published on 27 July 2015

Association Networks in a Matched Case-Control Design - Co-occurrence Patterns of Preexisting Chronic Medical Conditions in Patients with Major Depression versus their Matched Controls

scientific article published on 06 October 2018

Automated Diabetes Case Identification Using Electronic Health Record Data at a Tertiary Care Facility

scientific article published on 28 April 2017

Bias in recording of body mass index data in the electronic health record

scientific article

Biobanks and personalized medicine

scientific article

Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: The SHARPn project ⬇️

scientific article published on February 4, 2012

Characterizing the epidemiology of perioperative transfusion-associated circulatory overload

scientific article published on January 2015

Characterizing the epidemiology of postoperative transfusion-related acute lung injury

scientific article published on January 2015

Clinical Decision Support to Implement CYP2D6 Drug-Gene Interaction

scientific article published on 01 January 2015

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

scientific article

Comparative analysis of online health queries originating from personal computers and smart devices on a consumer health information portal

scientific article

Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG.

scientific article

Considerations for Improving the Portability of Electronic Health Record-Based Phenotype Algorithms

scientific article published on 01 January 2019

D2Refine: A Platform for Clinical Research Study Data Element Harmonization and Standardization

scientific article

Deep learning in mental health outcome research: a scoping review

scientific article published on 22 April 2020

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 Associations between Major Depressive Disorder Treatment and Essential Hypertension using Electronic Health Records

scientific article published on 7 April 2014

Developing EHR-driven heart failure risk prediction models using CPXR(Log) with the probabilistic loss function

scientific article published on February 2016

Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries

scientific article published on 14 October 2019

Developing a Standards-Based Information Model for Representing Computable Diagnostic Criteria: A Feasibility Study of the NQF Quality Data Model.

scientific article

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

scientific article

Developing a modular architecture for creation of rule-based clinical diagnostic criteria

scientific article published on 21 October 2016

Developing a portable natural language processing based phenotyping system

scientific article published on 04 April 2019

Development and validation of a machine learning algorithm for predicting the risk of postpartum depression among pregnant women

scientific article published on 30 September 2020

Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL.

scientific article published on 29 May 2013

Dissecting clinical heterogeneity of bipolar disorder using multiple polygenic risk scores

scientific article published on 18 September 2020

Effects of Plasma Transfusion on Perioperative Bleeding Complications: A Machine Learning Approach

scientific article published on January 2015

Electronic health record surveillance algorithms facilitate the detection of transfusion‐related pulmonary complications ⬇️

scientific article published on August 31, 2012

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

scientific article published on December 2013

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

scientific article published on April 2011

Empowering Personalized Medicine with Big Data and Semantic Web Technology: Promises, Challenges, and Use Cases

scientific article published on 01 October 2014

Ensemble learning approaches to predicting complications of blood transfusion

scientific article published on August 2015

Evaluating Phenotypic Data Elements for Genetics and Epidemiological Research: Experiences from the eMERGE and PhenX Network Projects ⬇️

scientific article published on March 7, 2011

Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study

scientific article published on 01 January 2019

Evaluating the process of online health information searching: a qualitative approach to exploring consumer perspectives.

scientific article

Formalizing ICD coding rules using Formal Concept Analysis

scientific article published on 21 February 2009

Further revamping VA's NDF-RT drug terminology for clinical research ⬇️

scientific article published on March 17, 2011

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

scientific article

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

scientific article published on 05 March 2013

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

scientific article

Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: a case study

scientific article

Health behaviors and quality of life predictors for risk of hospitalization in an electronic health record-linked biobank

scientific article

Healthcare utilization among patients with psychiatric hospitalization admitted through the emergency department (ED): A claims-based study

scientific article published on 07 October 2020

Hospitalizations and emergency department use in Mayo Clinic Biobank participants within the employee and community health medical home

scientific article

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

scientific article

Identifying sub-phenotypes of acute kidney injury using structured and unstructured electronic health record data with memory networks

scientific article published on 03 January 2020

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

scientific article published on March 2012

Improvement in Cardiovascular Risk Prediction with Electronic Health Records

scientific article published on 09 March 2016

Improving risk prediction for depression via Elastic Net regression - Results from Korea National Health Insurance Services Data

scientific article

Incorporating expert terminology and disease risk factors into consumer health vocabularies

scientific article published on January 2013

Increased risk of hospitalization for ultrarapid metabolizers of cytochrome P450 2D6

scientific article published on 14 February 2017

Integrating VA's NDF-RT drug terminology with PharmGKB: preliminary results ⬇️

scientific article published on January 1, 2012

Leveraging an Electronic Health Record-Linked Biorepository to Generate a Metformin Pharmacogenomics Hypothesis

scientific article published on 23 March 2015

Leveraging electronic health records to study pleiotropic effects on bipolar disorder and medical comorbidities.

scientific article published on 16 August 2016

Leveraging informatics for genetic studies: use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease ⬇️

scientific article published on September 1, 2010

LexGrid: a framework for representing, storing, and querying biomedical terminologies from simple to sublime

scientific article

LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies ⬇️

scientific article published on October 26, 2009

LexValueSets: an approach for context-driven value sets extraction

scientific article (publication date: 6 November 2008)

Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience ⬇️

scientific article published on May 19, 2011

Mayo Genome Consortia: a genotype-phenotype resource for genome-wide association studies with an application to the analysis of circulating bilirubin levels

scientific article

Measuring the impact of ambulatory red blood cell transfusion on home functional status: study protocol for a pilot randomized controlled trial

scientific article published on 31 March 2017

Minimum information required for a DMET experiment reporting

scientific article published on 22 August 2016

Mining Genotype-Phenotype Associations from Public Knowledge Sources via Semantic Web Querying

scientific article (publication date: 2013)

Mining the human phenome using semantic web technologies: a case study for Type 2 Diabetes

scientific article (publication date: 2012)

Modeling and executing electronic health records driven phenotyping algorithms using the NQF Quality Data Model and JBoss® Drools Engine

scientific article

Modular ontology techniques and their applications in the biomedical domain ⬇️

scientific article (publication date: 5 August 2008)

Multimodal mental health analysis in social media

scientific article published on 10 April 2020

Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium

scientific article

Online information seeking for cardiovascular diseases: a case study from Mayo Clinic

scientific article published on January 2014

PharmGKB Drug Data Normalization with NDF-RT.

scientific article

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

scientific article

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

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

Predicting Prolonged Stay in the ICU Attributable to Bleeding in Patients Offered Plasma Transfusion

scientific article published on January 2016

Predictive Modeling of the Risk of Acute Kidney Injury in Critical Care: A Systematic Investigation of The Class Imbalance Problem.

scientific article published on 6 May 2019

Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol

scientific article

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

scientific article published on 13 September 2017

Quantifying the impact of chronic conditions on a diagnosis of major depressive disorder in adults: a cohort study using linked electronic medical records

scientific article

Quantifying the importance of disease burden on perceived general health and depressive symptoms in patients within the Mayo Clinic Biobank

scientific article published on 3 July 2015

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

scientific article

Risk Factors for Depression Among Civilians After the 9/11 World Trade Center Terrorist Attacks: A Systematic Review and Meta-Analysis.

scientific article

Scalable and High-Throughput Execution of Clinical Quality Measures from Electronic Health Records using MapReduce and the JBoss® Drools Engine

scientific article published on 14 November 2014

Simplifying complex clinical element models to encourage adoption

scientific article published on 07 April 2014

Social determinants of health in mental health care and research: a case for greater inclusion

scientific article published on 01 August 2019

Some experiences and opportunities for big data in translational research.

scientific article

Standardized Representation of Clinical Study Data Dictionaries with CIMI Archetypes

scientific article

Stratified Mortality Prediction of Patients with Acute Kidney Injury in Critical Care

scientific article published on 01 August 2019

Survey of modular ontology techniques and their applications in the biomedical domain ⬇️

scientific article (publication date: August 2009)

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

scientific article

Terminology representation guidelines for biomedical ontologies in the semantic web notations ⬇️

scientific article published on September 28, 2012

The ATXN2-SH2B3 locus is associated with peripheral arterial disease: an electronic medical record-based genome-wide association study

scientific article

The Mayo Clinic Biobank: a building block for individualized medicine

scientific article

The SHARPn project on secondary use of Electronic Medical Record data: progress, plans, and possibilities ⬇️

scientific article published on October 22, 2011

The phenotypic legacy of admixture between modern humans and Neandertals

scientific article

The potential value of social determinants of health in predicting health outcomes

scientific article published on 01 August 2018

Time to achieving therapeutic international normalized ratio increases hospital length of stay after heart valve replacement surgery

scientific article published on 16 February 2017

Understanding the research landscape of major depressive disorder via literature mining: an entity-level analysis of PubMed data from 1948 to 2017

scientific article published on 03 April 2018

Use of computerized algorithm to identify individuals in need of testing for celiac disease

scientific article published on 16 August 2013

Use of standard drug vocabularies in clinical research: a case study in pediatrics ⬇️

scientific article published on November 13, 2010

Using EHR-Linked Biobank Data to Study Metformin Pharmacogenomics

scientific article

Using EHRs and Machine Learning for Heart Failure Survival Analysis.

scientific article published on January 2015

Using EHRs for Heart Failure Therapy Recommendation Using Multidimensional Patient Similarity Analytics

scientific article published on January 2015

Using Electronic Health Records and Machine Learning to Predict Postpartum Depression

scientific article published on 01 August 2019

Using RxNorm and NDF-RT to classify medication data extracted from electronic health records: experiences from the Rochester Epidemiology Project ⬇️

scientific article published on October 22, 2011

Using association rule mining for phenotype extraction from electronic health records

scientific article published on 18 March 2013

Using clinical element models for pharmacogenomic study data standardization

scientific article

Using electronic health records for population health sciences: a case study to evaluate the associations between changes in left ventricular ejection fraction and the built environment

scientific article published on 28 October 2020

Using electronic health records to characterize prescription patterns: focus on antidepressants in nonpsychiatric outpatient settings

scientific article published on 24 September 2018

Using linked data for mining drug-drug interactions in electronic health records

scientific article (publication date: 2013)

Using semantic web technologies for cohort identification from electronic health records for clinical research ⬇️

scientific article published on March 19, 2012

Validation and discovery of genotype-phenotype associations in chronic diseases using linked data

scientific article

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

scientific article

Variation in Cohorts Derived from EHR Data in Four Care Delivery Settings

scientific article

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

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