Shawn N. Murphy

Thomas H. McCoy Jr.

J. Am. Medical Informatics Assoc., 2022

The Mass General Brigham Biobank Portal: an i2b2-based data repository linking disparate and high-dimensional patient data to support multimodal analytics.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2022

The Informatics of RECOVER: Understanding the Post Acute Sequelae of SARS-CoV-2 Infection.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2022, 2022

Research Patient Data Repositories: Perspectives from JAMIA Special Issue Editors on the Next Generation of Multi-Institutional Data Sharing.

[BibT_eX]

[DOI]

Genevieve Melton-Meaux

Leslie Lenert

Michael J. Becich

Thomas R. Campion Jr.

Proceedings of the AMIA 2022, 2022

Distinguishing Admissions Specifically for COVID-19 from Incidental SARS-CoV-2 Admissions.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2022, 2022

Informatics for Integrating Biology and the Bedside (i2b2) in 2022: Single Sign On and Synthetic Data.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2022, 2022

A Deductive Data-Driven Pipeline Powered by MLHO for Post-Acute Sequelae of COVID-19 (PASC) Phenotyping.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2022, 2022

2021

Quantitative disease risk scores from EHR with applications to clinical risk stratification and genetic studies.

[BibT_eX]

[DOI]

npj Digit. Medicine, 2021

Clinical knowledge extraction via sparse embedding regression (KESER) with multi-center large scale electronic health record data.

[BibT_eX]

[DOI]

npj Digit. Medicine, 2021

Predicting COVID-19 mortality with electronic medical records.

[BibT_eX]

[DOI]

npj Digit. Medicine, 2021

Multi-channel attention-fusion neural network for brain age estimation: Accuracy, generality, and interpretation with 16, 705 healthy MRIs across lifespan.

[BibT_eX]

[DOI]

Medical Image Anal., 2021

ATLAS: an automated association test using probabilistically linked health records with application to genetic studies.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2021

Validation of an internationally derived patient severity phenotype to support COVID-19 analytics from electronic health record data.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2021

The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment.

[BibT_eX]

[DOI]

Christopher P. Austin

Ken R. Gersing

J. Am. Medical Informatics Assoc., 2021

Generative transfer learning for measuring plausibility of EHR diagnosis records.

[BibT_eX]

[DOI]

Sebastien Vasey

J. Am. Medical Informatics Assoc., 2021

High-throughput phenotyping with temporal sequences.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2021

A Novel Data Portal to Enable COVID-19 Data Integration and Analysis.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

A Machine Learning Approach for Identifying Emergent Phenotypes Associated with a Previous COVID Infection.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Evaluation of the Portability of Natural Language Processing-based Computable Phenotypes in the eMERGE Network.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Temporal Phenotypic Pathways of Post-Acute Sequelae of SARS-CoV-2 by an International Consortium for Clinical Characterization of COVID-19 (4CE).

[BibT_eX]

[DOI]

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Combining Chart Review and Hospital System Dynamics for Electronic Health Record Phenotyping in an International COVID-19 Research Network.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

Integrating Informatics for Integrating Biology and the Bedside with tranSMART: Flexible Data Warehousing with Complex Analytics.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

2020

Transitive Sequencing Medical Records for Mining Predictive and Interpretable Temporal Representations.

[BibT_eX]

[DOI]

Patterns, 2020

International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium.

[BibT_eX]

[DOI]

Brett K. Beaulieu-Jones

Arnaud Serret-Larmande

Alba Gutiérrez-Sacristán

npj Digit. Medicine, 2020

sureLDA: A multidisease automated phenotyping method for the electronic health record.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2020

Individualized Prediction of COVID-19 Adverse outcomes with MLHO.

[BibT_eX]

[DOI]

CoRR, 2020

Polar labeling: silver standard algorithm for training disease classifiers.

[BibT_eX]

[DOI]

Marykate Murphy

Bioinform., 2020

Brain Age Estimation Using LSTM on Children's Brain MRI.

[BibT_eX]

[DOI]

Proceedings of the 17th IEEE International Symposium on Biomedical Imaging, 2020

HistoriView: An Interactive and Scalable Visual Exploratory Plugin for Longitudinal Patient Data Review.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2020, 2020

High-throughput Phenotyping with EHR Sequences.

[BibT_eX]

[DOI]

Victor M. Castro

Proceedings of the AMIA 2020, 2020

National Informatics Infrastructure Responding to the COVID-19 Pandemic.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2020, 2020

Informatics for Integrating Biology and the Bedside (i2b2) in 2020: Supporting Large Ontologies and REDcap Surveys.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2020, 2020

Generative Transfer Learning for Measuring Plausibility of EHR Diagnosis Records Over Time.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2020, 2020

Transitive Sequential Pattern Mining for Discrete Clinical Data.

[BibT_eX]

[DOI]

Sebastien Vasey

Proceedings of the Artificial Intelligence in Medicine, 2020

2019

A clustering approach for detecting implausible observation values in electronic health records data.

[BibT_eX]

[DOI]

BMC Medical Informatics Decis. Mak., 2019

Facilitating phenotype transfer using a common data model.

[BibT_eX]

[DOI]

J. Biomed. Informatics, 2019

High-throughput multimodal automated phenotyping (MAP) with application to PheWAS.

[BibT_eX]

[DOI]

Christopher J. O'Donnell

J. Am. Medical Informatics Assoc., 2019

A federated EHR network data completeness tracking system.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2019

Semi-supervised encoding for outlier detection in clinical observation data.

[BibT_eX]

[DOI]

Comput. Methods Programs Biomed., 2019

Plugin for importing spreadsheets into Informatics for Integrating Biology and the Bedside platform.

[BibT_eX]

[DOI]

Akshay Zagade

Vishal Vernekar

Shek-Wayne Chan

Proceedings of the AMIA 2019, 2019

Scalable Process to Generate Aggregated Patient Data for Analysis.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2019, 2019

Stratification of Patient Population for enabling data-driven Clinical Interventions using I2b2.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2019, 2019

Dynamic Phenotyping to facilitate Accrual for Prospective Clinical studies: A Case Study in Heart Failure.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2019, 2019

Patient Stratification Process for enabling Clinical Interventions.

[BibT_eX]

[DOI]

Samuel J. Aronson

Benjamin Morgan Scirica

Akshay S. Desai

Proceedings of the AMIA 2019, 2019

Ontologies Enabling Computable Tables.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2019, 2019

EHR Sequencing: A Novel Approach for Constructing Predictive and Interpretable Data Representations from EHR Data.

[BibT_eX]

[DOI]

Thomas H. McCoy

Proceedings of the AMIA 2019, 2019

sureLDA: A Novel Multi-Disease Automated Phenotyping Method for the Electronic Health Record.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2019, 2019

2018

Data Warehousing for Clinical Research.

[BibT_eX]

[DOI]

Jayashree Kalpathy-Cramer

Proceedings of the Encyclopedia of Database Systems, Second Edition, 2018

Field of View Normalization in Multi-Site Brain MRI.

[BibT_eX]

[DOI]

Elizabeth R. Gerstner

Bruce R. Rosen

Patricia Ellen Grant

Randy L. Gollub

Neuroinformatics, 2018

Implementation of informatics for integrating biology and the bedside (i2b2) platform as Docker containers.

[BibT_eX]

[DOI]

BMC Medical Informatics Decis. Mak., 2018

Extraction of Ejection Fraction from Echocardiography Notes for Constructing a Cohort of Patients having Heart Failure with reduced Ejection Fraction (HFrEF).

[BibT_eX]

[DOI]

Christina M. Fischer

Alyssa P. Goodson

J. Medical Syst., 2018

Enabling phenotypic big data with PheNorm.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2018

Web services for data warehouses: OMOP and PCORnet on i2b2.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2018

Exploring completeness in clinical data research networks with DQe-c.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2018

Empowering genomic medicine by establishing critical sequencing result data flows: the eMERGE example.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2018

<i>kluster</i>: An Efficient Scalable Procedure for Approximating the Number of Clusters in Unsupervised Learning.

[BibT_eX]

[DOI]

Behzad Abounia Omran

Big Data Res., 2018

Automated Population of an i2b2 Clinical Data Warehouse using FHIR.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2018, 2018

High-Throughput Multimodal Automated Phenotyping (MAP) Incorporating Natural Language Processing with Application to PheWAS.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2018, 2018

Accessible Research Commons for Health: Four Years Into the PCORnet Journey.

[BibT_eX]

[DOI]

Sebastian Schneeweiss

Kenneth D. Mandl

Proceedings of the AMIA 2018, 2018

Using HL7 FHIR to Improve Standardization and Interoperability of Common Data Models for Clinical and Translational Research.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2018, 2018

2017

Surrogate-assisted feature extraction for high-throughput phenotyping.

[BibT_eX]

[DOI]

Sheng Yu

Abhishek Chakrabortty

Katherine P. Liao

Tianrun A. Cai

J. Am. Medical Informatics Assoc., 2017

Biases introduced by filtering electronic health records for patients with "complete data".

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2017

SMART-on-FHIR implemented over i2b2.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2017

Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization.

[BibT_eX]

[DOI]

Jorge L. Bernal-Rusiel

Frontiers Neuroinformatics, 2017

Evolving Research Data Sharing Networks to Clinical App Sharing Networks.

[BibT_eX]

[DOI]

Proceedings of the Summit on Clinical Research Informatics, 2017

i2b2 on OMOP CDM.

[BibT_eX]

[DOI]

Proceedings of the Summit on Clinical Research Informatics, 2017

Creating a Patient Information Commons from Multiple Research Informatics Platforms.

[BibT_eX]

[DOI]

Proceedings of the Summit on Clinical Research Informatics, 2017

Needs-Driven Data Completeness Assessment for Clinical Research.

[BibT_eX]

[DOI]

Proceedings of the Summit on Clinical Research Informatics, 2017

Needs-Driven Data Completeness Dashboard in a Multi-Site Research Network.

[BibT_eX]

[DOI]

Proceedings of the Summit on Clinical Research Informatics, 2017

Data Fitness-for-Use: A Method to Maximize Utility of Poor-Quality Data?

[BibT_eX]

[DOI]

Proceedings of the Summit on Clinical Research Informatics, 2017

Applying Computed Phenotypes Derived from Electronic Health Records in the Partners HealthCare Biobank Using i2b2.

[BibT_eX]

[DOI]

Proceedings of the Summit on Clinical Research Informatics, 2017

Strategic Assessment and Planning for the PCORnet Common Data Model.

[BibT_eX]

[DOI]

Ania Berchuck

Michael G. Kahn

Shelley A. Rusincovitch

Proceedings of the Summit on Clinical Research Informatics, 2017

Instrumenting the Health Care Enterprise for Discovery in the Course of Clinical Care.

[BibT_eX]

[DOI]

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

High-throughput Phenotyping via Denoised Normal Mixture Transformation.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2017, 2017

Building Better Timeline Interactions for Patient Chart Reviews.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2017, 2017

Web-Service-Enabled Apps for Research: SMART-on-FHIR for OMOP and PCORNet.

[BibT_eX]

[DOI]

Matthew A. Joss

Proceedings of the AMIA 2017, 2017

Reuse of PCORnet Data to Support the Precision Medicine Initiative: Data Model Harmonization.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2017, 2017

Integrating Patient Registries into Enterprise wide Patient-Discovery Strategies.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2017, 2017

Applying unsupervised learning to characterize rare observations in clinical data: the DQe-p tool.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2017, 2017

2016

Data interchange using i2b2.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2016

Read only SMART on FHIR Façade for I2b2.

[BibT_eX]

[DOI]

Proceedings of the Summit on Clinical Research Informatics, 2016

Using Medication Terminologies NDF-RT and RxNorm for Implementing a Medications Ingredient Hierarchy in a SHRINE/i2b2 use case.

[BibT_eX]

[DOI]

Proceedings of the Summit on Clinical Research Informatics, 2016

Improving i2b2 Ontology Medications Mappings with RxMix.

[BibT_eX]

[DOI]

Proceedings of the Summit on Clinical Research Informatics, 2016

Multi-site Data Completeness Analysis: Application to Laboratory Results in a Large Distributed Research Network.

[BibT_eX]

[DOI]

Proceedings of the Summit on Clinical Research Informatics, 2016

Comparison of Two Distributed Data Network Approaches: Democratic and Self-Governed vs. Centrally Managed.

[BibT_eX]

[DOI]

Proceedings of the Summit on Clinical Research Informatics, 2016

Defining a Statistically Valid Type 2 Diabetes Cohort in the Partners HealthCare EMR.

[BibT_eX]

[DOI]

Alyssa P. Goodson

Andrew Cagan

Vivian S. Gainer

Kelly Bell

Tianxi Cai

Proceedings of the Summit on Clinical Research Informatics, 2016

Export data from i2b2 using the new download data web client plugin.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2016, 2016

Evaluation of SMART-on-FHIR I2b2 cell using PCORNET data model.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2016, 2016

Cajun Codefest 4.0 on SMART-on-FHIR apps for Diabetes.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2016, 2016

Data Topography of a Large Multi-Site Research Network.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2016, 2016

Comparison of Data Models used in Research Data Repositories for Electronic Phenotyping.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2016, 2016

2015

Brain extraction in pediatric ADC maps, toward characterizing neuro-development in multi-platform and multi-institution clinical images.

[BibT_eX]

[DOI]

NeuroImage, 2015

A numerical similarity approach for using retired Current Procedural Terminology (CPT) codes for electronic phenotyping in the Scalable Collaborative Infrastructure for a Learning Health System (SCILHS).

[BibT_eX]

[DOI]

BMC Medical Informatics Decis. Mak., 2015

High Throughput Tools to Access Images from Clinical Archives for Research.

[BibT_eX]

[DOI]

Katherine P. Andriole

J. Digit. Imaging, 2015

Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2015

Taking advantage of continuity of care documents to populate a research repository.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2015

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

[BibT_eX]

[DOI]

Proceedings of the AMIA 2015, 2015

Computable Phenotypes enabled by the i2b2 Validation Platform.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2015, 2015

SCILHS Data Mart Creation Plugin.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2015, 2015

Supporting Multi-sourced Medication Information in i2b2.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2015, 2015

The Scalable Collaborative Infrastructure for a Learning Health System: Facilitating Agile Comparative Effectiveness Research.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2015, 2015

The Scalable Collaborative Infrastructure for a Learning Health System.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2015, 2015

Demonstrating the Advantages of Applying Data Mining Techniques on Time-Dependent Electronic Medical Records.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2015, 2015

2014

Evaluation of matched control algorithms in EHR-based phenotyping studies: A case study of inflammatory bowel disease comorbidities.

[BibT_eX]

[DOI]

Victor M. Castro

W. Kay Apperson

Vivian S. Gainer

Alyssa P. Goodson

Taowei David Wang

J. Biomed. Informatics, 2014

Brief communication: Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): Architecture.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2014

Query Health: standards-based, cross-platform population health surveillance.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2014

Improving the Review of Individual Patients in a Clinical Data Repository.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2014, 2014

Informatics for Integrating Biology and the Bedside (I2b2) Clinical Trials (CT) Patient Ascertainment Suite.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2014, 2014

Handling Clinical and Next Generation Sequencing data: new strategies in i2b2 and tranSMART.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2014, 2014

Enabling Patient-Centric Comparative Effectiveness Research in i2b2.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2014, 2014

Integrating Information from Unstructured Text with Structured Clinical Data from an Electronic Medical Record to Improve Patient Cohort Identification.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2014, 2014

2013

Research Informatics : Re-engineering the Research Enterprise.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2013, 2013

Integrating the CCDA for Real-Time Patient Data in the i2b2 Platform.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2013, 2013

Organization and Transformation of Next-Generation Sequencing Data for Use within i2b2.

[BibT_eX]

[DOI]

Isaac S. Kohane

Proceedings of the AMIA 2013, 2013

Amassing Pediatric Brain MRI's to Understand "Normal" using Mi2b2.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2013, 2013

Using SMART and i2b2 to Efficiently Identify Adverse Events.

[BibT_eX]

[DOI]

Rachel L. Ramoni

Proceedings of the AMIA 2013, 2013

Query Health: One Step Toward a Learning Health System.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2013, 2013

2012

The SMART Platform: early experience enabling substitutable applications for electronic health records.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2012

A translational engine at the national scale: informatics for integrating biology and the bedside.

[BibT_eX]

[DOI]

Isaac S. Kohane

Susanne E. Churchill

J. Am. Medical Informatics Assoc., 2012

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

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2012

Clinical Bioinformatics: challenges and opportunities.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

Integrating Substitutable Medical Apps, Reusable Technologies (SMART) in the i2b2 Platform.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2012, 2012

Apps to display patient data, making SMART available in the i2b2 platform.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2012, 2012

Rethinking the "Honest Broker" in the Changing Face of Security and Privacy.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2012, 2012

Supporting Population Queries and Clinical Trials in i2b2 with SMART.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2012, 2012

Building the SMART Platforms Ecosystem: Toward an Apps-Based Health Information Economy.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2012, 2012

The Medical App Store, Research Data Repositories, and Physician Cognitive Overload: Uniting Three Large, Multisite Grants for Health Care Transformation.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2012, 2012

Query Health and i2b2: Enabling Standards-based, Multiplatform Population Health Queries.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2012, 2012

Implementing a pharmacovigilance framework using data from electronic medical records.

[BibT_eX]

[DOI]

Wannapa Kay Mahamaneerat

Proceedings of the AMIA 2012, 2012

Data Sharing: Incentives and Governance Issues in Industry and Academia.

[BibT_eX]

[DOI]

Proceedings of the AMIA 2012, 2012

2011

Strategies for maintaining patient privacy in i2b2.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2011

2010

Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2).

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2010

2009

Data Warehousing for Clinical Research.

[BibT_eX]

[DOI]

Proceedings of the Encyclopedia of Database Systems, 2009

Application of Information Technology: The Shared Health Research Information Network (SHRINE): A Prototype Federated Query Tool for Clinical Data Repositories.

[BibT_eX]

[DOI]

J. Am. Medical Informatics Assoc., 2009

A PSO/ACO approach to knowledge discovery in a pharmacovigilance context.

[BibT_eX]

[DOI]

Margarita Sordo

Gabriela Ochoa