S. Murphy

Qing Zeng-Treitler, Shawn N Murphy, Isaac S Kohane, 2014, The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry.

Read only SMART on FHIR Façade for I2b2

Kavishwar B. Wagholikar, Christopher G. Chute, Kenneth D. Mandl, 2016, CRI.

iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources

Arthur W. Toga, Ron Kikinis, H. V. Jagadish, 2008, PloS one.

Association of intracranial aneurysm rupture with smoking duration, intensity, and cessation

T. Cai, S. Weiss, V. Gainer, 2017, Neurology.

Distribution of agitation and related symptoms among hospitalized patients using a scalable natural language processing method.

S. Berretta, S. Murphy, T. McCoy, 2020, General hospital psychiatry.

Genetic basis of autoantibody positive and negative rheumatoid arthritis risk in a multi-ethnic cohort derived from electronic health records.

Peter Szolovits, Tianxi Cai, Shawn N Murphy, 2011, American journal of human genetics.

Genetic validation of bipolar disorder identified by automated phenotyping using electronic health records

T. Cai, Chia-Yen Chen, J. Smoller, 2017, bioRxiv.

Combining clinical and genomics queries using i2b2 – Three methods

Lori C. Phillips, R. Bellazzi, I. Kohane, 2017, PloS one.

Common Genetic Variants Influence Circulating Vitamin D Levels in Inflammatory Bowel Diseases

Tianxi Cai, Shawn N Murphy, Isaac Kohane, 2015, Inflammatory bowel diseases.

Mortality and extraintestinal cancers in patients with primary sclerosing cholangitis and inflammatory bowel disease.

I. Kohane, T. Cai, Su-Chun Cheng, 2014, Journal of Crohn's & colitis.

Association between low density lipoprotein and rheumatoid arthritis genetic factors with low density lipoprotein levels in rheumatoid arthritis and non-rheumatoid arthritis controls

Peter Szolovits, Tianxi Cai, Jing Cui, 2013, Annals of the rheumatic diseases.

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

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

Modeling Disease Severity in Multiple Sclerosis Using Electronic Health Records

Peter Szolovits, Tianxi Cai, Guergana K. Savova, 2013, PloS one.

Definition of Crohns Disease and Ulcerative Colitis in Electronic Medical Records Using Natural Language Processing

T. Cai, Su-Chun Cheng, Peter Szolovits, 2013 .

Rapid Identification of Myocardial Infarction Risk Associated With Diabetes Medications Using Electronic Medical Records

M. Sordo, J. Brownstein, I. Kohane, 2009, Diabetes Care.

The CoMorbidity Burden of Children and Young Adults with Autism Spectrum Disorders

Douglas MacFadden, Isaac S. Kohane, Nich Wattanasin, 2012 .

Electronic health records: high-quality electronic data for higher-quality clinical research.

Michael Weiner, Shawn Murphy, Jason A Lyman, 2007, Informatics in primary care.

Current State of Information Technologies for the Clinical Research Enterprise across Academic Medical Centers

Shawn N Murphy, Paul A Harris, Peter J Embi, 2012, Clinical and translational science.

Morphological variables associated with ruptured basilar tip aneurysms

T. Cai, S. Weiss, V. Gainer, 2021, Scientific Reports.

Age and morphology of posterior communicating artery aneurysms

T. Cai, S. Weiss, V. Gainer, 2020, Scientific Reports.

Geometric Features Associated with Middle Cerebral Artery Bifurcation Aneurysm Formation: A Matched Case-Control Study.

T. Cai, V. Gainer, S. Murphy, 2021, Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association.

Geometric variations associated with posterior communicating artery aneurysms

T. Cai, S. Weiss, V. Gainer, 2021, Journal of NeuroInterventional Surgery.

Surrounding vascular geometry associated with basilar tip aneurysm formation

T. Cai, S. Weiss, V. Gainer, 2020, Scientific Reports.

Information Technology Systems

Jeffrey G. Klann, Shawn N. Murphy, Jim Meeks-Johnson, 2016 .

Normalization of Plasma 25-Hydroxy Vitamin D Is Associated with Reduced Risk of Surgery in Crohn’s Disease

Peter Szolovits, Tianxi Cai, Shawn N Murphy, 2013, Inflammatory bowel diseases.

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

Randy L. Gollub, P. Ellen Grant, Rudolph Pienaar, 2021, Medical Image Anal..

Voxelwise and Regional Brain Apparent Diffusion Coefficient Changes on MRI from Birth to 6 Years of Age.

P. Grant, R. Gollub, S. Murphy, 2020, Radiology.

Kenneth D. Mandl, Alexander Turchin, Jeffrey G. Klann, 2015, BMC Medical Informatics and Decision Making.

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

Brett K. Beaulieu-Jones, Jeffrey G. Klann, Robert W. Follett, 2020, npj Digital Medicine.

Validation of a Derived International Patient Severity Phenotype to Support COVID-19 Analytics from Electronic Health Record Data

Jason W. Moore, Brett K. Beaulieu-Jones, Jeffrey G. Klann, 2020, medRxiv.

Antihyperglycemic Agents Are Inversely Associated With Intracranial Aneurysm Rupture

T. Cai, S. Weiss, V. Gainer, 2018, Stroke.

Pharmacotherapy for Hospitalized Patients with COVID-19: Treatment Patterns by Disease Severity

J. Gagne, S. Schneeweiss, S. Murphy, 2020, Drugs.

Alcohol Consumption and Aneurysmal Subarachnoid Hemorrhage

T. Cai, S. Weiss, V. Gainer, 2018, Translational Stroke Research.

Informative Missingness: What can we learn from patterns in missing laboratory data in the electronic health record?

Harrison G. Zhang, G. Omenn, K. Ngiam, 2022, medRxiv.

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

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

Improving the Review of Individual Patients in a Clinical Data Repository

Kenneth D. Mandl, Isaac S. Kohane, Nich Wattanasin, 2014, AMIA.

Surrogate-assisted feature extraction for high-throughput phenotyping

Peter Szolovits, Sheng Yu, Tianxi Cai, 2016, J. Am. Medical Informatics Assoc..

Creating a Patient Information Commons from Multiple Research Informatics Platforms

Griffin M. Weber, Isaac S. Kohane, Michael Mendis, 2017, CRI.

High-throughput Phenotyping via Denoised Normal Mixture Transformation

Peter Szolovits, Sheng Yu, Tianxi Cai, 2017, AMIA.

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

Isaac S. Kohane, Shawn N. Murphy, Lori C. Phillips, 2013, AMIA.

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

Tianxi Cai, Boris P. Hejblum, Griffin M. Weber, 2021, medRxiv.

Prenatal antidepressant exposure is associated with risk for attention deficit-hyperactivity disorder but not autism spectrum disorder in a large health system

Isaac S. Kohane, Shawn N. Murphy, Jordan W. Smoller, 2014, Molecular Psychiatry.

Stratification of risk for hospital admissions for injury related to fall: cohort study

I. Kohane, S. Murphy, T. McCoy, 2014, BMJ.

A framework for employing longitudinally collected multicenter electronic health records to stratify heterogeneous patient populations on disease history

J. Smoller, S. Raychaudhuri, S. Murphy, 2022, J. Am. Medical Informatics Assoc..

External Validation of an Algorithm to Identify Patients with High Data-Completeness in Electronic Health Records for Comparative Effectiveness Research

K. Mandl, S. Schneeweiss, R. Glynn, 2020, Clinical epidemiology.

Validation of an Electronic Health Record-Based Suicide Risk Prediction Modeling Approach Across Multiple Health Care Systems.

Jeffrey G. Klann, Ben Y. Reis, Emily M. Madsen, 2020, JAMA network open.

Validation of Electronic Health Record Phenotyping of Bipolar Disorder and Controls

Alisha R Pollastri, I. Kohane, T. Cai, 2015 .

GWAS and enrichment analyses of non-alcoholic fatty liver disease identify new trait-associated genes and pathways across eMERGE Network

John J. Connolly, Marc S. Williams, H. Hakonarson, 2019, BMC Medicine.

Electronic Medical Records for Discovery Research in Rheumatoid Arthritis Citation

I. Kohane, T. Cai, S. Raychaudhuri, 2011 .

Using web technology and Java mobile software agents to manage outside referrals

Dean F. Sittig, G. Octo Barnett, Shawn N. Murphy, 1998, AMIA.

Integrating outside modules into the i2b2 architecture.

Shawn N Murphy, Michael Mendis, Lori C. Phillips, 2008, AMIA ... Annual Symposium proceedings. AMIA Symposium.

Needs-Driven Data Completeness Assessment for Clinical Research

Chunhua Weng, Kenneth D. Mandl, Jeffrey G. Klann, 2017, CRI.

International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality

Jason W. Moore, Brett K. Beaulieu-Jones, Florence T. Bourgeois, 2022, npj Digital Medicine.

Development of a COVID-19 Application Ontology for the ACT Network

Jeffrey G. Klann, S. Reis, V. Gainer, 2021, medRxiv.

Statin Use Is Associated With Reduced Risk of Colorectal Cancer in Patients With Inflammatory Bowel Diseases.

I. Kohane, T. Cai, V. Gainer, 2016, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association.

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

Adam Wright, Allison B. McCoy, Jeffrey G. Klann, 2012, AMIA.

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

Douglas MacFadden, Kenneth D. Mandl, Stanley Boykin, 2018, AMIA.

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

Kenneth D. Mandl, Isaac S. Kohane, Nich Wattanasin, 2013, AMIA.

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

Kenneth D. Mandl, Shawn N. Murphy, Brian D. Athey, 2012, AMIA.

Enabling Patient-Centric Comparative Effectiveness Research in i2b2

Kenneth D. Mandl, Jeffrey G. Klann, Shawn N. Murphy, 2014, AMIA.

Data Topography of a Large Multi-Site Research Network

Douglas MacFadden, Kenneth D. Mandl, Jeffrey G. Klann, 2016, AMIA.

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

Douglas MacFadden, Kenneth D. Mandl, Jeffrey G. Klann, 2016, AMIA.

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

Rahul Jain, Kavishwar B. Wagholikar, Kenneth D. Mandl, 2016, AMIA.

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

Kenneth D. Mandl, Jeffrey G. Klann, Shawn N. Murphy, 2017, CRI.

Supporting Population Queries and Clinical Trials in i2b2 with SMART

Kenneth D. Mandl, Isaac S. Kohane, Nich Wattanasin, 2012, American Medical Informatics Association Annual Symposium.

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

Douglas MacFadden, Kenneth D. Mandl, Jeffrey G. Klann, 2016, CRI.

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

Douglas MacFadden, Kenneth D. Mandl, Jeffrey G. Klann, 2015, AMIA.

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

Kenneth D. Mandl, Isaac S. Kohane, Nich Wattanasin, 2012, AMIA.

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

Rahul Jain, Kavishwar B. Wagholikar, Prasad Patil, 2016, AMIA.

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

Douglas MacFadden, Kenneth D. Mandl, Jeffrey G. Klann, 2016, CRI.

The Association of Black Cardiologists (ABC) Cardiovascular Implementation Study (CVIS): A Research Registry Integrating Social Determinants to Support Care for Underserved Patients

Kevin L. Thomas, K. Mandl, S. Murphy, 2019, International journal of environmental research and public health.

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

Harrison G. Zhang, I. Kohane, T. Cai, 2021, medRxiv.

Decreased Total Iron Binding Capacity May Correlate with Ruptured Intracranial Aneurysms

T. Cai, V. Gainer, S. Murphy, 2019, Scientific Reports.

International electronic health record-derived post-acute sequelae profiles of COVID-19 patients

Florence T. Bourgeois, Jeffrey G. Klann, Harrison G. Zhang, 2022, npj Digital Medicine.

Elevated International Normalized Ratio Is Associated With Ruptured Aneurysms

T. Cai, V. Gainer, S. Murphy, 2018, Stroke.

Peter Szolovits, Tianxi Cai, Shawn N Murphy, 2013, The American Journal of Gastroenterology.

Association between reduced plasma 25-hydroxy vitamin D and increased risk of cancer in patients with inflammatory bowel diseases.

Peter Szolovits, Tianxi Cai, Shawn N Murphy, 2013, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association.

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

Peter Szolovits, Jiehuan Sun, Isaac S. Kohane, 2018, AMIA.

Use of Narrative Concepts in Electronic Health Records to Validate Associations Between Genetic Factors and Response to Treatment of Inflammatory Bowel Diseases

Kristin E. Burke, R. Xavier, I. Kohane, 2020 .

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

Isaac S. Kohane, Nich Wattanasin, Vivian S. Gainer, 2014, AMIA.

Lipid and Lipoprotein Levels and Trend in Rheumatoid Arthritis Compared to the General Population

I. Kohane, T. Cai, V. Gainer, 2013, Arthritis care & research.

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

Kavishwar B. Wagholikar, Jeffrey G. Klann, Shawn N. Murphy, 2017, AMIA.

Low Serum Calcium and Magnesium Levels and Rupture of Intracranial Aneurysms

T. Cai, V. Gainer, S. Murphy, 2018, Stroke.

A first update on mapping the human genetic architecture of COVID-19

Eurie L. Hong, E. F. Perez, Rachel G Liao, 2022, Nature.

Deriving Patient Profiles from Clinical Repositories

Henry C. Chueh, G. Octo Barnett, Shawn N. Murphy, 1999, AMIA.

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

Nich Wattanasin, Vivian S. Gainer, Bhaswati Ghosh, 2016, AMIA.

Lipid-Lowering Agents and High HDL (High-Density Lipoprotein) Are Inversely Associated With Intracranial Aneurysm Rupture

T. Cai, V. Gainer, S. Murphy, 2018, Stroke.

Natural Language Processing to Improve Prediction of Incident Atrial Fibrillation Using Electronic Health Records

Jeffrey M. Ashburner, S. Murphy, K. Liao, 2022, Journal of the American Heart Association.

Association between aspirin dose and subarachnoid hemorrhage from saccular aneurysms

T. Cai, V. Gainer, S. Murphy, 2018, Neurology.

Implementing a pharmacovigilance framework using data from electronic medical records

Vivian S. Gainer, Shawn N. Murphy, Christopher Herrick, 2012, AMIA.

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

Bradley Malin, Andrew D. Boyd, Luke V. Rasmussen, 2012, American Medical Informatics Association Annual Symposium.

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

Nich Wattanasin, Vivian S. Gainer, Bhaswati Ghosh, 2017, CRI.

Building Better Timeline Interactions for Patient Chart Reviews

Vivian S. Gainer, Shawn N. Murphy, Taowei David Wang, 2017, AMIA.

i2b2 on OMOP CDM

Shawn N. Murphy, Lori C. Phillips, Christopher Herrick, 2017, CRI.

Strategic Assessment and Planning for the PCORnet Common Data Model

Keith Marsolo, Daniella Meeker, Lemuel R. Waitman, 2017, CRI.

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

Philip Trevvett, Bhanu Bahl, Shawn N. Murphy, 2016, CRI.

Chapter 13 – Information Technology

Henry C. Chueh, Shawn N. Murphy, Christopher D. Herrick, 2017 .

Query Health: One Step Toward a Learning Health System

Douglas B. Fridsma, Jeffrey G. Klann, Shawn N. Murphy, 2013, AMIA.

Improving i2b2 Ontology Medications Mappings with RxMix

Shawn N. Murphy, Lori C. Phillips, S. Murphy, 2016, CRI.

Patient Stratification Process for enabling Clinical Interventions

Kavishwar B. Wagholikar, Samuel J. Aronson, Shawn N. Murphy, 2019, AMIA.

Claims‐Based Algorithms for Identifying Patients With Pulmonary Hypertension: A Comparison of Decision Rules and Machine‐Learning Approaches

Jeffrey G. Klann, K. Mandl, S. Murphy, 2020, Journal of the American Heart Association.

Multiview Incomplete Knowledge Graph Integration with application to cross-institutional EHR data harmonization

S. Murphy, G. Weber, K. Liao, 2022, J. Biomed. Informatics.

Vascular geometry associated with anterior communicating artery aneurysm formation.

T. Cai, V. Gainer, S. Murphy, 2020, World neurosurgery.

International Changes in COVID-19 Clinical Trajectories Across 315 Hospitals and 6 Countries: a 4CE Consortium Study (Preprint)

Jeffrey G. Klann, Robert W. Follett, Darren W. Henderson, 2021 .

Data Sharing: Incentives and Governance Issues in Industry and Academia

Suzanne Bakken, Lisa M. Schilling, Shawn N. Murphy, 2012, American Medical Informatics Association Annual Symposium.

Feasibility of Homomorphic Encryption for Sharing I2B2 Aggregate-Level Data in the Cloud

Jean-Pierre Hubaux, Jean Louis Raisaro, Jeffrey G Klann, 2018, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

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

Griffin M. Weber, Isaac S. Kohane, Vivian S. Gainer, 2010, J. Am. Medical Informatics Assoc..

Calculating the Benefits of a Research Patient Data Repository

Henry C. Chueh, Shawn N. Murphy, Diane Keogh, 2006, AMIA.

kluster: An Efficient Scalable Procedure for Approximating the Number of Clusters in Unsupervised Learning

Shawn N. Murphy, Behzad Abounia Omran, Hossein Estiri, 2018, Big Data Res..

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

Philip R. O. Payne, Jeffrey G. Klann, Haendel Melissa, 2020, J. Am. Medical Informatics Assoc..

Strategies for maintaining patient privacy in i2b2

Isaac S. Kohane, Vivian S. Gainer, Michael Mendis, 2011, J. Am. Medical Informatics Assoc..

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

Douglas MacFadden, Griffin M. Weber, Isaac S. Kohane, 2014 .

Architecture of the Open-source Clinical Research Chart from Informatics for Integrating Biology and the Bedside

Isaac S. Kohane, Vivian S. Gainer, Henry C. Chueh, 2007, AMIA.

SHRINE: Enabling Nationally Scalable Multi-Site Disease Studies

Douglas MacFadden, Philip Trevvett, Isaac S. Kohane, 2013, PloS one.

Individualized prediction of COVID-19 adverse outcomes with MLHO

Shawn N. Murphy, Hossein Estiri, Zachary H. Strasser, 2020, Scientific Reports.

Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network.

Robert C. Green, Keith Marsolo, Casey Overby Taylor, 2019, American journal of human genetics.

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

Keith Marsolo, Casey Overby Taylor, Pedro J. Caraballo, 2018, J. Am. Medical Informatics Assoc..

Mapping the human genetic architecture of COVID-19

Mattia G. Bergomi, Christopher M. DeBoever, Matthew A. Wiles, 2021, Nature.

Rare Copy Number Variation in Treatment-Resistant Major Depressive Disorder

M. Fava, I. Kohane, J. Smoller, 2014, Biological Psychiatry.

Transitive Sequential Pattern Mining for Discrete Clinical Data

Shawn N. Murphy, Hossein Estiri, Sebastien Vasey, 2020, AIME.

Semi-supervised Encoding for Outlier Detection in Clinical Observation Data

Shawn N Murphy, Hossein Estiri, S. Murphy, 2018, bioRxiv.

Longitudinal validation of an electronic health record delirium prediction model applied at admission in COVID-19 patients

S. Murphy, T. McCoy, R. Perlis, 2021, General Hospital Psychiatry.

Evolving phenotypes of non-hospitalized patients that indicate long COVID

Jason W. Moore, Brett K. Beaulieu-Jones, Tiago K. Colicchio, 2021, BMC Medicine.

Hospitalizations Associated With Mental Health Conditions Among Adolescents in the US and France During the COVID-19 Pandemic

Jason W. Moore, Brett K. Beaulieu-Jones, Florence T. Bourgeois, 2022, JAMA network open.

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

Jeffrey G. Klann, Robert W. Follett, I. Krantz, 2020, npj Digital Medicine.

The Biobank Portal for Partners Personalized Medicine: A Query Tool for Working with Consented Biobank Samples, Genotypes, and Phenotypes Using i2b2

Nich Wattanasin, Vivian S. Gainer, Shawn N. Murphy, 2016, Journal of personalized medicine.

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

S. Murphy, I. Ionita-Laza, I. Kullo, 2021, npj Digital Medicine.

Clinical Bioinformatics: challenges and opportunities

Marco Masseroli, Riccardo Bellazzi, Amnon Shabo, 2012, BMC Bioinformatics.

Large-scale identification of patients with cerebral aneurysms using natural language processing

Tianxi Cai, Scott T. Weiss, Dmitriy Dligach, 2016, Neurology.

Out-of-system Care and Recording of Patient Characteristics Critical for Comparative Effectiveness Research

Shawn N Murphy, Sebastian Schneeweiss, Robert J Glynn, 2017, Epidemiology.

High-throughput Phenotyping with Temporal Sequences

Kavishwar B. Wagholikar, Shawn N. Murphy, Alyssa P. Goodson, 2019, bioRxiv.

Hypertension prevalence in the All of Us Research Program among groups traditionally underrepresented in medical research

Katherine K. Kim, Sally L. Baxter, Cheryl R. Clark, 2021, Scientific Reports.

Validation of an Internationally Derived Patient Severity Phenotype to Support COVID-19 Analytics from Electronic Health Record Data

Jeffrey G. Klann, Robert W. Follett, R. Bellazzi, 2021, J. Am. Medical Informatics Assoc..

A security architecture for query tools used to access large biomedical databases

Henry C. Chueh, Shawn N. Murphy, H. Chueh, 2002, AMIA.

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

Peter Szolovits, Sheng Yu, Tianxi Cai, 2015, J. Am. Medical Informatics Assoc..

Genetic Differences in the Immediate Transcriptome Response to Stress Predict Risk-Related Brain Function and Psychiatric Disorders

N. Wray, H. Stefánsson, S. Cichon, 2015, Neuron.

A National Human Neuroimaging Collaboratory Enabled by the Biomedical Informatics Research Network (BIRN)

David B. Keator, H. Jeremy Bockholt, Syam Gadde, 2008, IEEE Transactions on Information Technology in Biomedicine.

Higher plasma 25(OH)D is associated with reduced risk of Clostridium difficile infection in patients with inflammatory bowel diseases

I. Kohane, Su-Chun Cheng, Peter Szolovits, 2014 .

Predictors of severe outcomes associated with Clostridium difficile infection in patients with inflammatory bowel disease

I. Kohane, T. Cai, V. Gainer, 2012, Alimentary pharmacology & therapeutics.

Thromboprophylaxis is associated with reduced post-hospitalization venous thromboembolic events in patients with inflammatory bowel diseases.

Elizabeth A. Scoville, I. Kohane, T. Cai, 2014, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association.

Colonoscopy is associated with a reduced risk for colon cancer and mortality in patients with inflammatory bowel diseases.

I. Kohane, T. Cai, V. Gainer, 2015, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association.

Serum inflammatory markers and risk of colorectal cancer in patients with inflammatory bowel diseases.

I. Kohane, T. Cai, Su-Chun Cheng, 2014, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association.

Mode of Childbirth and Long-Term Outcomes in Women with Inflammatory Bowel Diseases

I. Kohane, T. Cai, V. Gainer, 2015, Digestive Diseases and Sciences.

Psychiatric co‐morbidity is associated with increased risk of surgery in Crohn's disease

I. Kohane, V. Gainer, S. Murphy, 2013, Alimentary pharmacology & therapeutics.

Psychiatric comorbidity is associated with increased risk of surgery in Crohn ' s disease

I. Kohane, T. Cai, Peter Szolovits, 2013 .

Comparative Effectiveness of Infliximab and Adalimumab in Crohn's Disease and Ulcerative Colitis

I. Kohane, T. Cai, V. Gainer, 2016, Inflammatory bowel diseases.

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

Jamie R. Robinson, John J. Connolly, Nephi A. Walton, 2019, World Journal of Surgery.

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

J Michael McCoy, Shawn N Murphy, Joshua C. Mandel, 2012, J. Am. Medical Informatics Assoc..

Identification of Nonresponse to Treatment Using Narrative Data in an Electronic Health Record Inflammatory Bowel Disease Cohort

Tianxi Cai, Vivian S. Gainer, Shawn N. Murphy, 2016, Inflammatory bowel diseases.

Use of narrative concepts in the EHR to validate genetic determinants of treatment response in a virtual inflammatory bowel disease cohort.

Kristin E. Burke, R. Xavier, I. Kohane, 2019, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association.

Predicting COVID-19 mortality with electronic medical records

S. Murphy, K. Wagholikar, H. Estiri, 2021, npj Digital Medicine.

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

Jeffrey G. Klann, Shawn N. Murphy, Hossein Estiri, 2019, bioRxiv.

Field of View Normalization in Multi-Site Brain MRI

Randy L. Gollub, Bruce R. Rosen, P. Ellen Grant, 2018, Neuroinformatics.

An electronic health records study of long-term weight gain following antidepressant use.

M. Fava, I. Kohane, J. Smoller, 2014, JAMA psychiatry.

Research Paper: The GuideLine Interchange Format: A Model for Representing Guidelines

Robert A. Greenes, Lucila Ohno-Machado, Edward H. Shortliffe, 1998, J. Am. Medical Informatics Assoc..

International Analysis of Electronic Health Records of Children and Youth Hospitalized With COVID-19 Infection in 6 Countries

Jeffrey G. Klann, Deanne M. Taylor, I. Kohane, 2021, JAMA network open.

Association between inflammation and systolic blood pressure in RA compared to patients without RA

S. Murphy, K. Liao, D. Solomon, 2018, Arthritis Research & Therapy.

What Every Reader Should Know About Studies Using Electronic Health Record Data but May Be Afraid to Ask (Preprint)

Jason W. Moore, Brett K. Beaulieu-Jones, Jeffrey G. Klann, 2020 .

High-throughput Multimodal Automated Phenotyping (MAP) with Application to PheWAS

Peter Szolovits, Jiehuan Sun, Isaac S. Kohane, 2019, bioRxiv.

Data model harmonization for the All Of Us Research Program: Transforming i2b2 data into the OMOP common data model

Jeffrey G Klann, Shawn N Murphy, Jeffrey G. Klann, 2019, PloS one.

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

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

Integration of Clinical and Genetic Data in the i2b2 Architecture

Isaac S. Kohane, Henry C. Chueh, Michael Mendis, 2006, AMIA.

Long-term kidney function recovery and mortality after COVID-19-associated acute kidney injury: An international multi-centre observational cohort study

Jason W. Moore, Brett K. Beaulieu-Jones, Florence T. Bourgeois, 2022, eClinicalMedicine.

The Digital Analytic Patient Reviewer (DAPR) for COVID-19 Data Mart Validation

T. Wang, V. Gainer, S. Murphy, 2021, Methods of Information in Medicine.

Development of a Coronavirus Disease 2019 (COVID-19) Application Ontology for the Accrual to Clinical Trials (ACT) network

Amy Y. Wang, Jeffrey G. Klann, Matthew C. Wyatt, 2021, JAMIA open.

Transitive Sequencing Medical Records for Mining Predictive and Interpretable Temporal Representations

Kavishwar B. Wagholikar, Shawn N. Murphy, Sebastien Vasey, 2020, Patterns.

Accrual to Clinical Trials (ACT): A Clinical and Translational Science Award Consortium Network

Shyam Visweswaran, Douglas MacFadden, Shawn N Murphy, 2018, JAMIA open.

Enabling phenotypic big data with PheNorm

Peter Szolovits, Sheng Yu, Tianxi Cai, 2018, J. Am. Medical Informatics Assoc..

Data interchange using i2b2

Kenneth D. Mandl, Jeffrey G. Klann, Shawn N. Murphy, 2016, J. Am. Medical Informatics Assoc..

Morphological Variables Associated With Ruptured Middle Cerebral Artery Aneurysms.

Tianxi Cai, Dmitriy Dligach, Sean Finan, 2018, Neurosurgery.

Heroin Use Is Associated with Ruptured Saccular Aneurysms

T. Cai, V. Gainer, S. Murphy, 2017, Translational Stroke Research.

Web services for data warehouses: OMOP and PCORnet on i2b2

Kavishwar B. Wagholikar, Jeffrey G. Klann, Shawn N. Murphy, 2018, J. Am. Medical Informatics Assoc..

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

Randy L. Gollub, P. Ellen Grant, Steven D. Pieper, 2015, NeuroImage.

Facilitating phenotype transfer using a common data model

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

Computing Health Quality Measures Using Informatics for Integrating Biology and the Bedside

Jeffrey G Klann, Shawn N Murphy, Jeffrey G. Klann, 2013, Journal of medical Internet research.

Evaluation of the portability of computable phenotypes with natural language processing in the eMERGE network

Agnes S. Sundaresan, Justin H. Gundelach, Nephi A. Walton, 2023, Scientific Reports.

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

T. Wang, V. Gainer, M. Mendis, 2021, J. Am. Medical Informatics Assoc..

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

Xiaobo Zhou, Keith Marsolo, George Hripcsak, 2014, J. Am. Medical Informatics Assoc..

The association between low density lipoprotein ( LDL ) and RA genetic factors with LDL levels in rheumatoid arthritis and non-RA controls

Y. Okada, I. Kohane, T. Cai, 2014 .

Incident user cohort study of risk for gastrointestinal bleed and stroke in individuals with major depressive disorder treated with antidepressants

M. Fava, I. Kohane, J. Smoller, 2012, BMJ Open.

Temporal Cohort Identification for Alzheimer's Disease with Sequences of Clinical Records

D. Blacker, S. Murphy, Hossein Estiri, 2023, medRxiv.

Biases introduced by filtering electronic health records for patients with “complete data”

Keith Marsolo, Xiaobo Zhou, Elmer V. Bernstam, 2017, J. Am. Medical Informatics Assoc..

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

Kavishwar B. Wagholikar, Shawn N. Murphy, Christopher Herrick, 2018, Journal of Medical Systems.

Decreased Total Iron Binding Capacity May Correlate with Ruptured Intracranial Aneurysms

T. Cai, V. Gainer, S. Murphy, 2019, Scientific Reports.

Mining multi-site clinical data to develop machine learning MRI biomarkers: application to neonatal hypoxic ischemic encephalopathy

P. Grant, R. Gollub, S. Murphy, 2019, Journal of Translational Medicine.

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

Randy L. Gollub, Steven D. Pieper, Rudolph Pienaar, 2017, Front. Neuroinform..

High Throughput Tools to Access Images from Clinical Archives for Research

Randy L. Gollub, Bruce R. Rosen, Steven D. Pieper, 2014, Journal of Digital Imaging.

Tobacco use and age are associated with different morphologic features of anterior communicating artery aneurysms

T. Cai, V. Gainer, S. Murphy, 2021, Scientific Reports.

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

Isaac S. Kohane, Shawn N. Murphy, Susanne E. Churchill, 2012, J. Am. Medical Informatics Assoc..

Antidepressant response in patients with major depression exposed to NSAIDs: a pharmacovigilance study.

M. Fava, I. Kohane, J. Smoller, 2012, The American journal of psychiatry.

High-throughput phenotyping with electronic medical record data using a common semi-supervised approach (PheCAP)

Peter Szolovits, Sheng Yu, Jiehuan Sun, 2019, Nature Protocols.

What Every Reader Should Know About Studies Using Electronic Health Record Data but May Be Afraid to Ask

Jeffrey G. Klann, Deanne M. Taylor, Andrew K Vallejos, 2021, Journal of medical Internet research.

Extracting principal diagnosis, co-morbidity and smoking status for asthma research: evaluation of a natural language processing system

Scott T. Weiss, Qing Zeng-Treitler, Margarita Sordo, 2006, BMC Medical Informatics Decis. Mak..

Heroin Use Is Associated with Ruptured Saccular Aneurysms

T. Cai, V. Gainer, S. Murphy, 2018, Translational Stroke Research.

A Visual Interface Designed for Novice Users to find Research Patient Cohorts in a Large Biomedical Database

Vivian S. Gainer, Henry C. Chueh, Shawn N. Murphy, 2003, AMIA.

The Association Between Arthralgia and Vedolizumab Using Natural Language Processing.

Shawn N Murphy, Andrew Cagan, Tianrun Cai, 2018, Inflammatory bowel diseases.

Probabilistic record linkage of de-identified research datasets with discrepancies using diagnosis codes

Peter Szolovits, Tianxi Cai, Boris P Hejblum, 2019, Scientific Data.

Aligning temporal data by sentinel events: discovering patterns in electronic health records

Ben Shneiderman, Catherine Plaisant, Alexander J. Quinn, 2008, CHI.

NATURAL LANGUAGE PROCESSING IMPROVES PHENOTYPIC ACCURACY IN AN ELECTRONIC MEDICAL RECORD COHORT OF TYPE 2 DIABETES AND CARDIOVASCULAR DISEASE

Peter Szolovits, Tianxi Cai, Isaac S. Kohane, 2014 .

Combining clinical and genomics queries using i2b2 – Three methods

Riccardo Bellazzi, Isaac S. Kohane, Matteo Gabetta, 2017, PloS one.

Information Technology Systems

Jeffrey G. Klann, S. Murphy, J. Meeks-Johnson, 2016 .

Automated Population of an i2b2 Clinical Data Warehouse using FHIR

Guoqian Jiang, Harold R. Solbrig, Shawn N. Murphy, 2018, AMIA.

Polar labeling: silver standard algorithm for training disease classifiers

Shawn N Murphy, Hossein Estiri, Kavishwar B Wagholikar, 2020, Bioinform..

Diabetes and the risk of infections with immunomodulator therapy in inflammatory bowel diseases

I. Kohane, T. Cai, V. Gainer, 2015, Alimentary pharmacology & therapeutics.

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

Lina M. Sulieman, Melissa A. Basford, David J. Schlueter, 2022, Patterns.

Scalable Process to Generate Aggregated Patient Data for Analysis

Nich Wattanasin, Vivian S. Gainer, Shawn N. Murphy, 2019, American Medical Informatics Association Annual Symposium.

Mapping the human genetic architecture of COVID-19

Mattia G. Bergomi, Christopher M. DeBoever, Matthew A. Wiles, 2021, Nature.

Mapping the human genetic architecture of COVID-19

Eurie L. Hong, E. F. Perez, Rachel G Liao, 2021 .

SurvMaximin: Robust Federated Approach to Transporting Survival Risk Prediction Models

J. H. Moore, G. Omenn, K. Ngiam, 2022, medRxiv.

Detecting Drug Interactions From Adverse‐Event Reports: Interaction Between Paroxetine and Pravastatin Increases Blood Glucose Levels

R. Altman, R. Altman, I. Kohane, 2011, Clinical pharmacology and therapeutics.

Higher plasma vitamin D is associated with reduced risk of Clostridium difficile infection in patients with inflammatory bowel diseases

I. Kohane, T. Cai, V. Gainer, 2014, Alimentary pharmacology & therapeutics.

International Comparisons of Harmonized Laboratory Value Trajectories to Predict Severe COVID-19: Leveraging the 4CE Collaborative Across 342 Hospitals and 6 Countries: A Retrospective Cohort Study

Jeffrey S. Morris, Jeffrey G. Klann, R. Bellazzi, 2020, medRxiv.

Visual query tool for finding patient cohorts from a clinical data warehouse of the partners HealthCare system

Henry C. Chueh, G. Octo Barnett, Shawn N. Murphy, 2000, AMIA.

Brain Age Estimation Using LSTM on Children's Brain MRI

Randy L. Gollub, P. Ellen Grant, Sheng He, 2020, 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI).

Geographic Variation in Obesity at the State Level in the All of Us Research Program

Mark J. Ommerborn, Andrea H. Ramirez, E. Boerwinkle, 2021, Preventing chronic disease.

Health Care Transformation Through Collaboration on Open-Source Informatics Projects: Integrating a Medical Applications Platform, Research Data Repository, and Patient Summarization

Dean F Sittig, Adam Wright, Dean F. Sittig, 2013, Interactive journal of medical research.

A federated EHR network data completeness tracking system

Elmer V. Bernstam, William G. Adams, Kenneth D. Mandl, 2019, J. Am. Medical Informatics Assoc..

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

I. Kohane, T. Cai, J. Denny, 2013, Arthritis and rheumatism.

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

Lilla Zöllei, R. Gollub, S. Murphy, 2015, NeuroImage.

Higher plasma vitamin D is associated with reduced risk of Clostridium difficile infection in patients with inflammatory bowel diseases

I. Kohane, T. Cai, V. Gainer, 2014, Alimentary pharmacology & therapeutics.

Mortality and extraintestinal cancers in patients with primary sclerosing cholangitis and inflammatory bowel disease.

I. Kohane, T. Cai, Su-Chun Cheng, 2014, Journal of Crohn's & colitis.

Development of phenotype algorithms using electronic medical records and incorporating natural language processing

I. Kohane, T. Cai, Peter Szolovits, 2015, BMJ : British Medical Journal.

Evolving Research Data Sharing Networks to Clinical App Sharing Networks

Joshua C. Mandel, Jeffrey G. Klann, K. Mandl, 2017, CRI.

Electronic medical records for discovery research in rheumatoid arthritis

I. Kohane, T. Cai, S. Raychaudhuri, 2010, Arthritis care & research.

BMC Medical Informatics and Decision Making

M. Sordo, S. Murphy, R. Lazarus, 2006 .

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

Jorge L. Bernal-Rusiel, R. Gollub, S. Murphy, 2017, Front. Neuroinform..

Generative transfer learning for measuring plausibility of EHR diagnosis records

Shawn N Murphy, Hossein Estiri, Sebastien Vasey, 2020, J. Am. Medical Informatics Assoc..

I am Not Dead Yet: Identification of False-Positive Matches to Death Master File.

S. Murphy, A. Turchin, M. Shubina, 2010, AMIA ... Annual Symposium proceedings. AMIA Symposium.

Feasibility of Homomorphic Encryption for Sharing I2B2 Aggregate-Level Data in the Cloud

Jeffrey G. Klann, J. Hubaux, S. Murphy, 2018, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

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

I. Kohane, S. Murphy, G. Weber, 2009, J. Am. Medical Informatics Assoc..

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

Joshua C. Mandel, Jeffrey G. Klann, Jonathan P. Bickel, 2014, Journal of the American Medical Informatics Association : JAMIA.

Chapter 10 – Information Technology

Henry C. Chueh, Shawn N. Murphy, H. Chueh, 2009 .

A Web Portal that Enables Collaborative Use of Advanced Medical Image Processing and Informatics Tools through the Biomedical Informatics Research Network (BIRN)

Randy L. Gollub, Bruce R. Rosen, David N. Kennedy, 2006, AMIA.

Optimizing healthcare research data warehouse design through past COSTAR query analysis

Henry C. Chueh, G. Octo Barnett, Mary Morgan, 1999, AMIA.

Informatics can help providers incorporate context into care

Shawn N. Murphy, Hossein Estiri, S. Murphy, 2018, JAMIA open.

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

Jeffrey G Klann, Shawn N Murphy, Jeffrey G. Klann, 2014, J. Am. Medical Informatics Assoc..