N. Shah

Nigam H. Shah, Paea LePendu, Srinivasan Iyer, 2012, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

Comparison of Ontology-based Semantic-Similarity Measures

Mark A. Musen, Nigam H. Shah, Wei-Nchih Lee, 2008, AMIA.

Rapid identification of slow healing wounds

R. Kirsner, K. Jung, N. Shah, 2016, Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society.

A dataset quantifying polypharmacy in the United States

N. Shah, K. Quinn, 2017, Scientific Data.

A Value Proposition for AI-Enabled Population Health Management

N. Shah, C. Derienzo, Cardinal Analytx, 2019 .

Development and Performance of the Pulmonary Embolism Result Forecast Model (PERFORM) for Computed Tomography Clinical Decision Support

Robyn L. Ball, Jonathan H. Chen, N. Shah, 2019, JAMA network open.

Big Data and Adverse Drug Reaction Detection

N H Shah, R Harpaz, N. Shah, 2016, Clinical pharmacology and therapeutics.

Developing a delivery science for artificial intelligence in healthcare

Nigam H. Shah, Ron C. Li, Steven M. Asch, 2020, npj Digital Medicine.

New Paradigms for Patient-Centered Outcomes Research in Electronic Medical Records: An Example of Detecting Urinary Incontinence Following Prostatectomy

J. Brooks, N. Shah, S. Tamang, 2016, EGEMS.

Unexpected Effect of Proton Pump Inhibitors: Elevation of the Cardiovascular Risk Factor Asymmetric Dimethylarginine

N. Shah, P. LePendu, J. Cooke, 2013, Circulation.

Deep phenotyping of 34,128 adult patients hospitalised with COVID-19 in an international network study

Rae Woong Park, Andrew E. Williams, M. Suchard, 2020, Nature Communications.

Automated Detection of Systematic Off-label Drug Use In Free Text of Electronic Health Records

K. Jung, N. Shah, P. LePendu, 2013 .

Baseline characteristics, management, and outcomes of 55,270 children and adolescents diagnosed with COVID-19 and 1,952,693 with influenza in France, Germany, Spain, South Korea and the United States: an international network cohort study

Andrew E. Williams, M. Suchard, N. Shah, 2020, medRxiv.

Treatment Patterns for Chronic Comorbid Conditions in Patients With Cancer Using a Large-Scale Observational Data Network

N. Shah, G. Hripcsak, P. Ryan, 2020, JCO clinical cancer informatics.

Estimating the efficacy of symptom-based screening for COVID-19

Jason Alan Fries, Conor K. Corbin, N. Shah, 2020, npj Digital Medicine.

Influence of age on androgen deprivation therapy-associated Alzheimer’s disease

N. Shah, J. Dudley, N. Leeper, 2016, Scientific Reports.

Development and validation of a prognostic model predicting symptomatic hemorrhagic transformation in acute ischemic stroke at scale in the OHDSI network

Ross D. Williams, Andrew E. Williams, N. Shah, 2020, PloS one.

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

Madeleine K. D. Scott, Hongyu Zhao, F. Martinez, 2019, The Lancet. Respiratory medicine.

Ensuring Reproducibility in Observational Research: Building and Sharing Knowledge Resources in the OHDSI Network

George Hripcsak, Patrick B. Ryan, Jon D. Duke, 2016, AMIA.

Treatment Pathways in Patients with Cancer Using a Large-scale Observational Data Network

George Hripcsak, Patrick B. Ryan, Nigam H. Shah, 2018, AMIA.

Association of Hemoglobin A1c Levels With Use of Sulfonylureas, Dipeptidyl Peptidase 4 Inhibitors, and Thiazolidinediones in Patients With Type 2 Diabetes Treated With Metformin

George Hripcsak, Patrick B. Ryan, Kipp W. Johnson, 2018, JAMA network open.

Research and Reporting Considerations for Observational Studies Using Electronic Health Record Data

Jonathan H. Chen, N. Shah, A. Callahan, 2020, Annals of Internal Medicine.

Deep phenotyping: Embracing complexity and temporality—Towards scalability, portability, and interoperability

George Hripcsak, Chunhua Weng, Chunhua Weng, 2020, Journal of Biomedical Informatics.

Risk of angioedema associated with levetiracetam compared with phenytoin: Findings of the observational health data sciences and informatics research network

George Hripcsak, Patrick B. Ryan, Jon D. Duke, 2017, Epilepsia.

MINING THE PHARMACOGENOMICS LITERATURE – Workshop Introduction

U. Hahn, K. Cohen, N. Shah, 2010 .

Erratum: The BioPAX community standard for pathway data sharing (Nat. Biotechnol. (2010) 28 (935-942)

Gary D. Bader, Frank Schacherer, Edgar Wingender, 2010 .

The BioPAX community standard for pathway data sharing (Nature Biotechnology (2010) 28, (935-942))

Kei-Hoi Cheung, Gary D. Bader, Frank Schacherer, 2012 .

DISCOVERY OF MOLECULARLY TARGETED THERAPIES.

Philip R. O. Payne, Zachary B. Abrams, Michael F. Sharpnack, 2016, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

Call for papers: Deep phenotyping for Precision Medicine

George Hripcsak, Chunhua Weng, Nigam H. Shah, 2018, J. Biomed. Informatics.

The Effectiveness of Transfer Learning in Electronic Health Records Data

Nigam H. Shah, Sébastien Dubois, Kenneth Jung, 2017, ICLR.

Early Detection of Adverse Drug Reactions in Social Health Networks: A Natural Language Processing Pipeline for Signal Detection (Preprint)

N. Shah, A. Callahan, Azadeh Nikfarjam, 2018 .

Business Process Optimization

Zhi-Hua Zhou, Goetz Graefe, Sameer Antani, 2002, Encyclopedia of Database Systems.

Detecting unplanned care from clinician notes in electronic health records.

Suzanne Tamang, Yohan Vetteth, Manali I Patel, 2015, Journal of oncology practice.

Occurrence and Timing of Subsequent Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-transcription Polymerase Chain Reaction Positivity Among Initially Negative Patients

Jacob E. Sunshine, N. Shah, J. Zehnder, 2020, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Occurrence and Timing of Subsequent SARS-CoV-2 RT-PCR Positivity Among Initially Negative Patients.

Jacob E. Sunshine, N. Shah, J. Zehnder, 2020, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Occurrence and Timing of Subsequent SARS-CoV-2 RT-PCR Positivity Among Initially Negative Patients

Jacob E. Sunshine, N. Shah, J. Zehnder, 2020, medRxiv.

Response to letters regarding article, "unexpected effect of proton pump inhibitors: elevation of the cardiovascular risk factor asymmetric dimethylarginine".

N. Shah, P. LePendu, J. Cooke, 2014, Circulation.

Ontologies for Bioinformatics (Computational Molecular Biology).Kenneth Baclawski and Tianhua Niu The MIT Press; ISBN: 0-262-02591-4; Hardcover; 440pp; 2005; £29.95.

Daniel L. Rubin, Nigam H. Shah, N. Shah, 2006 .

FIND FH – A phenotype model to identify patients with familial hypercholesterolemia

N. Shah, J. Knowles, J. Banda, 2015 .

BioPAX – A community standard for pathway data sharing

Gary D Bader, Alexander R. Pico, Joanne S. Luciano, 2010, Nature Biotechnology.

Development and utility assessment of a machine learning bloodstream infection classifier in pediatric patients receiving cancer treatments

Conor K. Corbin, N. Shah, G. Tomlinson, 2020, BMC cancer.

Temporal evolution of the Arabidopsis oxidative stress response

N. Shah, N. Fedoroff, R. Mahalingam, 2005, Plant Molecular Biology.

Predictors of diagnostic transition from major depressive disorder to bipolar disorder: a retrospective observational network study

N. Shah, P. Ryan, C. Reich, 2021, Translational Psychiatry.

Characteristics and outcomes of 627 044 COVID-19 patients with and without obesity in the United States, Spain, and the United Kingdom

N. Shah, P. Ryan, C. Reich, 2020, medRxiv.

Proton pump inhibitors and vascular function: A prospective cross-over pilot study

N. Shah, J. Cooke, N. Leeper, 2015, Vascular medicine.

Big Data for Healthcare and Life Sciences: Learning Useful Insights from Imperfect Data

Patrick B. Ryan, Jianying Hu, Bradley Malin, 2016, AMIA.

Baseline phenotype and 30-day outcomes of people tested for COVID-19: an international network cohort including >3.32 million people tested with real-time PCR and >219,000 tested positive for SARS-CoV-2 in South Korea, Spain and the United States

Jason A. Thomas, Andrew E. Williams, M. Suchard, 2020, medRxiv.

Data from "A Time-indexed Reference Standard of Adverse Drug Reactions"

Olivier Bodenreider, Ryen W. White, Eric Horvitz, 2014 .

Pharmacovigilance Using Textual Data: The Need to Go Deeper and Wider into the Con(text)

N. Shah, Tavpritesh Sethi, 2017, Drug Safety.

An Unexpected Effect of Proton Pump Inhibitors: Elevation of the Cardiovascular Risk Factor ADMA

N. Shah, P. LePendu, J. Cooke, 2013 .

Using public clinical trial reports to evaluate observational study methods

N. Shah, Nikolaos Ignatiadis, S. Yadlowsky, 2020, 2006.14102.

Prediction of Major Depressive Disorder Following Beta-Blocker Therapy in Patients with Cardiovascular Diseases

N. Shah, C. Reich, P. Rijnbeek, 2020, Journal of personalized medicine.

Normalizing Clinical Document Titles to LOINC Document Ontology: an Initial Study

Hua Xu, N. Shah, G. Hripcsak, 2020, AMIA.

Research and Applications Synergistic drug combinations from electronic health records and gene expression

Maya B. Mathur, Yen S. Low, Aaron C. Daugherty, 2017 .

Use of dialysis, tracheostomy, and extracorporeal membrane oxygenation among 842,928 patients hospitalized with COVID-19 in the United States

M. Suchard, N. Shah, J. Jonnagaddala, 2020, medRxiv.

A network paradigm predicts drug synergistic effects using downstream protein–protein interactions

R. Altman, N. Shah, E. Steinberg, 2022, CPT: pharmacometrics & systems pharmacology.

The Age of Data-Driven Medicine: Mining the Electronic Health Record

Mark A. Musen, Nigam H. Shah, Paea LePendu, 2011, ICBO.

A computational approach to measure the linguistic characteristics of psychotherapy timing, responsiveness, and consistency

Jason Alan Fries, Adam S. Miner, Tim Althoff, 2022, npj Mental Health Research.

Characteristics and outcomes of COVID-19 patients with COPD from the United States, South Korea, and Europe

M. Suchard, N. Shah, K. Verhamme, 2022, Wellcome open research.

An international characterisation of patients hospitalised with COVID-19 and a comparison with those previously hospitalised with influenza

Andrew E. Williams, M. Suchard, N. Shah, 2020, medRxiv.

SARS-CoV-2 Antibody Responses Correlate with Resolution of RNAemia But Are Short-Lived in Patients with Mild Illness

R. Tibshirani, N. Shah, K. Nadeau, 2020, medRxiv.

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

Csongor Nyulas, Tania Tudorache, Mark A. Musen, 2011, Nucleic Acids Res..

BioPortal: ontologies and integrated data resources at the click of a mouse

Christopher G. Chute, Margaret-Anne D. Storey, Mark A. Musen, 2009, Nucleic Acids Res..

Rates of Co-infection Between SARS-CoV-2 and Other Respiratory Pathogens.

N. Shah, B. Pinsky, J. Quinn, 2020, JAMA.

Thirty-Day Outcomes of Children and Adolescents With COVID-19: An International Experience

Andrew E. Williams, M. Suchard, N. Shah, 2021, Pediatrics.

Predictive Modeling of Risk Factors and Complications of Cataract Surgery

Nigam H Shah, Suzann Pershing, N. Shah, 2016, European journal of ophthalmology.

Use of repurposed and adjuvant drugs in hospital patients with covid-19: multinational network cohort study

M. Suchard, N. Shah, J. Jonnagaddala, 2021, BMJ.

Novel Data‐Mining Methodologies for Adverse Drug Event Discovery and Analysis

P Ryan, R Harpaz, W DuMouchel, 2012, Clinical pharmacology and therapeutics.

Implications of non-stationarity on predictive modeling using EHRs

Nigam H. Shah, Kenneth Jung, K. Jung, 2015, J. Biomed. Informatics.

Ontology-driven indexing of public datasets for translational bioinformatics

Rong Chen, Atul J. Butte, Mark A. Musen, 2009, BMC Bioinformatics.

Biomedical ontologies: a functional perspective

Daniel L. Rubin, Nigam H. Shah, Natalya Fridman Noy, 2007, Briefings Bioinform..

Estimate the hidden deployment cost of predictive models to improve patient care

Nigam H. Shah, Keith E. Morse, Steven C. Bagley, 2020, Nature Medicine.

Scalable and accurate deep learning with electronic health records

Jeffrey Dean, Quoc V. Le, Andrew M. Dai, 2018, npj Digital Medicine.

Medical device surveillance with electronic health records

Christopher Ré, Alison Callahan, Nigam H. Shah, 2019, npj Digital Medicine.

Persistent detection of SARS-CoV-2 RNA in patients and healthcare workers with COVID-19

N. Shah, J. Zehnder, S. Boyd, 2020, Journal of Clinical Virology.

STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation

Uday S. Evani, N. Shah, T. Wittkop, 2013, BMC Bioinformatics.

Can we identify cellular pathways implicated in cancer using gene expression data?

Nigam H. Shah, Gustavo Stolovitzky, Yuhai Tu, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

Computational drug repositioning of atorvastatin for ulcerative colitis

Purvesh Khatri, Ethan Steinberg, Laurynas Kalesinskas, 2021, J. Am. Medical Informatics Assoc..

Precision screening for familial hypercholesterolaemia: a machine learning study applied to electronic health encounter data.

N. Shah, J. Knowles, D. Rader, 2019, The Lancet. Digital health.

The digital revolution in phenotyping

Olivier Bodenreider, Michel Dumontier, Hongfang Liu, 2015, Briefings Bioinform..

Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop

Karin M. Verspoor, N. Shah, L. Soldatova, 2016, Journal of Biomedical Semantics.

Special issue on bio-ontologies and phenotypes

Karin M. Verspoor, N. Shah, L. Soldatova, 2015, Journal of Biomedical Semantics.

Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers

Yu-Chuan Li, George Hripcsak, Patrick B. Ryan, 2015, MedInfo.

The Stanford Tissue Microarray Database

Nigam H. Shah, Gavin Sherlock, Yasodha Natkunam, 2007, Nucleic Acids Res..

Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome

R. Tibshirani, N. Shah, B. Narasimhan, 2020, Science Immunology.

A curated and standardized adverse drug event resource to accelerate drug safety research

Juan M Banda, Nigam H Shah, Nicholas P Tatonetti, 2016, Scientific Data.

Using Annotations from Controlled Vocabularies to Find Meaningful Associations

Louiqa Raschid, Padmini Srinivasan, Adam Woei-Jyh Lee, 2007, DILS.

Annotation and query of tissue microarray data using the NCI Thesaurus

Daniel L. Rubin, Mark A. Musen, Nigam H. Shah, 2007, BMC Bioinformatics.

Translational Bioinformatics Embraces Big Data

N H Shah, N. Shah, Nigam H. Shah, 2012, Yearbook of Medical Informatics.

The coming age of data-driven medicine: translational bioinformatics' next frontier

Nigam H. Shah, Jessica D. Tenenbaum, N. Shah, 2012, J. Am. Medical Informatics Assoc..

Comparison of concept recognizers for building the Open Biomedical Annotator

Daniel L. Rubin, Mark A. Musen, Clement Jonquet, 2009, BMC Bioinformatics.

Association Between Androgen Deprivation Therapy and Risk of Dementia

N. Shah, N. Leeper, Greg Gaskin, 2017, JAMA oncology.

Androgen Deprivation Therapy and Future Alzheimer's Disease Risk.

Joel T Dudley, Nigam H Shah, Greg Gaskin, 2016, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

Unraveling COVID-19: A Large-Scale Characterization of 4.5 Million COVID-19 Cases Using CHARYBDIS

Jason A. Thomas, Andrew E. Williams, M. Suchard, 2022, Clinical epidemiology.

Unraveling COVID-19: a large-scale characterization of 4.5 million COVID-19 cases using CHARYBDIS

Andrew E. Williams, M. Suchard, N. Shah, 2021, Research square.

Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop

Michel Dumontier, Karin M. Verspoor, Nigel Collier, 2016, Journal of Biomedical Semantics.

Special issue on bio-ontologies and phenotypes

Michel Dumontier, Karin M. Verspoor, Nigel Collier, 2015, Journal of Biomedical Semantics.

The National Center for Biomedical Ontology

Christopher G. Chute, Barry Smith, Margaret-Anne D. Storey, 2012, J. Am. Medical Informatics Assoc..

Chapter 9: Analyses Using Disease Ontologies

Mark A. Musen, Nigam H. Shah, Tyler Cole, 2012, PLoS Comput. Biol..

Enabling enrichment analysis with the Human Disease Ontology

Mark A. Musen, Nigam H. Shah, Paea LePendu, 2011, J. Biomed. Informatics.

The Impact of Acute Organ Dysfunction on Long-Term Survival in Sepsis*

G. Escobar, V. Liu, N. Shah, 2018, Critical care medicine.

A new paradigm for accelerating clinical data science at Stanford Medicine pdf

Somalee Datta, Jose Posada, Garrick Olson, 2020, ArXiv.

Translational Bioinformatics

N. Shah, J. Tenenbaum, Russ B. Altman, 2021, Biomedical Informatics.

Characteristics and outcomes of 627 044 COVID-19 patients living with and without obesity in the United States, Spain, and the United Kingdom

N. Shah, C. Reich, M. Matheny, 2021, International Journal of Obesity.

COVID-19 in patients with autoimmune diseases: characteristics and outcomes in a multinational network of cohorts across three countries

M. Suchard, N. Shah, J. Jonnagaddala, 2021, Rheumatology.

Clinical characteristics, symptoms, management and health outcomes in 8,598 pregnant women diagnosed with COVID-19 compared to 27,510 with seasonal influenza in France, Spain and the US: a network cohort analysis

M. Suchard, N. Shah, J. Jonnagaddala, 2020, medRxiv.

DLMM as a lossless one-shot algorithm for collaborative multi-site distributed linear mixed models

Md Nazmul Islam, Andrew E. Williams, D. Asch, 2022, Nature Communications.

Characteristics and outcomes of COVID-19 patients with and without asthma from the United States, South Korea, and Europe

M. Suchard, N. Shah, K. Verhamme, 2022, The Journal of asthma : official journal of the Association for the Care of Asthma.

Characteristics and Outcomes of Over 300,000 Patients with COVID-19 and History of Cancer in the United States and Spain

M. Suchard, N. Shah, I. Soerjomataram, 2021, Cancer Epidemiology, Biomarkers & Prevention.

Characteristics, outcomes, and mortality amongst 133,589 patients with prevalent autoimmune diseases diagnosed with, and 48,418 hospitalised for COVID-19: a multinational distributed network cohort analysis

M. Suchard, N. Shah, J. Jonnagaddala, 2020, medRxiv.

Current progress in network research: toward reference networks for key model organisms

Nigam H. Shah, Serafim Batzoglou, Jason Flannick, 2007, Briefings Bioinform..

Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations

Dominique T. Alessi, N. Shah, Francesco Vallania, 2018, Scientific Reports.

An evaluation of clinical order patterns machine-learned from clinician cohorts stratified by patient mortality outcomes

Nigam H. Shah, Mary K. Goldstein, Jonathan H. Chen, 2018, J. Biomed. Informatics.

Developing a delivery science for artificial intelligence in healthcare

Ron C. Li, N. Shah, S. Asch, 2020, npj Digital Medicine.

Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations

Mark A. Musen, Winston Haynes, Francesco Vallania, 2017, Scientific Reports.

Bridging the implementation gap of machine learning in healthcare

Nigam H. Shah, Martin G. Seneviratne, Larry F. Chu, 2019, BMJ Innovations.

NCBO Resource Index: Ontology-based search and mining of biomedical resources

Mark A. Musen, Clement Jonquet, Nigam H. Shah, 2010, J. Web Semant..

UMLS-Query: A Perl Module for Querying the UMLS

Mark A. Musen, Nigam H. Shah, N. Shah, 2008, AMIA.

A method for systematic discovery of adverse drug events from clinical notes

Guan Wang, Nigam H. Shah, Kenneth Jung, 2015, J. Am. Medical Informatics Assoc..

Ontologies for Formal Representation of Biological Systems

Mark A. Musen, Nigam H. Shah, N. Shah, 2009, Handbook on Ontologies.

Web-scale pharmacovigilance: listening to signals from the crowd

Ryen W. White, Eric Horvitz, Russ B. Altman, 2013, J. Am. Medical Informatics Assoc..

Mining clinical text for signals of adverse drug-drug interactions

Nigam H. Shah, Paea LePendu, Anna Bauer-Mehren, 2014, J. Am. Medical Informatics Assoc..

Comparative safety and effectiveness of alendronate versus raloxifene in women with osteoporosis

D. Madigan, M. Suchard, Yonghui Wu, 2020, Scientific Reports.

Language models are an effective representation learning technique for electronic health record data

Nigam H Shah, Ethan Steinberg, Ken Jung, 2020, J. Biomed. Informatics.

Language Models Are An Effective Patient Representation Learning Technique For Electronic Health Record Data

Jason Alan Fries, Conor K. Corbin, K. Jung, 2020, ArXiv.

Advances in Electronic Phenotyping: From Rule-Based Definitions to Machine Learning Models.

Tina Hernandez-Boussard, Juan M Banda, Martin Seneviratne, 2018, Annual review of biomedical data science.

Detecting Chemotherapeutic Skin Adverse Reactions in Social Health Networks Using Deep Learning

N. Shah, Azadeh Nikfarjam, K. Sarin, 2018, JAMA oncology.

The Open Biomedical Annotator

Mark A. Musen, Clement Jonquet, Nigam H. Shah, 2009, Summit on translational bioinformatics.

Treatment and Monitoring Variability in US Metastatic Breast Cancer Care.

Jennifer L. Caswell-Jin, Summer S. Han, N. Shah, 2021, JCO clinical cancer informatics.

A time-indexed reference standard of adverse drug reactions

Olivier Bodenreider, Ryen W. White, William DuMouchel, 2014, Scientific Data.

Toward personalizing treatment for depression: predicting diagnosis and severity

Nigam H. Shah, David Carrell, Paea LePendu, 2014, J. Am. Medical Informatics Assoc..

Combing signals from spontaneous reports and electronic health records for detection of adverse drug reactions

Carol Friedman, William DuMouchel, Hojjat Salmasian, 2013, J. Am. Medical Informatics Assoc..

MINIMAR (MINimum Information for Medical AI Reporting): Developing reporting standards for artificial intelligence in health care

Selen Bozkurt, John P A Ioannidis, Tina Hernandez-Boussard, 2020, J. Am. Medical Informatics Assoc..

Automated Detection of Systematic Off-label Drug Use in Free Text of Electronic Medical Records

Kenneth Jung, Paea LePendu, Nigam Shah, 2013, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

Distribution of Opioids by Different Types of Medicare Prescribers.

Jonathan H. Chen, N. Shah, K. Humphreys, 2016, JAMA internal medicine.

Predicting patient ‘cost blooms’ in Denmark: a longitudinal population-based study

Lucas Janson, Arnold Milstein, Lester Mackey, 2017, BMJ Open.

Estimating the efficacy of symptom-based screening for COVID-19

Jason Alan Fries, Conor K. Corbin, N. Shah, 2020, npj Digital Medicine.

RegenBase: a knowledge base of spinal cord injury biology for translational research

Ubbo Visser, Alison Callahan, Nigam H. Shah, 2016, Database J. Biol. Databases Curation.

Proton Pump Inhibitor Usage and the Risk of Myocardial Infarction in the General Population

Nigam H. Shah, Paea LePendu, Anna Bauer-Mehren, 2015, PloS one.

Machine Learning in Healthcare

Alison Callahan, Nigam H. Shah, N. Shah, 2017 .

Inpatient Clinical Order Patterns Machine-Learned From Teaching Versus Attending-Only Medical Services

Nigam H. Shah, Alejandro Schuler, Michael T. M. Baiocchi, 2018, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

Quantifying the relative change in physical activity after Total Knee Arthroplasty using accelerometer based measurements

Nigam H. Shah, Vibhu Agarwal, Mathew Smuck, 2017, CRI.

Estimation of SARS-CoV-2 Infection Prevalence in Santa Clara County

S. Yadlowsky, J. Steinhardt, J. Steinhardt, 2020, medRxiv.

Scalable and accurate deep learning with electronic health records

Quoc V. Le, Andrew M. Dai, Peter J. Liu, 2018, npj Digital Medicine.

A predictive tool for identification of SARS-CoV-2 PCR-negative emergency department patients using routine test results

David M. Liebovitz, N. Shah, S. Mooney, 2020, Journal of Clinical Virology.

Contributions to the formal ontology of functions and dispositions : An application of non-monotonic reasoning 9 : 00 9 : 20

N. Shah, Susie Stephens, Johnson Larisa Soldatova, 2009 .

Predicting need for advanced illness or palliative care in a primary care population using electronic health record data

Walter F. Stewart, Nigam H. Shah, Kenneth Jung, 2019, J. Biomed. Informatics.

Inferring Physical Function From Wearable Activity Monitors: Analysis of Free-Living Activity Data From Patients With Knee Osteoarthritis

Nigam H Shah, Matthew Smuck, Vibhu Agarwal, 2018, JMIR mHealth and uHealth.

Inferring Physical Function From Wearable Activity Monitors: Analysis of Free-Living Activity Data From Patients With Knee Osteoarthritis (Preprint)

N. Shah, M. Smuck, V. Agarwal, 2018 .

Monitoring physical function in patients with knee osteoarthritis using data from wearable activity monitors

Nigam H Shah, Vibhu Agarwal, N. Shah, 2018, 1801.08668.

Automated model versus treating physician for predicting survival time of patients with metastatic cancer

Nigam H. Shah, Douglas J. Wood, Solomon Henry, 2020, J. Am. Medical Informatics Assoc..

Characteristics and outcomes of patients with COVID-19 with and without prevalent hypertension: a multinational cohort study

M. Suchard, N. Shah, G. Hripcsak, 2021, BMJ Open.

Comparing methods for estimation of heterogeneous treatment effects using observational data from health care databases

K Jung, T Wendling, A Callahan, 2018, Statistics in medicine.

An unsupervised learning method to identify reference intervals from a clinical database

Nigam H. Shah, Sarah Poole, Lee Frederick Schroeder, 2016, J. Biomed. Informatics.

Creating Fair Models of Atherosclerotic Cardiovascular Disease Risk

Ben J. Marafino, Nigam H. Shah, Adrien Coulet, 2018, AIES.

Estimating the efficacy of symptom-based screening for COVID-19.

Jason Alan Fries, Conor K. Corbin, N. Shah, 2020, NPJ digital medicine.

Assessing the accuracy of automatic speech recognition for psychotherapy

Jason Alan Fries, Adam S. Miner, A. Milstein, 2020, npj Digital Medicine.

The number needed to benefit: estimating the value of predictive analytics in healthcare

Nigam H Shah, Jenna Wiens, David W Bates, 2019, J. Am. Medical Informatics Assoc..

Predicting hospital visits from geo-tagged Internet search logs

Nigam H. Shah, Vibhu Agarwal, Isaac Madan, 2016, CRI.

An Empirical Characterization of Fair Machine Learning For Clinical Risk Prediction

Nigam H. Shah, Stephen R. Pfohl, Agata Foryciarz, 2020, J. Biomed. Informatics.

A model to forecast regional demand for COVID-19 related hospital beds

P. Glynn, A. Milstein, N. Shah, 2020, medRxiv.

Author ' s personal copy Using text to build semantic networks for pharmacogenomics

Russ B. Altman, Mark A. Musen, Nigam H. Shah, 2010 .

Nursing Workflow Change in a COVID-19 Inpatient Unit Following the Deployment of Inpatient Telehealth: Observational Study Using a Real-Time Locating System

N. Shah, M. Lough, S. Vilendrer, 2022, Journal of medical Internet research.

Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA

Atul J. Butte, Nigam H. Shah, A. Butte, 2011, J. Am. Medical Informatics Assoc..

Repurposing cAMP-modulating medications to promote β-cell replication.

Yen S. Low, N. Shah, J. Ryu, 2014, Molecular endocrinology.

A quality assessment tool for artificial intelligence-centered diagnostic test accuracy studies: QUADAS-AI

Charles E. Kahn, Jérémie F. Cohen, D. Webster, 2021, Nature Medicine.

Learning statistical models of phenotypes using noisy labeled training data

Nigam H. Shah, Juan M. Banda, Tanya Podchiyska, 2016, J. Am. Medical Informatics Assoc..

A comparison of approaches to improve worst-case predictive model performance over patient subpopulations

M. Ghassemi, N. Shah, S. Pfohl, 2021, Scientific Reports.

Funding and Publication of Research on Gun Violence and Other Leading Causes of Death

N. Shah, David E. Stark, 2017, JAMA.

Occurrence and Timing of Subsequent Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-transcription Polymerase Chain Reaction Positivity Among Initially Negative Patients.

Jacob E. Sunshine, N. Shah, J. Zehnder, 2021, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Integration and publication of heterogeneous text-mined relationships on the Semantic Web

Russ B. Altman, Michel Dumontier, Mark A. Musen, 2011, J. Biomed. Semant..

It is time to learn from patients like mine

Alison Callahan, Nigam H. Shah, Robert Harrington, 2019, npj Digital Medicine.

Performing an Informatics Consult: Methods and Challenges.

Alison Callahan, Kenneth Jung, Nigam H Shah, 2018, Journal of the American College of Radiology : JACR.

A formal concept analysis and semantic query expansion cooperation to refine health outcomes of interest

Olivier Curé, Nigam H. Shah, Paea LePendu, 2015, BMC Medical Informatics and Decision Making.

ACE: the Advanced Cohort Engine for searching longitudinal patient records

Alison Callahan, Juan M Banda, Nigam H Shah, 2021, J. Am. Medical Informatics Assoc..

Identifying cases of metastatic prostate cancer using machine learning on electronic health records

Nigam H. Shah, Juan M. Banda, James D. Brooks, 2018, AMIA.

Electronic phenotyping with APHRODITE and the Observational Health Sciences and Informatics (OHDSI) data network

Nigam H. Shah, Juan M. Banda, David Sontag, 2017, CRI.

Annotation analysis for testing drug safety signals using unstructured clinical notes

Cédrick Fairon, Nigam H. Shah, Paea LePendu, 2012, J. Biomed. Semant..

Mapping between the OBO and OWL ontology languages

Daniel P. Miranker, Juan Sequeda, Chris Mungall, 2011, J. Biomed. Semant..

Building a biomedical ontology recommender web service

Mark A. Musen, Clement Jonquet, Nigam H. Shah, 2010, J. Biomed. Semant..

What Four Million Mappings Can Tell You about Two Hundred Ontologies

Mark A. Musen, Clement Jonquet, Nigam H. Shah, 2009, SEMWEB.

Biomedical ontologies: a functional

Natalya F. Noy, Nigam H. Shah, L. Rubin, 2007 .

Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting

Michel Dumontier, Nigam H. Shah, Susanna-Assunta Sansone, 2013, J. Biomed. Semant..

Learning Effective Treatment Pathways for Type-2 Diabetes from a clinical data warehouse

Nigam H. Shah, Ken Jung, Rohit Vashisht, 2016, AMIA.

Ontology-driven weak supervision for clinical entity classification in electronic health records

Jason Alan Fries, N. Shah, A. Callahan, 2021, Nature Communications.

A Second Opinion From Observational Data on Second-line Diabetes Drugs.

N. Shah, A. Callahan, 2018, JAMA network open.

Assessment of Extractability and Accuracy of Electronic Health Record Data for Joint Implant Registries

Jason Alan Fries, Alex H. S. Harris, Christopher Ré, 2021, JAMA network open.

Reply to R.L. Bowen et al, M. Froehner et al, J.L. Leow et al, and C. Brady et al.

N. Shah, J. Dudley, N. Leeper, 2016, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

Synth-Validation: Selecting the Best Causal Inference Method for a Given Dataset

Trevor Hastie, Robert Tibshirani, Ken Jung, 2017, 1711.00083.

A Clinical Trial Derived Reference Set for Evaluating Observational Study Methods

Nigam H. Shah, Steve Yadlowsky, Ethan Steinberg, 2020 .

Using clinical data text-mining analysis to examine the association between androgen deprivation therapy and depression.

N. Shah, N. Leeper, Greg Gaskin, 2015 .

The Emotional Toll of Inflammatory Bowel Disease: Using Machine Learning to Analyze Online Community Forum Discourse

Dan Jurafsky, N. Shah, Azadeh Nikfarjam, 2019, Crohn's & Colitis 360.

Use of Machine Learning and Lay Care Coaches to Increase Advance Care Planning Conversations for Patients With Metastatic Cancer

N. Shah, K. Ramchandran, N. Myall, 2022, JCO oncology practice.

Predicting Emergency Department Visits

Shaun J. Grannis, Nigam H. Shah, Sarah F. Poole, 2016, CRI.

Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting

Nigam H. Shah, Susanna-Assunta Sansone, Larisa N. Soldatova, 2011, J. Biomed. Semant..

Democratizing Health Data for Translational Research.

Philip R. O. Payne, N. Shah, L. Mangravite, 2018, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

SARS-CoV-2 infection and COVID-19 severity in individuals with prior seasonal coronavirus infection

N. Shah, T. Bergquist, B. Pinsky, 2020, Diagnostic Microbiology and Infectious Disease.

Analyzing Information Seeking and Drug-Safety Alert Response by Health Care Professionals as New Methods for Surveillance

Jure Leskovec, Alison Callahan, Gregor Stiglic, 2015, Journal of medical Internet research.

Use of Electronic Health Record Data for Drug Safety Signal Identification: A Scoping Review

Sharon E. Davis, Joshua C. Smith, N. Shah, 2023, Drug Safety.

Empirical bayes model to combine signals of adverse drug reactions

William DuMouchel, Nigam H. Shah, Paea LePendu, 2013, KDD.

The accuracy vs. coverage trade-off in patient-facing diagnosis models

Jen Jen Chen, Xavier Amatriain, Anitha Kannan, 2019, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

PGEN: A Novel Approach to Sequential Circuit Test Generation

Sunil R. Das, Nigam Shah, Wen-Ben Jone, 1996, VLSI Design.

Pharmacovigilance using Clinical Text

Paea LePendu, Anna Bauer-Mehren, Nigam H Shah, 2013, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

Predicting the need for a reduced drug dose, at first prescription

N. Shah, M. Dumontier, Adrien Coulet, 2018, Scientific Reports.

Mining the pharmacogenomics literature - a survey of the state of the art

K. Bretonnel Cohen, Udo Hahn, Nigam H. Shah, 2012, Briefings Bioinform..

Pathway knowledge base: An integrated pathway resource using BioPAX

Nigam H. Shah, Nikesh Kotecha, Kyle Bruck, 2008, Appl. Ontology.

Characteristics and outcomes of 118,155 COVID-19 individuals with a history of cancer in the United States and Spain

N. Shah, I. Soerjomataram, J. Jonnagaddala, 2021, medRxiv.

U-Index, a dataset and an impact metric for informatics tools and databases

Alison Callahan, Nigam H Shah, Rainer Winnenburg, 2018, Scientific Data.

Comparing Concept Recognizers for Ontology-Based Indexing : MGREP vs . MetaMap

Mark A. Musen, Nigam H. Shah, Annie P. Chiang, 2008 .

CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology

N. H. Shah, Nina V. Fedoroff, N. Shah, 2004, Bioinform..

Ontology-driven weak supervision for clinical entity classification in electronic health records

Jason Alan Fries, N. Shah, A. Callahan, 2020, Nature Communications.

A comparison of methods for model selection when estimating individual treatment effects

Robert Tibshirani, Alejandro Schuler, Nigam Shah, 2018, 1804.05146.

General-purpose validation and model selection when estimating individual treatment effects pdf

Nigam H. Shah, Alejandro Schuler, N. Shah, 2018, ArXiv.

Translational Bioinformatics

Fernando Martin-Sanchez, Isabel Hermosilla-Gimeno, N. Shah, 2021, Biomedical Informatics.

Using natural language processing to construct a metastatic breast cancer cohort from linked cancer registry and electronic medical records data pdf

Nigam H. Shah, George W. Sledge, Allison W. Kurian, 2019, JAMIA open.

Effective Representations of Clinical Notes

Kenneth Jung, Sebastien Dubois, David C. Kale, 2017 .

Countdown Regression: Sharp and Calibrated Survival Predictions

Nigam H. Shah, Anand Avati, Kenneth Jung, 2018, UAI.

Synergistic drug combinations from electronic health records and gene expression

Maya B. Mathur, Trevor J. Hastie, Nigam H. Shah, 2016, J. Am. Medical Informatics Assoc..

Biomedical ontologies: a functional perspective.

Natasha Noy, N. Shah, D. Rubin, 2008, Briefings in bioinformatics.

Missingness as Stability: Understanding the Structure of Missingness in Longitudinal EHR data and its Impact on Reinforcement Learning in Healthcare pdf

Emma Brunskill, Nigam Shah, Tony Duan, 2019, ArXiv.

Unexpected Effect of Proton Pump Inhibitors: Elevation of the Cardiovascular Risk Factor Asymmetric Dimethylarginine

N. Shah, P. LePendu, J. Cooke, 2013, Circulation.

Postmarket Surveillance of Point-of-Care Glucose Meters through Analysis of Electronic Medical Records.

Nigam H Shah, Lee F Schroeder, Milo Engoren, 2016, Clinical chemistry.

Functional evaluation of out-of-the-box text-mining tools for data-mining tasks

Bethany Percha, Nigam H. Shah, Kenneth Jung, 2014, J. Am. Medical Informatics Assoc..

Mining the internet for drug information.

N. Shah, 2014, Clinical advances in hematology & oncology : H&O.

Unsupervised Learning for Automated Detection of Coronary Artery Disease Subgroups

N. Shah, J. Cooke, E. Ross, 2021, Journal of the American Heart Association.

Accurate and interpretable intensive care risk adjustment for fused clinical data with generalized additive models

Ben J. Marafino, R. Adams Dudley, Nigam H. Shah, 2018, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis

Cui Tao, Hongfang Liu, Stephen T. Wu, 2012, J. Am. Medical Informatics Assoc..

Assessing Screening Guidelines for Cardiovascular Disease Risk Factors using Routinely Collected Data

Sarah F. Poole, N. Shah, J. Pannu, 2017, Scientific Reports.

Provenance-Centered Dataset of Drug-Drug Interactions pdf

Michel Dumontier, Tobias Kuhn, Nigam H. Shah, 2015, SEMWEB.

Extraction of Conditional Probabilities of the Relationships Between Drugs, Diseases, and Genes from PubMed Guided by Relationships in PharmGKB

Martin Theobald, Jeff Shrager, Nigam Shah, 2009, Summit on translational bioinformatics.

Statin Intensity or Achieved LDL? Practice-based Evidence for the Evaluation of New Cholesterol Treatment Guidelines

Nigam Shah, N. Shah, E. Ross, 2016, PloS one.

Addressing vital sign alarm fatigue using personalized alarm thresholds

Nigam H. Shah, Sarah Poole, Sarah F. Poole, 2019, PSB.

Open Data for Discovery Science

Kun Huang, Nigam H. Shah, Philip R. O. Payne, 2017, PSB.

Toward multimodal signal detection of adverse drug reactions

Olivier Bodenreider, Ryen W. White, Eric Horvitz, 2017, J. Biomed. Informatics.

Mining the pharmacogenomics literatureça survey of the state of the art

K. Bretonnel Cohen, Nigam H. Shah, Yael Garten, 2012 .

DENMARK: A LONGITUDINAL POPULATION-BASED STUDY

Lester W. Mackey, A. Milstein, N. Shah, 2016 .

Accurate and interpretable intensive care risk adjustment for fused clinical data with generalized additive models

Ben J. Marafino, Jonathan H. Chen, N. Shah, 2018, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

Development and validation of phenotype classifiers across multiple sites in the observational health data sciences and informatics network

George Hripcsak, Borim Ryu, Sooyoung Yoo, 2020, J. Am. Medical Informatics Assoc..

Web-scale pharmacovigilance: listening to signals from the crowd

Ryen W. White, E. Horvitz, R. Altman, 2013, J. Am. Medical Informatics Assoc..

Making Machine Learning Models Clinically Useful.

A. Milstein, N. Shah, Steven C Bagley PhD, 2019, JAMA.

Ontology-driven weak supervision for clinical entity classification in electronic health records

Alison Callahan, Jose Posada, Jason Alan Fries, 2020, Nature Communications.

Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature

N. Shah, R. Winnenburg, 2016, BMC Bioinformatics.

Quantifying the relative change in physical activity after Total Knee Arthroplasty using accelerometer based measurements

N. Shah, V. Agarwal, Mathew Smuck, 2017, CRI.

Early Detection of Adverse Drug Reactions in Social Health Networks: A Natural Language Processing Pipeline for Signal Detection

N. Shah, A. Callahan, Azadeh Nikfarjam, 2019, JMIR public health and surveillance.

A Comprehensive Analysis of Five Million UMLS Metathesaurus Terms Using Eighteen Million MEDLINE Citations.

Rong Xu, Mark A Musen, Nigam H Shah, 2010, AMIA ... Annual Symposium proceedings. AMIA Symposium.

A case study in pathway knowledgebase verification

Nigam H. Shah, Stephen A. Racunas, Nina V. Fedoroff, 2006, BMC Bioinformatics.

Erratum: The BioPAX community standard for pathway data sharing (Nat. Biotechnol. (2010) 28 (935-942)

Kei-Hoi Cheung, Frank Schacherer, Edgar Wingender, 2010 .

Changing computational research. The challenges ahead

Egon L. Willighagen, Peter Murray-Rust, Gaël Varoquaux, 2012, Source Code for Biology and Medicine.

Mining Biomedical Ontologies and Data Using RDF Hypergraphs

Ruoming Jin, Dejing Dou, Nigam H. Shah, 2013, 2013 12th International Conference on Machine Learning and Applications.

What This Computer Needs Is a Physician: Humanism and Artificial Intelligence.

N. Shah, R. Harrington, A. Verghese, 2018, JAMA.

The Open Biomedical Annotator

N. Shah, M. Musen, C. Jonquet, 2009, Summit on translational bioinformatics.

STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation

Sean D. Mooney, Nigam H. Shah, Corey Powell, 2013, BMC Bioinformatics.

Using ontology-based annotation to profile disease research

Yi Liu, Nigam H. Shah, Adrien Coulet, 2012, J. Am. Medical Informatics Assoc..

An ontology-neutral framework for enrichment analysis.

Mark A Musen, Nigam H Shah, Sean D Mooney, 2010, AMIA ... Annual Symposium proceedings. AMIA Symposium.

The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies.

Clement Jonquet, Rong Xu, Mark A Musen, 2010, AMIA ... Annual Symposium proceedings. AMIA Symposium.

Building a biomedical ontology recommender web service

N. Shah, M. Musen, C. Jonquet, 2010, J. Biomed. Semant..

- 1-Building a biomedical ontology recommender web service

Clement Jonquet, Mark Musen, Nigam Shah, 2010 .

Prototyping a Biomedical Ontology Recommender Service

Mark A. Musen, Clement Jonquet, Nigam H. Shah, 2009 .

A System for Ontology-Based Annotation of Biomedical Data

Mark A. Musen, Clement Jonquet, Nigam H. Shah, 2008, DILS.

Biomedical Data/Content Acquisition, Curation

N. Shah, 2009, Encyclopedia of Database Systems.

Ontology-based Annotation and Query of Tissue Microarray Data

Daniel L. Rubin, Mark A. Musen, Nigam H. Shah, 2006, AMIA.

Proceedings of the Joint Workshop on Semantic Technologies Applied to Biomedical Informatics and Individualized Medicine in Conjunction with the 11th International Semantic Web Conference 2012 (ISWC 2012)

Nigam H. Shah, Mark D. Wilkinson, Alejandro Rodríguez González, 2012 .

The use of machine learning for the identification of peripheral artery disease and future mortality risk.

N. Shah, J. Cooke, R. Dalman, 2016, Journal of vascular surgery.

Addressing vital sign alarm fatigue using personalized alarm thresholds

Sarah F. Poole, N. Shah, 2019, PSB.

An Unexpected Effect of Proton Pump Inhibitors: Elevation of the Cardiovascular Risk Factor ADMA

N. Shah, P. LePendu, J. Cooke, 2013 .

Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA

A. Butte, N. Shah, 2011, J. Am. Medical Informatics Assoc..

Electronic phenotyping with APHRODITE and the Observational Health Sciences and Informatics (OHDSI) data network

D. Sontag, N. Shah, J. Banda, 2017, CRI.

Ranitidine Use and Incident Cancer in a Multinational Cohort

M. Suchard, N. Shah, G. Hripcsak, 2023, JAMA network open.

BioPortal: A Web Repository for Biomedical Ontologies and Data Resources

Daniel L. Rubin, Mark A. Musen, Clement Jonquet, 2008, SEMWEB.