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List of works by Nigam H. Shah

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

scientific article

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

scientific article published on 07 December 2018

A System for Ontology-Based Annotation of Biomedical Data

article

A UIMA wrapper for the NCBO annotator

scientific article

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

scientific article

A dataset quantifying polypharmacy in the United States.

scientific article published on 31 October 2017

A framework for making predictive models useful in practice

scientific article published on 22 December 2020

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

scientific article published on 31 July 2015

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

scientific article published on 30 March 2020

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

scientific article published on 10 June 2020

A survey of extant organizational and computational setups for deploying predictive models in health systems

scientific article

A time-indexed reference standard of adverse drug reactions

scientific article

ACE: the Advanced Cohort Engine for searching longitudinal patient records

scientific article

APLUS: A Python library for usefulness simulations of machine learning models in healthcare

scientific article published in 2023

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

scientific article published on 18 May 2018

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

scientific article published on 23 May 2018

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

scientific article published on 07 September 2018

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

scientific article published on 26 April 2020

An ontology-neutral framework for enrichment analysis

scientific article

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

scientific article published on 19 December 2015

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

scientific article

Analyzing patterns of drug use in clinical notes for patient safety ⬇️

scientific article published on March 19, 2012

Analyzing search behavior of healthcare professionals for drug safety surveillance

scientific article published on January 2015

Androgen Deprivation Therapy and Future Alzheimer's Disease Risk

scientific article

Androgen Deprivation Therapy and Subsequent Dementia-Reply

scientific article published on 4 May 2017

Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes ⬇️

scientific article published on April 24, 2012

Annotation and query of tissue microarray data using the NCI Thesaurus

scientific article

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

scientific article

Assessing the accuracy of automatic speech recognition for psychotherapy

scientific article published on 03 June 2020

Association Between Androgen Deprivation Therapy and Risk of Dementia

scientific article published on 13 October 2016

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

scientific article published on 03 August 2018

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

scientific article published on 14 April 2020

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

scientific article published on 18 March 2013

Automated detection of off-label drug use

scientific article (publication date: 2014)

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

scientific article published on 14 December 2020

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

scientific article published on 30 October 2020

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

scientific article published on 27 October 2020

BioPortal: A Web Repository for Biomedical Ontologies and Data Resources

scientific article published in iswc2008 posters and demonstrations

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

scientific article (publication date: July 2011)

Biological Resource Discovery

Biomedical ontologies: a functional perspective

scientific article published on 12 December 2007

Bridging the implementation gap of machine learning in healthcare

scientific article

Building a biomedical ontology recommender web service

scientific article (publication date: 22 June 2010)

Building the graph of medicine from millions of clinical narratives

scientific article

Call for Papers: Deep Phenotyping for Precision Medicine

scientific article published on 29 September 2018

Chapter 9: Analyses using disease ontologies

scientific article

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

scientific article published on 27 November 2020

Characterizing treatment pathways at scale using the OHDSI network

scientific article

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

scientific article published on October 31, 2012

Comment on: "Zoo or savannah? Choice of training ground for evidence-based pharmacovigilance".

scientific article published in January 2015

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

scientific article published on 06 July 2020

Comparison of concept recognizers for building the Open Biomedical Annotator

scientific article

Comparison of ontology-based semantic-similarity measures

scientific article

Computational drug repositioning of atorvastatin for ulcerative colitis

scientific article

Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured inJAMIA ⬇️

scientific article published on July 1, 2011

Conflicting information from the Food and Drug Administration: Missed opportunity to lead standards for safe and effective medical artificial intelligence solutions

scholarly article by Tina Hernandez-Boussard et al published 1 March 2021 in Journal of the American Medical Informatics Association

DISCOVERING PATIENT PHENOTYPES USING GENERALIZED LOW RANK MODELS

scientific article published on January 2016

Deep Phenotyping: Embracing Complexity and Temporality-Towards Scalability, Portability, and Interoperability

scientific article published on 23 April 2020

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

scientific article published on 06 October 2020

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

scientific article published on 01 December 2020

Detecting unplanned care from clinician notes in electronic health records

scientific article published on May 2015

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

scientific article published on 02 August 2019

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

scientific article published on 13 November 2020

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

scientific article published on 07 January 2020

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

scientific article published on 06 May 2020

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

scientific article published on 03 June 2019

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

scientific article

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

scientific article

Enabling enrichment analysis with the Human Disease Ontology

scientific article

Enhanced Quality Measurement Event Detection: An Application to Physician Reporting.

scientific article

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

scientific article published on 01 January 2020

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

scientific article published on 13 July 2020

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

scientific article (preprint)

Ethics of Using and Sharing Clinical Imaging Data for Artificial Intelligence: A Proposed Framework

scientific article published on 24 March 2020

Evaluation of Domain Generalization and Adaptation on Improving Model Robustness to Temporal Dataset Shift in Clinical Medicine

scientific article

Extraction of genotype-phenotype-drug relationships from text: from entity recognition to bioinformatics application

scientific article published on January 2010

Finding missed cases of familial hypercholesterolemia in health systems using machine learning

scientific article published on 11 April 2019

Finding progression stages in time-evolving event sequences

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

scientific article

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

scientific article

HyQue: evaluating hypotheses using Semantic Web technologies ⬇️

scientific article (publication date: 17 May 2011)

Identifying Cases of Metastatic Prostate Cancer Using Machine Learning on Electronic Health Records.

scientific article

Identifying phenotypic signatures of neuropsychiatric disorders from electronic medical records ⬇️

scientific article published on August 16, 2013

Impact of Predicting Health Care Utilization Via Web Search Behavior: A Data-Driven Analysis

scientific article (publication date: 21 September 2016)

Implications of non-stationarity on predictive modeling using EHRs

scientific article

Improving palliative care with deep learning

scholarly article by Anand Avati et al published 12 December 2018 in BMC Medical Informatics and Decision Making

In silico functional profiling of human disease-associated and polymorphic amino acid substitutions

scientific article

Inferring Physical Function from Wearable Activity Monitors: Analysis of Activity Data from Patients with Knee Osteoarthritis (Preprint)

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

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

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

scientific article published on 18 October 2016

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

scientific article

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

scientific article (publication date: 17 May 2011)

Interpretation errors related to the GO annotation file format.

scientific article published on 11 October 2007

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

scientific article published on 23 March 2018

It is time to learn from patients like mine

scientific article published on 19 March 2019

LEARNING ATTRIBUTES OF DISEASE PROGRESSION FROM TRAJECTORIES OF SPARSE LAB VALUES.

scientific article published on January 2016

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

scientific article published on 05 December 2020

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

scientific article

Learning decision thresholds for risk stratification models from aggregate clinician behavior

scientific article

Learning signals of adverse drug-drug interactions from the unstructured text of electronic health records

scientific article published on 18 March 2013

Learning signals of adverse drug-drug interactions from the unstructured text of electronic health records

scientific article

Learning statistical models of phenotypes using noisy labeled training data

scientific article

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

scientific article published on 28 June 2020

Mapping between the OBO and OWL ontology languages

scientific article

Measure what matters: Counts of hospitalized patients are a better metric for health system capacity planning for a reopening

scientific article published on 17 June 2020

Measure what matters: counts of hospitalized patients are a better metric for health system capacity planning for a reopening

scientific article published on 23 April 2020

Medical device surveillance with electronic health records

scientific article published on 25 September 2019

Meeting Report: BioSharing at ISMB 2010

scientific article (publication date: 4 December 2010)

Mining clinical text for signals of adverse drug-drug interactions

scientific article published on 24 October 2013

NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources

scientific article

Network analysis of unstructured EHR data for clinical research

scientific article

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

scientific article published on 12 May 2016

OBO & OWL: Roundtrip Ontology Transformations ⬇️

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

scientific article

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

scientific article published on 08 May 2020

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

scientific article published on 07 June 2020

Ontology-based annotation and query of tissue microarray data.

scientific article

Ontology-driven indexing of public datasets for translational bioinformatics

scientific article

Optimize First, Buy Later: Analyzing Metrics to Ramp-Up Very Large Knowledge Bases

article published in 2010

Performing an Informatics Consult: Methods and Challenges

scientific article published on 22 January 2018

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

scientific article published on 30 May 2020

Pharmacovigilance using Clinical Text

scientific article published on 18 March 2013

Practice-Based Evidence: Profiling the Safety of Cilostazol by Text-Mining of Clinical Notes ⬇️

scientific article published on May 23, 2013

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

scientific article published on 21 October 2019

Predicting Future Cardiovascular Events in Patients With Peripheral Artery Disease Using Electronic Health Record Data

scientific article published on 01 March 2019

Predicting hospital visits from geo-tagged Internet search logs

scientific article published on 20 July 2016

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

scientific article published on 10 February 2019

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

scientific article published in Scientific Reports

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

scientific article published on 18 December 2020

Profiling risk factors for chronic uveitis in juvenile idiopathic arthritis: a new model for EHR-based research

scientific article

Proposed SKOS Extensions for BioPortal Terminology Services

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

scientific article

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

scientific article

Provenance-Centered Dataset of Drug-Drug Interactions

scientific article published at ISWC 2015

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

scientific article

Refining Health Outcomes of Interest using Formal Concept Analysis and Semantic Query Expansion ⬇️

article

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

scientific article published on 7 April 2016

Reply

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

scientific article

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

scientific article published on 01 June 2020

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

scientific article published on April 2014

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

scientific article

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

scientific article published on 17 August 2020

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

scholarly article by Nigam H. Shah published in 2020

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

scientific article

Scalable and accurate deep learning with electronic health records

article

Searching ontologies based on content

Selected papers from the 12th annual Bio-Ontologies meeting

scientific article

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

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting

scientific article (publication date: 24 April 2012)

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

scientific article (publication date: 15 April 2013)

Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting.

scientific article published on 3 June 2014

Special issue on bio-ontologies and phenotypes

scientific article

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

scientific article

Text mining for adverse drug events: the promise, challenges, and state of the art.

scientific article

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

scientific article

The National Center for Biomedical Ontology

scientific article

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

scientific article published in November 2007

The Stanford Tissue Microarray Database

scientific article

The digital revolution in phenotyping

scientific article published on 29 September 2015

The open biomedical annotator

scientific article

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

scientific article published on 3 June 2016

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

scientific article published on 12 December 2016

Toward multimodal signal detection of adverse drug reactions

scientific article published on 25 October 2017

Toward personalizing treatment for depression: predicting diagnosis and severity

scientific article

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

scientific article published on 01 March 2020

Trove: Ontology-driven weak supervision for medical entity classification

scientific article published on 05 August 2020

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

scientific article

Unexpected effect of proton pump inhibitors: elevation of the cardiovascular risk factor asymmetric dimethylarginine.

scientific article published on 03 July 2013

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

scientific article

Use of dialysis, tracheostomy, and extracorporeal membrane oxygenation among 240,392 patients hospitalized with COVID-19 in the United States

scientific article published on 27 November 2020

Using ontology-based annotation to profile disease research ⬇️

scientific article published on April 11, 2012

Using temporal patterns in medical records to discern adverse drug events from indications ⬇️

scientific article published on March 19, 2012

Using text to build semantic networks for pharmacogenomics

scientific article

Web-scale pharmacovigilance: listening to signals from the crowd

scientific article

What Four Million Mappings Can Tell You about Two Hundred Ontologies

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