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View article: Implementing integrated genomic risk assessments for breast cancer: lessons learned from the Electronic Medical Records and Genomics study
Implementing integrated genomic risk assessments for breast cancer: lessons learned from the Electronic Medical Records and Genomics study Open
Objectives To implementation an automated multi-institutional pipeline that delivers breast-cancer risk integrated with polygenic risk scores, monogenic variants, family history, and clinical factors, emphasizing operational challenges and…
View article: Achieving a rapid and continuous learning health system requires socio-technical harmonization of research and operational IT
Achieving a rapid and continuous learning health system requires socio-technical harmonization of research and operational IT Open
This perspective identifies challenges in integrating clinical research and care delivery in a rapid and continuous Learning Health System (LHS), focusing on Information technology (IT) systems and workforce harmonization. Based on our exp…
View article: Announcing the Biomedical Data Translator: Initial Public Release
Announcing the Biomedical Data Translator: Initial Public Release Open
The growing availability of biomedical data offers vast potential to improve human health, but the complexity and lack of integration of these datasets often limit their utility. To address this, the Biomedical Data Translator Consortium h…
View article: Announcing the Biomedical Data Translator: Initial Public Release
Announcing the Biomedical Data Translator: Initial Public Release Open
The growing availability of biomedical data offers vast potential to improve human health, but the complexity and lack of integration of these datasets often limit their utility. To address this, the Biomedical Data Translator Consortium h…
View article: Implementing Integrated Genomic Risk Assessments for Breast Cancer: Lessons Learned from the eMERGE Study
Implementing Integrated Genomic Risk Assessments for Breast Cancer: Lessons Learned from the eMERGE Study Open
Objective To develop and implement a pipeline for integrated breast cancer risk assessment using the BOADICEA model within the eMERGE study, incorporating polygenic risk scores (PRS), monogenic variants, family history, and clinical factor…
View article: Identifying Phenotypes for Earlier Diagnosis of Rare Diseases
Identifying Phenotypes for Earlier Diagnosis of Rare Diseases Open
Rare diseases, while individually rare, cumulatively affect a large population, and patients often undergo long and arduous diagnostic odysseys. Toward the goal of supporting earlier diagnosis of rare diseases, we developed generalizable m…
View article: Current Limitations of Electronic Health Record Systems in Supporting Pragmatic Clinical Trials: Insights from the eMERGE Consortium
Current Limitations of Electronic Health Record Systems in Supporting Pragmatic Clinical Trials: Insights from the eMERGE Consortium Open
Pragmatic clinical trials (PCTs) evaluate interventions in real-world settings, often using electronic health records (EHRs) for efficient data collection. We report on the challenges in performing EHR analysis of health-care provider orde…
View article: Mini-mental status examination phenotyping for Alzheimer’s disease patients using both structured and narrative electronic health record features
Mini-mental status examination phenotyping for Alzheimer’s disease patients using both structured and narrative electronic health record features Open
Objective This study aims to automate the prediction of Mini-Mental State Examination (MMSE) scores, a widely adopted standard for cognitive assessment in patients with Alzheimer’s disease, using natural language processing (NLP) and machi…
View article: An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges
An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges Open
Knowledge graphs have become a common approach for knowledge representation. Yet, the application of graph methodology is elusive due to the sheer number and complexity of knowledge sources. In addition, semantic incompatibilities hinder e…
View article: Clinical Data: Sources and Types, Regulatory Constraints, Applications
Clinical Data: Sources and Types, Regulatory Constraints, Applications Open
Access to clinical data is critical for the advancement of translational research. However, the numerous regulations and policies that surround the use of clinical data, although critical to ensure patient privacy and protect against misus…
View article: Phenotype-Driven Molecular Genetic Test Recommendation for Diagnosing Pediatric Rare Disorders
Phenotype-Driven Molecular Genetic Test Recommendation for Diagnosing Pediatric Rare Disorders Open
Rare disease patients often endure prolonged diagnostic odysseys and may still remain undiagnosed for years. Selecting the appropriate genetic tests is crucial to lead to timely diagnosis. Phenotypic features offer great potential for aidi…
View article: <i>EvidenceMap</i>: a three-level knowledge representation for medical evidence computation and comprehension
<i>EvidenceMap</i>: a three-level knowledge representation for medical evidence computation and comprehension Open
Objective To develop a computable representation for medical evidence and to contribute a gold standard dataset of annotated randomized controlled trial (RCT) abstracts, along with a natural language processing (NLP) pipeline for transform…
View article: Principal Investigators' Perceptions on Factors Associated with Successful Recruitment in Clinical Trials.
Principal Investigators' Perceptions on Factors Associated with Successful Recruitment in Clinical Trials. Open
Participant recruitment continues to be a challenge to the success of randomized controlled trials, resulting in increased costs, extended trial timelines and delayed treatment availability. Literature provides evidence that study design f…
View article: Uncovering key clinical trial features influencing recruitment
Uncovering key clinical trial features influencing recruitment Open
Background: Randomized clinical trials (RCT) are the foundation for medical advances, but participant recruitment remains a persistent barrier to their success. This retrospective data analysis aims to (1) identify clinical trial features …
View article: An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges
An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges Open
Knowledge graphs have become a common approach for knowledge representation. Yet, the application of graph methodology is elusive due to the sheer number and complexity of knowledge sources. In addition, semantic incompatibilities hinder e…
View article: Can Race-sensitive Biomedical Embeddings Improve Healthcare Predictive Models?
Can Race-sensitive Biomedical Embeddings Improve Healthcare Predictive Models? Open
This reproducibility study presents an algorithm to weigh in race distribution data of clinical research study samples when training biomedical embeddings. We extracted 12,864 PubMed abstracts published between January 1st, 2000 and Januar…
View article: Clinical and temporal characterization of COVID-19 subgroups using patient vector embeddings of electronic health records
Clinical and temporal characterization of COVID-19 subgroups using patient vector embeddings of electronic health records Open
Objective To identify and characterize clinical subgroups of hospitalized Coronavirus Disease 2019 (COVID-19) patients. Materials and Methods Electronic health records of hospitalized COVID-19 patients at NewYork-Presbyterian/Columbia Univ…
View article: Evaluation of Criteria2Query: Towards Augmented Intelligence for Cohort Identification
Evaluation of Criteria2Query: Towards Augmented Intelligence for Cohort Identification Open
Electronic healthcare records data promises to improve the efficiency of patient eligibility screening, which is an important factor in the success of clinical trials and observational studies. To bridge the sociotechnical gap in cohort id…
View article: Towards Better Diagnosis Prediction Using Bidirectional Recurrent Neural Networks
Towards Better Diagnosis Prediction Using Bidirectional Recurrent Neural Networks Open
Bidirectional recurrent neural networks (RNN) improved performance of various natural language processing tasks and recently have been used for diagnosis prediction. Advantages of general bidirectional RNN, however, are not readily applied…
View article: Progress toward a universal biomedical data translator
Progress toward a universal biomedical data translator Open
Clinical, biomedical, and translational science has reached an inflection point in the breadth and diversity of available data and the potential impact of such data to improve human health and well‐being. However, the data are often siloed…
View article: Risk Factors Associated With SARS-CoV-2 Breakthrough Infections in Fully mRNA-Vaccinated Individuals: Retrospective Analysis
Risk Factors Associated With SARS-CoV-2 Breakthrough Infections in Fully mRNA-Vaccinated Individuals: Retrospective Analysis Open
Background COVID-19 messenger RNA (mRNA) vaccines have demonstrated efficacy and effectiveness in preventing symptomatic COVID-19, while being relatively safe in trial studies. However, vaccine breakthrough infections have been reported. O…
View article: A machine learning approach to identifying delirium from electronic health records
A machine learning approach to identifying delirium from electronic health records Open
The identification of delirium in electronic health records (EHRs) remains difficult due to inadequate assessment or under-documentation. The purpose of this research is to present a classification model that identifies delirium using retr…