Jonathan C. Silverstein
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View article: Predicting Alzheimer’s Disease Diagnosis, a Decade or more Years before Onset using the Electronic Health Record and Random Forest Machine Learning Models
Predicting Alzheimer’s Disease Diagnosis, a Decade or more Years before Onset using the Electronic Health Record and Random Forest Machine Learning Models Open
INTRODUCTION There is need to detect and intervene in pre-clinical phases of Alzheimer’s disease (AD). Electronic health records (EHRs) may help predict AD using machine learning methods. METHODS We identified EHRs for 19,473 cases with AD…
View article: The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data
The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data Open
The Data Distillery Knowledge Graph (DDKG) is a framework for semantic integration and querying of biomedical data across domains. Built for the NIH Common Fund Data Ecosystem, it supports translational research by linking clinical and exp…
View article: Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage Open
View article: Homo Sapiens Chromosomal Location Ontology: A Framework for Genomic Data in Biomedical Knowledge Graphs
Homo Sapiens Chromosomal Location Ontology: A Framework for Genomic Data in Biomedical Knowledge Graphs Open
The Homo sapiens Chromosomal Location Ontology (HSCLO) is designed to facilitate the integration of human genomic features into biomedical knowledge graphs from releases GRCh37 and GRCh38 at multiple resolutions. HSCLO comprises two distin…
View article: Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data
Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data Open
View article: An open source knowledge graph ecosystem for the life sciences
An open source knowledge graph ecosystem for the life sciences Open
View article: Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage
Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage Open
The Human BioMolecular Atlas Program (HuBMAP) aims to construct a reference 3D structural, cellular, and molecular atlas of the healthy adult human body. The HuBMAP Data Portal ( https://portal.hubmapconsortium.org ) serves experimental da…
View article: Organizational Breast Cancer Data Mart: A Solution for Assessing Outcomes of Imaging and Treatment
Organizational Breast Cancer Data Mart: A Solution for Assessing Outcomes of Imaging and Treatment Open
PURPOSE In the United States, a comprehensive national breast cancer registry (CR) does not exist. Thus, care and coverage decisions are based on data from population subsets, other countries, or models. We report a prototype real-world re…
View article: Association between SARS-CoV-2 infection and select symptoms and conditions 31 to 150 days after testing among children and adults
Association between SARS-CoV-2 infection and select symptoms and conditions 31 to 150 days after testing among children and adults Open
Background An increasing number of studies have described new and persistent symptoms and conditions as potential post-acute sequelae of SARS-CoV-2 infection (PASC). However, it remains unclear whether certain symptoms or conditions occur …
View article: Presentation Acuity and Surgical Outcomes for Patients With Health Insurance Living in Highly Deprived Neighborhoods
Presentation Acuity and Surgical Outcomes for Patients With Health Insurance Living in Highly Deprived Neighborhoods Open
Importance Insurance coverage expansion has been proposed as a solution to improving health disparities, but insurance expansion alone may be insufficient to alleviate care access barriers. Objective To assess the association of Area Depri…
View article: Association Between Hypertension and Diabetes Control and COVID‐19 Severity: National Patient‐Centered Clinical Research Network, United States, March 2020 to February 2022
Association Between Hypertension and Diabetes Control and COVID‐19 Severity: National Patient‐Centered Clinical Research Network, United States, March 2020 to February 2022 Open
Background Hypertension and diabetes are associated with increased COVID‐19 severity. The association between level of control of these conditions and COVID‐19 severity is less well understood. Methods and Results This retrospective cohort…
View article: REDCap and the National Mesothelioma Virtual Bank—a scalable and sustainable model for rare disease biorepositories
REDCap and the National Mesothelioma Virtual Bank—a scalable and sustainable model for rare disease biorepositories Open
Objective Rare disease research requires data sharing networks to power translational studies. We describe novel use of Research Electronic Data Capture (REDCap), a web application for managing clinical data, by the National Mesothelioma V…
View article: Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging
Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging Open
View article: A Surgical Desirability of Outcome Ranking (DOOR) Reveals Complex Relationships Between Race/Ethnicity, Insurance Type, and Neighborhood Deprivation
A Surgical Desirability of Outcome Ranking (DOOR) Reveals Complex Relationships Between Race/Ethnicity, Insurance Type, and Neighborhood Deprivation Open
Objective: Develop an ordinal Desirability of Outcome Ranking (DOOR) for surgical outcomes to examine complex associations of Social Determinants of Health. Background: Studies focused on single or binary composite outcomes may not detect …
View article: An Open-Source Knowledge Graph Ecosystem for the Life Sciences
An Open-Source Knowledge Graph Ecosystem for the Life Sciences Open
Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challen…
View article: ReDWINE: A clinical datamart with text analytical capabilities to facilitate rehabilitation research
ReDWINE: A clinical datamart with text analytical capabilities to facilitate rehabilitation research Open
View article: Combination of antidepressants and antipsychotics as a novel treatment option for psychosis in Alzheimer's disease
Combination of antidepressants and antipsychotics as a novel treatment option for psychosis in Alzheimer's disease Open
Psychotic symptoms are reported as one of the most common complications of Alzheimer's disease (AD), in whom they are associated with more rapid deterioration and increased mortality. Empiric treatments, namely first and second‐generation …
View article: ReDWINE: A Clinical Datamart with Text Analytical Capabilities to Facilitate Rehabilitation Research
ReDWINE: A Clinical Datamart with Text Analytical Capabilities to Facilitate Rehabilitation Research Open
Rehabilitation research focuses on determining the components of a treatment intervention, the mechanism of how these components lead to recovery and rehabilitation, and ultimately the optimal intervention strategies to maximize patients' …
View article: Independent Associations of Neighborhood Deprivation and Patient-Level Social Determinants of Health With Textbook Outcomes After Inpatient Surgery
Independent Associations of Neighborhood Deprivation and Patient-Level Social Determinants of Health With Textbook Outcomes After Inpatient Surgery Open
Objective: Assess associations of social determinants of health (SDoH) using area deprivation index (ADI), race/ethnicity and insurance type with textbook outcomes (TO). Background: Individual- and contextual-level SDoH affect health outco…
View article: Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data
Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data Open
The use of biomedical knowledge graphs (BMKG) for knowledge representation and data integration has increased drastically in the past several years due to the size, diversity, and complexity of biomedical datasets and databases. Data extra…
View article: Combination of Antidepressants and Antipsychotics as A Novel Treatment Option for Psychosis in Alzheimer’s Disease
Combination of Antidepressants and Antipsychotics as A Novel Treatment Option for Psychosis in Alzheimer’s Disease Open
Background Psychotic symptoms are reported as one of the most common complications of Alzheimer’s disease (AD), affecting approximately half of AD patients, in whom they are associated with more rapid deterioration and increased mortality.…
View article: Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis
Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis Open
The AURORA US Metastasis Project was established with the goal to identify molecular features associated with metastasis. We assayed 55 females with metastatic breast cancer (51 primary cancers and 102 metastases) by RNA sequencing, tumor/…
View article: ReDWINE: A Clinical Datamart with Text Analytical Capabilities to Facilitate Rehabilitation Research
ReDWINE: A Clinical Datamart with Text Analytical Capabilities to Facilitate Rehabilitation Research Open
View article: Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis
Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis Open
The AURORA US Metastasis Project was established with the goal to identify molecular features associated with metastasis. We assayed 55 females with metastatic breast cancer (51 primary cancers and 102 metastases) by RNA sequencing, tumor/…
View article: NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health
NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health Open
View article: Tissue registration and exploration user interfaces in support of a human reference atlas
Tissue registration and exploration user interfaces in support of a human reference atlas Open
View article: Assessing the impact of privacy-preserving record linkage on record overlap and patient demographic and clinical characteristics in PCORnet®, the National Patient-Centered Clinical Research Network
Assessing the impact of privacy-preserving record linkage on record overlap and patient demographic and clinical characteristics in PCORnet®, the National Patient-Centered Clinical Research Network Open
Objective This article describes the implementation of a privacy-preserving record linkage (PPRL) solution across PCORnet®, the National Patient-Centered Clinical Research Network. Material and Methods Using a PPRL solution from Datavant, …
View article: Establishing a framework for privacy-preserving record linkage among electronic health record and administrative claims databases within PCORnet®, the National Patient-Centered Clinical Research Network
Establishing a framework for privacy-preserving record linkage among electronic health record and administrative claims databases within PCORnet®, the National Patient-Centered Clinical Research Network Open
View article: NIH SenNet Consortium: Mapping Senescent Cells in the Human Body to Understand Health and Disease
NIH SenNet Consortium: Mapping Senescent Cells in the Human Body to Understand Health and Disease Open
Cells respond to a myriad of stressors by senescing, acquiring stable growth arrest, morphologic and metabolic changes, and a senescence-associated-secretory-phenotype (SASP). The heterogeneity of senescent cells (SnCs) and their SASP is v…
View article: Establishing a Framework for Privacy-Preserving Record Linkage among Electronic Health Record and Administrative Claims Databases within PCORnet®, the National Patient-Centered Clinical Research Network
Establishing a Framework for Privacy-Preserving Record Linkage among Electronic Health Record and Administrative Claims Databases within PCORnet®, the National Patient-Centered Clinical Research Network Open
Objective: The aim of this study was to determine whether a secure, privacy-preserving record linkage (PPRL) methodology can be implemented in a scalable manner for use in a large national clinical research network.Results: We established …