Joel T. Dudley

A public resource of single cell transcriptomes and multiscale networks from persons with and without Alzheimer's disease

The paper provides a public resource of single nucleus RNA sequencing data and multiscale networks from Alzheimer's disease and non-disease individuals, linking genetic variants to molecular features and revealing novel disease biology.

Orally active mGluR2/3 metabotropic antagonist pro-drug mimics the beneficial effects of physical exercise on neurogenesis, behavior, and exercise-related molecular pathways in an Alzheimer's disease mouse model

This study shows that BCI-838, a mGluR2/3 antagonist, mimics exercise's benefits on neurogenesis, behavior, and molecular pathways in an Alzheimer's mouse model.

Saracatinib, a Selective Src Kinase Inhibitor, Blocks Fibrotic Responses in In Vitro, In Vivo and Ex Vivo Models of Pulmonary Fibrosis

This study identifies saracatinib as a potential anti-fibrotic drug effective in multiple models of pulmonary fibrosis, showing equal or superior efficacy compared to existing treatments.

Deep Learning-Based Brain Transcriptomic Signatures Associated with the Neuropathological and Clinical Severity of Alzheimer's Disease

The paper uses deep learning to analyze RNA-seq data from Alzheimer's disease brain donors, identifying transcriptomic signatures linked to neuropathology and clinical severity.

Pleiotropic Variability Score: A Genome Interpretation Metric to Quantify Phenomic Associations of Genomic Variants

The paper introduces the Pleiotropic Variability Score (PVS) to quantify the phenomic associations of genomic variants using semantic reasoning and validates it with electronic health records.

Further evidence of increased human Herpesvirus in Alzheimer's disease

The paper investigates the association between herpesviruses and Alzheimer's disease using multiomic data and simulations, finding increased HHV-6A abundance in AD brains.

Early life stress alters transcriptomic patterning across reward circuitry in male and female mice

This study shows that early life stress alters transcriptomic patterns in reward circuitry of male and female mice, increasing sensitivity to adult stress.

Identification and genetic validation of drug-comorbidity interactions in type 2 diabetes using data-driven disease trajectory analysis

This study identifies drug-comorbidity interactions in T2D using EMR data and genetic validation, finding protective effects of certain drugs against comorbidities.

Integrative transcriptome imputation reveals tissue-specific and shared biological mechanisms mediating susceptibility to complex traits

This study integrates transcriptome data with genetic variation to identify gene-trait associations and uncover biological mechanisms underlying complex traits in humans and mice.

Designing robust N-of-1 studies for precision medicine

The paper develops a stochastic time series model to optimize N-of-1 study designs for precision medicine, showing how design parameters affect treatment efficacy detection.

Multiscale analysis of acne connects molecular subnetworks with disease status

This study performs a multi-omic analysis of acne patients and non-acne individuals to identify molecular subnetworks associated with disease status.

fragilityindex: An R Package for Statistical Fragility Estimates in Biomedicine

The paper introduces an R package for calculating fragility index in clinical trials and extends the method to survival analysis and logistic regression.

Meta-analysis of Cytometry Data Reveals Racial Differences in Immune Cells

MetaCyto enables meta-analysis of flow and mass cytometry data, revealing racial differences in immune cell populations across 2926 samples.

Prioritizing Small Molecule as Candidates for Drug Repositioning using Machine Learning

This study uses machine learning to prioritize small molecules for drug repositioning by analyzing chemical properties and leveraging public drug databases.

Rapid Therapeutic Recommendations in the Context of a Global Public Health Crisis using Translational Bioinformatics Approaches: A proof-of-concept study using Nipah Virus Infection

This study uses computational drug repositioning and gene expression analysis to identify potential therapies for Nipah Virus infection.

Learning and Mapping Lyme Disease Patient Trajectories from Electronic Medical Data for Stratification of Disease Risk and Therapeutic Response

The paper uses machine learning on electronic medical records to identify comorbidities and medications associated with Lyme disease and its treatment outcomes.

Estimate of disease heritability using 7.4 million familial relationships inferred from electronic health records

The paper uses next-of-kin data from electronic health records to estimate heritability for 500 disease phenotypes, finding results consistent with existing literature.