John Peter Quinn

This study uses long-read sequencing to map transposable element variation in human brain tissue, revealing regulatory and epigenetic effects across cell types and ancestries.

This study benchmarks TE detection tools on long-read data, showing significant variation in performance and highlighting tool-specific strengths and limitations.

The paper introduces the NeuroBooster Array, a genome-wide genotyping platform designed to study neurological disorders across diverse populations by capturing genetic variation and enabling imputation of disease-related variants.

The paper evaluates bioinformatics tools for detecting human endogenous retroviral insertions in short-read genome sequencing data, finding performance variability across datasets and recommending a consensus approach.

This study identifies 3,154 high-confidence structural variants in Parkinson's disease using short-read sequencing and validates some with long-read data, highlighting limitations of short-read methods.

The paper investigates how mitochondrial function affects ALS severity but not risk, identifying specific genetic and expression factors linked to disease progression.

RetroSnake detects HERVs in NGS data using an end-to-end pipeline validated by wet-lab experiments, producing annotated insertions in an interactive HTML file.

This study analyzes intronic RNA-Seq data from Parkinson's Disease patients over time, revealing significant changes in nascent transcription specific to the disease.

The paper identifies human-lineage-specific genomic elements, called CNCRs, and shows their enrichment in neurological disease genes and APOE intron-3 retention transcripts in Alzheimer's disease.

This study identifies cell-type-specific expression of dystonia-associated genes and links them to shared genetic and biological mechanisms with psychiatric disorders.

The paper identifies disease-relevant regulatory loci in human basal ganglia using genomic and transcriptomic data from 117 brains, highlighting splicing eQTLs and ASE analyses as sources of cell-specific regulatory information.

This study connects Parkinson’s disease heritability to cell-type-specific gene regulation, finding enrichment in lysosomal genes in astrocytic and microglial subtypes rather than specific cell types or brain regions.

The paper examines how maternal depression affects child behavior, finding sex-dependent mediation by NR3C1 methylation in a longitudinal study from pregnancy to age 5.