Alan E Murphy

Challenging selective vulnerability in Parkinson's disease: a systematic review and meta-analysis

This paper challenges the assumption of selective vulnerability in Parkinson's disease by analyzing post-mortem data and finding substantial neuronal loss beyond dopaminergic and pigmented populations.

orthogene: a Bioconductor package to easily map genes within and across hundreds of species

orthogene simplifies gene mapping across species and identifier systems, providing a unified framework for reproducible and scalable workflows.

Genome-wide analyses of quantitative generalised anxiety symptom severity

This study conducts a genome-wide association analysis of generalised anxiety symptom severity, identifying 80 significant variants and showing genetic correlations with other mental and physical health traits.

Genome-wide meta-analysis of panic attacks and disorder identifies genetic risk factors and implicates multiple body systems in panic and other psychiatric disorders

This study identifies genetic risk factors for panic attacks and disorder through genome-wide meta-analysis and links them to multiple body systems and neuronal functions.

Predicting gene expression from histone marks using chromatin deep learning models depends on histone mark function, regulatory distance and cellular states

This study shows that histone mark function, genomic distance, and cellular states collectively influence gene expression predictions using deep learning models, with no single mark consistently predicting expression across contexts.

Predicting cell type-specific epigenomic profiles accounting for distal genetic effects

This paper introduces a deep learning model, Enformer Celltyping, that predicts cell type-agnostic epigenomic profiles and outperforms existing methods, while highlighting limitations in genetic variant effect predictions.

Avoiding false discoveries: Revisiting an Alzheimer's disease snRNA-Seq dataset

The paper reanalyzes an Alzheimer's disease snRNA-Seq dataset using improved methods, finding 549 times fewer differentially expressed genes at an FDR of 0.05.

EpiCompare: R package for the comparison and quality control of epigenomic peak files

EpiCompare is an R package that compares and quality controls epigenomic peak files, providing an interactive HTML report with minimal user input.

A balanced measure shows superior performance of pseudobulk methods over mixed models and pseudoreplication approaches in single-cell RNA-sequencing analysis

This paper reanalyzes differential expression methods in scRNA-seq using corrected simulations, finding pseudobulk methods outperform mixed models and pseudoreplication approaches.

Transcriptomic analyses reveal neuronal specificity of Leigh syndrome associated genes

This study identifies the cellular specificity of Leigh syndrome genes using transcriptomic analyses and finds enrichment in neuronal cells and pre-synaptic structures.

MungeSumstats: A Bioconductor package for the standardisation and quality control of many GWAS summary statistics

MungeSumstats standardises and quality controls GWAS summary statistics, enabling secondary analysis and meta-analysis by converting them into a common format.

scFlow: A Scalable and Reproducible Analysis Pipeline for Single-Cell RNA Sequencing Data

scFlow provides a scalable, reproducible pipeline for analyzing single-cell RNA-seq data, demonstrating its utility with public datasets and extensibility as an open-source tool.