Owen J. L. Rackham

The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.

PathPinpointR predicts scRNA-seq sample positions along reference trajectories using switching-gene events to assign pseudo-time values.

The paper expands and refines a reference catalog of human non-canonical open reading frames (ncORFs) by incorporating more datasets and introducing a translation signature score framework to prioritize high-quality ncORFs.

The paper shows that loss of chromosome Y in immune cells of aging men affects cell fate and X-chromosome inactivation patterns.

ShinyCell2 provides an interactive R package for visualizing spatial, peak-based, and multi-omic single-cell data with advanced features and ease of use.

The paper examines 5' untranslated regions (UTRs) to show their role in translational regulation of dosage-sensitive genes and introduces a web tool for analyzing 5UTR composition.

This study shows that PKN2 deficiency causes prenatal congenital cardiomyopathy and impairs angiotensin II-induced cardiac hypertrophy in adult mice.

CLIPreg integrates RNA, Ribo, and CLIP-seq data to construct translational regulatory networks mediated by RNA-binding proteins.

ShinyCell converts single-cell RNA sequencing data into interactive, shareable visualizations for easier exploration and sharing.

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.

The paper systematically studies uORF variants in 15,708 genomes, showing they are under strong negative selection and contribute to disease.

GeneSwitches identifies the order of gene-expression and functional events along pseudo-time trajectories in single-cell experiments.

The paper introduces Xtail, a method to identify differentially translated genes by analyzing Ribo-seq data while accounting for mRNA abundance variations.

The paper identifies translational regulators of fibrogenic genes in human cardiac fibroblasts and shows their role in cardiac fibrosis through ribosome profiling and RNA-binding protein analysis.

The paper identifies drugs for leukaemia differentiation therapy using network pharmacology, finding that dimaprit and mebendazole enhance ATRA-mediated differentiation in leukaemia cells.

This study identifies that amyloid plaque phagocytosis through Hif1α controls microglial phenotypes in Alzheimer’s disease in both mice and humans.

This paper creates a single-cell brain atlas of Alzheimer’s disease, identifying cell-type specific gene expression patterns and regulatory networks associated with disease.

ABBA detects differentially methylated regions in WGBS data, identifies disease-associated methylation changes, and proposes a mechanism for glomerulonephritis via Ifitm3 promoter hypermethylation.