Thomas Keane

The paper shows that satellite DNA composition affects PRC1-mediated heterochromatin formation and mitotic spindle interactions in early embryos.

The paper presents a mouse pangenome with 17 strains, resolving structural complexity and improving RNA-Seq analysis by identifying non-reference genes and VNTR polymorphisms.

The paper analyzes young KRAB-zinc finger gene clusters in mice, showing ERVs drive genetic heterogeneity through recombination and duplication mechanisms.

This study identifies molecular adaptations in Onychomys species that confer toxin resistance through genome analysis and positive selection detection.

The paper presents a chromosome-level genome assembly of the Hispid cotton rat, annotating 24,878 protein-coding genes and identifying genetic innovations.

The paper presents T2T mouse genomes for C57BL/6J and CAST/EiJ, revealing structural diversity in telomeres, centromeres, and key loci like PAR and KZFPs.

The GWAS Catalog now holds 625,113 curated SNP-trait associations from 6,921 publications plus >85K summary statistics datasets, with a new GWAS-SSF submission standard and GRCh38 harmonisation.

The paper identifies IFI207 as a rapidly evolving protein that controls retroviral replication through the STING pathway, highlighting its role in host-pathogen co-evolution.

The paper describes a unified data infrastructure for rare disease research, enabling collaborative analysis of multi-omics data across institutions.

The paper identifies and characterizes spontaneous mutations causing deafness in mice from a targeted knockout program, showing these mutations are a common side effect of intensive breeding.

The paper introduces refget, an API for standardized access to reference sequences using identifiers derived from the sequences themselves.

HTSlib provides a C library for efficient programmatic access to high-throughput sequencing data formats, with performance improvements and new features.

The paper assesses the value and sustainability of ELIXIR Core Data Resources, showing their critical role in preserving biological data and highlighting funding challenges.

The paper compares germline mutation rates and spectra between mice and humans using whole genome sequencing of multi-sibling pedigrees, finding significant differences including a reduced mutation rate in human spermatogonial stem cells.

The paper introduces Ragout, a reference-assisted assembly tool that improves chromosome assembly for large and complex genomes, achieving high accuracy with less than 5% unlocalized sequence.

The paper annotates pseudogenes in the mouse genome and strains, finding similar overall characteristics to humans but distinct age distributions and transcriptional patterns.

The paper introduces CAT, a toolkit for simultaneous clade and personal genome annotation, demonstrating its ability to discover novel genes and improve cross-species RNA expression analysis.

The paper compares genome assemblies of Mus caroli and Mus pahari with Mus musculus and Rattus norvegicus to reveal lineage-specific evolutionary mechanisms, particularly repeat-associated processes.

The paper presents full-length de novo genome assemblies for 16 inbred mouse strains, identifying strain-specific haplotypes and novel functional loci, including a large unannotated gene with potential developmental roles.

The paper deep sequences 13 inbred mouse strains to identify SNPs, indels, and private mutations linked to disease phenotypes.

This paper introduces a population BWT data structure to efficiently store and analyze sequencing reads from thousands of human genomes, enabling variant calling and viral detection.