Graham M. Hughes

The paper introduces a metric called DLR to identify population bottlenecks by analyzing olfactory receptor gene evolution across multiple mammalian species.

The paper identifies OR14 gene family expansion in fossorial and insectivorous mammals, linking it to ecological adaptation and convergent evolution.

GENE-FAM is an automated pipeline for gene family mining applied to MADS-box genes in Cannabis sativa, identifying conserved and divergent subfamilies across species.

The paper describes the European Reference Genome Atlas (ERGA) pilot project, which tests a decentralized model for producing high-quality reference genomes across 98 European species.

The paper identifies proteins and regulatory elements associated with vocal learning by analyzing bat neural activity and epigenomic data.

TOGA integrates gene annotation and orthology inference across hundreds of genomes, improving ortholog detection and creating large comparative gene resources.

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

The paper curates TE content in 248 mammalian genomes, finding trends in recent TE accumulation and associations with dietary habits.

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

The paper uses evolutionary constraint scores to identify functional genomic regions and finds they are enriched for variants associated with common diseases.

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

The paper generates bat induced pluripotent stem cells and finds they contain endogenous viral sequences, suggesting a deep entanglement between bats and viruses.

The paper identifies a new nematode species from Siberian permafrost and shows it shares cryptobiosis mechanisms with C. elegans dauer larvae.

The paper predicts the broad host range of SARS-CoV-2 by analyzing ACE2 conservation across vertebrates and identifying high-risk species.

The paper generates six reference-quality bat genomes, identifies genomic adaptations related to echolocation, immunity, and viral tolerance, and reveals regulatory elements contributing to bat traits.