David Thybert

The paper studies gene regulatory evolution in salmonids after autotetraploidization, finding that it is influenced by developmental and tissue-specific factors, with constraints at advanced embryogenesis.

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

This study uses long-read sequencing to analyze 88 Lepidoptera genomes, identifying genomic signatures linked to conservation concerns like low heterozygosity and high inbreeding.

The paper describes the Ensembl COVID-19 resource, which integrates SARS-CoV-2 genomic data and variant annotations to support research on virus variants and their impact on therapeutics and vaccines.

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 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 identifies strain-specific genomic regions associated with metabolic syndrome in rats by integrating genomic variation and regulatory conservation.

The paper investigates cis and trans mechanisms influencing transcription factor binding and gene expression evolution in mice by analyzing allele-specific occupancy in crosses of two inbred strains.

The paper reconstructs the evolutionary history of a segmental duplication in mice, showing gene conversion, structural variation, and meiotic drive associated with the duplication.