Tobias Baril

Earl Grey ParTEA annotates transposable elements across multiple genomes, revealing shared and private TE families and improving annotation consistency.

This study compares 3D genome architectures across 55 fungal species, identifying novel configurations and challenging existing classifications.

The paper identifies transposable elements, particularly R1-like LINE retrotransposons, as contributors to chromosomal fusions and fissions in butterflies, but also finds gene-related factors play a role.

MycoMobilome is a non-redundant fungal TE consensus sequence database curated from 4,309 genomes, providing standardized naming and metadata for TE classification and curation.

The paper analyzes TE dynamics in Zymoseptoria tritici genomes to show how historical TE mobilization waves contribute to adaptive variation in a fungal pathogen.

This study integrates genomic, transcriptomic, and morphological data from the small-spotted catshark to uncover molecular mechanisms underlying sensory organ evolution in jawed vertebrates.

This study identifies genomic signatures of domestication in a fungus farmed by leafcutter ants using long-read sequencing, revealing gene expansions and losses linked to cultivation adaptation.

Earl Grey improves TE annotation by addressing fragmentation and poor end capture, outperforming existing methods in benchmarking and providing user-friendly outputs.

The paper examines TE accumulation at xenobiotic gene family loci across 20 aphid genomes, finding significant TE enrichment at these genes compared to others.

The paper presents a chromosome-scale genome of the Mongolian gerbil with sequenced centromeres, revealing new insights into centromere structure and heterochromatin distribution.

The paper annotates and analyzes transposable elements (TEs) in the monarch butterfly genome, finding reduced TE content compared to related species and identifying novel TE families and their associations with immune genes.

This study analyzes the evolutionary patterns of DDE transposons across eukaryotic hosts, finding host conservation, horizontal transfer, and trade-offs in host adaptation.

The paper presents a chromosomal-level genome assembly for Aquilaria sinensis and identifies genes involved in sesquiterpenoid and agarwood production.