Ongoing project

2+ genomes make a parTEA! This pangenome TE annotation pipeline extends EarlGrey for multi-genome comparative analysis - TobyBaril/EarlGreyParTEA

The three-dimensional architecture of genomes plays major roles in biological processes such as gene expression and DNA replication. The architecture of genomes has evolved substantially with distinct...

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Abstract. Retrotransposons are mobile, repetitive DNA sequences that are ubiquitous across eukaryotes and widely recognised as key drivers of both gene and

Helitrons are a recently identified category of transposons. This study reveals that heat stress combined with reduced DNA methylation can mobilize a Helitron family in wheat. Its mobilization is gene...

Swave is a method to call structural variants from pangenome graphs using a recurrent neural network to identify structural variant patterns, including complex structural variants.

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Abstract. Transposable elements (TEs) are found in nearly all eukaryotic genomes. Despite significant advances in the sequencing of genomes, TE resources r

BMC Genomics - Transposable elements (TEs) are major components of plant genomes, shaping genome architecture, gene regulation, and evolutionary innovation. While the Extensive de novo TE Annotator...

Transposable elements (TEs) are ubiquitous components of the genome whose mobility can be triggered by environmental stress and influenced by genotype…

Earl Grey: A fully automated TE curation and annotation pipeline - TobyBaril/EarlGrey

In this study, the authors analysed a large genomic dataset to trace how jumping genes shaped the global spread of a major wheat pathogen and reveal bursts of activity over decades that drove adaptati...

Background. Paramecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual gene...

Transposable elements (TEs) are repetitive DNA sequences that can alter their position and abundance within genomes. While TEs are known to have various impacts on genome structure and function, our u...

Long terminal repeat retrotransposons (LTR-RTs) are recognised as a significant evolutionary force capable of shaping the structure and function of the genomes in eukaryotes, including animals, plant...

Transposable elements (TEs) make up half of mammalian genomes and shape genome regulation by harboring binding sites for regulatory factors. These include binding sites for architectural proteins, such as CTCF, RAD21, and SMC3, that are involved in ...