Clément Goubert

GraffiTE v1.1 is a Nextflow pipeline that genotypes structural variants, annotates polymorphic mobile elements, and maps epigenetic data to transposable elements using pangenome graphs, revealing hypomethylated elements and age-related demethylation.

The paper updates Drosophila melanogaster transposable element (TE) libraries in Dfam 4.0 by integrating new data, resolving redundancies, and improving consensus sequences.

This study uses long-read sequencing to map transposable element variation in human brain tissue, revealing regulatory and epigenetic effects across cell types and ancestries.

The paper identifies 1296 human genes with dual-coding regions (DCRs) and shows their conservation in mice, tissue-specific expression, and functional implications in gene regulation.

The paper directly identifies de novo mobile element insertions in human sperm using long-read sequencing and finds age-related increases in retrotransposition rates.

The paper identifies and quantifies transposable elements in chromosomal inversion breakpoints in Atlantic cod, showing their role in driving ectopic recombination and chromosomal reorganization.

The paper examines TE accumulation in Scalesia species and finds no significant variation despite hybridization and niche shifts, challenging the role of TEs in diversification.

GraffiTE analyzes transposable element insertion polymorphisms using genome-graphs, achieving high precision and recall across multiple species and sequencing technologies.

This study uses long-read RNA-seq to identify and quantify transposable element transcripts at the copy level in Drosophila germline tissues, revealing differences in their transcriptional landscape between testes and ovaries.

The paper refines the annotation of endogenous retrovirus LTRs in primates by identifying new subfamilies and their regulatory roles through phylogenetic analysis and functional validation.

The paper identifies genomic features that enable SVA transposons to function as cis-regulatory elements in human pluripotent stem cells, showing their impact on gene expression.

The paper presents the genome of Sitophilus oryzae, revealing high transposable element content and host-symbiont metabolic interactions.

With a new structural LTR module, RepeatModeler2 recovers 2.9 to 4.7 times more curated TE families near-perfectly than RepeatModeler 1.0.11 in fruit fly, zebrafish, and rice.

TypeTE improves Alu insertion genotype accuracy from 83% to 92% in the 1000 Genomes dataset by reassembling and re-mapping sequencing data.

The paper identifies TE-eQTL in lymphoblastoid and stem cell lines, showing unfixed TEs influence gene expression and regulatory elements across cell types.

The paper identifies 92 outlier transposable element insertion loci showing differentiation between temperate and tropical Aedes albopictus populations, suggesting adaptive evolution in temperate environments.