Clément Goubert

Please spread the word:

We invite applications to a two-week Computational Biology workshop in Singapore, June 14-27.

This NSF-funded workshop brings together 16-20 US grad students with international peers.
Apply by March 21: compbioasia.net
🧵 Details below:

ColabCuraTE: an easy-to-use, web-based pipeline for the manual curation of transposable elements - Mobile DNA Background Transposable elements (TEs) are widespread mobile DNA sequences that shape genome structure, function, and evolution. Although automated tools exist for the de novo identification and class...

WOW! Very promising new tool to facilitate collaborative manual curation of TEs link.springer.com/article/10.1...

Transposable elements drive much of naturally occurring genetic lethality in Drosophila melanogaster Recessive lethal mutations are widespread across studied species, with estimates suggesting that each individual carries at least one. Numerous lethal alleles persist in wild populations at higher fre...

www.biorxiv.org/content/10.1...

Long-term monitoring of a North American cheese cave reveals mechanisms and consequences of fungal adaptation Using a unique longitudinal sampling approach, Louw et al. demonstrate how a cheese-associated Penicillium population has adapted in an artisan cheese production facility in Vermont, USA. Adaptation i...

Yummy! www.cell.com/current-biol...

Rapid emergence of non-autonomous elements may stop P-element invasions in the absence of a piRNA-based host defence Author summary Transposable elements (TEs) are short, self-replicating DNA sequences found in nearly all genomes. While they can be harmful to their hosts, many organisms have evolved defence systems,...

Rapid emergence of non-autonomous elements may stop P-element invasions in the absence of a piRNA-based host defence journals.plos.org/plosgenetics...

A Concise Guide for the Characterization and Curation of Transposable Elements in Insect Genomes Transposable elements (TEs) can play a huge role in shaping the structure and evolution of genes and genomes, but it can be difficult, especially in non-model organisms, to confidently characterize th...

A Concise Guide for the Characterization and Curation of Transposable Elements in Insect Genomes -- by the excellent @valentinapeona.bsky.social link.springer.com/protocol/10....

Adaptive P-element insertions in a long non-coding RNA are associated with unique silencing properties Transposable elements are genetic parasites whose mobilization throughout the genome is a major source of deleterious mutations. However, some TE insertions are beneficial because they improve host fi...

Adaptive P-element insertions in a long non-coding RNA are associated with unique silencing properties

www.biorxiv.org/content/10.1...

A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage A phylogenetic approach reveals cryptic LTR subfamilies and functional insights at nucleotide resolution in primates.

How the complex issue of delineating #Transposons families plays out in the interpretation of epigenetic experiments. Congrats Xun Chen and @guilbourque.bsky.social for leading this work, and thank you for having me on this! www.science.org/doi/10.1126/... #TEsky

No evidence of transposable element bursts in the Galápagos Scalesia adaptive radiation despite hybridization, diversification and ecological niche shifts - Mobile DNA Transposable elements (TEs) have been hypothesized to play a pivotal role in driving diversification by facilitating the emergence of novel phenotypes and the accumulation of divergence between specie...

Challenging the TE burst hypothesis in the adaptive radiation of Galápagos Asteraceae trees (Scalesia) with @naturalselection.bsky.social and team!
mobilednajournal.biomedcentral.com/articles/10....

GitHub - zeqianli/tgv: Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion. Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion. - zeqianli/tgv

Waho this is impressive: github.com/zeqianli/tgv

Genomic and genetic insights into Mendel’s pea genes - Nature Characterization of the genetic architecture underlying the 7 pairs of contrasting traits studied by Mendel and the over 70 additional agronomic traits in pea (Pisum sativum) reveals their m...

New genomic & genetic insights into Mendel’s pea genes, including previously uncharacterised alleles

159 years after Mendel published his work, this is a real delight (especially for a geneticist)

🧪
@nature.com

www.nature.com/articles/s41...

Manual validation finds only ultra-long long-read sequencing enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin www.biorxiv.org/content/10.1...

🧬🖥️
Thanks to Evangelos Karatzas at @ebi.embl.org, our _nail_ software for fast and sensitive protein sequence search
is now available as an @nf-co.re module (nf-co.re/modules/nail...)

(crates.io/crates/nail, github.com/TravisWheele...)

Thanks Evangelos!

Celebrating DNA Day with transposable elements Each year on DNA Day, we celebrate the DNA double helix structure and the Human Genome Project's completion. Here we dive into a fascinating genomic component: transposable elements. Once seen as mere...

go.nature.com/3S27sLp

Column | Delete your DNA from 23andMe right now The genetic information company declared bankruptcy on Sunday, and California’s attorney general has issued a privacy “consumer alert.”

The writing’s been on the wall for a while, and in case anyone was unaware: YOUR GENOMIC DATA IS THE MOST VALUABLE ASSET THEY HAVE LEFT.

Delete your data. Make sure you opt-out of any opt-outable options.

Tell your friends and family - you know that technophobe cousin missed the memo. 🧪

Polymorphic transposable elements contribute to variation in recombination landscapes (drosohila 🪰) www.pnas.org/doi/full/10.... #TEsky

Rapid emergence of hyperparasitic elements may stop P-element invasions in the absence of a piRNA-based host defence Transposable element (TE) invasions pose risks to both the TE and the host. All copies of a TE may be lost via genetic drift, or host populations may suffer fitness declines, potentially leading to ex...

Rapid emergence of hyperparasitic elements may stop P-element invasions in the absence of a piRNA-based host defence www.biorxiv.org/content/10.1...

#Transposons are just the best!

Here, we demonstrate that Starships, a newly discovered group of cargo-mobilizing transposable elements, are active vectors of horizontally transferred DNA among eukaryotic species.

Worth mentioning that hmm models for D. melanogaster elements in DFAM are now seeded from additional genomes (beyond the dm6 reference), including 13 genomes from Rech. et al., 2022 (www.nature.com/articles/s41...)

P element entry: dfam.org/family/DF003...

Following new user submissions many previously DFAM fly model of TE families were revisited/updated, absent elements (such as P) were added, and when applicable, aliases between DFAM/Repbase/Flybase/BGDP and other publications are reported!

DFAM (database of transposable elements) 3.9 is out! A lot of cool new stuff and a special update for Drosophila melanogaster... 1/2 #Transposon #DFAM

Cool stuff from the Trono lab, as usual! Zinc-finger proteins with a co-opted capsid domain
anchor nucleosomes over transposon sequences www.biorxiv.org/content/10.1...

LOCATE: using Long-read to Characterize All Transposable Elements Transposons constitute ~45% of the human genome, driving gene evolution and contributing to disease, but their repetitive nature complicates the identification of new insertions. We present LOCATE (Lo...

LOCATE: using Long-read to Characterize All Transposable Elements
doi.org/10.1101/2025...

Mapping-based Genome Size Estimation
doi.org/10.1101/607390

#Genomics #Bioinformatics #OpenScience

Do you want to annotate your #pangenome graph and its embedded genome ? Then GrAnnoT is for you !
🖥️🧬 🧪

In the present paper, our PhD student Nina Marthe developed a Python tool, a user friendly one, that allows to
1/5

www.biorxiv.org/content/10.1...

Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells - Nature Genetics The N6-methyladenosine reader YTHDC2 recruits TET1 to remove 5-methylcytosine from LTR7/HERV-H loci in human embryonic stem cells. The YTHDC2/LTR7 pathway inhibits neural fate commitment.

RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate
www.nature.com/articles/s41...

Pannagram: unbiased pangenome alignment and the Mobilome calling Pannagram is a toolkit for unbiased pangenome alignment and Mobilome detection based on full-genome assemblies. It consists of two components: a command-line interface for performing the multiple geno...

Very promising approach to characterize the mobilome in pangenomes from ! I wonder how this compares/complements to Pantera (@piosierra.bsky.social) and GraffiTE www.biorxiv.org/content/10.1... #TESky #SV #Pangenomes

Exploring the role of transposable elements to sex gap in longevity in Drosophila species In Drosophila, like in many other animal species, females tend to live longer than males, a phenomenon known as sex gap in longevity (SGL). One of the possible causes underlying this phenomenon could ...

www.biorxiv.org/content/10.1... #TEsky

Highly recommend!