Clément Goubert @clementgoubert@qoto.org

#introduction Hi there! My name is Clément, I am an evolutionary biologist interested in #transposons (Jumping Genes 🧬➰🧬) !

#transposons are really cool! They turn Cabernet 🍷 into Chardonnay, protect us from viruses 👾and also give their nice smell to roses🌹!

I really like to pretend I'm doing bioinformatics by playing Lego with software and making pipelines and methods for #transposon analysis and annotation. Here are some of them:
- #dnaPipeTE : find and quantity transposons in short-reads data https://github.com/clemgoub/dnaPipeTE
- #GraffiTE : detect and genotype polymorphic #Transposon insertions using #pangenome approaches https://github.com/cgroza/GraffiTE
- #TE+Aid : a little tool to help manual curation of #Transposons libraries https://github.com/clemgoub/TE-Aid

I am also a contributor to the #TEhub a community centered ressource to learn and share how to analyze #Transposons -- find out more here https://tehub.org -- YouTube: https://youtube.com/@tehub

Always excited to talk about anything, please reach out if you are interested in #Transposons!

When I don't do science, I am passionate about music (I'm into DIY synthetizers these days), vinyl records, photography, skiing, video games and ah yes I am quite passionate about politics too!

Cheers!

Insights into mammalian TE diversity through the curation of 248 genome assemblies https://www.science.org/doi/10.1126/science.abn1430#.ZFEdDQyAPFg.twitter

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning https://www.science.org/doi/10.1126/science.abm7993#.ZFEc8vGDQGE.twitter

I ♥️ 🛏️⚒️ !
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RT @aaronquinlan
It's been a while, but version 2.31.0 of #bedtools is out!

This includes a new "summary" command for basic stats, sanity checks, and QC on interval files.

It also supports gzipped FASTA files. Thanks to @brent_p, @38, @jomarnz for their contributions. https://bedtools.readthedocs.io/en/latest/content/tools/summary.html
https://twitter.com/aaronquinlan/status/1651954456714694656

https://rdcu.be/c7aKM

What the hell!!! 🤯
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RT @CedricFeschotte
This cutie is the Antarctic krill. Its genome is 48 Gb, 15x the human genome! 92% repeats! CMC/CACTA elements, an enigmatic and relatively rare group of DNA transposons in other animals, alone account for 42%!! Why these and why in krill?…🤔😯🤯
https://www.cell.com/cell/fulltext/S0092-8674(23)00107-1
https://twitter.com/CedricFeschotte/status/1631760070596755462

Evolution of the germline mutation rate across vertebrates https://www.nature.com/articles/s41586-023-05752-y#citeas

Congrats @OggenfussUrsula et al!
#PLOSPathogens: Recent transposable element bursts are associated with the proximity to genes in a fungal pla ... https://dx.plos.org/10.1371/journal.ppat.1011130

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009935

Stop everything and read this 👇(especially if "gene enrichment analysis" rings a 🔔)
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RT @mdziemann
I want to talk today about a methodological issue in #genomics research that has been around a long time but is still a major problem.
The reason is that today I reviewed another manuscript that has this exact problem.
https://twitter.com/mdziemann/status/1626407797939384320

🌿👾 #plant #transposon friends: I'm looking for a good dataset to benchmark a program detecting insertion polymorphisms. Ideally the samples would have different type of raw sequencing (long+short reads), and a trusted list of known insertion polymorphisms. Open to collab! 🤝

Reproducible evaluation of short-read transposable element detectors and species-wide data mining of insertion patterns in yeast https://www.biorxiv.org/content/10.1101/2023.02.13.528343v1

Highly recommended!!!
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RT @guilbourque
Come work with us this summer! https://twitter.com/c3genomics/status/1622626415362310144
https://twitter.com/guilbourque/status/1622646034030596097