Clément Goubert @clementgoubert@qoto.org

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

@trinsec those 'repeats' are actually repeats of transposons which are for most part selfish... So unfortunately they can't be seen as a backup of the genome, more of a parasite that sometimes may evolve as a partner.

@trinsec it's very hard to predict! But transposons can be both good and evil, so the more there are, and the more are still active (usually many have been rendered inactive, like in our genome) the more 'anything' can happen. Active transposons create change in the DNA, this is evolution! I may lead to pathologies and cancer (https://www.nature.com/articles/nrc.2017.35) but indeed, sometimes it can lead to cancer resistance! https://www.nature.com/articles/s41590-021-01027-8

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