Clément Goubert
🤘🧬 Transposable
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Elements 🧬🤘
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Assistant Research Professor @wheelerlab.org
University of Arizona
- WOW! Very promising new tool to facilitate collaborative manual curation of TEs link.springer.com/article/10.1...
- 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 journals.plos.org/plosgenetics...
- 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 www.biorxiv.org/content/10.1...
- 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
- 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....
- Waho this is impressive: github.com/zeqianli/tgv
- 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...
- 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 www.biorxiv.org/content/10.1...
- #Transposons are just the best!
- 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
- Today we released Dfam 3.9 with many new community submissions and the result of a thorough curation and update of the Drosophila Melanogaster library. www.dfam.org (release notes: www.dfam.org/releases/Dfa...)
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View full threadP element entry: dfam.org/family/DF003...
- 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...)
- 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!
- 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...
- RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate www.nature.com/articles/s41...
- 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
- Highly recommend!
- We are recruiting a Bioinformatics PostDoctoral Research to join our team @ibb-botanic.bsky.social @csic.es. Reach out if you have questions! #transposons #Drosophila bioinformaticsbarcelona.eu/job/bioinfor...
- The great @johannconfais.bsky.social on a reference-free approach (panREPET) to annotate #Transposons in #pangenomes 🧬
- #PAG32 I'd bet that every genome studied at PAG has a least 1 #Transposon, if not thousands! Find us on Sunday for an exciting session on #mobileDNA!
- #PAG32 About to discuss #Transposons in the grain weevil genomes using pangenomic tools! Weevilomics workshop, Pacific room F!
- Let me know If Google does that!
- Posting this to remember the day I have more followers than @cedricfeschotte.bsky.social 🤣🤣🤣
- I use this example in all my intros to TEs!
- It is so much fun to add new discoveries (made this year!) to my undergraduate Genetics lectures. Yesterday's topic was mutations and DNA repair, and my students loved learning about the cool phenotypes that transposons can cause. +link to Bo Xia in @itaiyanai.bsky.social's Night Science podcast.
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- all my*
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- Should I add "legendary creature" to my bio? 🐸🤣
- Ahahah excellent! Is this card any good? At least the art is neat!
- If you like #Transposons 👾 check out this feed and tag your posts with #TEsky! Thanks @tobybarilbio.bsky.social 🤗 bsky.app/profile/did:...
- Come to Tucson!
- I am recruiting graduate students this year to join my lab in Tucson! If you are interested in studying the evolution of plant diversity, polypoidy, and chromosomal evolution, please reach out about opportunities in my lab! Details about applying to EEB and our new CAMBIUM NRT in the thread below! 🧪
- Welcome to Bsky everybody! Remember: TE RULES!!!
- Genomics, evolution, and more starter pack! Help build community with this starter pack. This list is currently incomplete. Want to be included? Reply and I will remedy that! go.bsky.app/JjvzkWUat://did:plc:yn4knmhptpotqk6hjdcxxfii/app.bsky.graph.starterpack/3lammzgqnp52c
- Awesome!
- 🎉 Our #GraffiTE paper is out!!! t.co/TmoSL3WQ1P If you are interested in #Transposon insertion polymorphism, this is for you!
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- That's real good to know Artem! Be sure I'll reach out if need be! 😊
- But you are right, DFAM received a lot of new data but we are terribly underfunded, and it's hard to update regularly. There is no full time curator, and only a couple of person (including me when I can) trying to push everything forward while working on software maintenance and improvement.
- But our motivation is intact and we know we have the support of the community! Don't hesitate to reach out if you have specific questions!
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- On dfam.org, go to "Browse" and fill "Mus" in the taxon box. Click "ancestor" and "descendant" to get all the families. You can then download (at the bottom) in the format you like (HMM profile, fasta or embl)
- You should be able to find the relevant mouse library at DFAM, these were actually made in collaboration with Repbase at the inception of DFAM...
- #TEhub workshop on #benchmark starts with a full room listening to the wisdom of @hquesneville and Arian Smit on the considerations, pitfalls and ways to assess #Transposons annotation. Soon on our YouTube channel! #TEsky
- DANTE and DANTE_LTR: computational pipelines implementing lineage-centered annotation of LTR... - goo.gl/scholar/sbGXRW #ScholarAlerts #TESky
- Just discovered sra-explorer.info and my life changed! Get directly the url to a fastq via EBI ENA!
