Clément Goubert
🤘🧬 Transposable
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Elements 🧬🤘
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Assistant Research Professor @wheelerlab.org
University of Arizona
- Reposted by Clément GoubertPlease 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:
- 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
- Reposted by Clément GoubertNew 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...
- Reposted by Clément Goubert🧬🖥️ 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!
- Reposted by Clément GoubertThe 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 www.biorxiv.org/content/10.1...
- #Transposons are just the best!
- Reposted by Clément GoubertHere, we demonstrate that Starships, a newly discovered group of cargo-mobilizing transposable elements, are active vectors of horizontally transferred DNA among eukaryotic species.
- 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...)
- 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!
- P 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...)
- 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...
- Reposted by Clément GoubertLOCATE: 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
- Reposted by Clément GoubertDo 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...
- 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...
- Reposted by Clément GoubertVery excited to share our paper on Gene and Transposable Element expression in mammalian preimplantation development, online today! www.cell.com/cell/fulltex... A short thread to highlight some of our findings 🧵
- The great @johannconfais.bsky.social on a reference-free approach (panREPET) to annotate #Transposons in #pangenomes 🧬
- Reposted by Clément GoubertAfter @tehub.bsky.social satellite workshop at #ICTE2024 and the creation of a working group on benchmark, what about the next step ? A manual curation workshop ? Share your thougth with the TEhub
- Reposted by Clément Goubert@johannconfais.bsky.social and @clementgoubert.bsky.social are presenting @tehub.bsky.social at #PAG2025, an amazing resource and driven community for anyone interested in transposable element
- Reposted by Clément GoubertAmazing talk of @nico971.bsky.social from @urgi-inrae.bsky.social on RepetDB #PAG32 urgi.versailles.inra.fr/repetdb/begi...
- #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!
- Reposted by Clément GoubertI have received a Wellcome Discovery Award to study the initiation of eukaryotic DNA replication, with 8 years of funding at the Francis Crick Institute. Looking for a postdoc in molecular mechanisms, cryo-EM, cryo-FIB and in situ structure? Contact me now! 3 postdoc positions advertised soon.
- Reposted by Clément GoubertI would really appreciate a wide sharing of this post, as the candidate profile I am looking for is outside of my regular circle. Thank you so much. More info and how to apply here: uu.varbi.com/se/what:job/... (2/2)
- Reposted by Clément GoubertIt was only a matter of time. www.cell.com/cell/fulltex...
- Let me know If Google does that!
- Reposted by Clément GoubertApple & AI There I was hoping Apple would make this opt-in… 😑
- Posting this to remember the day I have more followers than @cedricfeschotte.bsky.social 🤣🤣🤣
- Reposted by Clément GoubertWe've got to do better. This field of 'social epigenomics' looks to be very lacking in self-criticism and necessary rigour, it is no wonder that these studies are wide open to criticism.
- Reposted by Clément GoubertWe found this ghost redwood tree this weekend while camping this weekend @jrossibarra.bsky.social . It's a rare chlorophyll mutant growing clonally off of the base of huge coastal redwood
- Reposted by Clément GoubertTracking transposable element (TE) activity in genomics data can be a pain, but there are solutions! Our lab built TEtranscripts -- which we've updated to work for small RNAs (TEsmall), bulk RNA at the locus level (TElocal), and in single-cell data (TEsingle). Check it out! www.mghlab.org/software
- Reposted by Clément GoubertPlease register for the course on Transposable elements in #genomics and #datascience. We will be sharing the magic of #nanopore long reads for #transposon expression #tesky
- 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.
- 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! 🧪
- Reposted by Clément GoubertEvolutionary biologists teaching intro courses: "Hardy-Weinberg is the null model of evolution." Evolutionary biologists studying bacteria/archaea/asexual eukaryotes: #evolution
- Reposted by Clément GoubertDelighted to share that our paper on discovering selective sweeps with haplotype statistics in aDNA is now out in Nat. Comm! www.nature.com/articles/s41... Wonderful collaboration with Vagheesh Narasimhan, Devansh Pandey, and @mharris.bsky.social
- Reposted by Clément GoubertNews has moved on, but here in Asheville it's been almost 7 weeks since Hurricane Helene knocked out drinking water for over 150,000 of us. At this point, we're hoping we'll be off bottled water by Christmas and more businesses can reopen.
- Reposted by Clément GoubertBioinformaticians of the world, it’s your time to shine! The SIB #Bioinformatics Awards are now open to entries. They promote excellence, diversity & innovation in the field. Submit your best work & share with colleagues. www.sib.swiss/bioinformati...
- Reposted by Clément GoubertOrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes academic.oup.com/nar/advance-... #jcampubs
- Welcome to Bsky everybody! Remember: TE RULES!!!
- Reposted by Clément GoubertWe are excited to share our latest work: Transposable elements (TE) are deregulated in #Preeclampsia placenta, which correlates with elevated type-I IFN. We then show "TE signature in maternal cell-free RNA can predict preeclampsia before the appearance of symptoms" biorxiv.org/content/10.1...
- Reposted by Clément GoubertCool to see so many new people here! Is this finally going to become the place for science with all the new faces!? #TEsky #TEworldwide
- Reposted by Clément GoubertScraping who is on the platform working on #TransposableElements or other types of #RepetitiveDNA Have fun! go.bsky.app/7t5GQAPat://did:plc:ebur4kpwnz66tpsbldned4bo/app.bsky.graph.starterpack/3lamuxwqbvg2g
- 🎉 Our #GraffiTE paper is out!!! t.co/TmoSL3WQ1P If you are interested in #Transposon insertion polymorphism, this is for you!
- #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!
