Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23

Excited to be in Barcelona for ISCO2026 to learn more about new innovations in the single cell genomics and transcriptomics space and reconnect with old friends and making new connections

🚨 Excited to share a new manuscript from the lab. Here, we have developed a new method, HiCPotts, to identify significant interactions in 3D chromatin data www.biorxiv.org/content/10.6...; package bioconductor.org/packages/HiC.... Big shoutout to an amazing previous PhD in the lab Godwin. 1/n

Exciting #CtrlEpiEdit conference update: Maja Jagodic @ki.se will be joining us in Paris! Check out her fantastic in vivo epigenome editing preprint here: www.biorxiv.org/content/10.6... And register for the symposium here 😉: ctrlepiedit.sciencesconf.org Please repost!

👋 Transposon lovers: registration is now open for the CSHL TE meeting! We have a 🔥 lineup of invited speakers and many slots for short talks selected upon abstract across all areas of TE biology. 🧬➰🧬 #TEsky Abstract deadline: July 10 meetings.cshl.edu/meetings.asp...

Hello world! So proud of our own @germainekaram.bsky.social presenting her PhD project during the #FragileNucleosome seminar! Great line-up with Ujani and Ethan! Please join if you wanna know how rapidly evolving H2A histones regulate maternal chromatin in mammals... #MolaroLab #Histones @igred.fr

OK Kids, our ERK story is finally heading out into the world. After 9 years of having funding, losing funding, losing staff, getting funding, gaining staff...it's ready! We discovered a novel stage of what is an otherwise extensively studied process: how cells respond to extracellular signals. 1/n

Do you want to move to Oxford and join our lab? There is a computational biologist position open atm to develop and implement tools to analyse TE expression in single cell long read data and more. Apply! #TEsky #UniversityofOxford #postdoc

Fun primer with @ForeverYHChang highlighting a lovely Travis Thomson lab paper! Did animals co-opt viral gag for intercellular (trans synaptic) communication? Or did viruses co-opt retrotransposon gags that animals had previously co-opted for intercellular use?

Integrated small and long RNA sequencing reveals piRNA mediated transposon repression during human oogenesis www.nature.com/articles/s41...

🎉🧬 Multiple genomes/pangenome? Time for a parTEA! 🧬 ☕️ Tired of annotating TEs one genome at a time? Same. So we organised a parTEA! Introducing EarlGrey ParTEA v0.1.3 — consistent TE annotation across all your genomes, in parallel, with one command: github.com/TobyBaril/Ea... #TEworldwide #TEsky

#TEsky TEffectBayes: a nextflow pipeline for exploring the potential effect of transposable elements in gene regulatory network with multi-omic Bayesian network model doi.org/10.1007/s004...

This fish has cloned itself for 100,000 years. Scientists just figured out how. #evolutionsoup #evolution #gynogenesis #science #fossils #cloning 👇🏿👇🏽 is.gd/PUwN0s

Potapenko et al. studied two species of barley, finding that TE silencing is central to genome size regulation, with selection maintaining smaller genomes among individuals with higher fitness in favorable habitats. 🔗 doi.org/10.1093/molbev/msag051 #evobio #molbio #TEsky #PlantSky

We are looking for a Postdoc to join our lab at @oxfordbiochemistry.bsky.social. This is a dry-lab focused post on the computational analysis of long read single-cell sequencing data to understand the role of transposable elements (TEs) in early development. my.corehr.com/pls/uoxrecru... #TEsky

#TEsky A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions pubmed.ncbi.nlm.nih.gov/41797537/

I'm so happy to share our latest paper! Now out in @narjournal.bsky.social 🥳 Did you know that transposable elements embedded in mRNAs can form dsRNA and activate innate immunity? 🧬🦠 Have a look! academic.oup.com/nar/article/... #TEsky #RNAsky #RNAbiology #immunity #NAR

Join us at the EMBO Workshop “RNA-guided genome protection” 🇨🇭 June 16–20. Transposon silencing • stem cell biology • RNA-guided immunity. Keynotes: Déborah Bourc’his + Ian MacRae. Register now + submit your abstract! meetings.embo.org/event/26-gen...

Transposable elements are increasingly studied in single-cell data, but how reliable are current locus-level quantification methods in short-read scRNA-seq data? If you work with single-cell RNA-seq or TEs, we hope this is a useful resource — feedback very welcome!

Happy to share our new preprint! 📊 We benchmarked methods for locus-level transposable element quantification in short-read scRNA-seq, using both real datasets and simulations with read-level ground truth. Huge thanks to @catavallejos.bsky.social and @antonio-scialdone.bsky.social! #TEsky

How does the piRNA system first recognize a new transposon or virus as foreign? https://www.biorxiv.org/content/10.1101/2024.01.24.577019

🚨📢📄 Article in press in Genome Biology doi.org/10.1186/s130... We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics #TEsky 🧵👇

How does the piRNA pathway solve the self vs. non-self problem? 🧬 Since piRNAs come from single-stranded RNA, how does the cell choose the right ones? For years, "piRNA clusters" were seen as THE privileged source. But are they really special and earmarked for biogenesis? (1/19)

Very last chance to join us (Deadline tomorrow Feb 10!) at this Developmental Biology meeting! Have a nice story? Come and discuss it with editors from @embojournal.org @plosbiology.org and @dev-journal.bsky.social ! A one hour info session from @erc.europa.eu will also be presented!

We're recruiting a #devbio Postdoctoral Fellow to explore the hTLS system! If you know any fab PhD students finishing, or candidates wanting to get their hands on #SCBEM embryo models, do get them to apply! 🌟https://www.crick.ac.uk/careers-study/vacancies/2026-02-03-postdoctoral-fellow-moris-lab

We've got two exciting chromatin talks coming up on Wednesday next week: @epijenatics.bsky.social from @jbuenrostro.bsky.social's lab and @ambystoma22.bsky.social! register and join us: us06web.zoom.us/webinar/regi...

Sad to hear that Oxford Nanopore wants to discontinue the P2Solo later this year in favor of the P2i (the very pricey P2Solo that comes with a GPU to do the basecalling in it) It feels like such a big step in the wrong direction. They are a great sequencing company, not a great GPU upseller...

The speed at which Oxford Nanopore is cancelling support for their devices is just mind boggling 😳 P2 solo will be decommissioned soon!!! This is not sustainable! @nanoporetech.com

🍄Transposon traffic in the mycocosmos🍄 Fascinating work reveals extensive horizontal TE transfer across fungi (@jromeijn.bsky.social, Iñigo Bañales & @mfseidl.bsky.social; doi.org/10.1016/j.cu...). I wrote a Dispatch to prime non-specialists,check it out here: doi.org/10.1016/j.cu.... #TEworldwide

Schaepe et al, 2026. Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells www.cell.com/cell/fulltex...

📣Excited to announce a new pre-print from the lab 📣 Led by my student @storiesofisobel.bsky.social in collab with Hemali Phatnani @nygenome.org We discovered a novel class of TDP-43 dependent cryptic gene-TE spliced transcripts: crypTEs #TEsky #RNAsky #ALS doi.org/10.64898/2026.01.09.698641

Really excited to share our recent work here today and connect all of you :)

What a cool story. Particularly like the fact of expansion and different TF bdg sites! Really speaks for each locus being differential key regulated.

☕Earl Grey v7.0.0 brewed fresh☕ Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix. Happy new year to the TE folks! 🧬 github.com/TobyBaril/Ea...

#TEsky still have to read the paper but sounds very interesting.

#TEsky Heterogeneous Lineages of DNA Transposons Encode a TET/JBP Dioxygenase in Fungi doi.org/10.3390/biol...

🪱 Selfish genes are everywhere and drive some of biology’s biggest innovations (CRISPR, antibody recombination, epigenetics). Yet almost no one asks the obvious question: how does a selfish gene begin? Our new manuscript uncovers how selfishness can emerge directly from the host genome.

@biorxivpreprint.bsky.social Chronic alcohol exposure drives inflammaging and transposon derepression in hematopoietic stem and progenitor cells www.biorxiv.org/content/10.6...

ISCO (Innovations in Single-Cell OMICS) will be back in beautiful Barcelona! 🗓️ 28th/29th of May 2026 📍Barcelona Biomedical Research Park @prbb.org (beachfront!) Keynotes: @bartdeplancke.bsky.social and @bocklab.bsky.social Submit your abstract and present your research! www.isco-conference.eu

Nice paper from @robertife.bsky.social on how metabolism-induced H4K16 acylations correlate with (and may cause) chromatin opening through disruption of tail-acidic patch internucleosomal interactions. www.cell.com/molecular-ce...

More than one-third of polar bear genome is made up of transposable elements. By contrast, transposons make up about 45% of the human genome Polar bears in southern Greenland are 'using jumping genes to rapidly rewrite their own DNA' to survive melting sea ice www.livescience.com/animals/pola...

🚨Our story is published! Same bones but + dissection of MERVL’s role integrating signals from #ZGA factors, & + about pathological DUX4 activation of NOXA #TEsky. Thanks to all revs for their helpful comments improving the ms. Even #rev3 - until they ghosted us 😜 www.science.org/doi/epdf/10....

Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway. And found a hidden RNA-decay axis from Piwi to the RNA exosome.

Very excited to share our work on locus level transposable elements in development with the @fnucleosome.bsky.social community!

Very excited to take part in ISCO in Barcelona next year. Looking forward to great discussions and new ideas!

Despite having been scooped big time by this paper from William Pastor's lab, really quite enjoyed reading it. Congrats to the authors.

TEs aren’t just genomic parasites, they’re also engines of genomic novelty. Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion. With @danielcroll.bsky.social & @guidopuccetti.bsky.social 🧬 www.nature.com/articles/s41... #TEworldwide

www.nature.com/articles/s41... Human inflammatory responses have been linked to adaptive genetic changes during human evolution. It is proposed that primate-specific transposons facilitated the evolution of inflammatory responses in great apes, w/Alus shaping adaptive potential in modern humans.

#TEsky A comparative analysis of transposable element diversity and evolution across 75 bee genomes doi.org/10.1186/s128...