EarlGrey ParTEA v0.2.0 is out! Pangenome TE annotation across multiple genomes just got a major upgrade — now fully compatible with RepeatMasker 4.2.4, RepeatModeler 2.0.9, RMBlast 2.17, and Dfam 4.0 / FamDB 3.0.0 🧬 🔗 github.com/TobyBaril/EarlGreyParTEA #TEworldwide #TEsky #genomics #transposons

GitHub - TobyBaril/EarlGreyParTEA: 2+ genomes make a parTEA! This pangenome TE annotation pipeline extends EarlGrey for multi-genome comparative analysis

2+ genomes make a parTEA! This pangenome TE annotation pipeline extends EarlGrey for multi-genome comparative analysis - TobyBaril/EarlGreyParTEA

github.com

Huge congrats to @alicelaigle.bsky.social for driving this work - excited to share this preprint! Comparative analyses reveal rapid turnover and emergence of transitory 3D genome architectures in the fungal kingdom www.biorxiv.org/content/10.6... #fungi #bioinformatics #evolution #preprint

Comparative analyses reveal rapid turnover and emergence of transitory 3D genome architectures in the fungal kingdom

The three-dimensional architecture of genomes plays major roles in biological processes such as gene expression and DNA replication. The architecture of genomes has evolved substantially with distinct...

biorxiv.org

Hi #TEsky, please remember that we have an amazing community in the TransposonsWorldWide slack channel (join.slack.com/t/transposon...), which I encourage you to join. Another great resource is tehub.org. Please share !

Join TransposonsWorldwide on Slack

Slack is a new way to communicate with your team. It’s faster, better organized, and more secure than email.

join.slack.com

This is huge! Very excited to hear this great news!

RepeatMasker Project@repeatmasker.bsky.social · last mo.

A New Open Foundation for TE Research: GIRI is transitioning the full Repbase collection to an open-access license and joining the Dfam effort to help build a unified open resource for transposable element research. Full announcement: tinyurl.com/48665xss

An exciting day for TE research and open science. #tesky

RepeatMasker Project@repeatmasker.bsky.social · last mo.

A New Open Foundation for TE Research: GIRI is transitioning the full Repbase collection to an open-access license and joining the Dfam effort to help build a unified open resource for transposable element research. Full announcement: tinyurl.com/48665xss

Congratulations to the authors (and my friends), @alex-stuart.bsky.social and Chandler on their paper on CR1 retrotransposons across vertebrates! And thanks for letting me tag along! #TEsky academic.oup.com/gbe/advance-...

Ancient persistence and newfound diversity of CR1-group retrotransposons across vertebrates

Abstract. Retrotransposons are mobile, repetitive DNA sequences that are ubiquitous across eukaryotes and widely recognised as key drivers of both gene and

academic.oup.com

#TEsky #TEworldwide

Abby Buchwalter@abbybuch.bsky.social · 2mo ago

After some good funding news, we are hiring! Looking for a postdoc to join our team and lead our explorations into transposon repression by the nuclear lamina. Check out the full ad on our lab website at buchwalter-lab.github.io/postdoc-ad.pdf + contact me to learn more!

📣 POSTDOC position available in the Feschotte Lab at Cornell to work on #TRANSPOSONS! More details below. Pls send informal application or inquiry ASAP by DM or email to cf458_at_cornell.edu. Pls spread the word 🙏 #TEsky www.thefeschottelabatcornell.com

#TEsky #TEworldwide

Camille Cornet@camillecornet.bsky.social · 2mo ago

To tackle this, we assembled high-quality genomes for 11 Erebia species and combined them with 25 additional assemblies from @projectpsyche.bsky.social, the Darwin Tree of Life project and @ergabiodiv.bsky.social Huge thanks to these initiatives for enabling exciting science!

Really great to see this preprint out! Amazing effort by @camillecornet.bsky.social, and a privilege to have been involved in this one, thanks for beginning me back to butterflies, Camille! 😉 #TEsky #TEworldwide #Genomics #Bioinformatics #Chromosome #Evolution #Butterflies

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 2mo ago

Transposable elements underlie chromosomal fusions and fissions in a highly species-rich group of butterflies https://www.biorxiv.org/content/10.64898/2026.06.15.732387v1

We just published our new paper about an active Helitron transposon in wheat 🌾🧬 We found that it can be mobilised by heat stress when DNA methylation is reduced. We document its full lifecycle: RNA -> circular DNA -> integration www.nature.com/articles/s41... #TEsky

An active Helitron transposon family in wheat - Nature Plants

Helitrons are a recently identified category of transposons. This study reveals that heat stress combined with reduced DNA methylation can mobilize a Helitron family in wheat. Its mobilization is gene...

nature.com

Looking for small pot of funding approx £5,000 to conduct some exciting genomics for a pilot transposons and climate resilience project in vulnerable species. If anyone knows of any pots available to UK-based researchers please let me know :) #funding #research #academia #NERC #UKRI

Population-level structural variant characterization using pangenome graphs www.nature.com/articles/s41...

Population-level structural variant characterization using pangenome graphs - Nature Genetics

Swave is a method to call structural variants from pangenome graphs using a recurrent neural network to identify structural variant patterns, including complex structural variants.

nature.com

🎉 EarlGrey ParTEA v0.1.6 is here! Huge thanks to everyone who's tried the pipeline and shared feedback — your suggestions directly shaped these new features. 🍵 #TEworldwide #transposableelements #bioinformatics #genomics

🎉🧬 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

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

Had a great chat with Sophie about this work back in Heidelberg, excited to dive into this preprint! #TEsky #TEworldwide

Tony Heitkam🌱🔍💚@toheitka.bsky.social · 5mo ago

🧬🔎 Deep dive into plant #TransposableElements ❓ If you identify all autonomous #TEs, you will automatically also have all non-coding derivates, right? Right? Well, no! Not even close. Check out here, how much you are missing: 📚 www.biorxiv.org/content/10.6... #TEsky

#TEsky a short paper from @mbonar.bsky.social , myself and others on our reannotation of TEs in the Octopus vulgaris genome. More work to come using genome ecology to analyze TEs in this species bsky.app/profile/bior...

bioRxiv Genomics@biorxiv-genomic.bsky.social · 5mo ago

Biological implications of a detailed repeat annotation in Octopus vulgaris https://www.biorxiv.org/content/10.64898/2026.03.03.709284v1

#TEworldwide #TEsky

Toby Baril@tobybarilbio.bsky.social · 5mo ago

Need to annotate transposons in fungal genomes? 🧬 Good news #MycoMobilome is now live! Check it out here: doi.org/10.1093/narg... Access the sequences through our Zenodo community (you can also contribute seqs with credit), and synchronisation with @dfam.bsky.social! w/ @danielcroll.bsky.social

Need to annotate transposons in fungal genomes? 🧬 Good news #MycoMobilome is now live! Check it out here: doi.org/10.1093/narg... Access the sequences through our Zenodo community (you can also contribute seqs with credit), and synchronisation with @dfam.bsky.social! w/ @danielcroll.bsky.social

MycoMobilome: a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom

Abstract. Transposable elements (TEs) are found in nearly all eukaryotic genomes. Despite significant advances in the sequencing of genomes, TE resources r

doi.org

#TEsky EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis doi.org/10.1186/s128...

EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis - BMC Genomics

BMC Genomics - Transposable elements (TEs) are major components of plant genomes, shaping genome architecture, gene regulation, and evolutionary innovation. While the Extensive de novo TE Annotator...

doi.org

Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics #TEworldwide #TEsky www.sciencedirect.com/science/arti...

Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics

Transposable elements (TEs) are ubiquitous components of the genome whose mobility can be triggered by environmental stress and influenced by genotype…

sciencedirect.com

👏 Congratulations Toby for this Current Biology dispatch! 🎨 Happy to see my watercolours in it to illustrate this so-cool topic! #illustration #sciart #scicomm #TE #fungi #watercolours #TEworldwide

Toby Baril@tobybarilbio.bsky.social · 7mo ago

🍄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

I'm recruiting 1-2 grad students through the AITHYRA-CeMM PhD program! Applications are due January 30th. This is a fully-funded PhD program, combining AI and biology to advance biological discovery. Please forward to anyone who may be interested! You can apply here: apply.cemm.at

🍄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

#TEworldwide

Manvendra Singh@manusingh.bsky.social · 7mo ago

🔥🎉 🧠 SuperThrilled to share our paper (preprint) - Human erythropoietin (rhEPO) reshapes the adult hippocampal chromatin landscape, around transposons to promote neurogenesis. 🧵1/8 Massive kudos to #UmutCakir who drove multi-omics through dark roads of the genome. www.biorxiv.org/content/10.1...

#TEsky #TEworldwide #Transposons #Bioinformatics #Bioconda #GenomeAnnotation #TransposableElements #Genomics #ComparativeGenomics

Toby Baril@tobybarilbio.bsky.social · 7mo ago

☕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...

☕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...

GitHub - TobyBaril/EarlGrey: Earl Grey: A fully automated TE curation and annotation pipeline

Earl Grey: A fully automated TE curation and annotation pipeline - TobyBaril/EarlGrey

github.com

Transposable elements can insert into genes, disrupting protein-coding potential. Researchers discover a mode of RNA processing, ‘SOS splicing’, that provides a quick fix @nature.com @harvardmed.bsky.social www.nature.com/articles/d41... www.nature.com/articles/s41...

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

Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen - Nature Communications

In this study, the authors analysed a large genomic dataset to trace how jumping genes shaped the global spread of a major wheat pathogen and reveal bursts of activity over decades that drove adaptati...

nature.com