Nature research paper: Specificity, length and luck drive gene rankings in association studies go.nature.com/47Fsqax

New OA Article: "Major alleles of CDCA7 shape CG methylation in Arabidopsis thaliana" rdcu.be/ePaOY GWAS identifies CDCA7 as a regulator of DNA methylation in Arabidopsis thaliana . CDCA7 binds the chromatin remodeller DDM1 and modulates the control of CG methylation.

Lifestyles shape genome size and gene content in fungal pathogens. buff.ly/tec1Tds

Packed room for Emma Corre's PhD defense on transposable elements in rust fungi genomes. Congratulations Dr @emma--c.bsky.social 👏👏👏 And what a lovely tribute to Barbara McClintock who discovered transposable elements in 🌽!!!

My awesome grad student Shashank and I wrote this paper trying to look at broader patterns of HT in TEs. HT is happening everywhere! DNA transposons jump further than other classes! www.biorxiv.org/content/10.1...

Very happy to see our paper published online natcomms.nature.com. Thank you to @wellcometrust.bsky.social for funding this work during my time with @robklose.bsky.social and David Booth! Thanks also to collaborators @garcialabms.bsky.social @alexdemendoza.bsky.social and the other authors!

Epigenetics Update - RNA m6A regulates the transcription and heterochromatin state of retrotransposons in Arabidopsis go.nature.com/47jvfiF Guifang Jia (Peking University) in Nat Plants #Epigenetics #Plants #Chromatin --- Empower your research with high-res epigenetic insight at epigenometech.com

1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start? We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes! www.biorxiv.org/content/10.1...

Want to understand how entire fungal chromosomes can be horizontally transferred? Join us to unravel the mechanism/consequences of horizontal chromosome transfer in a fungal pathogen as part of an ERC-funded project. Postdoc/PhD positions available. fungal-evolutionary-genetics.de/open-positio...

Thrilled to share our most recent paper describing the antimicrobial activity of engineered mesoporous silica nanoparticles targeting intracellular mycobacteria in macrophages and zebrafish. Outstanding work headed by Yara Tasrini, John Jairo Aguilera Correa, Miguel Gisbert and others. rdcu.be/eAcN4

Hominoid-specific retrotransposons fuel regulatory novelty in early brain development , by @retrogenomics.bsky.social. ➡️ www.cell.com/cell-genomic...

🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China

🚨 First pre-print from my team !! TL;DR: presence of polymorphism (sequence differences between the homologous chromosomes) can *increase* the local rate of recombination in Arabidopsis thaliana, turning cold regions of the genome hot (purple v. grey) !

Weng et al. examined 431 genomes of butterflies and related lineages, revealing that horizontal transfer of digestion and detoxification genes facilitated the evolution of herbivory, enabling butterflies to co-evolve with angiosperm hosts. 🔗 doi.org/10.1093/gbe/evaf156 #genome #evolution #HGTsky

Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance www.nature.com/articles/s41...

📝New preprint! #MicroSky 🕰️We chart the full, synchronized lifecycle of a predatory bacterium using Hi-C, RNA-seq, ChIP-seq & microscopy. 🧬We uncover dramatic shifts in nucleoid architecture & transcription, tightly coordinated with predation. www.biorxiv.org/content/10.1...

Apple is entering the protein folding arena. SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...

Thrilled to share that our TEtrimmer paper has just been published in Nature Communications! A big thank you to all collaborators — the article is now online ;) www.nature.com/articles/s41...

Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life. www.nature.com/articles/s41...

Job Alert! We're hiring a BIOINFORMATICIAN / NGS SPECIALIST to support our new Molecular Biodiversity Lab in the @terra-cluster.org at @unituebingen.bsky.social. Like the idea to use your skills for understanding biodiversity? To work on diverse questions in a wonderful place? Apply! Please repost!

Come and join our team! A 2-year postdoc position is available in our "Genome Evolution" department at Univ Paris Saclay. We want to play with phylogenetic models accounting for horizontal transfers of transposable elements. Application& details on the official portal: emploi.cnrs.fr/Offres/CDD/U...

Check out our new preprint! We compare sequence versus synteny approaches for resolving a challenging #phylogenetic problem. In this case, synteny is far more informative! Also includes the first chromosome-level #genome for the enigmatic #fish family Gyrinocheilidae. doi.org/10.1101/2025...

New OA Article: "A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution" rdcu.be/eHce3 Chromatin accessibility in rice & related grasses: how regulatory DNA elements evolve across cell types & species; identifying potential silencers.

Happy to share the results of a long-haul post-doc project, now online @science.org, aiming at understanding the rules of transgeneration epigenetic inheritance over TEs in plants and its extent and impact in nature. More below! doi.org/10.1126/scie...

PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity. But how does piRNA-guided target interaction translate into silencing? PhD student Júlia Portell Montserrat has an intriguing answer www.cell.com/molecular-ce...

Active learning enables discovery of transcriptional activators across fungal evolutionary space https://www.biorxiv.org/content/10.1101/2025.09.12.675635v1

Our new review is out in Trends in Cancer. We had fund writing this :) We discuss the roles of retrotransposons in immune modulation in normal and malignant hematopoiesis. www.cell.com/trends/cance...

Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods https://www.biorxiv.org/content/10.1101/2025.08.29.672809v1

Vesalius 2.0 is in ‪‪@natcomms.nature.com‬ ! We show how using spatial context improves cell-to-cell mapping across heterogenous spatial samples. Thanks to the reviewers, editors, and collaborators for making this possible. GitHub: github.com/WonLab-CS/Ve... Paper: www.nature.com/articles/s41...

Nature research paper: Elementary 3D organization of active and silenced E. coli genome go.nature.com/4n1DTY7

📣 NEW PREPRINT 📝 We identified evolutionary origins of many fungal effectors! We show that fungi secrete lots of antimicrobial proteins, and that some of them were repurposed by plant pathogens for host immune suppression. www.biorxiv.org/content/10.1... cc @teamthomma.bsky.social

Paper led by @movillome.bsky.social on unbiased detection of (somatic) #TE insertions in #Arabidopsis with @pacbio.bsky.social long reads out after peer review. Thanks to academic editor Leandro Quadrana for shepherding it through the review process. #plantscience link.springer.com/article/10.1...?

📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social rdcu.be/exBSp

I am so happy to announce that our Drosophila testis multiome paper is now published in Nature Communications !!! I am very happy and proud of all who contributed, in particular Patrick and Pallavi who did an amazing job! www.nature.com/articles/s41...

We are looking for a student to continue our work on chromatin evolution: www.nature.com/articles/s41... www.biorxiv.org/content/10.1... The project with @seanamontgomery.bsky.social will focus on chromatin state readers across eukaryotes. More info: recruitment.crg.eu/content/jobs...

1/2 Somatic TE transposition in plants is getting traction again (70 years after McClintock's discovery of "controlling elements")! A very large collection of somatic TE insertions in A. thaliana described by Ambreen et al.(www.biorxiv.org/content/10.1...).

New Pre-print! A long-standing question for transcription factor biology is how their chromatin context dependency works in plants. In this collaboration with Fred Berger lab, we present some new ideas not only in Arabidopsis but also in Marchantia. www.biorxiv.org/content/10.1...

OrthoFinder just dropped a major update It’s faster, more accurate, and ready for thousands of genomes Let’s break it down (1/10) github.com/OrthoFinder/... www.biorxiv.org/content/10.1...

How bats developed their wings? 🦇 Turns out they reutilize existing gene programs 🔧 Find out more in our paper @natecoevo.nature.com in collaboration with @fany-real.bsky.social and @stemundi.bsky.social labs www.nature.com/articles/s41...

🚨Our latest work on selfish centromeres is published @currentbiology.bsky.social 🐭🧬We found that the spindle checkpoint contributes to non-Mendelian segregation! Huge congrats to our lab manager, Zaak Walton, who led the project🎉 Free link: authors.elsevier.com/a/1lQzN3QW8S...

Our latest paper is out: rdcu.be/ev6Ym — one of my favorite projects. It began about 8 years ago when Nobel laureate Torsten Wiesel asked me: what transcription factors regulate new genes? I had no idea then. Now we have some answers.

Curious about how novel #plant #pathogens emerge? Check out our microreview on whether #fungal disease outbreaks are instigated by Starship #transposons. We present three examples that we think are evidence of outbreaks caused by Starship HGT. bsppjournals.onlinelibrary.wiley.com/doi/10.1111/...

An insightful @cp-trendsgenetics.bsky.social perspective on our recent article about the early evolution of genome regulation in animals. www.cell.com/trends/genet... Thank you Omar and @ferdix.bsky.social!

Viral genomes might encode more proteins than we initially thought! Intrigued? Come see my poster on the identification of potentially new ORFs in the potato virus X genome. Tuesday 9:55-11:30, P-266 @geminiteamlab.bsky.social #2025ISMPMI

In another fruitful collaboration with the @rokaslab.bsky.social, Hittinger Lab members @katarina-aranguiz.bsky.social and @linder-surprise.bsky.social , et al. established a ML framework to identify gene families in the yeast subphylum Saccharomycotina whose copy numbers predicted ROS resistance.

super-happy, three TE invasions in Dmel during the last 30 years; the crazy thing - Transib1 spread in just 2-3years in global populations academic.oup.com/mbe/advance-... great work everyone @rpianezza.bsky.social @almoroscarpa.bsky.social @signor-molevol.bsky.social Anna Haider

Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁 Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5

🚀 Thrilled to share our new review on how structural variants reshape 3D genome architecture and cause disease! 🧬🔀 Out now in Nature Reviews Genetics: www.nature.com/articles/s41... #3D-Genome #StructuralVariants #uksh

Relaxed Purifying Selection is Associated with an Accumulation of Transposable Elements in Flies academic.oup.com/mbe/article/...

The evolution of high-order genome architecture revealed from 1,000 species https://www.biorxiv.org/content/10.1101/2025.07.05.663309v1