Development of a CRISPR/Cas9-mediated transformation procedure for the wheat pathogen Zymoseptoria tritici https://www.biorxiv.org/content/10.64898/2026.05.27.728285v1

An Aspergillus lncRNA atlas reveals a novel modulator of aflatoxin biosynthesis https://www.biorxiv.org/content/10.64898/2026.05.29.728754v1

Giants within: a new class of microbial mobile elements review in @cp-trendsgenetics.bsky.social www.cell.com/trends/genet...

🚨 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

Going from the discovery of epigenetic silencing of CTCF insulators www.nature.com/articles/s41... to aberrant E-P looping www.cell.com/molecular-ce... to a successful clinical trial www.nature.com/articles/s41... all from Brad Bernstein's lab

New preprint! In an fun collaboration with @imaeso.bsky.social and @mirimiam.bsky.social led by Manu F-M, we set to explore the potential adaptation of transposable elements 👾 to host adenine DNA methylation by recruiting prokaryotic DAM methyltransferases: www.biorxiv.org/content/10.6.... 1/6

Nature research paper: A pathogen lncRNA secreted into rice sequesters a host miRNA for virulence go.nature.com/3RCU6IB

Host-transposable element coexistence: a matter of resistance, tolerance and trade-off Read this new review by Séverine Chambeyron, Charlotte Grimaud, Mikiko Siomi et al link.springer.com/article/10.1...

Thrilled to see this finally out!! Our new work suggests #Starships helped #Colletotrichum acquire the genes needed to infect lupin. A glimpse into how fungal pathogens emerge through horizontal transfer and genome reshaping. biorxiv.org/content/10.6... #Fungi #Genomics #Pathogenicity #evolution

📢 EffectorGeneP is finally here! Stop missing small, single-exon or orphan genes from your favourite pathogen genome. Current tools only annotate 15%-78% of effector genes, EffectorGeneP finds 95% - including the large AvrSr26 family in stem rust. #Bioinformatics 📖 www.biorxiv.org/content/10.6...

EffectorGeneP: accurate gene annotation in pathogen genomes from infection transcriptomes https://www.biorxiv.org/content/10.64898/2026.05.04.722827v1

New preprint out! We generated haplotype-phased genome assemblies for two poplar rust fungi. These resources open new opportunities to explore rust genome architecture, haplotype diversity, and TE-driven evolution. www.biorxiv.org/content/10.6...

📢Out now on bioRxiv: We used Plant STARR-seq to characterize the species- and condition-specific enhancer activity of over 350,000 sequences derived from four plant species. For more, see below and read the paper at: www.biorxiv.org/content/10.6...

CoCUT&Tag maps linked chromatin states at single-molecule, single-cell resolution https://www.biorxiv.org/content/10.64898/2026.04.27.721191v1

🎉 📰 Very happy to share the journal publication of our manuscript "Plant-associated fungi co-opt ancient antimicrobials for host manipulation"! #ScienceAdvancesResearch @science.org @teamthomma.bsky.social www.science.org/doi/10.1126/...

Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.

k-mer-based approaches to unlock genebank genomics for targeted crop improvement rdcu.be/ffBWh

If you want to read more about our recent work on how gene body methylation buffers noise in gene expression academic.oup.com/nar/article/... , @jamespblloyd.bsky.social has a excellent spotlight in @cp-trendsgenetics.bsky.social.

🎉Excited to share our new preprint! TIR domains from diverse animals, including human TLR4, are catalytically active and produce cyclic ADP-ribose (cADPR). This enzymatic activity is widespread in animals and conserved across the tree of life. www.biorxiv.org/content/10.6...

Really happy to share that our preprint is now published in @narjournal.bsky.social! 🎉

MAJEC: unified gene, isoform, and locus-level transposable element quantification from RNA-seq https://www.biorxiv.org/content/10.64898/2026.04.10.717472v1

Very proud of this work and all the efforts from my team and collaborators on this! You can now use DGRs for in vivo targeted hypermutagenesis in E. coli. We also included some early proof of concept in Yeast thanks to @seth-shipman.bsky.social !

DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci buff.ly/NRhk83b?utm_...

Ancestral Genome Reconstruction. https://www.biorxiv.org/content/10.64898/2026.04.16.718917v1

Contrasting transcriptional responses and genetic determinants underlie Zymoseptoria tritici adaptation mechanisms to simulated host defense environments https://www.biorxiv.org/content/10.64898/2026.04.14.718361v1

Happy to share our review of the past, recent, and future applications of synthetic genomics in studying the 3D functional organization of chromosomes, a set of approaches that are gaining momentum! www.sciencedirect.com/science/arti...

New Article: "Genome–host association mapping reveals wheat pathogen genes involved in host specialization" rdcu.be/fdBNC GHA: leverage natural epidemics to map the genetic landscape of host adaptation in Zymoseptoria tritici. Applied to 832 wheat fungal strains.

Thrilled to share our paper now out in Nature Plants 🎉 We developed a genome-host association (GHA) approach to study pathogen adaptation directly from field metadata by using the originating host cultivar as phenotype. www.nature.com/articles/s41...

Our linker histone H1 paper is featured on the cover of the April 10 issue of #ScienceAdvances. www.science.org/doi/10.1126/... A molecular dynamics simulation of nucleosomes and linker histone H1, with single-H1 trajectories (background). 🎉 Full cover caption: www.science.org/toc/sciadv/1...

Love Drosophila genetics — this journal club was a great way to share that enthusiasm and pay tribute to the pioneers of transposons regulation 🪰 How classical genetics uncovered key determinants of TE silencing #transposon @igred.fr @igred.fr 👇👇

#NatMicroPicks Same destination, different routes 🍄🧫🧪 Following 10,000 generations, parallel evolution occurred in separate yeast species, but took different genetic routes driven largely by transcriptomic and trans‑regulatory differences. #MicroSky www.nature.com/articles/s41...

Our latest publication is now out at Genome Biology! link.springer.com/article/10.1... We uncover a unique association between a H3K27me3 reader complex and active transcription. A thread with our key findings: (1/8) #TEsky #Polycomb #transcription #smallRNAs

Arnab et al. explored positive-unlabeled learning as a flexible framework for detecting adaptive events and introduced PULSe as a versatile tool for detecting adaptive regions across diverse genomic landscapes. 🔗 doi.org/10.1093/gbe/... #genome #evolution

🔬 Recruiting a Postdoc!!!! I’m looking for a motivated postdoc to join my lab and work on characterizing the role of a heterochromatin protein involved in a sex-ratio meiotic drive system in Drosophila. If you know someone who might be interested, please share widely!

DNA demethylation suppresses a state of enhanced cellular pluripotency and regeneration competence in Arabidopsis. https://www.biorxiv.org/content/10.64898/2026.03.27.714943v1

Studying DNA modification in microbes shouldn't be limited by methodology. 🧬 We’re excited to introduce MODIFI, our new scalable method for detecting DNA modifications in PacBio metagenomic data and estimating ECE-host linkage. Check out the preprint: www.biorxiv.org/content/10.6...

Chromatin plays a central role in gene regulation, but chromatin systems are only known for a few model species. This study analyses chromatin regulatory landscapes in brown algal lineages to elucidate their structural organization and evolution 🧪 www.nature.com/articles/s41...

Impacts of genome architecture on the repeatability of polygenic adaptation https://www.biorxiv.org/content/10.64898/2026.03.26.714499v1

"Machine learning for evolutionary genetics and molecular evolution" by Li Zhao & colleagues authors.elsevier.com/sd/article/S...

ChromSMF preprint is out!🚀 tinyurl.com/ChromSMF We often piece together chromatin regulation layer by layer from separate assays. But this can be limiting! In @arnaudkr.bsky.social's lab, we developed a method to directly study multiple layers on the same DNA molecule! 🧬 What does this unlock? ⬇️

Now out! We show that TEs can be horizontally transferred between fungal species via Starships. Once transferred, these TEs can become active, changing the genome organization and affecting the lifestyle of the recipient fungus. www.nature.com/articles/s41... @oggenfussursula.bsky.social #TEsky

Integrating Long-Read Structural Variant Analysis with single-nucleus RNA-seq to Elucidate Gene Expression Effects in Disease https://www.biorxiv.org/content/10.64898/2026.03.20.713192v1

Check out our new review on exciting advances in molecular tools for studying DNA and RNA biology of fungal pathogens! w/ Matthew Blango @femsjournals.bsky.social @trr124-funginet.bsky.social @leibniz-hki.de academic.oup.com/microlife/ar...

Super nice read!! And what a pleasure to see three ECR I have had the chance to see grow up as fully accomplished scientists writting this piece together! Congrats @minyaojhu.bsky.social @fabianvanbeveren.bsky.social and Bruno !

Position-dependent variant effects reveal importance of context in genomic regulation https://www.biorxiv.org/content/10.64898/2026.03.17.712488v1

Excited to share my PhD work! The question: How is genome organization established? Here, we developed a low-input Micro-C method, Pico-C, and used it to map chromatin architecture across early stages of fly development. Here’s a quick Blue-torial 🙂 (1/n) www.nature.com/articles/s41...

Fouché, @oggenfussursula.bsky.social, McDonald & @danielcroll.bsky.social retrace chromosomal degeneration in a fungal pathogen, identifying the exact sequence triggers that initiate chromosome instability and perpetuate degenerative cycles. 🔗 doi.org/10.1093/gbe/evag037 #genome #evolution

🔥Fantastic paper!🔥 TE with a role in vegetative phase change and gametogenesis, mediated by 24-nt siRNAs acting in trans to a wide range of genes. Found by GWAS in A. thaliana 🌱. Congratulations to the authors! 👏🏻👏🏻👏🏻 #epigenetics #plantscience www.pnas.org/doi/10.1073/...

Integrative analysis reveals extensive interactions among C2H2 zinc finger proteins at chromatin loop anchors https://www.biorxiv.org/content/10.64898/2026.03.06.710197v1

Nature research paper: Genome modelling and design across all domains of life with Evo 2 go.nature.com/4aMo9Vu