Very interesting and comprehensive study using synthetic activation of enhancers to probe the rules of distal vs. proximal gene regulations:

COMPARATIVE GENOMIC ANALYSIS OF CORE AND ACCESSORY GENES IN RUST FUNGI REVEALS PATHOGENICITY-ASSOCIATED GENE FAMILIES IN Phakopsora pachyrhizi https://www.biorxiv.org/content/10.64898/2026.07.03.736376v1

🐦 Why are bird genomes so difficult to assemble? Birds have dozens of tiny, gene-rich microchromosomes that are frequently fragmented, misplaced, or missing from genome assemblies despite containing important genetic information. 📖 Read the publication: lnkd.in/gar-GrKZ #BirdGenomics #Biodiversity

Gene regulatory networks to decipher tomato multi-pathogen interactions Multari et al. nph.onlinelibrary.wiley.com/doi/10.1111/...

Very excited to share our new Nature study! We discovered that replication stress stabilizes CTCF-dependent chromatin loops enclosing stressed nascent DNA, where G9a-mediated heterochromatin protects it from nucleolytic degradation. rdcu.be/frzLg Huge thanks to all our collaborators and co-authors!

A conserved architectural domain shapes centromere evolution in Drosophila https://www.biorxiv.org/content/10.64898/2026.06.30.735607v1

Interested on latest research on the evolution of the first forms of life? Drop by Inder Raj Sing's poster, where he will be showing work from his GBE paper on pre-LUCA TF evolution. 📋 Poster Session A 🗓️ June 29, 6 pm Read the paper here 👉 doi.org/10.1093/gbe/evag141 #SMBE2026 #societyjournal

🌾🧬Plants face multifactorial stress, not single stressors. Combination specific regulatory modules coordinate protective pathways like ROS buffering. Integrative tools offers a path to climate smart crops #plantscience @abioticstress.bsky.social www.sciencedirect.com/science/arti...

Novel Drosophila cis-regulatory elements can be uncovered by footprinting transcription factor binding sites in ATAC-seq data https://www.biorxiv.org/content/10.64898/2026.06.22.733832v1

PhD position open @inrae-bioger.bsky.social ⬇️

Hi-C data from the filamentous fungus Podospora anserina and associated 3D models to visualize the spatial organization of its chromosomes https://www.biorxiv.org/content/10.64898/2026.06.14.732207v1

"A role for epigenetics in rapid adaptation" by Reid S. Brennan & Melissa H. Pespeni "Epigenetic variation may be key to rapid adaptation and can interact with genetic change during evolutionary rescue. However, key questions remain.." FREE till Aug. 7th at authors.elsevier.com/a/1nH%7EscQb...

Nearly a year after our symposium on Repeat-Induced Point (RIP) mutations, I’m happy to share the fruit of some of our discussions. The fungal RIP hypermutator mechanism has deep eukaryotic roots www.sciencedirect.com/science/arti... We hope to spark interest in this underappreciated mechanism.

LIKE HETEROCHROMATIN PROTEIN 1: a Polycomb-beyond composite regulator of chromatin in development, stress, and defense doi.org/10.1093/plce... #PlantScience @aspbofficial

A funded PhD position for studying wheat pathogen adaptation to climate factors is open in my lab @inrae-bioger.bsky.social @univparissaclay.bsky.social in collab. @jki-research.bsky.social (Germany), with a start planned for autumn 2026 ▶️ eng-bioger.versailles-saclay.hub.inrae.fr/teams-and-pl...

#SMBE2026 S03: Genome Plasticity and Evolutionary Innovation 🗓️ Tue Jun 30, 10:20 am - Part 1 🗓️ Tue Jun 30, 1:20 pm - Part 2 🔗 smbe2026.org/programme

Happy to share our work! 🍄🍇 Botrytis cinerea grapevine-specialized strains harbor a specific repertoire of transposons. While retrotransposon-derived small RNAs do not appear to play a significant role in virulence on grapevine, a new giant transposon—a #Starship— confers arsenic resistance.

Capolavoro 🎨 alert 🚨! What is the role of gene body methylation in invertebrates? Despite extensive speculation linking it to plasticity and environmental responses, its mechanistic effects and heritability remain unclear. Our take out in @natecoevo.nature.com: www.nature.com/articles/s41... 1/

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