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 www.biorxiv.org/content/10.64898/2026.04...

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 DNA O-MAP enables proximity labeling at specific genomic loci in fixed cells using programmable oligonucleotides, revealing locus-proximal proteomes and chromatin interactions without genetic…

DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

buff.ly/NRhk83b?utm_...

Ancestral Genome Reconstruction. www.biorxiv.org/content/10.64898/2026.04...

Contrasting transcriptional responses and genetic determinants underlie Zymoseptoria tritici adaptation mechanisms to simulated host defense environments www.biorxiv.org/content/10.64898/2026.04...

Synthetic chromosomes for 3D functional genomics: from principles to AI-guided design The role of genome 3D organization for fundamental chromatin processes, such as long-range promoter-activator regulatory interactions, remains ambiguo…

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.

Functional validation showed 10 GHA-identified genes affecting virulence.

Here, we show that natural population metadata can be leveraged to map the genetic basis of pathogen adaptation, offering a scalable alternative to large controlled phenotyping experiments limiting classic GWAS.

Using 830 Zymoseptoria tritici field strains collected from 12 wheat cultivars during a natural epidemic, we identified pathogen loci associated with specific hosts.

Genome–host association mapping reveals wheat pathogen genes involved in host specialization - Nature Plants This study introduces genome–host association (GHA), leveraging natural epidemics to map the genetic landscape of host adaptation in the pathogen Zymoseptoria tritici. Applied to 832 wheat fungal stra...

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
👇👇

Parallel but distinct adaptive routes in the budding and fission yeasts after 10,000 generations of experimental evolution - Nature Ecology & Evolution Experimental evolution of fission yeast (Schizosaccharomyces pombe) in the same environment as a previous experiment with budding yeast (Saccharomyces cerevisiae) reveals parallel evolution but distin...

#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...

A H3K27me3 reader complex couples H3K27me3 accumulation to nascent transcription of transposable elements in Paramecium - Genome Biology Background The ability to deposit histone H3K27-trimethyl (me3) marks is essential for transcriptional repression by Polycomb Repressive Complex 2 (PRC2). This is largely attributed to Polycomb repres...

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

Identifying Adaptive Footprints in the Presence of Demographic Uncertainty Abstract. Identifying genomic regions shaped by natural selection is a central goal in evolutionary genomics. Existing machine learning methods for this ta

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. www.biorxiv.org/content/10.64898/2026.03...

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...

Evolution of a distinct chromatin regulatory landscape in brown algae - Nature Ecology & Evolution 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 elucidat...

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 www.biorxiv.org/content/10.64898/2026.03...

"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? ⬇️

Transposable elements hitchhike on Starships across fungal genomes - Nature Communications Large mobile genetic elements known as Starships act as vehicles for transferring transposable elements (TEs) between fungi. Here, Griem-Krey et al. show that these ‘hitchhiking’ TEs can drive rapid e...

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 www.biorxiv.org/content/10.64898/2026.03...

Advances in molecular tools for elucidating nucleic acid biology in fungal pathogens Check out this new review highlighting advances in DNA-, RNA-, and chromatin-based technologies and how they are used to keep pace with the emerging threat

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 www.biorxiv.org/content/10.64898/2026.03...

Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila - Nature Genetics Pico-C, a low-input Micro-C approach, reveals that dynamic three-dimensional genome folding precedes zygotic genome activation in Drosophila.

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...

Recurrent Chromosome Destabilization Through Repeat-Mediated Rearrangements in a Fungal Pathogen Abstract. Genomic instability caused by chromosomal rearrangements has severe consequences for organismal fitness and progression of cancerous cell lines.

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