Ruibao's first paper from the lab is out in @nature.com . www.nature.com/articles/s41.... Collab with @multicellgenome.bsky.social & @jennahed.bsky.social. How did cells stick together and form the first animals? The protist Ministeria suggests cellular aggregation had a role. @iuqcb.bsky.social

A unicellular relative links aggregative multicellularity to animal origins - Nature

Aggregative multicellularity was key to the evolution of the multicellular animal genetic toolkit.

nature.com

Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below

Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics

This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...

nature.com

This adds another piece to an emerging evolutionary picture: many fungal effectors may not have evolved de novo to manipulate hosts. Instead, they started as antimicrobial proteins to compete with other microbes — and were repeatedly repurposed as fungi adapted to host-associated lifestyles.

New GreenRobust publication by the group of Eric Kemen on using machine learning to identify beneficial microbiota: www.nature.com/articles/s41...

Machine learning reveals biocontrol agents shaping disease outcome in natural Arabidopsis populations - Nature Communications

Plants can recruit beneficial microbes to suppress pathogens, offering a route to rational biocontrol beyond empirical screening. Here, the authors use machine learning to identify disease-associated ...

nature.com

📣 New preprint! 🧵 Fantastic work led by @antonkraege.bsky.social Fact: Cerato-platanins are everywhere in fungi. Found across the fungal kingdom, implicated in everything from development to virulence to immune activation. But what do they *actually* do? We finally found the answer 👇

Excited to share that our paper on Horizontal Gene Transfer is now out in its final form in @gigascience.bsky.social! 🥳 By analysing 163 high-quality ant genomes, we show that HGT from bacteria is widespread across the ants and likely has adaptive functions! doi.org/10.1093/giga... 🐜📸: Alex Wild

RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...

Analog intrinsic recoding measures RNA dynamics without chemical conversion

Steady-state RNA abundance measurements mask the synthesis and decay rates that shape gene expression. Analog intrinsic recoding sequencing (AIR-seq) repurposes the base-pairing properties of N4-hydro...

biorxiv.org

New preprint: how are young and old proteins distributed in sequence space? 🌌 Comparing de novo, intergenic and canonical proteins from yeast and fly with length- and composition-matched randomized controls, using alignment-free k-mer distances. 1/7 doi.org/10.64898/202...

our paper starts with an analysis of the dynamics of 3D chromatin in cardiac differentiation, for ventricular and atrial cardiomyocytes. They are different! And by single cell methyl-HiC we can discern subtype differences. www.science.org/doi/10.1126/...

Dose-dependent sensitivity of human three-dimensional chromatin to a heart disease–linked transcription factor

Dosage-sensitive transcription factors (TFs) underlie altered gene regulation in human developmental disorders, and cell type–specific gene regulation is linked to the reorganization of three-dimensio...

science.org

Programmed chromosome elimination correlates with the overexpression of cohesin and additional B chromosome-encoded genes in Aegilops speltoides https://www.biorxiv.org/content/10.64898/2026.07.20.739560v1

Super proud and excited about this work, led masterfully by Peiwei Chen! A fun and fruitful collaboration with department colleagues Andy Clark & Alexei Aravin. After 30 yrs of studying transposons, this is one of the very first times I see them jump in real time in their natural host! Hurrah! 🥳

Peiwei Chen@peiwei-chen.bsky.social · 3w ago

How do transposons jump when they’re released from host control? I babysat two chromosomes for 2 years, making sure they are ok without most piRNAs. Here’s what we found & excited to share my 1st postdoc paper: “piRNA loss unleashes episodic transposition bursts” www.biorxiv.org/content/10.6...

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

Elias Friman@eliasfriman.bsky.social · 3mo ago

Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/ www.biorxiv.org/content/10.6...

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!

Replication-stress-induced chromatin loops protect fork stability - Nature

Replication stress induces the formation of transient chromatin loops that enclose de novo heterochromatin-enriched stalled replication forks.

nature.com

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

Early Evolution of the Prokaryotic Transcription Factor Repertoire

Abstract. Transcription initiation is regulated by transcription factors (TFs). Though TFs determine phenotype, they are nonessential for minimal cellular

doi.org

🌾🧬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...

Distinct regulatory networks mediate plant adaptation to multifactorial abiotic stress combinations: rethinking of plant stress genetics

Plants in natural environments often encounter multifactorial abiotic stress combinations that trigger regulatory responses distinct from those trigge…

sciencedirect.com

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 ⬇️

Frédéric Suffert@wheatpath.bsky.social · 2mo ago

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...

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

LIKE HETEROCHROMATIN PROTEIN 1: a Polycomb-beyond composite regulator of chromatin in development, stress, and defense

Abstract. Amid its dynamic roles within Polycomb group (PcG) complexes, a growing body of work shows that LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) interacts w

doi.org

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.

bioRxiv Genomics@biorxiv-genomic.bsky.social · 2mo ago

Role of transposons in the specialization of Botrytis cinerea to grapevine: Insights into small RNAs and a new Starship https://www.biorxiv.org/content/10.64898/2026.05.30.728154v1

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/

Gene body methylation suppresses intragenic transcription and permits epigenetic inheritance in a cnidarian - Nature Ecology & Evolution

Experiments in the cnidarian Nematostella vectensis show a role of gene body methylation in transposable element suppression and that epigenetic inheritance is constrained by chromatin context and tra...

nature.com

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