Spread the word ! LLMs "mistakes" are features, NOT bugs.

A thoughtful and beautifully written @quantamagazine.bsky.social article about genome regulatory innovation at the origin of animals. Featuring some of our work and highlighting key open questions. Thanks to @philipcball.bsky.social for this fantastic piece.

New paper! We generated and/or (re)analyzed ~100 #metagenomics Hi-C datasets to provide a comprehensive analysis of bacterial and viral metagenomes across VERY different environments. Congratulations to all authors especially Amaury Bignaud and @mmarbout.bsky.social for the huge work! #metaHiC

www.cell.com/cell/abstrac... A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis

"Transposable elements are vectors of recurrent transgenerational epigenetic inheritance" Congrats Vincent Colot and team! www.science.org/doi/10.1126/...

In the early days of quantum chemistry, before we had computers to calculate the shapes of electron orbitals, one man invented a mechanical machine that simulated their shapes. My latest column for @chemistryworld.com www.chemistryworld.com/opinion/the-...

Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9

Our paper is now out in Molecular Cell! Check the thread in this former post: www.cell.com/molecular-ce...

In @elife.bsky.social: Criticality-driven enhancer-promoter dynamics in Drosophila chromosomes doi.org/10.7554/eLif...

No new genes needed to fly - just rewire what you have! 🦇🧬 Great new paper from the labs of @fany-real.bsky.social @stemundi.bsky.social @dariloops.bsky.social doi.org/10.1038/s415... #EvoDevo #SingleCell #BatWings

Highly needed !

Today marks the end of en-JUNE-eering, the month where I focused mostly on the nitty gritty of improving genomics ML infrastructure. Here are some of the highlights:

📢 New paper out in Mol Syst Biol! During the development of WT yeast colonies, small cell subpopulations experience transient, high-intensity mutational bursts. Such hypermutation episodes are modulated by the DNA damage tolerance pathway 🧬 🔗 www.embopress.org/doi/full/10....

tree of life core lab has put together such a manuscript, detailing a lot of information on the lab work needed for reference genomes for biodiversity which you can find here: www.biorxiv.org/content/10.1...

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭 Check out our paper - fresh off the press!!! We find widespread functional conservation of enhancers in absence of sequence homology Including: a bioinformatic tool to map sequence-diverged enhancers! rdcu.be/enVDN github.com/tobiaszehnde...

Hi everyone! The latest method from the Whitehouse lab: PCP 
PCP uses a novel proximity barcoding strategy to simultaneously map 3D genome organization at various resolutions at the single molecule level: Out soon, check the updated BioRxiv – little thread: 1/11 www.biorxiv.org/content/10.1...

🚨 We're hiring! 🚨 A 2-year postdoc position is now open in our lab to explore the fascinating world of yeast polyploid genomes, their structure, stability, and adaptive potential. 🔗 More info here: docs.google.com/document/d/1... Please repost! #Postdoc #Genomics #Yeast #Polyploidy #Evolution

Interested in chromatin architecture?
 Checkout our new method - PCP - that can map genome organization as multi-way interactions as well as nucleosome footprint and nucleosome spacing at very high resolution. www.biorxiv.org/content/10.1...

Great opportunity to work at the frontier between genomics and deep learning. research.pasteur.fr/en/job/perma...

Last call: Tomorrow friday April 11th 🤘

@sorbonne-universite.fr et @mnhn.fr organise cet échange entres spécialistes sur les applications actuelles, les perspectives d’avenir et les verrous méthodologiques liés à l’adoption de l’IA dans l’étude et la conservation de la biodiversité. Gratuit, sur inscription

The importance of moving away from bulk! Occupancy of Pol II at promoters is dramatically different between fly and mouse cells! When looking single molecule! Proud of the team! @kasitc.bsky.social @molinalab.bsky.social doi.org/10.1038/s443...

The latest live-cell imaging work from the Boettiger lab measures chromosomal kinetics across genomic scales — it’s moving faster than you think! —, and puts a number on the ‘in vivo’ speed of cohesin loop extrusion itself. www.biorxiv.org/content/10.1...

Miloshev et al., 2025, Linker Histones Maintain Genome Stability and Drive the Process of Cellular Ageing [review] www.imrpress.com/journal/FBL/... Interesting figure: we did observe NRL increase with ageing (onlinelibrary.wiley.com/doi/10.1111/...). Not sure about about loop sizes, to be checked

Come start your lab in beautiful Strasbourg 🇫🇷 www.nature.com/naturecareer...

The DNA in our cells is not naked but instead is compacted by being wrapped around nucleosomes assembled from histone proteins. In our current view, this produces the chromatin architecture that leaves some regions open for transcription while others are more compacted & transcriptionally silent 1/n

We an open postdoc position (UK) generegulation.org/job-opening/

🧬🧪🦠🧫 @science.org www.science.org/doi/10.1126/... @rkoszul.bsky.social @leameneu.bsky.social @christophechapard.bsky.social @chromozz.bsky.social @pasteur.fr @sorbonne-universite.fr @institutcurie.bsky.social + PS www.science.org/doi/epdf/10.... @gfudenberg.bsky.social @vram142.bsky.social

Cette année, mon cours @collegedefrance.bsky.social traitera de la régulation des gènes par les séquences enhancers. Une des clés de notre développement. Premier cours le vendredi 21 février à 10h. Entrée libre, salle chauffée. Amis et Collègues parisiens, merci de diffuser!

Our latest work: how can compartmentalization emerge in a eukaryotic genome lacking canonical heterochromatin? By investigating bacterial genomes put in yeast, we show that the presence or absence of transcription is sufficient! #chromatin #3Dgenome #generegulation www.science.org/doi/10.1126/... 👇

Deep learning models (@chromozz.bsky.social) trained only on yeast chromosomes predict nucleosome positioning, RNA Poll II and cohesin tracks along foreign DNA, based on the sequence alone. This implies that the behavior of any DNA in a host cell follows deterministic sequence-based rules.

What happens to bacterial genomes when they're cloned into yeast? Do they transcribe, do they get silenced, do they get packaged away from the rest of the DNA? This cool study congrats to the Koszul lab team at Pasteur for this great work. www.science.org/doi/10.1126/...

#RésultatScientifique🔎 Quand un ADN étranger s'intègre dans une cellule hôte, comment s’adapte-t-il aux règles métaboliques de son nouvel occupant ? @rkoszul.bsky.social et ses collaborateurs ont enquêté ! 🕵️ 🤝 @cnrs.bsky.social @pasteur.fr @mnhn.fr https://buff.ly/40GvJL2