AlphaGenome, une nouvelle avancée en intelligence artificielle pour comprendre les effets des mutations génétiques Google vient de sortir un nouveau logiciel d’IA pour explorer les effets des intelligences artificielles. Décryptage de deux spécialistes qui ne font pas partie de l’équipe.

Nouvelle publication sur l'AlphaGenome, une nouvelle avancée en intelligence artificielle pour comprendre les effets des mutations génétiques par Julien Mozziconacci de StrInG & al. parue dans @france.theconversation.com
@mnhn.fr

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.

Agreed! But that's when it would be nice to see actual distributions instead of box plots.

the surprise in this plot is that the NRL is not quantized. Would be interesting to see a distribution of NRL for each point.

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

A host organelle integrates stolen chloroplasts for animal photosynthesis Sea slugs steal foreign chloroplasts and store them in specialized organelles that facilitate photosynthesis and eventual digestion to mediate starvation resistance.

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 DNA methylation loss at transposable elements (TEs) can affect neighboring genes and be epigenetically inherited in plants, yet the determinants and significance of this additional system of inheritan...

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

The simple machine that visualised atomic orbitals In 1931, Harvey Elliott White developed a device that traced out the shapes of electron clouds by approximating solutions to the Schrödinger equation

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....

On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species Since its inception in 2019, the Tree of Life programme at the Wellcome Sanger Institute has released high-quality, chromosomally-resolved reference genome assemblies for over 2000 species. Tree of Li...

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...

Conservation of regulatory elements with highly diverged sequences across large evolutionary distances Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...

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...

The 3D Genome Shapes the Regulatory Code of Developmental Genes We revisit the notion of gene regulatory code in embryonic development in the light of recent findings about genome spatial organization. By analogy w…

We wrote a piece a few years back discussing the existence of a gene regulatory "code". The take home message is that if you define properly what are: the "encoded objects", the "codewords" and the "adaptor" it can make sense to use this word. www.sciencedirect.com/science/arti...

Postdoc_Evol_Genomics_Sorbonne.docx Postdoctoral position in Yeast Evolutionary Genomics Hosting unit Laboratory of Computational, Quantitative, and Synthetic Biology (CQSB). The CQSB is an interdisciplinary research unit within the ...

🚨 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

Chromatin architecture mapping by multiplex proximity tagging Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed a novel proximity-tagging method which assigns unique DNA b...

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...

Group Head in AI and Mathematical Modeling Applied to Genomics - Research The Bioinformatics and Biostatistics Hub at Institut Pasteur provides computational biology support to research units and platforms at the Institut Pasteur. Our mission is to: As the head of the Algor...

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

Last call: Tomorrow friday April 11th 🤘

L'IA pour comprendre et préserver la biodiversité Dans le cadre du Sommet pour l'action sur l’IA 2025, du lancement de PostGenAI@Paris, et de l’initiative « IA responsable », SCAI propose un cycle de conférences sur les enjeux et les risques liés à l...

@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

Call For Two Group Leader Positions - Strasbourg-Ville, Bas-Rhin (FR) job with IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) | 12837602 The Institute of Genetics, Molecular and Cellular Biology (IGBMC) is seeking two outstanding group leaders to establish independent research teams.

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

Diagram of chromatin and nucleosomes from https://www.genome.gov/genetics-glossary/Nucleosome

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