Design and experimental characterization of specificity-switching mutational paths of WW domains Specific interactions between proteins and other biomolecules are ubiquitous in cellular processes. How specificity is encoded in the protein sequence and can be modified through a minimal set of conc...

Link: www.biorxiv.org/content/10.6...

We use energy-based generative models (RBM) to design full mutational paths connecting two natural proteins of different binding specificities, and verify experimentally that intermediate sequences stay functional.

New preprint: Design and experimental characterization of specificity-switching mutational paths of WW domains.

Cross-individual translation of spontaneous zebrafish brain activity through a shared latent representation Spontaneous activity is a hallmark of brain function, reflecting the underlying circuit organization. Identifying conserved structure across individuals in this self-sustained activity has remained a ...

Link: www.biorxiv.org/content/10.6...

We develop latent-aligned RBMs, to uncover a common representational space from cell-resolved whole-brain recordings spanning several distinct larval zebrafish individuals.

New preprint: Cross-individual translation of spontaneous zebrafish brain activity through a shared latent representation

Designing molecular RNA switches with Restricted Boltzmann machines - Nature Communications Riboswitches are allosteric RNA molecules that change conformation upon ligand binding to regulate downstream genes. Here, the authors use Restricted Boltzmann machines trained on natural sequences to...

Just published in @natcomms.nature.com : Designing molecular RNA switches with Restricted Boltzmann machines. Full paper: www.nature.com/articles/s41...

Master internship position available, with possibility of PhD after. More details here: sites.google.com/view/jorgefd...

See www.cofund-physics.universite-paris-saclay.fr for more information. Deadline to apply is July 31 2025.

We invite early-career researchers to apply for the STARφ programme of Université Paris-Saclay, funded by the European Union under the Marie Skłodowska-Curie COFUND action. Our team at the IPhT at CEA-Saclay is among the participating laboratories.

The candidate is expected to have a strong background in machine learning, computational biology and statistical physics.

For more details and to apply contact me (DM or email).

The work will be carried out in close collaboration with the experimental team of Frédéric Ducongé, at MIRCen, Institut de Biologie François Jacob of CEA.

The goal of the project is to develop machine learning approaches to infer fitness landscapes from large sequencing datasets obtained in such experiments.

Aptamers are often obtained through rounds of in vitro competitive selection (SELEX), starting from random artificial libraries of ~10^15 distinct distinct sequences. However, engineered libraries cannot fully explore sequence space diversity.

An 14 months months postdoctoral positions is available in my team, to work on computational models of artificial evolution for aptamer design.

The summer school “Molecular Evolution and Design: from Computational Models to Biological and Medical Applications”, which we are organizing in Cargèse on Corsica island, will take place from August 19-29 2025 - the place is fantastic in summer ! 🧵

For more details and to apply: adum.fr/as/ed/voirpr....
Deadline to apply is May 23, 2025. DM if you have questions.

By addressing the inherent biases and noise structures in these datasets, we will create more accurate computational frameworks for protein fitness landscape modeling.

This PhD project aims to develop novel machine learning approaches for robust characterization and modeling of noise in deep sequencing data from selection-amplification experiments.

We are looking for a candidate for a PhD position shared between Gen&Chem group (BGE/IRIG) at CEA-Grenoble and IPhT at CEA-Saclay, combining expertise in statistical physics, computational biology and computer science. 🧵

2025 This summer school will cover different topics in protein and RNA design as listed below, and will focus on teaching modern modeling approaches in this domain, from statistical physics, computer scien...

We would like to invite applications and propositions for contributed talks or posters from students, postdocs and young researchers. To register and for more details, see the website: sites.google.com/view/coevolc...

The school will cover different topics in protein and RNA design, and will focus on teaching modern modeling approaches in this domain, from statistical physics, computer science, and machine learning fields to recent experimental approaches.

The summer school “Molecular Evolution and Design: from Computational Models to Biological and Medical Applications”, which we are organizing in Cargèse on Corsica island, will take place from August 19-29 2025 - the place is fantastic in summer ! 🧵

Personal website - Open positions Jorge FERNANDEZ-DE-COSSIO-DIAZ CNRS Junior Professor Institut de Physique Théorique Contact: jorge[dot]fdcd[at]icloud[dot]com

See sites.google.com/view/jorgefd... for more details.

I have an 18 months postdoc position available in Paris-Saclay, starting in March 2025, to work at the interface of machine learning, computational biology and statistical physics.

The first list filled up, so here's a second list of AI for Science researchers on bluesky.

Let me know if I missed you / if you'd like to join!

bsky.app/starter-pack...

Hey folks! I got a bit swamped with all the new #julialang BlueSky people and made my own mega Julia #programmer starter pack!

go.bsky.app/Hv4RKzM

What other starter packs would you want to see? I'm in health research, mathematics, and open source/science. 🧪🛟🩺 📊

Thanks please add me

Hello, I'd love to join

Thanks ! Please add me :)