For today Methods Primer session, we will have Gabriel VICTORINO CARDOSO talking about the use of score-based generative models as informative priors for solving inverse problems and discussing how this approach can be used for denoising and anomaly detection.

For the 4th Method Primer of the spring, we will have Stephane FISCHER talking about single-cell analyses, introducing the building blocks of standard single-cell analyses (normalization, dimension reduction, clustering and visualization), and some common deviations (epigenetics, spatial,..)

For today Method Primer we will host Joëlle Barido-Sottani, who will talk about using birth-death processes as models for diversification in species phylogenies, discussing how these models are structured, how to derive their likelihood and how they can be applied to study species diversification.

For today's Methods Primer we will have @fdevicofallani.bsky.social talking about Duality in Complex Networks, discussing unappreciated topological properties of interconnected systems, and how those properties can be used across fields, from systems biology to neuroscience.

Our Methods Primer seminar are resuming! Today, March the 20th, we will have Ernest Mordret who will talk about Fine-tuning Protein Language Models for functional classification and discovery.

How did farming reach the Southern Andes? Through migration or cultural transmission? Our new paper in @nature.com combines ancient DNA, isotopes, archaeology & paleoclimate to reconstruct 2,000+ years of history in Uspallata, Mendoza. www.nature.com/articles/s41... A Thread🧵 (1/25+)

Local agricultural transition, crisis and migration in the Southern Andes - Nature

In the Uspallata Valley, agriculture was adopted by local populations, as evidenced by genetic continuity from earlier hunter-gatherers to farmers; maize-dependent groups from the same regional p...

nature.com

Kicking off the AI for Life Sciences course at @institutpasteur.bsky.social today! 🧬🤖 Special thanks to @bonomimax.bsky.social and Ernest Mordret for the co-organization, to the @pasteuredu.bsky.social and all the trainers. Excited to dive into how algorithms can help us understand life!

Institut Pasteur (@pasteur.fr) is recruiting new young PIs to open new groups in the Institute. Deadline is February 9th! Don't miss the opportunity!

New preprint from my team! Led by @jkobject.com "scPRINT-2: Towards the next-generation of cell foundation models and benchmarks" We perform an additive benchmark of single-cell Foundation Models (scFMs) and we present scPRINT-2 pre-trained on 350 million cells 📝 www.biorxiv.org/content/10.6...

ReCoN: REconstruction of multicellular COrdination Network We are releasing a new tool to model multicellular coordination and cellular responses in tissu! 🫀🫁 The package is just out, and the preprint should follow within a few days😇 If you want to have a look already: github.com/cantinilab/R...

GitHub - cantinilab/ReCoN: Exploring multicellular coordination from single-cell gene expression / multi-omics using mutlilayer network representations

Exploring multicellular coordination from single-cell gene expression / multi-omics using mutlilayer network representations - cantinilab/ReCoN

github.com

We are proud to share a recent preprint from our lab: Taxonomic-free metagenome GWAS to identify gut microbiome functions influencing host phenotypes doi.org/10.64898/202... which studies the potential of taxonomy-free GWAS approach of the human gut microbiome, using our implemented tool MOGS.

For the last Methods Primer of the winter session, we will have Jean-Baptiste Masson talking about Statistical testing in behavioural latent spaces --discussing methods to learned latent space and comparing frequentist and bayesian models to perform test on the resulting latent variables.

📣📣 very attractive junior group leader positions @pasteuredu.bsky.social 👇

Institut Pasteur | 130 years of biomedical research@pasteur.fr · 8mo ago

🔬 Call to create junior research groups at the Institut Pasteur Focus: Infectious diseases, host-microbe interactions, vaccines Special interest: AI methodologies 📅 Deadline: Feb 9, 2026 👥 2-12 years post-PhD Apply now 📝 research.pasteur.fr/en/call/crea... #JobOpportunity #Research

Our Methods Primer continue! Today, Dec 5th, we will have Hervé Perdy talking about assortative mating and vertical cultural transmission in genetic studies --discussing the polygenic model and how our estimation of the genetic component of traits is impacted by those two phenomena.

‪We're resuming our Methods Primer seminar! Today, we will have Alex Barbier–Chebbah talking about bandit problem --when an agent must decide between immediate gains or potential long-term rewards. He will present canonical solutions and new class of algorithms.

There a is a joint call between @pasteur.fr and @cnrsbiologie.bsky.social for a mid career group leader position in AI and genomics (or molecular biology). Don't hesistate to spread the word if you know anyone relevant. research.pasteur.fr/en/call/mid-...

Mid-career Group Leader position in AI in genomics at Institut Pasteur, Paris - Research

Institut Pasteur and the CNRS are launching a call for a mid-career group leader position in AI in genomics. We are looking for an experienced researcher (typically with > 8 years of research experien...

research.pasteur.fr

The INCEPTION is organizing its Annual Symposium. This year is about GWAS & beyond! We're happy to have @bpasaniuc.bsky.social, @caina89.bsky.social, Iuliana Ionita-Laza , Sriram Sankararaman, and others, who will talk about tools for understanding the genetic determinants of complex diseases

INCEPTION Symposium 2025 - Research

INCEPTION symposium 2025 - Focus on GWAS: paving the way for the future of genetics.

research.pasteur.fr

We are happy to share a new paper from our lab: The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals www.nature.com/articles/s42... which investigates environmental effects on microbiome interactions, using our previously published tool MANOCCA.

The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals - Communications Biology

Co-abundance analysis of 938 healthy individuals uncovers how host factors shape gut microbiome interactions, highlighting a core set of 200 impacted genera and additional factor-specific interactions...

nature.com

We're resuming our Methods Primer seminar! Today, we will have Thibault Lagache talking about statistical analysis of spatial relationships in biological imaging from both conventional and super-resolution microscopy.

DNA from Napoleon’s 1812 army identifies the pathogens likely responsible for the army’s demise during their Russian retreat. www.cell.com/current-biol... Nicolás Rascovan & colleagues @currentbiology.bsky.social

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

Please join us next Thursday (Nov 6th, 12am, in Jules Bordet Auditorium) for a presentation by Aryan Kamal from @unibas.ch. Aryan will talk about his recent work that examined safeguarding cell identity with PROX1 in liver and ZNF385D in blood.

Don't miss the upcoming DBC seminar by @juliosaezrod.bsky.social, head of Research at EMBL-EBI's! (on Friday 24 october at 2pm in Auditorium Jules Bordet for those at Pasteur). Julio will present works on knowledge-based machine learning to extract disease mechanisms from spatial multi-omics data.

MOTL is finally out in Genome Biology! Work led by David Hirst and @anaisbaudot.bsky.social If you are interested in multi-omics matrix factorization when few samples are available (e.g. rare diseases), have a look at it! #multiomics #machinelearning #transferlearning

Anaïs Baudot@anaisbaudot.bsky.social · last yr.

Excited to share David Hirst's PhD work! 🧬 When you only have a few datasets available for multi-omics integration, for instance because you work on rare diseases, one solution is Transfer Learning. Introducing #MOTL - now available in Genome Biology! doi.org/10.1186/s130...

www.youtube.com/watch?v=hMH1... I am very thankful to the @ec.europa.eu for highlighting my research at @institutpasteur.bsky.social . It is a privilege for me to have the opportunity of developing my professional life here.

From Ancient Bones to Modern Insights: Argentinian Scientist Uncovering History of Disease in Paris

YouTube video by European Commission

youtube.com

Super cool to see scPRINT, work of my team led by @jkobject.com, featured by @cnrsbiologie.bsky.social To access the work www.nature.com/articles/s41...

CNRS Biologie@cnrsbiologie.bsky.social · last yr.

#RésultatScientifique 🔎 Une IA pour lire le langage des cellules ! 🧬 Grâce à scPRINT, des chercheurs décryptent les réseaux de gènes qui contrôlent les états cellulaires à partir de millions de données single-cell. buff.ly/XMcDog0

Two weeks ago, I had the pleasure to discuss the research activity of my team @institutpasteur.bsky.social in the panel discussion "How is AI and data-driven innovation reshaping oncology" at @parissaclay.bsky.social SPRING 2025 in @ecolepolytechnique.bsky.social #ParisSaclaySPRING #SPRING25

🥇Congratulations to David Bikard @dbikard.bsky.social on winning the EMBO Gold Medal! Well-deserved recognition for advancing synthetic biology and microbial genetics. 🔬✨ @embo.org www.embo.org/press-releas...

This long-shot paper aimed to assess whether common GWAS pipelines are reaching their limits for prediction purposes. The review process was lengthy and painful. We're curious to see how it will fly! All comments are welcome! www.cell.com/hgg-advances...

Polygenic risk score prediction accuracy convergence

Polygenic risk prediction has the potential to transform the diagnosis, treatment, and prevention of many common human diseases. However, the timescale and breadth of this transformation is partly unk...

cell.com

The dpt is pleased to host John Lees, group leader at EMBL-EBI, for a seminar today (24/04) about the bacterial accessory genome adaptive! research.pasteur.fr/en/event/dep...