Computational Biology Dpt at Pasteur

🍽️ Eating: One Behavior, Many Sciences! Join us Nov 9 at Institut Pasteur for an interdisciplinary exploration of how genes, brains, cultures & environments shape what we eat. Where nutrition meets neuroscience, genetics, anthropology & more. 🧬🧠🌍 📍Paris | 9:30–17:30 🔗 docs.google.com/forms/d/e/1F...

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+)

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...

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 👇

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-...

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

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.

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

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.

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...

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...

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...

Excited to see scPRINT published in @natcomms.nature.com ! scPRINT is a large cell model for the inference of gene networks pre-trained on 50Mcells with innovative pretraining tasks inspired from biology. Work led by @jkobject.com

Always had a soft spot for @narjournal.bsky.social . Not just because I got my 1st first author paper there, but because they were the first traditional journal I knew that went for full open access. It was 20 years ago. Here's Richard Roberts editorial (in OA 😉): doi.org/10.1093/nar/...

Pour ou contre l'IA? "Ne pas confondre recherche et précipitation", par @chtruchet.bsky.social dans @maglarecherche.bsky.social www.larecherche.fr/intelligence...

Got invited with @Nucleate, to the @McDermott conference on health and life science last week. web.cvent.com/event/.... Loads of important business insights from leaders in the field!

Great to see this in its final form: our study showing that antibiotic resistance genes are more often found in families of plasmids that evolve faster than average (in terms of gain/loss of genes, homologous recombination...). Kudos to @charlescoluzzi.bsky.social now Junior Chair Professor @ U Lyon

📢Here WE go!!! AI for life sciences course kicking off at @pasteur.fr with a lecture from @laineelodie.bsky.social. Happy to see so many students on campus interested in AI! @bonomimax.bsky.social @pasteuredu.bsky.social

Avatar Medical, a spin-off from the Institut Pasteur, receives CE marking for its innovative solution «AVATAR MEDICAL Vision ». Avatar Medical turns 2D medical scans into 3D visuals, giving surgeons and patients clearer health insights. #MedTech

Take note, the next Pasteur Qbio mini-symposium "Simulated Bodies - Simulated Processes" is taking place on March the 12th!

The Evo 2 authors join us tomorrow in the reading group to discuss their paper: "Genome modeling and design across all domains of life with Evo 2" www.biorxiv.org/content/10.1... Join on zoom (Monday) at 9am PT / 12pm ET / 6pm CET: www.biorxiv.org/content/10.1...

We're hiring! Join the Hub of Bioinformatics and Biostatistics at @pasteur.fr as the Head of the "Algorithmics, AI, and Mathematical Modeling" pole. 🧬💻 Apply now: hub-jobs2025.pasteur.cloud #Bioinformatics #ScienceJobs

Are you curious about eukaryotic plasmids? PhD student Fabien Girard with Axel Cournac in the lab explore the positioning of plasmid 2u, one of these rare (known) episomes, in the budding yeast nucleus. The results were surprising. #plasmids #chromatin #3Dgenome www.embopress.org/doi/full/10....

🔔 Reminder! 🧠🔎 Why do we fall for fake news? Join philosophers & neuroscientists to explore how our brains shape our perception of truth. 📅 March 15, 2 PM | Hall Duclaux | Institut Pasteur 🎟 Free, registration required: www.eventbrite.fr/e/comprendre...

If you are at @pasteur.fr today, come see @bussigio.bsky.social at 11AM in Salle Retrovirus. You won’t regret it #rna #cryoEM #coolscience @ipdbsc.bsky.social

🧠🔎 Why do we fall for fake news? Join philosophers & neuroscientists to explore how our brains shape our perception of truth. 📅 March 15, 2 PM | Hall Duclaux | Institut Pasteur 🎟 Free, registration required : www.eventbrite.fr/e/comprendre...

We have updated all Logan contigs (now at version 1.1)! Contiguity has been much improved (2x) and a duplicated k-mers bug has been fixed. More information and changelog here: github.com/IndexThePlan...

Many years to get this one out, while gaining huge respect for people doing clinical trials (perseverance!). We show that antibiotic treatments spur changes in the phage composition of the human gut, with bursts of virulent phages that may facilitate homeostasis. Check Eugen's thread!👇

To conclude our Primer Method winter session, Aimee Taylor will talk about Bayesian models to classify recurrent infections in clinical trial participants. She will present key concepts underpinning these models, focusing on identity-by-descent and sibship graphs.

For today's Primer, @jkobject.com will talk about Foundation models of RNAseq data and biological networks, presenting deep learning and transformer models in the context of single cell data and discussing how to train these models on atlas-scale datasets.

Our Primer Methods session continue! This morning @bonomimax.bsky.social will talk about Bayesian inference in integrative structural biology, presenting theory and applications where different types of experimental data have to be combined to obtain accurate structural models of biological systems