Computational Biology Dpt at Pasteur

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...

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

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.

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...

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-...

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

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

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...

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.

Napoleon's retreat from Moscow CREDIT Barbieri et al., Current Biology

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

From Ancient Bones to Modern Insights: Argentinian Scientist Uncovering History of Disease in Paris YouTube video by European Commission

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

David Bikard has been awarded the EMBO Gold Medal in recognition of his pioneering work on gene editing, including his recent editing of a target bacterial population directly in the gut of mice.

🥇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...

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...

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

Looking back at 20 years of Open Access publishing at Nucleic Acids Research When Nucleic Acids Research (NAR) was launched in 1974, the concept of an Open Access publication model was not on anyone’s radar. Instead, the focus was o

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 Vision enables real-time conversion of patients' 2D medical images (such as MRIs and CT scans) into 3D, thus improving visualization and understanding of the patient's state of health. ...

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