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Computational Biology Dpt at Pasteur

@pasteur-dbc.bsky.social
178 followers 40 following 23 posts

A multidisciplinary community of researchers dedicated to better understanding complex biological mechanisms and systems, from bacteria to human

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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 17/04/2026
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.
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 10/04/2026
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,..)
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 03/04/2026
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.
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 27/03/2026
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.
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 20/03/2026
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.
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Nico Rascovan @nrascovan.bsky.social · 18/03/2026
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+)
nature.com
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...
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Laura Cantini @cantinilab.bsky.social · 09/03/2026
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!
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Nico Rascovan @nrascovan.bsky.social · 27/01/2026
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!
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Laura Cantini @cantinilab.bsky.social · 17/12/2025
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...
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Rémi Trimbour - MD-PhD student @remitrimbour.bsky.social · 20/01/2026
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.com
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
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Statistical Genetics Unit at Pasteur Paris @ggspasteur.bsky.social · 16/01/2026
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.
doi.org
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 19/12/2025
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.
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Nadia Izadi-Pruneyre @nadia-izadi.bsky.social · 09/12/2025
📣📣 very attractive junior group leader positions @pasteuredu.bsky.social 👇
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 05/12/2025
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.
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 28/11/2025
‪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.
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Levayer Lab @levayerr.bsky.social · 27/11/2025
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-...
research.pasteur.fr
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...
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 24/11/2025
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
research.pasteur.fr
INCEPTION Symposium 2025 - Research
INCEPTION symposium 2025 - Focus on GWAS: paving the way for the future of genetics.
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Statistical Genetics Unit at Pasteur Paris @ggspasteur.bsky.social · 10/11/2025
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.
nature.com
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...
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 07/11/2025
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.
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Cell Press @cellpress.bsky.social · 24/10/2025
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
Napoleon's retreat from Moscow CREDIT Barbieri et al., Current Biology
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Rayan Chikhi @rayanchikhi.bsky.social · 03/09/2025
🌎👩‍🔬 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...
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 30/10/2025
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.
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 15/10/2025
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.
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Laura Cantini @cantinilab.bsky.social · 26/07/2025
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
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Nico Rascovan @nrascovan.bsky.social · 10/07/2025
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.
youtube.com
From Ancient Bones to Modern Insights: Argentinian Scientist Uncovering History of Disease in Paris
YouTube video by European Commission
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Laura Cantini @cantinilab.bsky.social · 19/05/2025
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...
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Laura Cantini @cantinilab.bsky.social · 04/06/2025
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
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Institut Pasteur | 130 years of biomedical research @pasteur.fr · 06/06/2025
🥇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...
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.
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Statistical Genetics Unit at Pasteur Paris @ggspasteur.bsky.social · 03/06/2025
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...
cell.com
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...
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 24/04/2025
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...
research.pasteur.fr
Log In ‹ Research — WordPress
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Laura Cantini @cantinilab.bsky.social · 16/04/2025
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
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Eduardo Rocha @epcrocha.bsky.social · 18/04/2025
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/...
doi.org
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
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Frederic Lemoine @fredlem.bsky.social · 09/04/2025
Pour ou contre l'IA? "Ne pas confondre recherche et précipitation", par @chtruchet.bsky.social dans @maglarecherche.bsky.social www.larecherche.fr/intelligence...
larecherche.fr
Ne pas confondre recherche et précipitation
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Jeremie Kalfon 👨‍💻🧬🤖🚀 @jkobject.com · 10/04/2025
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!
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Eduardo Rocha @epcrocha.bsky.social · 31/03/2025
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
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Laura Cantini @cantinilab.bsky.social · 17/03/2025
📢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
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Institut Pasteur | 130 years of biomedical research @pasteur.fr · 14/03/2025
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
pasteur.fr
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. ...
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 10/03/2025
Take note, the next Pasteur Qbio mini-symposium "Simulated Bodies - Simulated Processes" is taking place on March the 12th!
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Hannes Stark @hannes-stark.bsky.social · 09/03/2025
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...
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Frederic Lemoine @fredlem.bsky.social · 03/03/2025
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
research.pasteur.fr
Permanent research engineer position as Head of Hub Algorithmics & AI pole - Research
The Hub of Bioinformatics and Biostatistics provides analytical support to research units and platforms at the Institut Pasteur. The Hub is committed to this mission through:  As head of the Algorithm...
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Romain Koszul @rkoszul.bsky.social · 03/03/2025
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....
embopress.org
Parasitic plasmids are anchored to inactive regions of eukaryotic chromosomes through a nucleosome signal | The EMBO Journal
imageimageThe naturally occurring S. cerevisiae 2µ plasmid is one of few documented cases of eukaryotic plasmids, undergoing equal distribution between mother and daughter cells during mitosis. Using ...
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Institut Pasteur | 130 years of biomedical research @pasteur.fr · 04/03/2025
🔔 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...
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Max Bonomi @bonomimax.bsky.social · 05/03/2025
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
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Institut Pasteur | 130 years of biomedical research @pasteur.fr · 18/02/2025
🧠🔎 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...
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Rayan Chikhi @rayanchikhi.bsky.social · 03/02/2025
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...
github.com
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Eduardo Rocha @epcrocha.bsky.social · 10/02/2025
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!👇
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 27/01/2025
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.
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 20/01/2025
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.
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 13/01/2025
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
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 06/01/2025
Our Primer MEthod seminar are resuming! Today Jean-Baptiste Masson will talk about variational Bayesian inference, presenting principles and associated methods, and introducing concepts and general approaches to amortized inferences.
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