Computational Biology Dpt at Pasteur
@pasteur-dbc.bsky.social
A multidisciplinary community of researchers dedicated to better understanding complex biological mechanisms and systems, from bacteria to human
Reposted by Computational Biology Dpt at Pasteur
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 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...
www.nature.com
November 10, 2025 at 5:00 PM
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 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.
Today, we will have Thibault Lagache talking about statistical analysis of spatial relationships in biological imaging from both conventional and super-resolution microscopy.
November 7, 2025 at 7:55 AM
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.
Today, we will have Thibault Lagache talking about statistical analysis of spatial relationships in biological imaging from both conventional and super-resolution microscopy.
Reposted by Computational Biology Dpt at Pasteur
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
Nicolás Rascovan & colleagues
@currentbiology.bsky.social
October 24, 2025 at 3:00 PM
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
Nicolás Rascovan & colleagues
@currentbiology.bsky.social
Reposted by Computational Biology Dpt at Pasteur
🌎👩🔬 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...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
September 3, 2025 at 8:39 AM
🌎👩🔬 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...
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.
October 30, 2025 at 8:16 AM
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.
October 15, 2025 at 9:34 AM
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.
Reposted by Computational Biology Dpt at Pasteur
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
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
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...
🧬 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...
MOTL: enhancing multi-omics matrix factorization with transfer learning - Genome Biology
Joint matrix factorization is popular for extracting lower dimensional representations of multi-omics data but loses effectiveness with limited samples. Addressing this limitation, we introduce MOTL (...
link.springer.com
July 26, 2025 at 10:55 AM
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
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
Reposted by Computational Biology Dpt at Pasteur
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.
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
www.youtube.com
July 10, 2025 at 10:19 AM
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.
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.
Reposted by Computational Biology Dpt at Pasteur
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...
To access the work www.nature.com/articles/s41...
#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
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
scPRINT : le premier modèle d'IA français pour déchiffrer les réseaux génétiques
Chaque cellule est un véritable monde moléculaire.
www.insb.cnrs.fr
May 19, 2025 at 8:06 AM
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...
To access the work www.nature.com/articles/s41...
Reposted by Computational Biology Dpt at Pasteur
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
#ParisSaclaySPRING #SPRING25
June 4, 2025 at 9:04 PM
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
#ParisSaclaySPRING #SPRING25
Reposted by Computational Biology Dpt at Pasteur
🥇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...
Well-deserved recognition for advancing synthetic biology and microbial genetics. 🔬✨ @embo.org www.embo.org/press-releas...
June 6, 2025 at 12:07 PM
🥇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...
Well-deserved recognition for advancing synthetic biology and microbial genetics. 🔬✨ @embo.org www.embo.org/press-releas...
Reposted by Computational Biology Dpt at Pasteur
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...
www.cell.com
June 3, 2025 at 9:05 AM
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...
Log In ‹ Research — WordPress
research.pasteur.fr
April 24, 2025 at 7:24 AM
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...
Reposted by Computational Biology Dpt at Pasteur
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
I am super happy to annonce that after 9 months under review the first paper of my PhD: scPRINT is finally available on Nature Comms! 🎉🧬
www.nature.com/artic...
www.nature.com/artic...
scPRINT: pre-training on 50 million cells allows robust gene network predictions
Nature Communications - Authors present a state-of-the-art cell foundation model trained on 50 million cells. They show that the model generates a meaningful gene network and has zero-shot...
www.nature.com
April 16, 2025 at 1:16 PM
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
Reposted by Computational Biology Dpt at Pasteur
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/...
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
doi.org
April 18, 2025 at 4:52 PM
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/...
Reposted by Computational Biology Dpt at Pasteur
Pour ou contre l'IA? "Ne pas confondre recherche et précipitation", par @chtruchet.bsky.social dans @maglarecherche.bsky.social www.larecherche.fr/intelligence...
Ne pas confondre recherche et précipitation
https://www.larecherche.fr/intelligence-artificielle/ne-pas-confondre-recherche-et-précipitation#
April 9, 2025 at 10:51 AM
Pour ou contre l'IA? "Ne pas confondre recherche et précipitation", par @chtruchet.bsky.social dans @maglarecherche.bsky.social www.larecherche.fr/intelligence...
Reposted by Computational Biology Dpt at Pasteur
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!
web.cvent.com/event/....
Loads of important business insights from leaders in the field!
April 10, 2025 at 12:40 PM
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!
web.cvent.com/event/....
Loads of important business insights from leaders in the field!
Reposted by Computational Biology Dpt at Pasteur
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
I'm very happy to share the last paper from my previous postdoc with the amazing @epcrocha.bsky.social! Thanks to the reviewers for their feedback, which improved our work!
#Plasmids #AMR #HorizontalGeneTransfer #Evolution
#Plasmids #AMR #HorizontalGeneTransfer #Evolution
March 31, 2025 at 4:20 PM
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
Reposted by Computational Biology Dpt at Pasteur
📢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
Happy to see so many students on campus interested in AI!
@bonomimax.bsky.social @pasteuredu.bsky.social
March 17, 2025 at 8:41 AM
📢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
Happy to see so many students on campus interested in AI!
@bonomimax.bsky.social @pasteuredu.bsky.social
Reposted by Computational Biology Dpt at Pasteur
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
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. ...
www.pasteur.fr
March 14, 2025 at 11:59 AM
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!
March 10, 2025 at 7:36 AM
Take note, the next Pasteur Qbio mini-symposium "Simulated Bodies - Simulated Processes" is taking place on March the 12th!
Reposted by Computational Biology Dpt at Pasteur
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...
Join on zoom (Monday) at 9am PT / 12pm ET / 6pm CET: www.biorxiv.org/content/10.1...
March 9, 2025 at 5:14 PM
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...
Join on zoom (Monday) at 9am PT / 12pm ET / 6pm CET: www.biorxiv.org/content/10.1...
Reposted by Computational Biology Dpt at Pasteur
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
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...
research.pasteur.fr
March 3, 2025 at 10:18 AM
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
Reposted by Computational Biology Dpt at Pasteur
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....
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....
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 ...
www.embopress.org
March 3, 2025 at 9:24 AM
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....
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....
Reposted by Computational Biology Dpt at Pasteur
🔔 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...
🧠🔎 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...
March 4, 2025 at 9:47 AM
🔔 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...
🧠🔎 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...