Paul Villoutreix
@paulvilloutreix.bsky.social
We develop machine learning frameworks to decode the geometry and topology of tissue development from spatial omics data | Junior Professor INSERM & Group Leader Turing Center for Living Systems | https://bioml.lis-lab.fr
Pinned
Looking back, 2024 has been our most productive year. Here is a short thread on the various lines of work we've been braiding.
Our aim is to understand the relationship between single cell molecular states and tissue dynamics.
We develop methods to bridge transcriptomics and bioimage analysis
Our aim is to understand the relationship between single cell molecular states and tissue dynamics.
We develop methods to bridge transcriptomics and bioimage analysis
Reposted by Paul Villoutreix
Are you passionate about the mathematics of data science, computational geometry and topology and want to apply your skills to a beautiful biological question?
Come do a PhD with us!
You will help us understand of how boundaries are established and maintained in early heart development.
Come do a PhD with us!
You will help us understand of how boundaries are established and maintained in early heart development.
November 15, 2025 at 3:42 PM
Are you passionate about the mathematics of data science, computational geometry and topology and want to apply your skills to a beautiful biological question?
Come do a PhD with us!
You will help us understand of how boundaries are established and maintained in early heart development.
Come do a PhD with us!
You will help us understand of how boundaries are established and maintained in early heart development.
Are you passionate about the mathematics of data science, computational geometry and topology and want to apply your skills to a beautiful biological question?
Come do a PhD with us!
You will help us understand of how boundaries are established and maintained in early heart development.
Come do a PhD with us!
You will help us understand of how boundaries are established and maintained in early heart development.
November 15, 2025 at 3:42 PM
Are you passionate about the mathematics of data science, computational geometry and topology and want to apply your skills to a beautiful biological question?
Come do a PhD with us!
You will help us understand of how boundaries are established and maintained in early heart development.
Come do a PhD with us!
You will help us understand of how boundaries are established and maintained in early heart development.
Reposted by Paul Villoutreix
Felix Zhou's u-Segment3D is out:
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
November 12, 2025 at 2:41 AM
Felix Zhou's u-Segment3D is out:
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
www.nature.com/articles/s41...
It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation.
It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
Reposted by Paul Villoutreix
Congratulations to Dr @baalberti.bsky.social !! 🎉
And many thanks to his jury members @randersson.bsky.social @arnausebe.bsky.social @olivier-gandrillon.mastodon.social.ap.brid.gy Marie Sémon Anouck Necsulea and co-supervizor @paulvilloutreix.bsky.social
And many thanks to his jury members @randersson.bsky.social @arnausebe.bsky.social @olivier-gandrillon.mastodon.social.ap.brid.gy Marie Sémon Anouck Necsulea and co-supervizor @paulvilloutreix.bsky.social
November 10, 2025 at 9:37 AM
Congratulations to Dr @baalberti.bsky.social !! 🎉
And many thanks to his jury members @randersson.bsky.social @arnausebe.bsky.social @olivier-gandrillon.mastodon.social.ap.brid.gy Marie Sémon Anouck Necsulea and co-supervizor @paulvilloutreix.bsky.social
And many thanks to his jury members @randersson.bsky.social @arnausebe.bsky.social @olivier-gandrillon.mastodon.social.ap.brid.gy Marie Sémon Anouck Necsulea and co-supervizor @paulvilloutreix.bsky.social
Excited to be in Paris later this week!
#Agenda
With
@batistaruan.bsky.social, Valentin Rineau, @ignacioq.bsky.social, Aleksandra Walczak, Guillaume Achaz, @k4tj4.bsky.social - @r3rto.bsky.social, Maël Montévil, @paulvilloutreix.bsky.social, Barbara Bravi, Cyril Rauch, Giuseppe Longo, Anton Robert, @charbelelhani.bsky.social , Ana Soto
With
@batistaruan.bsky.social, Valentin Rineau, @ignacioq.bsky.social, Aleksandra Walczak, Guillaume Achaz, @k4tj4.bsky.social - @r3rto.bsky.social, Maël Montévil, @paulvilloutreix.bsky.social, Barbara Bravi, Cyril Rauch, Giuseppe Longo, Anton Robert, @charbelelhani.bsky.social , Ana Soto
November 9, 2025 at 9:37 AM
Excited to be in Paris later this week!
Reposted by Paul Villoutreix
#Agenda
With
@batistaruan.bsky.social, Valentin Rineau, @ignacioq.bsky.social, Aleksandra Walczak, Guillaume Achaz, @k4tj4.bsky.social - @r3rto.bsky.social, Maël Montévil, @paulvilloutreix.bsky.social, Barbara Bravi, Cyril Rauch, Giuseppe Longo, Anton Robert, @charbelelhani.bsky.social , Ana Soto
With
@batistaruan.bsky.social, Valentin Rineau, @ignacioq.bsky.social, Aleksandra Walczak, Guillaume Achaz, @k4tj4.bsky.social - @r3rto.bsky.social, Maël Montévil, @paulvilloutreix.bsky.social, Barbara Bravi, Cyril Rauch, Giuseppe Longo, Anton Robert, @charbelelhani.bsky.social , Ana Soto
November 9, 2025 at 8:36 AM
#Agenda
With
@batistaruan.bsky.social, Valentin Rineau, @ignacioq.bsky.social, Aleksandra Walczak, Guillaume Achaz, @k4tj4.bsky.social - @r3rto.bsky.social, Maël Montévil, @paulvilloutreix.bsky.social, Barbara Bravi, Cyril Rauch, Giuseppe Longo, Anton Robert, @charbelelhani.bsky.social , Ana Soto
With
@batistaruan.bsky.social, Valentin Rineau, @ignacioq.bsky.social, Aleksandra Walczak, Guillaume Achaz, @k4tj4.bsky.social - @r3rto.bsky.social, Maël Montévil, @paulvilloutreix.bsky.social, Barbara Bravi, Cyril Rauch, Giuseppe Longo, Anton Robert, @charbelelhani.bsky.social , Ana Soto
Reposted by Paul Villoutreix
Happy to share STORIES out now on Nature Methods
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transport - Nature Methods
By learning a differentiation potential using an optimal transport-based approach, STORIES models and infers cell fate trajectories using spatiotemporal omics data.
www.nature.com
November 4, 2025 at 7:25 AM
Happy to share STORIES out now on Nature Methods
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
Great program, amazing scientists and beautiful facilities!! I visited for 6 months in 2023, a unique place in Europe at the intersection of maths, computer science and developmental biology
Our call for ELBE Visiting Faculty at the Center for Systems Biology Dresden is live with deadline 30 November: www.csbdresden.de/join-us/as-a... Please visit us during your sabbatical!
@mpi-cbg.de @math-mpicbg.bsky.social @csbdresden.bsky.social
@mpi-cbg.de @math-mpicbg.bsky.social @csbdresden.bsky.social
As a Visiting Faculty
© 2025 CSBD
www.csbdresden.de
October 31, 2025 at 1:46 PM
Great program, amazing scientists and beautiful facilities!! I visited for 6 months in 2023, a unique place in Europe at the intersection of maths, computer science and developmental biology
Reposted by Paul Villoutreix
🧬 Excited to share Nicheformer out now in Nature Methods!
A transformer foundation model linking single-cell & spatial omics, learning spatial context from gene expression to map tissue organization.
Led by Ale Tejada & Anna Schaar 👏
👉 www.nature.com/articles/s41...
A transformer foundation model linking single-cell & spatial omics, learning spatial context from gene expression to map tissue organization.
Led by Ale Tejada & Anna Schaar 👏
👉 www.nature.com/articles/s41...
October 30, 2025 at 7:19 PM
🧬 Excited to share Nicheformer out now in Nature Methods!
A transformer foundation model linking single-cell & spatial omics, learning spatial context from gene expression to map tissue organization.
Led by Ale Tejada & Anna Schaar 👏
👉 www.nature.com/articles/s41...
A transformer foundation model linking single-cell & spatial omics, learning spatial context from gene expression to map tissue organization.
Led by Ale Tejada & Anna Schaar 👏
👉 www.nature.com/articles/s41...
Reposted by Paul Villoutreix
Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding
The formation of neural circuits depends on the precise spatial and temporal organisation of neuronal populations during development. In the vertebrate spinal cord, progenitors are patterned into mole...
www.biorxiv.org
October 26, 2025 at 5:15 PM
Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇
www.biorxiv.org/content/10.1...
Had a very nice time visiting Granada for the annual heart ICDAR meeting! We presented Harshit Pateria's current work in collaboration with Robert Kelly following up from our recent publication on the second heart field www.nature.com/articles/s41...
October 17, 2025 at 3:51 PM
Had a very nice time visiting Granada for the annual heart ICDAR meeting! We presented Harshit Pateria's current work in collaboration with Robert Kelly following up from our recent publication on the second heart field www.nature.com/articles/s41...
Reposted by Paul Villoutreix
🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution.
www.biorxiv.org/cgi/content/...
www.biorxiv.org/cgi/content/...
October 16, 2025 at 7:09 AM
Reposted by Paul Villoutreix
Pleasure to announce the program of my new series of lectures at the College de France in Nov-Dec. Continuing on the theme of Biological information. I will focus on the computational aspects, building on David Marr's tri-level of analysis in biological systems. YouTube link sent when it starts.
October 7, 2025 at 6:13 AM
Pleasure to announce the program of my new series of lectures at the College de France in Nov-Dec. Continuing on the theme of Biological information. I will focus on the computational aspects, building on David Marr's tri-level of analysis in biological systems. YouTube link sent when it starts.
Reposted by Paul Villoutreix
🤩👍🏼💪🏼 Meet #TopoSPAM - a high-performance simulation platform for biological morphogenesis with a friendly Python interface. @tudresden.bsky.social @csbdresden.bsky.social @mpi-cbg.de. Solve both continuous and discrete active mechanics! Released today: arxiv.org/abs/2509.24905
TopoSPAM: Topology grounded Simulation Platform for morphogenesis and biological Active Matter
We present a topology grounded, multiscale simulation platform for morphogenesis and biological active matter. Morphogenesis and biological active matter represent keystone problems in biology with ad...
arxiv.org
October 1, 2025 at 10:21 AM
🤩👍🏼💪🏼 Meet #TopoSPAM - a high-performance simulation platform for biological morphogenesis with a friendly Python interface. @tudresden.bsky.social @csbdresden.bsky.social @mpi-cbg.de. Solve both continuous and discrete active mechanics! Released today: arxiv.org/abs/2509.24905
Reposted by Paul Villoutreix
Very elegant and efficient methodology to recover spatial patterns from multi-modal spatial datasets 👌!! Many congratulations @paulvilloutreix.bsky.social and to all authors👏😀!!
September 19, 2025 at 9:16 AM
Very elegant and efficient methodology to recover spatial patterns from multi-modal spatial datasets 👌!! Many congratulations @paulvilloutreix.bsky.social and to all authors👏😀!!
Very happy to introduce jsPCA, a fast and interpretable computational framework for spatial transcriptomics that simultaneously identifies spatial domains and variable genes across multi-slice and multi-sample data.
September 19, 2025 at 6:50 AM
Very happy to introduce jsPCA, a fast and interpretable computational framework for spatial transcriptomics that simultaneously identifies spatial domains and variable genes across multi-slice and multi-sample data.
Reposted by Paul Villoutreix
Are digits modified fins, or evolutionary innovations? Read how we tackled this old question from a new angle🧪
A story with @chasebolt.bsky.social, @homeobox.bsky.social and myself, coordinated by @denisduboule.bsky.social from @college-de-france.fr and published in @nature.com today!
#InHoxWeTrust
A story with @chasebolt.bsky.social, @homeobox.bsky.social and myself, coordinated by @denisduboule.bsky.social from @college-de-france.fr and published in @nature.com today!
#InHoxWeTrust
September 17, 2025 at 5:26 PM
Are digits modified fins, or evolutionary innovations? Read how we tackled this old question from a new angle🧪
A story with @chasebolt.bsky.social, @homeobox.bsky.social and myself, coordinated by @denisduboule.bsky.social from @college-de-france.fr and published in @nature.com today!
#InHoxWeTrust
A story with @chasebolt.bsky.social, @homeobox.bsky.social and myself, coordinated by @denisduboule.bsky.social from @college-de-france.fr and published in @nature.com today!
#InHoxWeTrust
Very happy to share MODIS - a new Multi-Omics Data Integration method for Small and unpaired datasets!
We solve a long-standing problem in the field: how to perform data integration for small unpaired datasets
Our solution: learning with class imbalance on both reference and target datasets!
We solve a long-standing problem in the field: how to perform data integration for small unpaired datasets
Our solution: learning with class imbalance on both reference and target datasets!
September 16, 2025 at 10:35 AM
Very happy to share MODIS - a new Multi-Omics Data Integration method for Small and unpaired datasets!
We solve a long-standing problem in the field: how to perform data integration for small unpaired datasets
Our solution: learning with class imbalance on both reference and target datasets!
We solve a long-standing problem in the field: how to perform data integration for small unpaired datasets
Our solution: learning with class imbalance on both reference and target datasets!
Reposted by Paul Villoutreix
#PressRelease 🗞️ The 2025 CNRS Gold Medal has been awarded to Stéphane Mallat, recognised the world over for his research on mathematics applied to signal processing and artificial intelligence.
👉 cnrs.fr/en/press/bet...
#CNRStalents 🏅
👉 cnrs.fr/en/press/bet...
#CNRStalents 🏅
September 11, 2025 at 9:31 AM
#PressRelease 🗞️ The 2025 CNRS Gold Medal has been awarded to Stéphane Mallat, recognised the world over for his research on mathematics applied to signal processing and artificial intelligence.
👉 cnrs.fr/en/press/bet...
#CNRStalents 🏅
👉 cnrs.fr/en/press/bet...
#CNRStalents 🏅
Reposted by Paul Villoutreix
Springboard for an international scientific career! 🧬🧪🔭⚛️🧠🌱 Call for #MaxPlanckResearchGroups launched; applications are possible until October 14, 2025 www.mpg.de/max-planck-r... #ScienceCareer
September 9, 2025 at 12:10 PM
Springboard for an international scientific career! 🧬🧪🔭⚛️🧠🌱 Call for #MaxPlanckResearchGroups launched; applications are possible until October 14, 2025 www.mpg.de/max-planck-r... #ScienceCareer
Reposted by Paul Villoutreix
Become a Theory Fellow at Janelia.
🔍 Use computation & theory to tackle biological problems.
🖥️ Leverage state-of-the-art computational infrastructure
🤝 Collaborate across scientific disciplines
Apply by Nov. 3 @ https://janelia.link/theoryfellowprogram
🔍 Use computation & theory to tackle biological problems.
🖥️ Leverage state-of-the-art computational infrastructure
🤝 Collaborate across scientific disciplines
Apply by Nov. 3 @ https://janelia.link/theoryfellowprogram
September 9, 2025 at 3:00 PM
Become a Theory Fellow at Janelia.
🔍 Use computation & theory to tackle biological problems.
🖥️ Leverage state-of-the-art computational infrastructure
🤝 Collaborate across scientific disciplines
Apply by Nov. 3 @ https://janelia.link/theoryfellowprogram
🔍 Use computation & theory to tackle biological problems.
🖥️ Leverage state-of-the-art computational infrastructure
🤝 Collaborate across scientific disciplines
Apply by Nov. 3 @ https://janelia.link/theoryfellowprogram
Reposted by Paul Villoutreix
Are you an AI expert who wants to stay in academia and change the world by understanding the most complex things we know - living organisms? Want to lead your own group, based in Heidelberg DE, working language English? @embl.org is hiring in AI embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Group Leader – AI in Biology
Are you ready to lead groundbreaking research in AI for Biology? Join us at EMBL! We are seeking a visionary scientist to establish their own independent research group bridging innovations in machine...
embl.wd103.myworkdayjobs.com
September 8, 2025 at 11:43 AM
Are you an AI expert who wants to stay in academia and change the world by understanding the most complex things we know - living organisms? Want to lead your own group, based in Heidelberg DE, working language English? @embl.org is hiring in AI embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Paul Villoutreix
Places available in our online courses this autumn: @embo.org Project Management (17-19.09), Negotiation for Scientists (18-19.09), Lab Leadership for Postdocs (07-09.10) and for Group Leaders (04-06.11) + Self-Leadership (14-16.10). Register now: www.embolableadership.org/our-courses/ #EMBOLabLead
September 5, 2025 at 6:30 AM
Places available in our online courses this autumn: @embo.org Project Management (17-19.09), Negotiation for Scientists (18-19.09), Lab Leadership for Postdocs (07-09.10) and for Group Leaders (04-06.11) + Self-Leadership (14-16.10). Register now: www.embolableadership.org/our-courses/ #EMBOLabLead
Reposted by Paul Villoutreix
Dresden researchers @paveltomancak.bsky.social @bruvellu.bsky.social, Carl Modes, @cuencam15.bsky.social & colleagues published in @nature.com that a tissue fold in fruit fly embryos buffers mechanical stresses & may have evolved in response to mechanical forces. www.mpi-cbg.de/news-outreac...
Mechanical forces drive evolutionary change
A small tissue fold present in fruit fly embryos buffers mechanical stresses and may have evolved in response to mechanical forces.
www.mpi-cbg.de
September 3, 2025 at 3:26 PM
Dresden researchers @paveltomancak.bsky.social @bruvellu.bsky.social, Carl Modes, @cuencam15.bsky.social & colleagues published in @nature.com that a tissue fold in fruit fly embryos buffers mechanical stresses & may have evolved in response to mechanical forces. www.mpi-cbg.de/news-outreac...
Reposted by Paul Villoutreix
📢We're #hiring Group Leaders!
Apply to lead a lab at Janelia & advance biology using theory, computational modeling & machine learning.
🔹5-year renewable appointment
🔹Pioneer new tools & approaches
🔹Collaborate across disciplines
Apply by Nov. 4👉 https://janelia.link/groupleader
Apply to lead a lab at Janelia & advance biology using theory, computational modeling & machine learning.
🔹5-year renewable appointment
🔹Pioneer new tools & approaches
🔹Collaborate across disciplines
Apply by Nov. 4👉 https://janelia.link/groupleader
August 26, 2025 at 7:00 PM
📢We're #hiring Group Leaders!
Apply to lead a lab at Janelia & advance biology using theory, computational modeling & machine learning.
🔹5-year renewable appointment
🔹Pioneer new tools & approaches
🔹Collaborate across disciplines
Apply by Nov. 4👉 https://janelia.link/groupleader
Apply to lead a lab at Janelia & advance biology using theory, computational modeling & machine learning.
🔹5-year renewable appointment
🔹Pioneer new tools & approaches
🔹Collaborate across disciplines
Apply by Nov. 4👉 https://janelia.link/groupleader