Paul Villoutreix

-> research group webpage: 

Embryogenesis is a fascinating process. It is the process by which a single fertilized cell is turned into a multi-cellular organism. It is a really beautiful phenomenon, studied in various species, from the sea urchin, to the fruit fly, to the zebrafish, to the chicken, to the mouse, to the human…

Recent technological developments in microscopy imaging and other measurement techniques have transformed embryology into a data intensive science. To address the question of how an embryo develops from a data driven perspective, I am starting an interdisciplinary research group at the intersection of developmental biology, mathematics and machine learning. Open positions available, please contact me 🙂


Dynamic multi-domain translation for high-throughput sequencing data
with Thierry Artières

In addition, I have been leading the open science project the Embryo Digital Atlas: a logoweb based platform for the visualization of complex experimental datasets of embryogenesis in an easy and beautiful way. You can contribute here. We are now extending the interactive visualization tool to Virtual Reality headsets, thanks to a mini grant award by the Mozilla Science Lab. All the code is developed openly and hosted on this github repository.

Twitter: @paulvilloutreix

Research Positions

2019 – Present | Group Leader – Turing Center for Living Systems – Marseille
2017 – 2018 | Postdoctoral Fellow – Zelzer Lab – Weizmann Institute of Science
2017 – 2018 | Visiting Fellow – Center for Data Arts – The New School, NYC
2015 – 2017 | Postdoctoral Fellow – Shvartsman Lab – Princeton University


Google Scholar Citations

Cross-View Kernel Transfer
Riikka Huusari, Cécile Capponi, Paul Villoutreix, Hachem Kadri – Pattern Recognition, 2022

Random walk informed community detection reveals heterogeneities in large networks 
Solène Song, Malek Senoussi, Paul Escande, Paul Villoutreix – Arxiv, 2022

Application of 3D MAPs pipeline identifies the morphological sequence chondrocytes undergo and the regulatory role of GDF5 in this process
Sarah Rubin, Ankit Agrawal, Johannes Stegmaier, Sharon Krief , Neta Felsenthal, Jonathan Svorai, Yoseph Addadi, Paul Villoutreix*, Tomer Stern*, Elazar Zelzer* – Nature Communications, 2021

Video explaining the main findings :

Weizmann News: Making Bone Growth Transparent

What machine learning can do for developmental biology
Paul Villoutreix, invited paper, Development, 2021

Towards a general framework for spatio-temporal transcriptomics
Julie Pinol, Thierry Artières, Paul Villoutreix, NeurIPS, LMRL workshop, 2020

Kernel transfer over multiple views for missing data completion
Riikka Huusari, Cécile Capponi, Paul Villoutreix, Hachem Kadri – arxiv (2019)

Entropic effects in cell lineage tree packings
Jasmin Imran Alsous*, Paul Villoutreix*, Norbert Stoop*, Stanislav Y. Shvartsman, Jörn Dunkel – Nature Physics, 14(10), 1016-1021, 2018.DomDrnaW4AEcrnq.jpg-large

MIT News
A mathematical view on cell packing
Sandi Miller | Department of Mathematics

News & Views
Connected development
Ben D. MacArthur, Nature Physics, 2018

Featured in Nature (with Jasmin Imran Alsous):
The visualizations transforming biology
Ewan Callaway, Nature, 535(7610), 187-188, 2016.

Synthesizing developmental trajectories
Paul Villoutreix*, Joakim Andén*, Bomyi Lim, Hang Lu, Yannis Kevrekidis, Amit Singer, Stanislav Y. Shvartsman – PLoS Comput Biol 13(9): e1005742, 2017.

Cover of September’s issue of PLoS Computational Biology

Collective Growth in a Simple Cell Network
Jasmin Imran Alsous, Paul Villoutreix, Alexander M. Berezhkovskii, Stanislav Y. Shvartsman – Current Biology 27(17), 2670–2676, 2017.

A post by Jasmin Imran Alsous featured on The Node describing the story behind the paper “Collective Growth in a Simple Cell Network”
Allometry in a Simple Cell Network – The Node, 2017.

screen-shot-2017-02-17-at-6-47-51-pmAn integrated modelling framework from cells to organism based on a cohort of digital embryos
Paul Villoutreix*, Julien Delile*, Barbara Rizzi*, Louise Duloquin*, Thierry Savy, Paul Bourgine, René Doursat, Nadine Peyriéras, Scientific Reports, 6:37438, 2016.
Code and Datasets or github repository

Book Chapter

Vers une modélisation multi-échelle de la variabilité biologique?
Paul Villoutreix, Chap. 19 in Modéliser & Simuler. Epistémologies et pratiques de la modélisation et de la simulation. Tome 2, Franck Varenne, Marc Silberstein, Philippe Huneman et Sebastien Dutreuil, Eds. pp. 643 – 664, Editions matériologiques, Novembre 2014.

Ph.D Thesis

rplot_allred_eyeyellowRandomness and variability in animal embryogenesis, a multi-scale approach
Paul Villoutreix, PhD Dissertation – Université René Descartes – Paris V, 2015


Piece of news on the Embryo Project Encyclopedia.

Showcase on the Information is Beautiful Award website.

Picture1Blog post describing The Embryo Digital Atlas’ journey to the Global Sprint.

Interview on Mozilla Science Lab blog – The Embryo Digital Atlas.

@mozillascienceBlog post discussing our work on data-driven visualizations of developing embryos and its relationships to art. This is a supporting webpage for Mozilla Science Lab  community call on art and science.


2015 | PhD in Mathematical Biology
Paris Descartes University – Frontiers of Life Science Program
2014 | Visiting Student Researcher
Stanford University – Department of Mathematics
2011 | MSc. Interdisciplinary Approaches of Life Sciences
Paris Diderot University
2011 | MSc. Applied Mathematics
Supélec Engineering School



Turing Center for Living Systems
Luminy Campus
Marseille, France

Marseille Machine Learning Team
Marseille, France