Publications

Google scholar list

What can machine learning 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

3D MAPs discovers the morphological sequence chondrocytes undergo in the growth plate and the regulatory role of GDF5 in this process
Sarah Rubin, Ankit Agrawal, Johannes Stegmaier, Jonathan Svorai, Yoseph Addadi, Paul Villoutreix*, Tomer Stern*, Elazar Zelzer* – in review, 2020

Video explaining the main findings : http://vimeo.com/463129275

Kernel transfer over multiple views for missing data completion
Riikka Huusari, Cécile Capponi, Paul Villoutreix, Hachem Kadri – in review (2020)

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

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 LimHang 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.

An 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

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

Others

Piece of news on the Embryo Project Encyclopedia.

Showcase on the Information is Beautiful Award website.

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

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

Blog 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.