Machine Learning
MODIS: Multi-omics data integration for small and unpaired datasets
Daniel Lepe-Soltero, Thierry Artières, Anaïs Baudot, Paul Villoutreix, LMRL workshop, ICLR 2025
Hierarchical novel class discovery for single-cell transcriptomic profiles
Malek Senoussi, Thierry Artières, Paul Villoutreix – arXiv, 2024
MOTL: enhancing multi-omics matrix factorization with transfer learning
David Hirst, Morgane Térézol, Laura Cantini, Paul Villoutreix, Matthieu Vignes, Anaïs Baudot – in review
Partial label learning for automated classification of single cell transcriptomic profiles
Malek Senoussi, Thierry Artieres*, Paul Villoutreix* – PLoS Computational Biology
Hierarchical classification for weakly supervised transcriptomics data
Malek Senoussi, Thierry Artieres, Paul Villoutreix – CAp, 2022
Cross-View Kernel Transfer
Riikka Huusari, Cécile Capponi, Paul Villoutreix, Hachem Kadri – Pattern Recognition, 2022
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
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.
Single cell morphometrics
Single-cell morphometrics reveals T-box gene-dependent patterns of epithelial tension in the Second Heart field
Clara Guijarro+, Solène Song+, Benoit Aigouy, Raphael Clement, Paul Villoutreix*, Robert G. Kelly* – in press, Nature Communications, 2024
Limited column formation in the embryonic growth plate implies divergent growth mechanisms during pre- and postnatal bone development
Sarah Rubin, Ankit Agrawal, Anne Seewald, Meng-Jia Lian, Livia Gottdenker, Paul Villoutreix, Adrian Baule, Tomer Stern, Elazar Zelzer – eLife, 2024
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, Jonathan Svorai, Yoseph Addadi, Paul Villoutreix*, Tomer Stern*, Elazar Zelzer* – Nature Communications, 2021
Video explaining the main findings : http://vimeo.com/463129275
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
Single-cell transcriptomics
Spatial reconstruction of single-cell enhancer activity in a multicellular organism
Baptiste Alberti, Séverine Vincent, Isabelle Stévant, Damien Lajoignie, Hélène Tarayre, Paul Villoutreix, Yad Ghalvi-Helm – bioRxiv 2024
Left/right asymmetrically expressed ephrin and Flamingo proteins regulate lateralized axon growth in C. elegans
Khulganaa Buyannemekh, Paul Villoutreix, Vincent Bertrand – Developmental Biology, 2024
Biologically informed modeling
Assessing the relative contributions of mosaic and regulatory developmental modes from single-cell trajectories
Solène Song, Paul Villoutreix – bioRxiv, 2024
Random walk informed heterogeneity detection reveals how the lymph node conduit network influences T cells collective exploration behavior
Solène Song, Malek Senoussi, Paul Escande, Paul Villoutreix – PLoS Computational Biology 2023, in press
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
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.
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.