{"id":28,"date":"2020-08-24T14:18:08","date_gmt":"2020-08-24T14:18:08","guid":{"rendered":"https:\/\/bioml.lis-lab.fr\/?page_id=28"},"modified":"2025-03-06T07:55:47","modified_gmt":"2025-03-06T07:55:47","slug":"publications","status":"publish","type":"page","link":"https:\/\/bioml.lis-lab.fr\/index.php\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n

Google scholar list<\/a><\/p>\n\n\n\n

Machine Learning<\/strong><\/p>\n\n\n\n

MODIS: Multi-omics data integration for small and unpaired datasets<\/em>
Daniel Lepe-Soltero, Thierry Arti\u00e8res, Ana\u00efs Baudot, Paul Villoutreix, LMRL workshop, ICLR 2025<\/p>\n\n\n\n

Hierarchical novel class discovery for single-cell transcriptomic profiles<\/a>
<\/em>Malek Senoussi, Thierry Arti\u00e8res, Paul Villoutreix – arXiv, 2024<\/p>\n\n\n\n

MOTL: enhancing multi-omics matrix factorization with transfer learning <\/a>
<\/em>David Hirst, Morgane T\u00e9r\u00e9zol, Laura Cantini, Paul Villoutreix, Matthieu Vignes, Ana\u00efs Baudot – in review<\/p>\n\n\n\n

Partial label learning for automated classification of single cell transcriptomic profiles<\/span><\/em>
Malek Senoussi, Thierry Artieres*, Paul Villoutreix* – PLoS Computational Biology<\/p>\n\n\n\n

Hierarchical classification for weakly supervised transcriptomics data<\/span><\/em>
Malek Senoussi, Thierry Artieres, Paul Villoutreix – CAp, 2022<\/p>\n\n\n\n

Cross-View Kernel Transfer<\/a><\/em>
Riikka Huusari, C\u00e9cile Capponi, Paul Villoutreix, Hachem Kadri \u2013 Pattern Recognition, 2022<\/p>\n\n\n\n

What can machine learning do for developmental biology
<\/a><\/em>Paul Villoutreix, invited paper, Development,<\/em> 2021<\/p>\n\n\n\n

Towards a general framework for spatio-temporal transcriptomics<\/a><\/em>
Julie Pinol, Thierry Arti\u00e8res, Paul Villoutreix, NeurIPS LMRL workshop, <\/em>2020<\/p>\n\n\n\n

Synthesizing developmental trajectories<\/a>
<\/em>Paul Villoutreix*, <\/em>Joakim And\u00e9n*,<\/em> Bomyi Lim, <\/em>Hang Lu, Yannis Kevrekidis, Amit Singer, Stanislav Y. Shvartsman – PLoS Comput Biol 13(9): e1005742, 2017.<\/p>\n\n\n\n

Single cell morphometrics<\/strong><\/p>\n\n\n\n

Single-cell morphometrics reveals T-box gene-dependent patterns of epithelial tension in the Second Heart field<\/a><\/em>
<\/span>Clara Guijarro+, Sol\u00e8ne Song+, Benoit Aigouy, Raphael Clement, Paul Villoutreix*, Robert G. Kelly* – in press, Nature Communications, 2024<\/p>\n\n\n\n

Limited column formation in the embryonic growth plate implies divergent growth mechanisms during pre- and postnatal bone development<\/em><\/a>
Sarah Rubin, Ankit Agrawal, Anne Seewald, Meng-Jia Lian, Livia Gottdenker, Paul Villoutreix, Adrian Baule, Tomer Stern, Elazar Zelzer – eLife, 2024<\/p>\n\n\n\n

Application of 3D MAPs pipeline identifies the morphological sequence chondrocytes undergo and the regulatory role of GDF5 in this process<\/a><\/em>
Sarah Rubin, Ankit Agrawal, Johannes Stegmaier, Jonathan Svorai, Yoseph Addadi, Paul Villoutreix*, Tomer Stern*, Elazar Zelzer* – Nature Communications<\/em>, 2021<\/p>\n\n\n\n

Video explaining the main findings : http:\/\/vimeo.com\/463129275<\/a><\/p>\n\n\n\n

An integrated modelling framework from cells to organism based on a cohort of digital embryos<\/a>
<\/em>Paul Villoutreix*, Julien Delile*, Barbara Rizzi*, Louise Duloquin*, Thierry Savy, Paul Bourgine, Ren\u00e9 Doursat, Nadine Peyri\u00e9ras, Scientific Reports, 6:37438, 2016.
Code and Datasets<\/a> or github repository<\/a><\/p>\n\n\n\n

Single-cell transcriptomics<\/strong><\/p>\n\n\n\n

Spatial reconstruction of single-cell enhancer activity in a multicellular<\/a><\/em> organism<\/em><\/a>
Baptiste Alberti, S\u00e9verine Vincent, Isabelle St\u00e9vant, Damien Lajoignie, H\u00e9l\u00e8ne Tarayre, Paul Villoutreix, Yad Ghalvi-Helm – bioRxiv 2024<\/p>\n\n\n\n

Left\/right asymmetrically expressed ephrin and Flamingo proteins regulate lateralized axon growth in C. elegans<\/a>  <\/em>
Khulganaa Buyannemekh, Paul Villoutreix, Vincent Bertrand – Developmental Biology, 2024<\/p>\n\n\n\n

Biologically informed modeling<\/strong><\/p>\n\n\n\n

Assessing the relative contributions of mosaic and regulatory developmental modes from single-cell trajectories<\/a><\/em>
Sol\u00e8ne Song, Paul Villoutreix – bioRxiv, 2024<\/p>\n\n\n\n

Random walk informed heterogeneity detection reveals how the lymph node conduit network influences T cells collective exploration behavior<\/a>
<\/em>Sol\u00e8ne Song, Malek Senoussi, Paul Escande, Paul Villoutreix – PLoS Computational Biology 2023, in press<\/p>\n\n\n\n

Entropic effects in cell lineage tree packings<\/a>
<\/em>Jasmin Imran Alsous*, Paul Villoutreix*, Norbert Stoop*, Stanislav Y. Shvartsman, J\u00f6rn Dunkel – Nature Physics, 14(10), 1016-1021, 2018<\/p>\n\n\n\n

Collective Growth in a Simple Cell Network<\/a>
<\/em>Jasmin Imran Alsous, Paul Villoutreix, Alexander M. Berezhkovskii, Stanislav Y. Shvartsman – Current Biology 27(17), 2670\u20132676, 2017.<\/p>\n\n\n\n

Book Chapter<\/strong><\/p>\n\n\n\n

Vers une mod\u00e9lisation multi-\u00e9chelle de la variabilit\u00e9 biologique?<\/a><\/em>
Paul Villoutreix, Chap. 19 in Mod\u00e9liser & Simuler. Epist\u00e9mologies et pratiques de la mod\u00e9lisation et de la simulation. Tome 2<\/a>, Franck Varenne, Marc Silberstein, Philippe Huneman et Sebastien Dutreuil, Eds. pp. 643 – 664, Editions mat\u00e9riologiques, Novembre 2014.<\/p>\n\n\n\n

Ph.D Thesis<\/strong><\/p>\n\n\n\n

Randomness and variability in animal embryogenesis, a multi-scale approach<\/a>
<\/em>Paul Villoutreix, PhD Dissertation – Universit\u00e9 Ren\u00e9 Descartes – Paris V, 2015<\/p>\n\n\n\n

Others<\/strong><\/p>\n\n\n\n

Piece of news<\/a> on the Embryo Project Encyclopedia.<\/p>\n\n\n\n

Showcase on the Information is Beautiful Award website<\/a>.<\/p>\n\n\n\n

Blog post<\/a> describing The Embryo Digital Atlas’ journey to the Global Sprint<\/a>.<\/p>\n\n\n\n

Interview<\/a> on Mozilla Science Lab blog – The Embryo Digital Atlas<\/a>.<\/p>\n\n\n\n

Blog post<\/a> discussing our work on data-driven visualizations of developing embryos and its relationships to art. This is a supporting webpage for Mozilla Science Lab<\/a>  community call<\/a> on art and science.<\/p>\n","protected":false},"excerpt":{"rendered":"

Google scholar list Machine Learning MODIS: Multi-omics data integration for small and unpaired datasetsDaniel Lepe-Soltero, Thierry Arti\u00e8res, Ana\u00efs Baudot, Paul Villoutreix, LMRL workshop, ICLR 2025 Hierarchical novel class discovery for single-cell transcriptomic profilesMalek Senoussi, Thierry Arti\u00e8res, Paul Villoutreix – arXiv, 2024 MOTL: enhancing multi-omics matrix factorization with transfer learning David Hirst, Morgane T\u00e9r\u00e9zol, Laura Cantini, Paul Villoutreix, … <\/p>\n

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