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 techniques have transformed embryology into a data intensive science. As an interdisciplinary scientist, I am interested in topics at the intersection of developmental biology, mathematics and data visualization. Currently, I am a postdoc at the Weizmann Institute of Science in Rehovot (Israel) working in Eli Zelzer’s lab and a visiting fellow of the Center for Data Arts at the New School in New York. Previously, I was a postdoc in Stas Shvartsman’s lab at Princeton University
In addition, I am leading the open science project the Embryo Digital Atlas: a web 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.
Recent news: I will be presenting our work at the 2018 NEUBIAS Conference in Szeged, Hungary.
Multiscale analysis of 3D nuclear morphology reveals new insights into growth plate organization in mice
Sarah Rubin*, Tomer Stern*, Paul Villoutreix, Johannes Stegmaier, Yoseph Addadi, Elazar Zelzer – submitted, bioRxiv
Entropy effects in cell lineage tree packings
Jasmin Imran Alsous*, Paul Villoutreix*, Norbert Stoop*, Stanislav Y. Shvartsman, Jörn Dunkel – Nature Physics, AOP, 2018.
A mathematical view on cell packing
Sandi Miller | Department of Mathematics
News & Views
Ben D. MacArthur, Nature Physics, 2018
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.
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
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.
Randomness 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.
2017 – Present | Postdoctoral Fellow – Zelzer Lab – Weizmann Institute of Science
2017 – Present | Visiting Fellow – Center for Data Arts – The New School, NYC
2015 – 2017 | Postdoctoral Fellow – Shvartsman Lab – Princeton University
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
Department of Molecular Genetics
Weizmann Institute of Science
Center for Data Arts
The New School
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New York, NY, 10011