René Doursat
 PhD, Habil.

Research Scientist & Fmr. Director

Complex Systems Institute, Paris Ile-de-France (ISC-PIF)
French National Center for Scientific Research (CNRS)

Research Unit UPS3611

113, rue Nationale
75013 Paris, France


Edited Proceedings

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Activities, Grants
Education, Career

Computational models of collective cell behavior in 2D/3D, such as organism development (embryogenesis), tumor growth, or bacterial mats (synthetic biology)
One of the greatest challenges of biology is to create a generic model of multicellular development, in order to unify what Darwin called nature's "endless forms most beautiful", and construe them as variants around a common theme. The variants are the unique genetic (and epigenetic) information of each species; the common theme is the developmental dynamics that this information guides and parametrizes.
While the "modern synthesis" of genetics and evolution focused most of the attention on selection, it is only during the past decade that analyzing and understanding variation by comparing the developmental processes of different species, at both embryonic and genomic levels, became a major concern of evolutionary development, or "evo-devo". More →
MECAGEN – Mechanogenetic Model and Simulation of Biological Morphogenesis  
From cell behavior to tissue deformation: A platform for the computational modeling and simulation of animal early embryogenesis
Drawing from real data measured on microscopy imaging, my PhD student Julien Delile, under the co-supervision of Nadine Peyriéras (CNRS, Gif-sur-Yvette), designed a realistic model of animal embryogenesis. It is construed as the collective behavior of a myriad of individual cells implemented in an agent-based simulation centered on the mechanic-chemical coupling between cellular and genetic dynamics. The MecaGen platform can run both on a GPGPU array or on a cluster or computing grid.
The aim of the MecaGen platform is to provide a computational modeling and simulation environment for the multiscale dynamics of the early stages of biological morphogenesis. This virtual reconstruction is done under the control of experimental and quantitative reconstructions coming from live imaging (see BIOEMERG below). More →
BIOEMERG – BioEmergences: Reconstructing the Physiome of Model Organisms  
An integrative biology platform allowing the exhaustive detection and measurement of multicellular dynamics from in vivo observations
Since 2007, I have been contributing to the scientific and technical direction of a team working on European (FP6/7) and French (ANR) projects about animal morphogenesis, including Embryomics (ended 2009) and BioEmergences (continued). These initiatives were launched by Nadine Peyriéras (CNRS) and Paul Bourgine (Ecole Polytechnique), and have pioneered the design of methods and algorithms for reconstructing the complete dynamics of multicellular development observed by microscopy. The workflow runs on a computing grid, partly via the OpenMOLE platform developed at ISC-PIF.
The BioEmergences platform allows biologists to produce and annotate time-lapse shots of organism development, while mathematicians and computer scientists process these images to "reconstruct" and model collective cell dynamics. More →
SYNBIOTIC – Synthetic Biological Systems: From Design to Compilation  
Translating the principles of biological morphogenesis into a stack of formal programming languages compiled and implemented in a (virtual or real) synthetic biological substrate or "bioware"
The SynBioTIC project, whose WP1 I lead with my collaborator Taras Kowaliw and postdoc Jonathan Pascalie, proposes to design and develop tools to literally "compile" (as in programming languages) the overall behavior of a population of cells (bacteria) into processes local to each entity (one bacterium). The motivation is to exploit the collective properties of a cellular population to create artificial biosystems that can meet various needs in the fields of health care, nanotechnology, energy and chemistry.
Synthetic biology is an emerging scientific discipline that promotes a standardized design and manufacturing of biological system components without natural equivalents (Endy 2005). It is currently in search of design principles to achieve a reliable and secure level of functionality from reusable biological parts (e.g. BioBricks, Knight 2003). More →