Biomergence Website

Biomergence incubated at ISC-PIF from 2006 to 2014. It is now a full team of Laboratoire Matières et Systèmes Complexes (MSC), UMR CNRS 7057, Paris, France

Infos

Director
Nadine Peyriéras, Director/DR2, CNRS, started the team in 2005.

Senior scientist
– Paul Bourgine, Associated Director and Visiting Professor, Open University, Co-founder since 2005.
– René Doursat, Senior Scientist, CNRS, Collaborator since 2008
– Monique Frain, Permanent Researcher/CR1, CNRS, Joined in May 2010
– Yannick Kergosien, Professor/Professeur, Université de Cergy-Pontoise, Joined in 2013

BioEmergences members hosted at ISC-PIF
– Mathieu Bouryie, PhD student, Agro PariTech, joined in 2012.
– Matthieu Hermann, Engineer, CNRS, joined in 2012.

Keywords : Biology, Morphogenesis, Integrative Cell Biology

Publications

Villoutreix, P., Delile, J., Rizzi, B., Duloquin, L., Savy, T., Bourgine, P., Doursat, R., & Peyri’eras, N. (2016). An integrated modelling framework from cells to organism based on a cohort of digital embryos. Scientific Reports, 6, 37438. http://www.nature.com/articles/srep37438

Bouyrie, M., Cornuéjols, A., Manfredotti, C., & Peyriéras, N. (2016). Denoising 3D microscopy images of cell nuclei using shape priors on an anisotropic grid. Proc. of ICPRAM-2016. Int. Conf. on Pattern Recognition Applications and Methods, Rome, Italy.

Munjal, A., Philippe, J.-M., Munro, E., & Lecuit, T. (2015). A self-organized biomechanical network drives shape changes during tissue morphogenesis. Nature, 524(7565), 351–355. https://doi.org/10.1038/nature14603

Faure, E., Campana, M., Cunderlik, R., Drblikova, O., Duloquin, L., Keller, R., Lombardot, B., Melani, C., Remesikova, M., Rizzi, B., Savy, T., Recher, G., Zanella, C., Kollar, J., Fabrèges, D., Villoutreix, P., Delile, J., Affaticati, P., Maury, B., … Bourgine, P. (2015). From 3D+time imaging of developing model organisms to the reconstruction and analysis of their digital lineage trees with the BioEmergences workflow. Nature Methods, (In Press).

Castro-González, C., Luengo-Oroz, M. A., Duloquin, L., Savy, T., Rizzi, B., Desnoulez, S., Doursat, R., Kergosien, Y. L., Ledesma-Carbayo, M. J., Bourgine, P., Peyriéras, N., & Santos, A. (2014). A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis. PLoS Computational Biology, 10(6), e1003670. https://doi.org/10.1371/journal.pcbi.1003670

Olivier, N., Luengo-Oroz, M. A., Duloquin, L., Faure, E., Savy, T., Veilleux, I., Solinas, X., Debarre, D., Bourgine, P., Santos, A., Peyrieras, N., & Beaurepaire, E. (2010). Cell Lineage Reconstruction of Early Zebrafish Embryos Using Label-Free Nonlinear Microscopy. Science, 329(5994), 967–971. https://doi.org/10.1126/science.1189428

Zanella, C., Campana, M., Rizzi, B., Melani, C., Sanguinetti, G., Bourgine, P., Mikula, K., Peyrieras, N., & Sarti, A. (2010). Cells Segmentation From 3-D Confocal Images of Early Zebrafish Embryogenesis. IEEE Transactions on Image Processing, 19(3), 770–781. https://doi.org/10.1109/TIP.2009.2033629

BioEmergences

Tracking all cells of a living organism, their membranes and nucleus positions, their divisions, from the original stem cell to the embryo.

We develop original methodologies and tools for the in vivo multiscale and multimodal observation, quantification and multilevel theoretical modelling of biological processes. Our strategies are the basis for the predictive understanding of the morphogenesis of living organisms in normal and pathological conditions and open the way to new kind of pharmacology and toxicology screening schemes.

In this context we foresee the following missions:

anticipating the needs of integrative cell biology and developmental biology in terms of methods and tool
tackling challenging biological issues as proof of concept,
proposing collaborative services through an innovative platform for imaging, image processing and multilevel modeling,
fostering the expansion of a transdisciplinary community through the e-Laboratory Embryome-DC in the context of the Complex Systems UNESCO UNITWIN Complex Systems-DC

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BioEmergences and ISC-PIF

Bioemergence was incubated at ISC-PIF between 2007 and 2014 before becoming a CNRS Unit per se (USR3695 CNRS). The two CNRS units has strong interactions and some members of Bioemergences working on theoretical issues are still hosted at ISC-PIF.

BioEmergences

BioEmergences and ISC-PIF

ISC-PIF Partners