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MOrphogenesis Simulation and Analysis In siliCo (MOSAIC)

Personnel du RDP

Christophe GODIN

christophe.godin
(33) 4 72 72 XX XX
DR INRIA

Olivier ALI

olivier.ali
(33) 4 72 72 XX XX
CRCN INRIA

Romain AZAIS

romain.azais
(33) 4 72 72 XX XX
CRCN INRIA

Jonathan LEGRAND

jonathan.legrand
(33)4 72 72 86 04
IR CNRS

CERUTTI Guillaume

guillaume.cerutti
(33) 4 72 72 XX XX
IR INRAe

CHAUDHURY Ayan

ayan.chaudhury
(33) 4 72 72 XX XX
PostDoc INRIA

INGELS Florian

florian.ingels
(33) 4 72 72 XX XX
Thèse

KAR Anuradha

anuradha/kar
(33) 4 72 72 XX XX
PostDoc INRIA



2021


Yassin Refahi, Argyris Zardilis, Gaël Michelin, Raymond Wightman, Bruno Leggio, Jonathan Legrand, Emmanuel Faure, Laetitia Vachez, Alessia Armezzani, Anne-Evodie Risson, Feng Zhao, Pradeep Das, Nathanaël Prunet, Elliot M Meyerowitz, Christophe Godin, Grégoire Malandain, Henrik Jönsson, Jan Traas "A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control". Dev. Cell 56 540-556.e8 (2021)
A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control

Vernoux, T., Besnard, F. & Godin, C. "What shoots can teach about theories of plant form". Nature Plants (2021)
10.1038/s41477-021-00930-0

2020


Galvan-Ampudia CS, Cerutti G, Legrand J, Brunoud G, Martin-Arevalillo R, Azais R, Bayle V, Moussu S, Wenzl C, Jaillais Y, Lohmann JU, Godin C, Vernoux T. "Temporal integration of auxin information for the regulation of patterning.". Elife 9:e55832 (2020)
PMID : 32379043

Yuchen Long, Ibrahim Cheddadi, Gabriella Mosca, Vincent Mirabet, Mathilde Dumond, Annamaria Kiss, Jan Traas, Christophe Godin, Arezki Boudaoud "Cellular Heterogeneity in Pressure and Growth Emerges from Tissue Topology and Geometry". Current Biology 8 R344-R346 (2020)
PMID : 32169211

Feng Zhao,1,7 Fei Du,2,7 Hadrien Oliveri,1,7 Lu¨ wen Zhou,3,7 Olivier Ali,1,7 Wenqian Chen,1 Shiliang Feng,3 Qingqing Wang,2,4 Shouqin Lu¨ ,4,5 Mian Long,4,5 Rene Schneider, - 6 Arun Sampathkumar,6 Christophe Godin,1 Jan Traas,1, and Yuling Jiao "Microtubule-Mediated Wall Anisotropy Contributes to Leaf Blade Flattening". Curr Biol 30 3972–3985 (2020)
Microtubule-Mediated Wall Anisotropy Contributes to Leaf Blade Flattening

Godin C, Golé C, Douady S "Phyllotaxis as geometric canalization during plant development". Development 147 (2020)
PMID : 33046454
Voir en ligne

2018


Oliveri H, Traas J, Godin C, Ali O "Regulation of plant cell wall stiffness by mechanical stress : a mesoscale physical model". J Math Biol. 78(3):625-653 (2018)
PMID : 30209574

Armezzani A, Abad U, Ali O, Andres Robin A, Vachez L, Larrieu A, Mellerowicz EJ, Taconnat L, Battu V, Stanislas T, Liu M, Vernoux T, Traas J*, Sassi M "Transcriptional induction of cell wall remodelling genes is coupled to microtubule-driven growth isotropy at the shoot apex in Arabidopsis". Development 145(11) (2018)
PMID : 29739839

2015


Boudon F, Chopard J, Ali O, Gilles B, Hamant O, Boudaoud A, Traas J, Godin C. "A computational framework for 3D mechanical modeling of plant morphogenesis with cellular resolution.". PLoS Comput Biol. 11 e1003950 (2015)
PMID : 25569615

Cerutti, G., Ribes, S., Godin, C., Galvan-Ampudia, C., & Vernoux, T. "3-d Tessellation of Plant Tissue-A Dual Optimization Approach to Cell-Level Meristem Reconstruction from Microscopy Images". IEEE - 2015 International Conference on 3D Vision 443–451 (2015)
http://doi.org/10.1109/3DV.2015.57

2014


Sassi M, Ali O, Boudon F, Cloarec G, Abad U, Cellier C, Chen X, Gilles B, Milani P, Friml J, Vernoux T, Godin C, Hamant O, Traas J "An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis". Curr Biol. 24(19):2335-42 (2014)
PMID : 25264254

Besnard, F., Refahi, Y., Morin, V., Marteaux, B., Brunoud, G., Chambrier, P., Rozier F., Mirabet V., Legrand J., Lainé S., Thévenon E., Farcot E., Cellier C., Das P., Bishopp A., Dumas R., Parcy F., Helariutta Y., Boudaoud A., Godin C., Traas J., Guédon Y., & Vernoux, T. "Cytokinin signalling inhibitory fields provide robustness to phyllotaxis.". Nature. 505 417-21 (2014)
PMID : 24336201
Featured in F1000 (2★)

Band, L. R., Wells, D. M., Fozard, J. A., Ghetiu, T., French, A. P., Pound, M. P., Wilson M. H., Yu L., Li W., Hijazi H.I., Oh J., Pearce S.P., Perez-Amador M.A., Yun J., Kramer E., Alonso J.M., Godin C., Vernoux T., Hodgman T.C., Pridmore T.P., Swarup R., King J.R., & Bennett, M. J "Systems analysis of auxin transport in the Arabidopsis root apex". Plant Cell 3 862–875 (2014)
http://doi.org/10.1105/tpc.113.119495
Featured in F1000 (2★)

2010


Fernandez R, Das P, Mirabet V, Moscardi E, Traas J, Verdeil JL, Malandain G, Godin C. "Imaging plant growth in 4D : robust tissue reconstruction and lineaging at cell resolution.". Nat Methods. 7 547-53 (2010)




The MOSAIC team is interested in the morphogenesis of life forms such as plants and animal embryos. We focus on how the biochemical and biophysical processes interact to shape organisms. To address the complexity of the underlying mechanisms and of their interactions, we develop computational models based on 3D imaging of form development. Our aim is to progressively construct an approach inspired from the theory of dynamical systems applied to the development of life forms.

For this, the team is lead to develop and explore the use of computational and mathematical concepts within a large variety of domains : form algebra, ODE/PDE, dynamical systems, fractals, stochastic processes, continuum mechanics, FEM, information theory, graph theory, computational geometry, unconventional programming languages. The team collaborates tightly with several teams of biologists with whom it shares biological questions and develops new methods.

Main results :

 Stochastic model of phyllotaxis : we revisited the classical deterministic model of phyllotaxis to integrate a stochastic component able to reflect the stochastic nature of the molecular processes underlying the initiation of organs at the tip of plant stems. This model recapitulates all the spiral and whorl patterns explained by the previous classical model and explains precisely stochastic perturbation patterns observed recently in various plants. This work was done in collaboration with the Teva Vernoux’s group at RDP.

 Feedback between mechanical stresses and tissue anisotropy in growing plant tissues : We developed a multiscale model of tissue response to the mechanical stresses that built up within tissues during development, based on a realistic description of cell wall remodeling processes.

 Cell fate in Ascidian embryo development : In collaboration with Patrick Lemaire’s group, we developed a new imaging pipeline to image high-throughput sequences of ascidian embryo development. We used these high spatial and temporal resolution sequences to develop a model of cell fate acquisition at the level of the embryo and to show that contact surfaces between the cells are essential explicative variable of differential induction in ascidian cells.

 Gnomon : The team develops a computational platform to analyse and simulate the development of life forms in 3D.

Articles de cette rubrique

  • Publications

    , par yfesseli

    2010
    – Fernandez R, Das P, Mirabet V, Moscardi E, Traas J, Verdeil JL, Malandain G, Godin C. (2010) Imaging plant growth in 4D : robust tissue reconstruction and lineaging at cell resolution. Nat Methods. 7(7):547-53.