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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

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Fractionation of AgroResources and Environment lab


Yassin __

Address: UMR FARE, 2 esplanade Roland-Garros, BP 224, 51686 Reims, France

Phone : +33 (0)3 26 77 36 86

Fax : +33 (0)3 26 77 35 99

E-mail : 


Since 2017 – Researcher INRAE, Reims (UMR FARE)

2014-2017 – Research associate, Sainsbury Laboratory, University of Cambridge, UK.

2012-2014 – Post-doctoral researcher, École Normale Supérieure (ENS) Lyon, France & Sainsbury  Laboratory, University of Cambridge, UK.


2008-2012 – P.h.D. in computer science, University of Montpellier 2, France with Christophe Godin, Etienne Farcot (INRIA) and Jan Traas (ENS - Lyon) on Multi-scale modelling of Arabidopsis thaliana phyllotaxis perturbations.

2007-2008 – Msc in computer science, modelling by software, University of Lorraine, Metz, France. 


Multi-scale modelling of biological processes and systems, four dimensional (space + time) image processing.

Research interests

I use a combination of multi-scale modelling and four-dimensional (space+ time) image processing to study the transformation processes of lignocellulosic biomass.

Main publications

Fal K., Liu M., Duisembekova A., Refahi Y., Haswell E., Hamant O. (2017). Phyllotactic regularity requires the Paf1 complex in Arabidopsis, doi: 10.1242/dev.154369, Development.

Meyer H.M.*, Teles J.*, Jordan-Formosa P.*, Refahi Y., San-Bento R., Ingram G., Jönsson H., Locke J., Roeder A.H.K. (2017). Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal. eLife, 6, e19131 (*joint first author).

Willis L.*, Refahi Y.*, Wightman R., Landrein B., Teles J., Huang K.C., Meyerowitz E., Jönsson H. (2016). Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche. PNAS (Proceedings of the National Academy of Sciences), 113(51), E8238-E8246. (*joint first author).

Recommended by Kay Schneitz, member of Faculty of 1000.

Refahi Y., Brunoud G., Farcot E., Jean-Marie A., Pulkkinen M., Vernoux T., Godin C. (2016). Stochastic Multicellular Model Identies Biological Watermarks from Disorders in Self-organized Patterns of Phyllotaxis. eLife, 5, e14093.

Highlighted in Labtimes (05/2016), CNRS- France, national website - ENS Lyon, France, website.

Michelin G., Refahi Y., Wightman R., Jönsson H., Traas J., Godin G., Malandain G. (2016). Spatio-temporal registration of 3D microscopy image sequences of Arabidopsis oral meristem. ISBI-IEEE 13th International Symposium on Biomedical Imaging, pp. 1127-1130.

Gruel J. Landrein B., Tarr P., Schuster C., Refahi, Y., Sampathkumar A., Hamant O., Meyerowitz E.,Jönsson H. (2016). An epidermis-driven mechanism positions and scales stem cell niches in plants. Science Advances, 2(1), e1500989.

Besnard, F., Refahi, Y., Morin, V., Marteaux, B., Brunoud, G., Chambrier, P., ... & Vernoux, T. (2014). Cytokinin signalling inhibitory fields provide robustness to phyllotaxis, Nature, 505 :7483 :417-421.

Landrein B., Refahi Y., Besnard F., Hervieux N., Mirabet V., Vernoux T., Boudaoud A., Hamant O. (2014). Meristem size contributes to the robustness of phyllotaxis in Arabidopsis. Journal of Experimental Botany, eru482.

Guédon Y. Refahi Y., Besnard F., Farcot E., Godin C., Vernoux T. (2013). Pattern identification and characterization reveal permutations of organs as a key genetically controlled property of post-meristematic phyllotaxis. Journal of Theoretical Biology, 338 :94-110.

Refahi Y., Farcot E., Guédon Y., Besnard F., Vernoux T., Godin C. (2011). A Combinatorial model of phyllotaxis perturbations in Arabidopsis thaliana. Combinatorial Pattern Matching, Springer, Berlin Heidelberg, 6661/2011 :323-335.

Refahi Y., Guédon Y., Besnard F., Farcot E., Godin C., Vernoux T. (2010). Analyzing perturbations in phyllotaxis of Arabidopsis thaliana. FSPM, Functional-Structural Plant Models, pp. 185-187.


Over 100 hours of teaching at University of Montpellier 2, France and University of Cambridge, United Kingdom.