skip to primary navigationskip to content

Dr Yassin Refahi

Dr Yassin Refahi

Research Associate

Sainsbury Laboratory
University of Cambridge
Bateman Street

Cambridge CB2 1LR
Office Phone: +44(0)1223 761100

Research Interests

The shoot apical meristem (SAM) continuously generates leaves, flowers, and branches in higher plants. In the past decades, much progress has been achieved in understanding the dynamics and structure of gene regulatory networks in the SAM.  However, little is known about the spatiotemporal coordination between gene expression patterns and growth at cellular resolution. The lack of understanding is mainly due to the lack of comprehensive quantification of organ-wide cell properties over time with regards to underlying molecular networks. The aim of my work is to address this problem by using high-resolution, confocal, time-lapse live imaging and by developing image processing tools and computational models. In particular, I am developing a 3D+time early flower development atlas integrating transcription factors involved in organ identity, growth control and organ polarity. A detailed quantitative correlation analysis between gene expression patterns and growth will shed light on mechanisms by which morphogenesis is coordinated by gene networks. This project is closely related to a general interest in the regulation of cell size and growth kinetics that is the focus of another investigation, carried out jointly with  Lisa Willis, in which we characterize cell growth and division dynamics in the Arabidopsis SAM. Another focus of my work is on the investigation of perturbations observed in phyllotactic patterns. In close collaboration with Raymond Wightman, we developed a semi-automated pipeline that uses 3D scanners to measure and analyse divergence angles of Arabidopsis organs. This is a continuation of my previous Ph.D. work studying the phyllotactic patterns of Arabidopsis in Christophe Godin’s group in France.

Key Publications

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., ... & Jönsson, H. (2016). Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche. Proceedings of the National Academy of Sciences, 113(51), E8238-E8246 (*joint first author).

Refahi, Y., Brunoud, G., Farcot, E., Jean-Marie, A., Pulkkinen, M., Vernoux, T., & Godin, C. (2016). A stochastic multicellular model identifies biological watermarks from disorders in self-organized patterns of phyllotaxis. eLife, 5, e14093.

Michelin, G., Refahi, Y., Wightman, R., Jönsson, H., Traas, J., Godin, C., & Malandain, G. (2016). Spatio-temporal registration of 3D microscopy image sequences of Arabidopsis floral meristems. 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., 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. Functional-Structural Plant Models, pp. 185-

Filed under:


Quantification of reporter abundance in flower primordium, flower organ in its early developmental stage. (Top image) 3D projection of multichannel confocal images. Red: membrane marker pUBQ10::acyl-YFP, green: PIN1:GFP. (Middle image) 3D segmentation of membrane reporter. The colours indicate individual cells. (Bottom image) The quantification of PIN1:GFP reporter in individual cells. Red: cell membrane, white: low PIN1 concentration, green: high PIN1 concentration.