LinkedIn

https://www.linkedin.com/in/yassin-refahi-42450b197/

Career

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

Education 

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. 

Skills

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.

Teaching

Over 120 hours of teaching at University of Montpellier 2, France, University of Cambridge, United Kingdom, and University of Reims Champagne-Ardenne

Main publications

Hossein Khani, S., Ould Amer, K., Remy, N., Lebas, B., Habrant, A., Faraj, A., ... & Refahi, Y. (2024). A Distinct Autofluorescence Distribution Pattern Marks Enzymatic Deconstruction of Plant Cell Wall. bioRxiv, 2024-12. (co-corresponding author) DOI

Refahi, Y., Zoghlami, A., Viné, T., Terryn, C., Paës, G., 2024. Plant cell wall enzymatic deconstruction: Bridging the gap between micro and nano scales. Bioresource Technology 414, 131551. DOI

Kar, A., Petit, M., Refahi, Y., Cerutti, G., Godin, C., & Traas, J. (2022). Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets. PLoS computational biology, 18(4), e1009879. DOI

Refahi, Y., Zardilis, A., Michelin, G., Wightman, R., Leggio, B., Legrand, J., ... & Traas, J. (2021). A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control. Developmental Cell, 56(4), 540-556. (co-corresponding author) DOI

Fal, K., Korsbo, N., Alonso-Serra, J., Teles, J., Liu, M., Refahi, Y., ... & Hamant, O. (2021). Tissue folding at the organ–meristem boundary results in nuclear compression and chromatin compaction. Proceedings of the National Academy of Sciences, 118(8), e2017859118. DOI

Zoghlami, A., Refahi, Y., Terryn, C., & Paës, G. (2020). Three-dimensional imaging of plant cell wall deconstruction using fluorescence confocal microscopy. Sustainable Chemistry, 1(2), 75-85. DOI

Zoghlami, A., Refahi, Y., Terryn, C., & Paës, G. (2019). Multimodal characterization of acid-pretreated poplar reveals spectral and structural parameters strongly correlate with saccharification. Bioresource technology, 293, 122015. DOI

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. *Co-first author DOI

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. DOI

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. DOI

PhD thesis supervisor

Aya Zoghlami, 2019 (co-supervision with Gabriel Paës et Christine Terryn)
Solmaz Hossein Khani, 2022 - 2025 (co-supervision with Gabriel Paës)
Anna Kestel, 2024 - 2025 (co-supervision with Grégoire Malandain et Gabriel Paës)