Etienne Farcot

Contact

• workRoom C27 Mathematical Sciences Building
  University Park
  Nottingham
  NG7 2RD
  UK
• work0115 9514943
• Etienne.Farcot@nottingham.ac.uk
• http://www.maths.nottingham.ac.uk/personal/pmzef/

Biography

I have been a Assistant Professor in Systems Biology at the School of Mathematical Sciences since January 2013. In 2001 I received an Engineer's Degree from ENSIMAG and a Master's in applied mathematics from Université de Grenoble. In 2005 I completed a PhD in applied mathematics at the Institut National Polytechnique de Grenoble (France). From 2005 to 2007 I was a post-doctoral researcher at Inria Sophia-Antipolis. From 2007 to 2008, I was a post-doctoral researcher at the Theoretical Physics (CPT) and Immunology Centres (CIML) in Marseilles, France. I was hired in 2008 as a "Chargé de Recherches" at Inria, the French research institute in computational sciences, in the Virtual Plants team in Montpellier, France, until I moved to Nottingham.

My research interests include the use of dynamical systems theory and mathematical modelling to analyse and understand biological systems, in collaboration with scientists from various disciplines.

Research Summary

Broadly speaking, my research concerns dynamical systems and their application to complex phenomena, especially in biology. I study different formalisms: discrete or continuous in time and/or space,… read more

Recent Publications

• ELISA TONELLO, ETIENNE FARCOT and CLAUDINE CHAOUIYA, 2019. Local Negative Circuits and Cyclic Attractors in Boolean Networks with at most Five Components Read More: https://epubs.siam.org/doi/abs/10.1137/18M1173988 SIAM Journal on Applied Dynamical Systems. 18(1), 68-79
• JEAN-LOUIS DINH, ETIENNE FARCOT and CHARLIE HODGMAN, 2017. The logic of the floral transition: Reverse-engineering the switch controlling the identity of lateral organs PLoS Computational Biology.
• CHRISTOPHE GODIN, EUGENIO AZPEITIA and ETIENNE FARCOT, 2016. An introduction to modeling the initiation of the floral primordium. In: From Molecules to Living Organisms: An Interplay Between Biology and Physics 102. Oxford Scholarship.
• REFAHI, YASSIN, BRUNOUD, GERALDINE, FARCOT, ETIENNE, JEAN-MARIE, ALAIN, PULKKINEN, MINNA, VERNOUX, TEVA and GODIN, CHRISTOPHE, 2016. A stochastic multicellular model identifies biological watermarks from disorders in self-organized patterns of phyllotaxis. eLife. 5,

• View all publications

Current Research

Broadly speaking, my research concerns dynamical systems and their application to complex phenomena, especially in biology. I study different formalisms: discrete or continuous in time and/or space, as well as intermediary, hybrid systems, in particular piecewise-linear formulations. I am interested in the relationships between these types of models, as well as their applications to model real world phenomena, which often requires a combination of varied mathematical frameworks.

Future Research

I welcome any applications for PhD. For a few examples of potential PhD projects, see:

https://www.maths.nottingham.ac.uk/postgraduate/projects/index.php?proposer=pmzef

Do not hesitate to get in touch if you are interested.

• ELISA TONELLO, ETIENNE FARCOT and CLAUDINE CHAOUIYA, 2019. Local Negative Circuits and Cyclic Attractors in Boolean Networks with at most Five Components Read More: https://epubs.siam.org/doi/abs/10.1137/18M1173988 SIAM Journal on Applied Dynamical Systems. 18(1), 68-79
• JEAN-LOUIS DINH, ETIENNE FARCOT and CHARLIE HODGMAN, 2017. The logic of the floral transition: Reverse-engineering the switch controlling the identity of lateral organs PLoS Computational Biology.
• CHRISTOPHE GODIN, EUGENIO AZPEITIA and ETIENNE FARCOT, 2016. An introduction to modeling the initiation of the floral primordium. In: From Molecules to Living Organisms: An Interplay Between Biology and Physics 102. Oxford Scholarship.
• REFAHI, YASSIN, BRUNOUD, GERALDINE, FARCOT, ETIENNE, JEAN-MARIE, ALAIN, PULKKINEN, MINNA, VERNOUX, TEVA and GODIN, CHRISTOPHE, 2016. A stochastic multicellular model identifies biological watermarks from disorders in self-organized patterns of phyllotaxis. eLife. 5,
• LAVENUS J, GOH T, GUYOMARC'H S, HILL K, LUCAS M, VOSS U, KENOBI K, WILSON M, FARCOT E, HAGEN G, GUILFOYLE T, FUKAKI H, LAPLAZE L and BENNETT MJ, 2015. Inference of the Arabidopsis lateral root gene regulatory network suggests a bifurcation mechanism that defines primordia flanking and central zones The Plant Cell. 27(5), 1368-88
• FELLER C, FARCOT E and MAZZA C, 2015. Self-Organization of Plant Vascular Systems: Claims and Counter-Claims about the Flux-Based Auxin Transport Model. PloS one. 10(3), e0118238
• FARCOT E, LAVEDRINE C and VERNOUX T, 2015. A modular analysis of the auxin signalling network. PloS one. 10(3), e0122231
• LAVEDRINE C, FARCOT E and VERNOUX T, 2015. Modeling plant development: from signals to gene networks. Current opinion in plant biology. 27, 148-153
• BESNARD, FABRICE, REFAHI, YASSIN, MORIN, VALERIE, MARTEAUX, BENJAMIN, BRUNOUD, GERALDINE, CHAMBRIER, PIERRE, ROZIER, FREDERIQUE, MIRABET, VINCENT, LEGRAND, JONATHAN, LAINE, STEPHANIE, THEVENON, EMMANUEL, FARCOT, ETIENNE, CELLIER, CORALIE, DAS, PRADEEP, BISHOPP, ANTHONY, DUMAS, RENAUD, PARCY, FRANCOIS, HELARIUTTA, YKA, BOUDAOUD, AREZKI, GODIN, CHRISTOPHE, TRAAS, JAN, GUEDON, YANN and VERNOUX, TEVA, 2014. Cytokinin signalling inhibitory fields provide robustness to phyllotaxis Nature. 505(7483), 417-421
• SAN-BENTO, RITA, FARCOT, ETIENNE, GALLETTI, ROBERTA, CREFF, AUDREY and INGRAM, GWYNETH, 2014. Epidermal identity is maintained by cell–cell communication via a universally active feedback loop in Arabidopsis thaliana The Plant Journal. 77(1), 46-58
• VOß U, BISHOPP A, FARCOT E and BENNETT MJ, 2014. Modelling hormonal response and development Trends in Plant Science. (In Press.)
• GOH T, VOß U, FARCOT E, BENNETT MJ and BISHOPP A, 2014. Systems biology approaches to understand the role of auxin in root growth and development Physiologia Plantarum. 151(1), 73-82
• OLIVA, M., FARCOT, E. and VERNOUX, T., 2013. Plant hormone signaling during development: insights from computational models Current Opinion in Plant Biology. 16(1), 19-24
• CHAVES, M., FARCOT, E. and GOUZÉ, J.-L., 2013. Probabilistic approach for predicting periodic orbits in piecewise affine differential models Bulletin of Mathematical Biology. 75(6), 967-987
• WALKER, M. L., FARCOT, E., TRAAS, J. and GODIN, C., 2013. The Flux-Based PIN Allocation Mechanism Can Generate Either Canalyzed or Diffuse Distribution Patterns Depending on Geometry and Boundary Conditions PLoS ONE. 8(1), e54802
• FARCOT, E. and YUAN, Y., 2013. Homogeneous auxin steady states and spontaneous oscillations in flux-based auxin transport models SIAM Journal on Applied Dynamical Systems. 12(3), 1330-1353
• GUÉDON, Y., REFAHI, Y., BESNARD, F., FARCOT, E., GODIN, C. and 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
• EDWARDS, R., FARCOT, E. and FOXALL, E., 2012. Explicit construction of chaotic attractors in Glass networks Chaos, Solitons & Fractals. 45(5), 666-680
• MIDDLETON, A., FARCOT, E., OWEN, M. and VERNOUX, T., 2012. Modeling regulatory networks to understand plant development: small is beautiful The Plant Cell. 24(10), 3876-3891
• VERNOUX, T., BRUNOUD, G., FARCOT, E., MORIN, V., VAN DEN DAELE, H., LEGRAND, J., OLIVA, M., DAS, P., LARRIEU, A., WELLS, D., GUEDON, Y., ARMITAGE, LL, PICARD, F., GUYOMARC'H, S., CELLIER, C., PARRY, G., KOUMPROGLOU, R., DOONAN, J.H., ESTELLE, M., GODIN, C., KEPINSKI, S., BENNETT, M., DE VEYLDER, L. and TRAAS, J, 2011. The auxin signalling network translates dynamic input into robust patterning at the shoot apex Molecular Systems Biology. 7, 508
• REFAHI, Y., FARCOT, E., GUÉDON, Y., BESNARD, F., VERNOUX, T. and GODIN, C., 2011. A Combinatorial Model of Phyllotaxis Perturbations in Arabidopsis thaliana In: 22nd Annual Symposium on Combinatorial Pattern Matching, Palermo, Italy. 323-335
• LA ROTA, C., CHOPARD, J., DAS, P., PAINDAVOINE, S., ROZIER, F., FARCOT, E., GODIN, C., TRAAS, J. and MONÉGER, F., 2011. A data-driven integrative model of sepal primordium polarity in Arabidopsis The Plant Cell. 23(12), 4318-433
• FARCOT, E. and GOUZÉ, J.-L., 2010. Limit cycles in piecewise-affine gene network models with multiple interaction loops International Journal of Systems Science. 41(1), 119-130
• FARCOT, E., BONNET, M., JAEGER, S., SPICUGLIA, S., FERNANDEZ, B. and FERRIER, P., 2010. TCRb Allelic Exclusion in Dynamical Models of V(D)J Recombination Based on Allele Independence Journal of Immunology. 185(3), 1622-1632
• FARCOT, E. and GOUZÉ, J.-L., 2009. Periodic Solutions of Piecewise Affine Gene Network Models with Non Uniform Decay Rates: The Case of a Negative Feedback Loop Acta Biotheoretica. 57(4), 429-455
• FARCOT, E. and GOUZÉ, J.-L., 2008. A mathematical framework for the control of piecewise-affine models of gene networks Automatica. 44(9), 2326-2332
• FARCOT, E. and GOUZÉ, J.-L., 2007. Piecewise Constant Feedback Control of Piecewise Affine Gene Network Models In: Hybrid Systems: Computation and Control, HSCC 2007. 688-692
• FARCOT, E., 2006. Geometric properties of a class of piecewise affine biological network models Journal of Mathematical Biology. 52(3), 373-418
• FARCOT, E., 2006. Symbolic numeric analysis of attractors in randomly generated piecewise affine models of gene networks In: International Conference on Symbolic and Algebraic Computation. 79-86
• MOUSSU S., SAN BENTO R., GALLETTI R., CREFF A., FARCOT E. and INGRAM G., Embryonic cuticle establishment: The great (apoplastic) divide Plant Signaling and Behavior. 8(12),