Junior research scientist in computational modeling of multiscale integration in plant development and morphogenesis

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INRAE presentation

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player globally in research and innovation. Gathering a community of 12,000 people with 272 units including fundamental and experimental research, spread out throughout 18 regional centres in France.

Internationally, INRAE is among the top research organisations in agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment.  

Faced with a growing world population, climate change, the depletion of resources and declining biodiversity, the Institute has a major role to play in providing the knowledge base supporting the necessary acceleration of agricultural, food and environmental transitions, to address the major global challenges.

INRAE is recruiting researchers by open competition and offering permanent position.

Work environment, missions and activities

The Institute Jean-Pierre Bourgin for Plant Sciences (IJPB) is a very large research unit (300 people, 27 teams, 6 platforms and 6 general services) located on the INRAE campus adjacent to the gardens of the Royal Palace in Versailles. The IJPB comprises a unique set of multidisciplinary resources and skills (biology, chemistry, computer science, applied mathematics). The unit's research activities aim to produce fundamental knowledge in plant biology (development and morphogenesis, adaptation to environmental constraints, genome functioning, signaling and communication) and to integrate this knowledge for innovation aimed at current major scientific and societal challenges.

You will join the Modeling and Digital Imaging team (around ten people), which brings together mathematicians, biomathematicians, computer scientists and engineers. The research conducted in the team aims to develop original computational approaches for quantifying and modeling plant developmental and morphogenetic processes, based essentially on microscope imaging data. To this end, the team mobilizes a unique set of skills and approaches that combine image analysis, spatial statistics, and computational and mathematical modeling.

To enable the prediction and optimization of crop productivity, quality and resilience in a context of a transition to agroecology, it is essential to grasp the complexity of plant tissue development and organ growth. These processes are generally studied independently at different scales (sub-cellular, cellular, tissue and beyond). In your project, you will address the key scientific and methodological challenges of integrating these levels through multi-scale modeling in order to gain novel mechanistic knowledge. Actually, the complexity of plant development and morphogenesis results from bottom-up and top-down interactions between different levels of organization, such as the coupling between cytoskeleton and chromosome dynamics within the nucleus, or feedback loops between mechanical signals and growth during morphogenesis. 

The major questions you will tackle in this project are to gain a mechanistic understanding of the basis of these couplings and how they work together to generate and transduce mechanical signals between different levels of organization and contribute to the integrated functioning and development of genomes, cells and tissues.
To reach these objectives, you will build on an original modeling framework developed by the team to design new biophysical and computer models predicting the effect of mechanical couplings at the interfaces between levels of organizations or domains in cells and tissues. You will feed the models developed and validate your predictions by comparing them with biological dynamics or organizations observed in imaging data (confocal microscopy, super-resolution). Your activity will initially focus on modeling connections between the cytoskeleton and chromosomal dynamics within the nucleus, in order to benefit from a well-established intra-IJPB collaboration for the start of your project. The model developed will provide a methodological basis for the evolution of the project towards higher levels of integration, from sub-cellular/cellular to tissue scales.

By addressing the methodological challenges required to design a truly mechanistic multi-scale modeling, your research will help identify new mechanisms essential for reproduction, growth and integration of environmental signals in plants.

Your project will be at the heart of the themes of the INRAE DigitBio MetaProgramme. Increasing the explanatory and predictive potential of modeling by coupling models across scales has been identified by INRAE as a major challenge for quantitative biology. In this context, the scales you will integrate (from sub-cellular to cellular/tissue) and the approaches you will develop (computational modeling, biophysics and mechanistic) are original and complementary to other on-going projects at INRAE.

You will benefit from computational resources and skills available in the team (mathematical and computational modeling, image analysis, programming, storage and CPU/GPU computing servers). Thanks to the well-established collaboration with the IJPB MeioMe team, renowned internationally as a leader in meiosis, you will have access to the necessary biological expertise and unique imaging data on chromosome dynamics needed for your starting project. 
Your research will benefit from infrastructures and developments in microscope imaging that are part the IJPB’s assets (e.g., novel cytoskeletal markers of interphase, FRET/FLIM microscopy, optogenetics, super-resolution). You will build on the collaborative networks of the team and the unit, at regional, national and international levels to expand your own network of collaborators in computational and biophysical modeling.

Training and skills

You have a PhD (or equivalent) in a speciality such as biophysics, applied mathematics or computer science. 
You have a solid expertise in the modeling of biological phenomena (e.g., multi-agent systems, dynamical systems, ODE/PDE) and, if possible, you have training and/or experience in soft matter physics, biomechanics or numerical physics. 
You have a good command of programming in languages such as C++ or Java. Your additional skills in biological image processing and analysis will also be appreciated. 
Fluency in English is desirable, as is long-term international experience: successful candidates who have not already had such experience will be required to spend a year abroad at the end of the internship year.

Let’s talk about your future job in a video!

INRAE's life quality

By joining our teams, you benefit from:

- 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.

For international scientists: please visit your guide to facilitate your arrival and stay at INRAE. 

How to apply

1. I download the applicant guide Application guidelines CRCN 2025 pdf - 3.93 MB
2. I write down the profile number CR-2025-BAP-4
3. I apply GO