Post-doctorak position in Data management and data mining for trade-off predictions in plant biology

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INRAE presentation

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the 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. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.

Work environment, missions and activities

•  Research unit

UMR 1332 BFP brings together more than 150 staff members, including permanent and non-permanent personnel. It is a joint research unit between INRAE (Plant Biology and Plant Breeding; Plant Health and Environment Divisions) and the University of Bordeaux, and represents a major center for plant biology research in the Nouvelle-Aquitaine region. In addition to its research activities, BFP is strongly involved in teaching and training in Plant Sciences, as well as in Microbiology and Biochemistry. The unit has a high level of international visibility, as illustrated by its coordination of several EU-funded projects and international collaborative networks, the establishment of an International Associated Laboratory with the University of Tsukuba, Japan (LIA FReQUenCE), and its participation in numerous international projects. BFP also maintains active partnerships with industry and grower organizations. 

The Meta Team is a multidisciplinary group combining expertise in analytical chemistry, biochemistry, molecular biology, physiology, statistics, and bioinformatics. It develops systems biology approaches to understand plant metabolism and its contribution to plant performance, including yield and responses to biotic and abiotic stresses. The team generates large-scale datasets to develop, parameterize, and validate predictive models. Both bottom-up and top-down modeling approaches are implemented. Bottom-up models (from mechanisms to phenotype) are used to investigate the control of metabolic fluxes and metabolite concentrations. Top-down approaches (from phenotype to mechanisms) aim to identify metabolic markers associated with performance, providing entry points to uncover underlying mechanisms. The Meta Team also hosts the Bordeaux Metabolome Platform, which provides access to a wide range of targeted and untargeted metabolomics approaches.

• Context:

The Bordeaux Plant Science (BPS) project aims to better understand and ultimately control the trade-offs between biomass production, plant resistance to biotic and/or abiotic stresses, and the quality of plant-derived products. The project brings together 11 laboratories from the Bordeaux plant science community, spanning a wide range of disciplines and research themes. It represents the second phase of a long-term collaborative effort, building on five years of prior interactions and joint work between these laboratories and across work packages.

BPS is structured around three main objectives: (i) identifying the molecular, metabolic, and physiological mechanisms underlying plant trade-offs; (ii) investigating their (epi)genetic and environmental determinants; and (iii) improving the control of plant performance, cropping systems, and product quality in the context of societal demands and environmental change.

The project is in part coordinated by the Meta Team, and the successful candidate will join Work Package 12 (WP12), also led by this team. WP12 focuses on data and metabolomics related aspects of the project, including the collection of FAIR data, the integration and analysis of multi-level datasets and the development of predictive models of plant performance and trade-offs. In addition, WP12 will generate metabolomics data to support the scientific objectives of the other work packages.

• Objectives and work program of the post-doctoral fellow

The post-doctoral fellow will lead the collection and curation of FAIR-compliant data and metadata across the different laboratories involved in the project. The recruitee will also identify, evaluate and deploy tools (such as Madbot or similar platforms) to streamline data sharing and accessibility within the broader scientific community.

The candidate will contribute to the collection and metabolomic analysis of samples, conducted in collaboration with the Bordeaux Metabolome Platform. He or she will also identify and develop biologically relevant questions to drive theses analyses, within the framework of the project.

In addition, the post-doctoral fellow will develop predictive models to explore trade-offs based on the phenotypic and omics datasets generated throughout the project, leveraging state-of-the-art machine learning approaches.

University of Bordeaux will be the main employer.

Training and skills

The ideal candidate holds a PhD in computational biology, metabolomics, or a related field, and demonstrates will a strong interest in FAIR data principles and a background in plant physiology.

The candidate should possess strong analytical and problem-solving skills, with proficiency in statistical modelling and/or data visualisation. Experience or interest in machine-learning, metabolomics and/or plant metabolism is highly valued. Excellent interpersonal and communication skills are essential, as the position requires effective collaboration within a network and the ability to report on his/her results, both orally and in writing).

INRAE's life quality

By joining our teams, you benefit from (depending on the type of contract and its duration):

- up to 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.

How to apply

I send my CV and my motivation letter