Postdoctoral position OT-19262

Which similarity matrices to account for omics information in genetic studies?

31326 CASTANET-TOLOSAN

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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

  • You will be welcomed in the GenPhySE unit located near Toulouse, France.

     

The last 20 years have been marked by major biotechnological advances that have made it possible to acquire 'omics' and high-throughput phenotyping data on a large number of individuals. Various models/methods have been proposed in the literature to integrate these data into genetic mixed models in order to i) estimate variance components ii) improve predictions of phenotypic, genetic/genomic or transmissible potential of individuals. One of the key steps in integrating this information is the construction of a similarity matrix between individuals based on the new information available. There are many ways of constructing this similarity matrix. Unfortunately, there is no consensus as to which similarity measure should be used depending on the type of data and the purpose for which the model is to be used, as no objective approach to this has yet been proposed. Your project aims to remove this obstacle by proposing relevant criteria for comparing matrices depending on the objective: estimation of variance components, prediction of phenotypes, transmissible potential (global or specific to a mode of transmission, for example genetic, epigenetic or microbiota). This will make it possible to determine the most suitable matrix, and derive the statistical properties expected of it for each application.

 

You will be in charge of proposing new methods in order to:

  • Compare matrices independently of the target objective, for instance by adapting Flury's test to high-dimensional matrices.
  • Assess the differences between matrices in terms of prediction, using an analytical derivation of the correlation between predictions from different matrices, for instance as a function of the matrices themselves.
  • Compare matrices aimed at estimating variance components, for instance by proposing an analytical expression to qualify their properties.
  • Propose one or more innovative criteria for evaluating the quality of the matrix, depending on the target objective (variance component estimations, phenotypic and genetic predictions).

Teleworking possible

Training and skills

PhD

 

  • Recommended training: PhD in quantitative genetic, statistics
  • Knowledge required: Expertise in linear mixed models and predictions and use of omics large datasets (genomics, epigenomics, microbiome, metabolome …), Proficiency in UNIX/Linux scripting, programming (Fortran would be a plus)
  • Appreciated experience: analysis of genomic, epigenetic or microbiota data
  • Skills sought: Documented skills in verbal and written communication in English. Autonomous, enthusiasm and team player attitude.
  • Fluency in French is not required, but appreciated.

 

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: trainingcareer 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

Offer reference

  • Contract: Postdoctoral position
  • Duration: 18 months
  • Beginning: As soon as possible
  • Remuneration: from 2 643,53 € to 3 342,57 € gross monthly (depending on your experience)
  • Reference: OT-19262
  • Deadline: 30/06/2024

Contact

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