Host

Dr. Olivier Gandrillon / Dr. Fabien Crauste
Inria Team-Project Dracula (http://dracula.univ-lyon1.fr/)
Inria Research Center Grenoble Rhône Alpes (https://www.inria.fr/en/centre/grenoble)
56 boulevard Niels Bohr, 69100 Villeurbanne
France

Duration 36 months

Infering gene regulatory networks from single-cell data. 

Background

EU countries face large health challenges to combat chronic diseases including immune disorders. Recently, systems medicine has emerged as a promising discipline to accelerate the translation of basic research into applications for improved diagnostics and personalized treatment. Its power arises from the integration of laboratory and computational approaches crossing research disciplines and sectors to solve biomedical and clinical questions.
 
Approach
COSMIC will focus on B-cell lymphoma (BCL) and rheumatoid arthritis (RA), prototypical diseases originating from abnormal functioning of immune cells. The PhD candidate will investigate gene regulatory network inference from single-cell data. These networks aim at being plugged into computational multiscale models of the germinal center, developed by Consortium partners, that will help focusing on BCL and RA and in particular on the molecular perturbations that could affect the cellular level. In order to account for the stochasticity that arises from single-cell transcriptomics data, inference will be thought as a fitting procedure for a mechanistic gene network (coupled piecewise deterministic Markov processes) model followed by a statistical inference.
 
Our research team
The Inria Dracula team focuses on multiscale modeling of biological processes, with an emphasis on the development of tools and methods for multiscale modeling of differentiation processes in fast renewing cell populations. For more information see http://dracula.univ-lyon1.fr/ and https://www.inria.fr/en/teams/dracula
 
Your experience
  • Candidates should have a Master’s degree in mathematics, computer sciences, or similar with a strong interest in biology. 
  • Experience with Markov processes, differential equations and/or agent-based modeling
  • Basic statistical knowledge and experience with R
  • Strong programming skills
  • Excellent higher education track record and strong scientific curiosity.
  • Fluent spoken and written English skills
In addition, the following experience would be helpful, but not essential:
  • Experience in systems biology or systems medicine
  • Experience in interacting with biologists and medical doctors.
We seek a highly motivated scientist who enjoys an interdisciplinary environment and an interdisciplinary project, able to work independently but also as part of a team.
 
Our offer
This 3-year position is funded by the Marie Skłodowska-Curie actions of the European Union's Horizon 2020 research and innovation programme under grant agreement No 765158.  The appointment is with Inria Research Center Grenoble Rhône Alpes, FranceUnder recruitment procedure the general MC salary description is detailed. Due to local law and differences in family situation, the exact salary will be determined in the host institution upon recruitment.
 
Your application
See recruitment procedure. You can apply using the online application form. For more information about the position you can contact Dr. Olivier Gandrillon (olivier.gandrillon@inria.fr, +33-4-72728595) or Dr. Fabien Crauste (fabien.crauste@inria.fr, +33-4-72437489).
 
Inria
Inria, the French National Institute for computer science and applied mathematics, promotes “scientific excellence for technology transfer and society”. Graduates from the world’s top universities, Inria's 2,700 employees rise to the challenges of digital sciences. With its open, agile model, Inria is able to explore original approaches with its partners in industry and academia and provide an efficient response to the multidisciplinary and application challenges of the digital transformation. Inria is the source of many innovations that add value and create jobs.

 

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