Postdoc in computational Immunology, Inria, Lyon, France

About SMB Forums Open Positions Postdoc in computational Immunology, Inria, Lyon, France

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    Fabien Crauste

    Integration and validation of a Single-Cell-based Gene Regulatory Network in a Multiscale Model of the CD8 T Cell Immune Response

    A postdoctoral position is open in the Inria Dracula team. The position is to be funded by an ANR grant (MEMOIRE project). Partners of the project are Inria Dracula, Inserm Immunology team (Head Dr. J. Marvel), AltraBio (private company). While other partners will focus on single cell data analysis, our work will focus on the modeling part: inference of a gene regulatory network, integration into a multiscale model, and validation of the model by comparison with experimental data.

    The position is an opportunity to be involved in a strongly interdisciplinary consortium, and to strengthen experience in computational immunology or computational biology by working on single cell data modeling.

    The specific CD8+ T cell immune response is based on complex interactions between CD8+ T cells and other immune cells as well as target cells. These interactions are either direct cell-to-cell interactions, relying on cell membrane contact, or cytokine mediated. In each case, surface proteins integrate signals that influence CD8+ T cell gene regulatory networks (GRN) that code for cell survival, differentiation, proliferation, and death. Our group previously introduced a multi-scale model of the CD8+ T cell immune response based on the description and dynamical interaction of a CD8+ T cell dynamics model and a GRN model. The later, however, was focused on the interactions of only 6 genes, whose roles were identified in the literature.

    The aim of this post-doctoral position is 1st/ to implement in C++/Python a GRN inferred from single cell data and described by a piecewise deterministic Markov model, and 2nd/ to couple the GRN with an existing cell dynamics model, in order to 3rd/ use the multiscale model to describe experimental data and to investigate the dynamics of CD8+ T cells.

    The applicant will have an experience in computational biology, ideally in computational immunology, and will be able to implement C++ and Python codes. In addition, the usage of various (deterministic, stochastic) mathematical formalisms and an experience in parameter estimation with experimental data will be considered as a plus. Interdisciplinary meetings and research are at the core of the project, so it is expected that the Postdoc Fellow is confortable with researchers from other fields. Good ability for team playing will be appreciated.

    Details of the offer and application form:

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