The human microbiota plays a major role in host infections. It can have an impact on host susceptibility, outcome of infection and pathogen acquisition. Over the past decade, efforts have been made to develop realistic ecological models of pathogen growth in animals or humans. This project aims to consider, through a modeling and data integration approach, the intra- and inter-host scales to study the interaction of mechanisms at these two scales involved in the acquisition and transmission of pathogenic bacteria, especially those resistant to antibiotics.

More specifically, the aim is to :

• Develop a model for the simulation of intra-host dynamics, formalizing the interactions between the microbiota and the colonizing pathogen and also including the host immune response and the use of antibiotics.
• Develop a multi-scale model taking into account intra- and inter-host dynamics, describing in particular the interactions between hosts and their impact on the transmission of commensal bacteria and the pathogen.
  The main application of the project concerns the nasal microbiota and the Staphylococcus aureus bacterium, for which data are already available. The modeling framework that will be developed in this project could be adapted to various niches and species.

The post-doctoral project is part of the MICROMOD project funded by the INCEPTION Convergence Institute and of a collaboration between researchers from INRAE and Institut Pasteur. You will mainly collaborate with Lulla Opatowski (Institut Pasteur) and Béatrice Laroche and Elisabeta Vergu (INRAE).

You will be hosted jointly in :

• INRAE's MaIAGE unit (https://maiage.inrae.fr/), which brings together mathematicians, computer scientists, bioinformaticians and biologists around questions of biology and agro-ecology, ranging from the molecular scale to the landscape scale through the study of the individual, populations or ecosystems. The construction of parametric, mechanistic models for spatio-temporal dynamic phenomena, and the analysis of their behavior, the statistical inference for dependent data are strong competences of the unit and in particular of the Dynenvie team to which you will be integrated.
• The EMAE unit of the Institut Pasteur, which has a recognized expertise in epidemiology and mathematical modeling of the dynamics of antibiotic resistance in populations. In addition, EMAE has a good knowledge of the epidemiology of S. aureus and of mathematical models of interactions between pathogens (in particular of the respiratory tract) at both the population and individual levels.

Recommended background: PhD in applied mathematics, biomathematics, computational biology. Required knowledge: ODE/PDE or stochastic process modeling, parameter inference and/or data assimilation, programming (Python or C/C++, R). Experience appreciated: a first experience in modeling of biological phenomena and data analysis would be an asset. Desired skills: an appetite for life modeling and interdisciplinary collaboration is essential; rigor, adaptability, teamwork.

2-year contract
Starting date: from 01/04/2022, as soon as possible
Salary: to be adjusted according to the candidate's profile.
Main location: MaIAGE unit, INRAE, Domaine de Vilvert, 78350 Jouy-en-Josas.
Send a letter of motivation, a CV and the contact information of two referees to :
Elisabeta Vergu (elisabeta.vergu@inrae.fr) & Lulla Opatowski (lulla.opatowski&@pasteur.fr).