Postdoctoral Researcher in Hybrid Mechanistic & AI Modeling of Microbiomes

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is seeking a postdoctoral researcher to join the MaIAGE unit. The successful candidate will build a computational multi-scale modeling framework that integrates individual bacterial strain metabolism with whole microbial community dynamics. This role involves developing hybrid models that combine mechanistic genome-scale metabolic models with deep learning techniques to predict strain interactions. The researcher will work at the intersection of simulation and experimental data, collaborating with wet-lab and digital-twin teams to advance fermentation technology.

• Construct and curate genome-scale metabolic models for food-fermentation strains using deep-learning-based reconstruction.
• Perform static and dynamic flux balance analyses on large-scale simulated microbial consortia.
• Develop hybrid deep-learning models, such as compositional Neural ODEs, constrained by ecological equations.
• Integrate high-resolution experimental data with public datasets and synthetic data from forward simulations.
• Parameterize dynamic models using Physics-Informed Neural Networks to ensure biophysical consistency.
• Contribute to the development of a digital-twin fermentation platform by integrating multi-omics datasets.