Hybrid Mechanistic & AI Microbiome Modeling Scientist

SFBI; Jouy-en-Josas; On-site; EUR 42,000 - 62,000; Full time

Benefits offered by this job

Annual leave

Social assistance and loans

Holiday vouchers

Sport and cultural activities

Collective catering

Job summary

INRAE invites applications for a postdoctoral researcher to advance hybrid mechanistic–ML modeling of microbiomes. You will build a multi-scale framework linking GEMs and microbial community dynamics to predictive fermentation outcomes.

The role collaborates with MaIAGE, PROSE, and MICALIS teams, using PyTorch/JAX, Python, and COBRApy, and requires a PhD in systems biology or applied mathematics; English proficiency is required.

Qualifications

• PhD in systems biology, computational biology, bioinformatics, applied mathematics, biophysics, or equivalent.
• Strong mathematical/machine-learning skills: dynamical systems (ODEs, numerical simulation) and deep learning.
• Proficient Python development; ability to work in a multidisciplinary team and in English.

Responsibilities

• Build the computational backbone of a multi-scale modeling framework linking individual strain metabolism to community dynamics.
• Run static/dynamic flux balance analyses across thousands of simulated microbial consortia.
• Integrate metabolic descriptors into a hybrid mechanistic–ML model constrained by biological equations.

Skills

Dynamical systems

Deep learning

Python development

Machine learning

Education

PhD in systems biology/computational biology/bioinformatics/applied mathematics

Tools

PyTorch

JAX

COBRApy

Job description

INRAE invites applications for a postdoctoral researcher to advance hybrid mechanistic–ML modeling of microbiomes. You will build a multi-scale framework linking GEMs and microbial community dynamics to predictive fermentation outcomes.

The role collaborates with MaIAGE, PROSE, and MICALIS teams, using PyTorch/JAX, Python, and COBRApy, and requires a PhD in systems biology or applied mathematics; English proficiency is required.