Mots-Clés

AI Systems Biology Synthetic Biology Whole-Cell Models

Description

Context

We are seeking a motivated individual to join our research group within the MICALIS institute (INRAE & University of Paris-Saclay, website: https://www.micalis.fr), a leading research unit with over 350 researchers developing multidisciplinary approaches and promoting the development of synthetic biology for health and biotechnology.

The candidate will contribute to our ongoing efforts in developing cellular models, as highlighted in our recent publication (https://www.nature.com/articles/s41467-023-40380-0), which proposes combining AI-driven and mechanistic methods to better design strains and predict strain performance more effectively.

The candidate will participate in projects funded by the French funding research agency (ANR) and a European Project at MICALIS. Within MICALIS , the recruiting research team (~20 staff spread into wet and dry labs) specializes in developing computer-aided design tools for biotechnology (more details at https://jfaulon.com/). The candidate will closely collaborate with software developers and interact with Research and Data Scientists, Engineers, and Ph.D. fellows.

Missions

Begin work with innovative AI-driven whole-cell models designed to facilitate studies of transcription, translation, and metabolism. In this role, the candidate will undertake the following tasks:

• Participate in ANR-funded and European Project initiatives, aiming to enhance biotechnological applications through innovative cellular models.
• Benchmark existing mechanistic methods to model the kinetics of transcription, translation and metabolism.
• Contribute to the development of hybrid neural-mechanistic models based on physics-informed neural networks (PINNs) and/or graph neural networks (GNNs).
• Benchmark the hybrid models with experimental measurements collected by project partners or generated in the hosting lab.
• Develop strategies for applying hybrid models in cell engineering.

Profile

• Ph.D. degree in System Biology, Bioinformatics, Biophysics or a related field.
• Prior knowledge in metabolic networks, metabolomics, metabolic flux analysis or kinetics of transcription and translation is desired.
• Good programming skills in Python, testing practices, and Git versioning. Knowledge of continuous integration paradigms is a plus.
• Excellent communication skills and the ability to work effectively in an interdisciplinary team.
• Strong analytical skills and a keen interest in software development for biotechnological applications.

Contract and Salary

• Fixed-term, renewable 12-month contract, in compliance with French legislation.
• Salary will be commensurate with qualifications and experience.

Application

To apply, please submit Cover Letter, Curriculum Vitae (CV), and Contact References to Jean-Loup Faulon jean-loup.faulon@inrae.fr