PhD in Bioinformatics / Structural Modeling (M/F)
Doctoral project on deep‑learning protein‑protein interaction modeling for bacterial predation.
Best for:Best for candidates with strong computational biology skills, experience in deep‑learning protein structure prediction, and proficiency in Python programming.
Overview
The position is a three‑year PhD at the Laboratoire de Biologie et Modélisation de la Cellule (LBMC) of the École Normale Supérieure de Lyon. The research focuses on building a protein‑protein interaction network between the Kil apparatus and the T3SS of Myxococcus xanthus using state‑of‑the‑art deep‑learning structure prediction tools such as AlphaFold and RosettaFold. The candidate will run large‑scale GPU simulations, analyse intra‑ and inter‑complex contacts, and integrate the results into a mechanistic model of bacterial predation. The work is carried out within the DAMM team under the supervision of Riccardo Pellarin and Juliette Martin, and the PhD thesis will be submitted to the university.
What you'll do
- Generate a comprehensive protein‑protein interaction network for Kil and T3SS systems using AlphaFold2/3, Boltzmann‑2, and RosettaFold3.
- Analyse intra‑ and inter‑complex contacts to identify key determinants of contact‑dependent predation.
- Run large‑scale GPU‑accelerated simulations on the Centre Blaise Pascal clusters and manage computational resources.
- Integrate interaction data into a mechanistic model of Myxococcus xanthus predation and prepare scientific publications.
- Present results regularly within the DAMM team and at national/international conferences.
Requirements
Degree offered: PhD
- Proficiency in Python or similar programming language
- Experience with deep‑learning protein structure prediction tools (e.g., AlphaFold, RosettaFold)
- Knowledge of protein‑protein interaction analysis methods
- Familiarity with high‑performance computing environments and GPU clusters
Funding & terms
How to apply
Deadline: 2026-11-22
Apply through the CNRS online portal using the link provided. Upload a curriculum vitae, a cover letter, copies of your BSc/MSc transcripts, and up to three reference letters. The portal requires a user login and will confirm receipt of your application.
- CV
- Cover letter
- BSc and MSc transcripts
- Three reference letters
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