Postdoctoral Researcher (Computational Protein Design & Antigen Evolution)

Institut Pasteur

Paris, France

Join the Antigen Evolution & Design Lab as our first postdoctoral researcher and help define the future of AI-driven antigen evolution and vaccine design.

We are seeking a highly motivated early-career scientist to develop cutting-edge machine learning approaches for understanding and designing pathogen antigens. This is a unique opportunity to help shape a new research program at the intersection of computational biology, protein language models, structural biology, and immunology.

Main Missions

• Build and curate large-scale antigen sequence datasets for training and fine-tuning protein language models across a range of clinically relevant pathogens.
• Develop novel computational methods to infer biological function directly from protein sequences, including modeling epistatic interactions and residue-residue contacts.
• Leverage state-of-the-art protein structure prediction tools, including AlphaFold3, ESMFold, and ESM3, to study antigen evolution and guide protein design.
• Work in a collaborative group across as number of interlinked projects and help with mentoring students and other early-career researchers in the lab.
• Drive independent, high-impact research while contributing to the lab’s vibrant research environment.

Qualifications

• PhD in Computational Virology, Computer Science or other related field.
• Awarded the PhD before the start of this appointment (no previous postdoctoral experience required).

Required Skills

• Familiarity with training and using protein language models or similar experience with non-protein large language models.
• Expertise in python and machine learning implementations (e.g., pytorch). Expertise in other coding languages (e.g. Julia, C++) will also be considered for the application.
• Working well within a team and with external collaborators who have diverse scientific backgrounds ranging from molecular biology and immunology to computer science.
• Candidates should have a demonstrated track record of productive research.
• Recommended (but not required) Skills
• Previous experience or familiarity with molecular phylogenetics.
• Previous work on protein sequence data focusing on viruses.
• Previous work on protein structure predictions.