Engineer in Structural Bioinformatics

Fixed-term contract Research engineer Postdoc level 18 months October 2025 Structural bioinformatics Interactomics Université Paris Cité

Contact information:

Interested candidates are invited to send a CV and a cover letter to the following addresses:
nicolas.chevrollier@inserm.fr and pierre.tuffery@u-paris.fr

Important: please include “Application IR FORMULA” in the subject line of your message.

General context

The candidate will join the RPBS platform, a technology infrastructure embedded within Université Paris Cité and specialized in the structural modeling of biological systems. This recruitment takes place in the framework of the FORMULA project, funded by the IdEx Excellence Initiative of Université Paris Cité.

FORMULA explores the multiscale dynamics and organization of living systems through innovative interdisciplinary approaches combining biology, physics, bioinformatics, bioengineering, and imaging. It brings together several renowned research units (Institut Jacques Monod, Institut Pasteur, etc.) and platforms (ImagoSeine, ProtéoSeine, RPBS).

Within RPBS, the work will focus on the interactomics axis of the project: modeling protein–protein interaction (PPI) networks from experimental data, to better understand the organization and dynamics of complex protein assemblies.

Missions

Design a bioinformatics strategy to model PPI networks from experimental data (e.g., TurboID), by combining large-scale structural modeling tools (AlphaPulldown, Proteo3Dnet) with rational filtering approaches. Ensure the scientific and technical robustness of the pipeline, and act as a bridge between the biological and computational teams.

Tasks

  • Development of a pipeline for PPI prediction from proximity labeling / mass spectrometry data
  • Technology watch on structural interactomics methods
  • Integration of large-scale modeling tools such as AlphaPulldown
  • Development of upstream filtering methods (interologs, domain co-occurrence, PPI databases)
  • Construction of benchmark datasets for comparative evaluation
  • Analysis and interpretation of results with biology partners
  • Optimization of computing resources (GPU, task partitioning, accelerated tools)
  • Documentation, reproducibility, version tracking (scripts, configs)

Expected skills and knowledge

Specific technical skills:
  • Structural bioinformatics (AlphaFold, AlphaPulldown, MMseqs2, Foldseek...)
  • Development of bioinformatics methods and tools
  • UNIX/Linux environment
  • Python and Bash programming
  • Git, Docker/Apptainer
  • HPC usage and job scheduling (Slurm)
Valued skills:
  • Machine learning applied to biological data
  • Multiple sequence alignment (MSA)
  • Benchmarking and performance evaluation (statistics, visualization)
Transversal skills:
  • Ability to interact with non-specialist users
  • Curiosity, autonomy, scientific rigor
  • Ability to disseminate results (reports, publications, oral presentations)
  • Proficiency in scientific English

Desired profile

  • PhD in life sciences, bioinformatics, or related fields
  • 3 years of experience including bioinformatics tool development

Location

Ressource Parisienne en Bioinformatique Structurale (RPBS)
Lamarck A building
35 rue Hélène Brion
75013 Paris
(Grands Moulins Campus, Université Paris Cité)

Recruitment conditions

  • Desired contract start: October 2025
  • Contract duration: 18 months, renewable up to 36 months total (to be confirmed based on project progress)
  • Contract type: fixed-term – IdEx-funded project (FORMULA, Université Paris Cité)
  • Salary: according to public service pay scales, based on the candidate’s profile and experience (category A – research engineer with PhD and ≥ 3 years of experience)