The Bioinformatics Team at Phagos is seeking a Bioinformatics Engineer to spearhead our capabilities in high-throughput structural genomics. You will lead the development of automated pipelines that analyze protein-protein and protein-ligand interactions at scale, moving beyond sequence identity to leverage structure-based clustering and protein-protein coupling.

Main Responsibilities

• Design and build robust bioinformatics pipelines using Nextflow to automate the structural prediction and clustering of thousands of phage and bacterial genomes

• Implement and tune structural clustering algorithms to organize phage receptor binding proteins and bacterial membrane proteins into functional families

• Develop modules to detect and classify non-protein surface markers (specifically LPS) from bacterial genomes.

• Create logic and statistical models that link RBP structural clusters with bacterial surface profiles to predict host range and phage resistance and automate protein docking.

🎁 Our benefits :

• Healthcare 100% paid by Phagos

• Swile card (€9.87/day – 60% paid by Phagos)

• RTT

• Wellpass (ex Gymlib) subscription

Technical Skills

• Hands on experience benchmarking and scaling state of the art protein structure prediction and clustering tools (AlphaFold, ESMFold, Foldseek, TM-align) and automating docking workflows (HADDOCK, Chai-1) (Required)

• Strong scripting skills for biological and structural data analysis (Biopython, Pandas, Bio.PDB) (Required)

• Comfortable to work in cross-functional team projects, translating bioinformatic/computational concepts for laboratory biologists (Highly desired)

• Knowledge of microbial genomics and bacteriophage biology, including the ability to identify genomic features like LPS or membrane proteins (Nice to have)

Soft Skills

• Self motivated,  ability to work independently, and manage objectives, expectations, and deliverables

• Fluency in English (written and spoken)

Education & Experience

• PhD or Master’s degree in Bioinformatics or Computational Biology, or a related field.

• 3+ years of professional experience specifically focused on Bioinformatics Engineering and Pipeline Development

At Phagos we believe the recruitment process begins from the application. This is why we invite you to take your time and thoughtfully complete our application form.

Once we select your profile, we are committed to make sure you have a positive and seamless experience.

Step #1 Interview with Andrew, our Head of Bioinformatics

Step #2 Technical test, with Andris our Bioinformatic Infrastructure Engineer

Step #3 Chat with our co-founders

Team fit : Last but not least, you will meet 5 members of Phagos, randomly picked for a Team fit discussion in English. When possible, this meeting will be held in our office in Suresnes.