Post-doctoral researcher in bioinformatics (M/F): exploring biomolecular interactions for bacteriophage protein function prediction

Job Description

Missions

Bacteriophages (viruses that infect bacteria, also called phages) profoundly shape bacterial ecosystems. Yet, classifying their vast diversity remains a major obstacle to understanding their ecological roles and interactions with bacteria. This position is embedded in a larger Franco-German collaborative project funded by the ANR, which aims to develop high-level taxonomic classification (at family or order level) for phages. The project proposes to decompose phage genomes into coevolutionary genetic modules (which we dubbed phage genetic modules or PGM) that will be used for classification and to improve functional annotation of phage genomes.
In this framework, the postdoctoral researcher will combine evolutionary information derived from multiple sequence alignments of homologous sequences with structural properties to predict biomolecular interactions of phage proteins. To do this, they will begin by benchmarking recent deep-learning tools (such as AlphaFold or ESMFold) to predict structures of phage protein complexes, first at small scale, then for the modules (PGM) and their alignments that will be constructed by collaborating teams. These predictions will be extended to more challenging cases, such as interactions involving short linear motifs in disordered regions (such as motifs that viruses use to hijack the regulatory functions of their hosts) or interactions between proteins and nucleic acids involved in replication and recombination. To this effect, the selected candidate will fine-tune structural prediction methods and study the benefits of large-scale language models. Finally, the project will include broader-scale screening steps (up to whole-genome level) to predict novel protein interactions and develop a tool for assessing the propensity of two phage proteins to interact.
The project results will be made available to the scientific community. One of the participating teams is developing a viral sequence database (VirJenDB), which will be expanded to include the modules identified in this project and will integrate annotations from the different participating teams.

Activity

The selected candidate will undertake the following tasks:
- Data collection and curation
- Benchmarking of different 3D structure prediction tools and biological language models
- Multi-scale structural modeling and analysis of predicted 3D models
- Statistical modeling and machine learning to extract features and develop predictor tools
- Analysis of interaction networks
- Development of methods, scripts and software, and use of compute clusters
- Preparation of data for integration into a central database (VirJenDB)
In addition, the selected candidate will be expected to contribute to the project and team life by designing research strategies, updating relevant knowledge, writing papers and communicating project results, and possibly supervising masters and PhD students.
The project relies on a collaboration with other French and German teams. The selected candidate will therefore interact with the different project participants on a regular basis.

Your Profil

Skills

Candidates should be highly motivated by interdisciplinary research and the use of computational or mathematical tools to answer questions of biological interest. The selected post-doctoral researcher should have a PhD in bioinformatics, microbiology/viral ecology, or another field providing relevant skills for the project. Previous experience in data analysis and methods development is required, as well as the knowledge of a relevant programming language (ideally Python). Knowledge in the field of bacteriophages and experience in manipulating protein and RNA molecular and/or structural data are both highly desirable. Experience in statistical modeling and biological network analysis would be a plus. The selected candidate should also be able to carry out research independently, to work collaboratively and should be fluent in written and oral scientific English. Knowledge of French is not necessary for the project.

Your Work Environment

The post-doctoral research will take place in the “Molecular assemblies and genome integrity” team of I2BC (Institute for Integrative Biology of the Cell, UMR 9198 CEA/CNRS/Université Paris-Saclay).
I2BC is a research institute of Université Paris-Saclay that gathers 48 research teams. Research at I2BC covers a wide range of integrative biology projects in biophysics, biochemistry, structural biology, genome biology, cell biology, microbiology, virology and bioinformatics.
The “Molecular assemblies and genome integrity” team belongs to the Biophysics, Biochemistry and Structural Biology department and relies on a strong coupling between computational and experimental approaches to characterize, predict and inhibit macromolecular interactions. The team is located on the Gif-sur-Yvette campus, less than one hour from the center of Paris.
In recent years, the team developed original approaches for the structural prediction of protein interactions using evolutionary information (Andreani et al. Bioinformatics 2013; Yu et al. Nucleic Acids Res 2016, Proteins 2017; Quignot, Rey et al. Nucleic Acids Res 2018, 2021 and Bioinformatics 2021). The team thus has a strong expertise in structural bioinformatics, macromolecular interaction prediction and heterogeneous data integration. Furthermore, the team has recently published several studies using artificial intelligence-based techniques, notably AlphaFold, to model protein-protein interactions (Bret et al, Nat Comm 2024; Villa et al, PLOS Pathogens 2026) and protein-DNA interactions (Dalia et al, PNAS 2025; Dewailly, Fauconnet et al, PNAS 2025). The team has also recently published studies on protein-RNA interactions, addressing both methodological aspects (Mahmoudi et al, PLOS Comp Biol 2024) and applications to the study of RNA-based defense systems in phage-bacteria interactions (Saunier et al, PLOS Genetics 2025).
The research position will be funded as part of a Franco-German project selected by the ANR. The postdoctoral researcher will benefit from a stimulating interdisciplinary scientific environment, the team's expertise, and access to the computational resources necessary to carry out the project.
The position is funded for 13 months (with possible extension) with a start date in autumn 2026 (exact date flexible).

Compensation and benefits

Compensation

approximately 3131€ to 4341€ gross monthly salary (depending on previous experience)

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

The research professions