The Hub of Bioinformatics and Biostatistics provides analytical support to research units and platforms at the Institut Pasteur. The Hub is committed to this mission through:
- Collaborating on scientific projects, submitted by research teams of our institute, to the Hub.
- Training scientific staff from the Institut Pasteur Paris or from other institutes of the international network of Instituts Pasteur.
- Developing tools and applications to be shared with the broader scientific community.
- Interacting directly with scientist upon specific inquiries.
The Hub is hiring a research engineer in bioinformatics/biostatistics, to be detached in the French National Reference Center for viruses of respiratory infections for Northern France.
The engineer will be detached for 80% of his/her time in the team headed by Etienne Simon-Lorière. The remaining 20% will be dedicated to technical contribution and interaction with the Hub, as well as training and teaching activities.
This job offer aims at increasing capacity to respond to future viral outbreaks and better track endemic viruses. This project is particularly focused on:
- Tracking of pathogens and their evolution
- Identification and characterization of novel pathogens / variants
- Development of diagnostics
To answer these questions, numerous bioinformatics challenges emerge. With genomic data being generated at an unprecedent rate, it becomes imperative to develop highly efficient tools capable of routinely monitor local and global trends.
In this context, we plan to develop computational tools and workflows to support large quantities of genomic data to monitor outbreaks.
This will involve benchmarking and developing bioinformatics workflows capable of: i) identify pathogens (targeted and untargeted high throughput sequencing data, both Illumina and Oxford Nanopore Technologies), ii) track their evolution (phylogenetics), and iii) monitor the emergence of relevant mutations, and specific evolutionary events (e.g., recombination or reassortment). To do so, different methods can be applied, such as K-mer methods, or Bayesian and Maximum Likelihood phylogenetics methods.
Knowledge & skills
A good knowledge of evolutionary bioinformatics methods is required. In particular in sequence analysis, alignment and phylogenetic reconstruction. Prior experience of Bayesian methods (Mr Bayes, BEAST) would be beneficial.
A special interest in developing reproducible and maintainable workflows is encouraged (e.g., workflow systems, containers).
The candidate should have a PhD degree or equivalent in a relevant field (bioinformatics, computational biology, etc.), with a good publication record. Knowledge in viral evolution will be a plus.
Details on the GEVA group of Institut Pasteur can be found here:
Click on the following link and select the corresponding profile “Viral genomics data analysis (respiratory viruses surveillance)” when this will be proposed:
Please, submit your updated CV and a cover letter (motivation letter). You may indicate contact information for reference letters (3 max.). They will be automatically contacted when you validate your application.
We are a team committed to foster a fair, inclusive and diverse work environment. Diversity has been scientifically established as a key factor to improve scientific objectivity. Hence, all applicants will be evaluated solely based on qualification regardless of gender, gender identity, sexual orientation, race or disability.