The Microbial Paleogenomics Unit is offering a permanent position of research engineer expert in bioinformatics applied to genomics, and particularly to ancient human and microbial DNA data.
The main questions tackled in the lab include the emergence and spread histories of human-associated microbes (including pathogens) as well as the genetic histories of ancient human populations, with a special focus on the Americas.
The recruited candidate will play a central role in the lab and will be involved in multiple tasks and research projects, with the possibility of carrying her/his own projects. The main topic of the lab, and hence, of his/her activities, will be the analysis of ancient DNA data obtained from human archaeological remains, with a special focus on ancient human microbes.
The main activities will include the following:
- Contribute to the development of the research lines of the lab, with high encouragement to participate in scientific discussions, bring ideas and propose new projects.
- Developing and writing new software (e.g., ancient DNA and paleometagenomic data analysis, pathogen screening and identification, microbial phylogenomics, etc.)
- Supervision of students
- Setting-up analysis pipelines that will be routinely used in the lab. This includes pipelines to screen sequencing data for microbial species, recovering, reconstructing and analyzing whole ancient and modern microbial and human genomes, variant calling, pangenomic analyses, phylogenomic analyses, metagenomic analyses, plotting results, etc.
- Assist students and postdocs in terms of scripting, programming, and data analysis.
- Spread good bioinformatic practices in the lab.
- Installing and testing software for the lab.
The candidate will also have a second affiliation to the Hub of bioinformatics and Biostatistics. This will imply participation to Hub tasks like bioinformatics support to Institut Pasteur through teachings, open desks or other support activities.
Required expertise
- High level of scripting in Python, Bash and pipelines (e.g., Nextflow, Snakemake) languages,
- Experience in package management tools for data science (e.g., singularity, conda, anaconda, etc.)
- Experience in microbial genomics and NGS data handling and analysis
(Proven experience in ancient DNA and/or phylogenetics and/or metagenomics will be prioritized) - Basic system administration skills.
- Experience with R, other programming languages and/or database management, will be also a plus.
Other fields of experience considered for eligibility :
- Biostatistics/machine learning,
- Phylogenetics,
- Metagenomics,
- Microbial ecology,
- Ancient DNA/paleogenomics,
- Human genetics
- Population genetics.
Soft skills
- The person must excel in social and communications skills to contribute to creating a positive learning and cooperative environment and must have a good predisposition to train or assist other people in the lab. She/he must be proactive, creative and flexible, capable of developing his/her work autonomously, but also eager to bring, discuss and develop new ideas for the lab.
Training/diploma:
The candidate may be a graduate from bioinformatics/computer science or biology-related degrees with a strong background in bioinformatics. Holding a PhD diploma or postdoc experience would be preferable but not mandatory.
To apply or get more information about the position:
Please, submit your updated CV and a cover letter (motivation letter) to Nicolas Rascovan: nicolas.rascovan@pasteur.fr
