Mots-Clés

Ancient DNA, Paleogenomics, Phylogenomics, Metagenomics, Population Genetics,

Description

Website of the offer:

https://research.pasteur.fr/en/job/research-engieneer-in-bioinformaticvs-applied-to-paleogenomics-data/

To get information about the position, you can directly contact Nicolás Rascovan (head of the Microbial Paleogenomics Unit) at the following email address: nicolas.rascovan@pasteur.fr

The Microbial Paleogenomics Unit of Institut Pasteur in Paris 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 special focus in the Americas.

The recruited candidate will play a central role in the lab and will be involved in multiple tasks and research projects, with 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 special focus in 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 on 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 (C++/Java) 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 on social and communications skills to contribute creating a positive learning and cooperative environment, and must have 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 graduate from bioinformatics/computer science school, or biology-related degrees with strong background in bioinformatics. Holding a Ph.D. diploma or postdoc experience would be preferable but not mandatory.

To apply

Click on the following link and select the corresponding profile “paleogenomics” when this will be proposed:

https://hub-jobs2022.pasteur.cloud/

Please, submit your updated CV and a cover letter (motivational letter). You will be able to indicate contact information for reference letters (3 max.). They will be automatically contacted as soon as you validate your application.