Biocomputist in Roscoff, Bretagne, FR at IFREMER - ENGLISH

Date Posted: 9/27/2020

Job Snapshot

Job Description

Job title : Biocomputist

Reference:  PV-2020-077

Department/Office :  Département des Ressources Biologiques et Environnement

Unité de recherche Physiologie Fonctionnelle des Organismes Marins

Duty station:  Roscoff, Bretagne, FR , France

Starting date on the job :

Deadline for applications : 30/09/2020



The Institute and the recruiting departement

A pioneer in ocean science, IFREMER’s cutting-edge research is grounded in sustainable development and open science. Our vision is to advance science, expertise and innovation to:

- Protect and restore the ocean

- Sustainably use marine resources to benefit society

- Create and share ocean data, information & knowledge.

With more than 1,500 personnel spread along the French coastline in more than 20 sites, the Institute explores the 3 great oceans: the Indian, Atlantic and Pacific oceans. A leader in ocean science, IFREMER is managing the French Oceanographic Fleet and its dedicated scientists create ground-breaking technology to push the boundaries of ocean exploration and knowledge, from the abyss to the atmosphere-ocean interface.

Well-established in the international scientific community, our scientists, engineers and technicians are committed to advance knowledge about our planet’s last unexplored frontiers. They provide the science we need for informed decision-making and public policy and they transfer this knowledge and technology to businesses to fulfill public and private needs. Core to our mission is also to strengthen public awareness about the importance of understanding the ocean and its resources, and empowering future generations of leaders through education and outreach national campaigns.

Founded in 1984, IFREMER is a French public organization and its budget approximates 240 million euros. It is operating under the joint authority of the French Ministry for Higher Education, Research and Innovation, the French Ministry for the Ecological and Solidary Transition, and the French Ministry of Agriculture and Food.



General areas of responsibility

The Roscoff marine station (SBR) constitutes an ideal scientific and logistical environment for the research project of “Génomique des Vibrios” team thanks to the presence of technological platforms (bioinformatics, imaging, crystallography, aquariums) and basic research projects developed in the departments (ecology, biology of marine microorganisms). Conversely, the team roots its scientific questions and experimental models in the needs of applied research that Ifremer must conduct (pathogenic oyster bacteria).

The position is part of the ERC advanced DYNAMIC project, which aims to understand the role of phages in the eco-evolutionary dynamics of pathogenic hollow oyster vibrios.

Under the supervision of the scientific leader of the project, he/she will work in close collaboration with the team members for the in silico analysis of the data.


General areas of responsibility

  • He/she will be in charge of the analysis of genomes, transcriptomes (vibrio/phage) and viral metagenomes.
  • He/she will be in charge of the traceability of sequencing and assembly data and of the deposit in the databases including Mage at CEA.
  • A special effort will be required for the drafting of the laboratory notebook.
  • He/she will participate in team meetings and laboratory seminars.


Principal activities

  • Using bioinformatics, he/she will characterize the candidate genes involved in vibrio-phage interactions (receptor, defense and counterattack mechanisms).
  • He/she will characterize the different families of genes in the genomes of phages and bacteria as well as by classifying them according to their distribution, function and origin.
  • He/she will study the evolution of specific genes in order to decipher the supposed relationships with the biology of species/strains/groups, and to characterize the mobile genetic elements involved in resistance.
  • A phage metagenomics study will explore phage dynamics both temporally (samplings during V. crassostreae blooms) and spatially (oyster versus seawater).
  • Participation in the team's duties involve i) updating our website; ii) updating the storage of sequencing and assembly data at the station site and at Pasteur. iii) updating our VibrioScope and Phage on Mage platform (CEA).
  • He/she will benefit from the experimental data obtained by the team members and will collaborate with the Pasteur Institute. This collaboration will involve short stays at the Institut Pasteur and regular exchanges by videoconference.


Collaborative work environment

Internal collaborative relationship: Project team, (8 persons), from the LBI2M unit in Roscoff (100 persons) and from the station (350 persons) various meetings and seminars will promote interaction. Regular exchanges will take place with colleagues from the PFOM unit of Ifremer Plouzané/Argenton.


External collaborative relationship: He/she will work in close collaboration with Eduardo Rocha at the Pasteur Institute. He will also interact with the Claudine Medique team at the CEA, Evry, for updating the VibriosCope platform.




Required Knowledge, skills, and characteristics


PhD in microbiology, genomics or bioinformatics

Required knowledge

Skils and characteristics

  • a PhD in microbiology, genomics or bioinformatics
  • a good knowledge of microbiology, ecology and evolution
  • strong expertise in genome bioinformatics, especially in the analysis of DNA and protein sequence data
  • a good knowledge of statistical analysis and management of biological (incl. multivariate) data
  • a good knowledge of at least one programming language (preferably R or Python)


Human qualities

  • a high degree of motivation for the advertised project
  • desire to learn, curiosity and adaptability
  • a fondness for support of and interaction with other group members



Specific working conditions


  • In silico work in office (with a computer supported by the lab).
  • Short stays at the Pasteur Institute for meetings and trainings.

All applications are processed exclusively via our website. Informal enquiries may be made to, scientific leader of the ERC advanced DYNAMIC project





How to apply for this position

Deadline for applications: 30/09/2020

All applications are processed exclusively via our website. Interested candidates can apply by clicking the “Apply” button.