The National Institute for Ocean Science (Ifremer) is an integrated marine sciences research institute, which contributes to national research and innovation, as well as to the European research landscape. As such, IFREMER produces:

basic knowledge using a systemic approach that aims to better comprehend the processes that govern ecosystems and understand the changes that affect them;
targeted research results to provide answers to society’s questions based on its capacity for observation, monitoring, and assessment.

IFREMER dedicates its efforts to high-quality research founded on diverse disciplines and topics by drawing on its partnerships with universities and research institutes. It is also the driving force on the international and European levels behind joint programming initiatives, targeting research or infrastructures (fleets, observatories, databases).

The Marine Invertebrate Health Adaptation Unit (ASIM) conducts projects related to i) the study of diseases affecting marine mollusks; ii) the detection and study of disease outbreaks; iii) host adaptation to these diseases (resistance development and associated determinism).

The ASIM unit serves as a strong integration point between research activities and surveillance/reference functions, thanks to its internationally recognized expertise. It is both a National Reference Laboratory (NRL) and a European Union Reference Laboratory (EURL) for marine mollusk diseases. The main objectives of the ASIM unit are to enhance knowledge and data on the genomes of marine invertebrates and their pathogenic microorganisms, to better understand the evolutionary and adaptive mechanisms of marine invertebrates and associated pathogenic microorganisms in their ecosystem, and to develop risk analysis approaches within a broader "One Health" framework.

General areas of responsibility

The postdoctoral position is funded by an ANR JCJC project named IDEAL. You will work on quantifying the contribution of genomic analyses to the understanding of marine pathogen spread and identification of drivers. You will be specialized in spatial and molecular epidemiology and aim at exploring relevant contrasting scenarios to compare and integrate together spatio-statistical and phylogeographic models to detect factor impacts on pathogen spatial distribution and spread.

Principal activities

You will:

develop a simulation pipeline using an existing agent-based transmission chain simulator to simulate entire epidemics of farmed marine bivalves in space and time, and subsequently generate fictitious occurrence and molecular data compatible with real datasets.
compare both spatio-statistical and phylogeographic analytical to assess to what extent and under which specific conditions the different analytical methodologies allow identifying and quantifying the impact of factors on the distribution and dispersal of pathogenic organisms.

Three aspects will receive particular attention: i) impacted epidemiological parameters; ii) monitoring and diagnosis conditions; and iii) evolutionary rates of pathogens. The data simulated within the framework of the different scenarios identified will be used to evaluate and compare the methods available for testing the impact of factors on the spread of pathogens.

You will be responsible for leading the publication resulting from this research.

Collaborative work environment

Internal collaborative relationship

You will be supervised by the coordinator of the project Maude Jacquot (IFREMER, ASIM), researcher in molecular epidemiology and will be working closely with project collaborators at IFREMER (ASIM, LPI, SeBiMER).

External collaborative relationship

You will be co-supervised by Simon Dellicour from the Spatial Epidemiology Lab (SpELL) hosted at the University of Brussels (ULB, Belgium), who is an expert on methodological developments and applications in landscape phylogeography. Regular remote meetings with S. Dellicour will be organized and you will visit him at SpELL at least twice during its contract.

Required Knowledge, skills, and characteristics

PhD in relevant field (spatial or molecular epidemiology, computational biology (obtained maximum 3 years ago).

Required knowledge, skills and characteristics

Knowledge, skills and abilities

Knowledge of spatial and molecular epidemiology
Proficiency in bio-statistical tools and programming languages (R, Python, Linux shell)
Proficiency in concepts and tools for characterizing genomic diversity and spatiotemporal evolution of pathogenic organisms
Understanding of various molecular genotyping and high-throughput sequencing approaches and their potential applications in population health research
Familiarity with pathogenic organisms in invertebrates appreciated
English language proficiency
Project coordination skills
Strong writing abilities

Human qualities

Autonomy and rigor
Curiosity
Ability to work in a team
Synthesis skills

Specific working conditions

The post is full time; 18 months contract.

All applications are processed exclusively via our website. Informal enquiries may be made to maude.jacquot@ifremer.fr and simon.dellicour@ulb.be.

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 of the Sea, the French Ministry for the Ecological and Solidary Transition, and the French Ministry of Agriculture and Food.

How to apply for this position

Deadline for applications: 30/11/2023

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

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