Careers

Two years post-doc position on viral phylodynamics

Title of the position: Post-doc on viral phylodynamics

Department: CERP (Center of Excellence in Respiratory Pathogens) and GenEPII (GENomique à visée diagnostique et EPIdémiologie des maladies Infectieuses)

Location: Lyon, France

Duration: 24 months (beginning at the latest January 2026)

ORGANIZATIONS

• CERP

The research carried out at the CERP (https://cerp-epi.com) aims to support decision-making related to respiratory pathogens. CERP based at Laennec (69008 Lyon) is part of the International Center for Research in Infectiology (CIRI), the University Claude Bernard Lyon 1 and the Hospices Civils de Lyon. The CERP’s goals are: to create excellence in multidisciplinary research combining virology, epidemiology, data analysis, bioinformatics and modeling; ensure a continuum from data collection to their use in policy decisions; be a convener for the main international actors working on this theme.

• GenEPII

The GenEPII sequencing platform (https://teamhcl.chu-lyon.fr/genepii; https://genepii.univ-lyon1.fr) is located in the Hopital de la Croix Rousse (69004 Lyon) within the Hospices Civils de Lyon. The team includes microbiologists, bioinformaticians, engineers and technicians working on microbiology genomics. The platform is associated with four National Reference Centers (NRC), including the NRC for respiratory viruses and has been deeply involved in SARS-CoV-2 genome sequencing. The lab has on-site robotic sample processing, high-throughput computing resources as well as next-gen sequencing facilities (NextSeq, NovaSeq, Oxford nanopore gridion).

JOB SUMMARY

CERP and GenEPII are looking for a highly motivated postdoctoral researcher, specialized in viral phylodynamics. The main aim of the project is to define and implement phylogenetic and phylodynamic methods to better monitor viral epidemics (Influenza, SARS-CoV-2 and other respiratory viruses).

Projects will focus on:

• Implementation of phylodynamic methods to monitor within-outbreak pathogen dynamics, to study the local spread of specific viral lineages (known or emergent) and to estimate key epidemiological parameters.
• Analysis of viral transmission dynamics across population structures (vaccination, age, hospital vs community…).

This is a unique opportunity for a post-doc to join a recent, motivated and experienced research team in an international working environment to address the main health challenges related to respiratory diseases.

TRAINING AND PROFESSIONAL EXPERIENCE

• PhD in genomics, population genetics, bioinformatics, computational biology, or biostatistics
• Experience with maximum-likelihood and Bayesian phylogenetic methods
• Knowledge of at least one programming language (R, python)
• A strong track record in phylodynamics is a plus
• Strong problem-solving skills and a record of self-directed, innovative research

SKILLS

• Fluent written English
• Ability to work on several projects simultaneously and adapt to the constraints of multidisciplinary research projects
• Integrity, curiosity, proactivity, organization and ability to work autonomously
• Good judgment and anticipation, able to propose solutions
• Enthusiastic and professional approach to working with colleagues and external collaborators.
• Good communication

HOW TO APPLY

If you are interested in the position, please send an email to Dr Marta Nunes (marta.nunes@univ-lyon1.fr) and Dr Laurence Josset (laurence.josset@chu-lyon.fr) attaching the following documents:

• A cover letter
• A curriculum vitae
• Contact information for 2 references