Post-doctoral position in Plasmodium genomics/transcriptomics

 CDD · Postdoc  · 24 mois (renouvelable)    Bac+8 / Doctorat, Grandes Écoles   LPHI UMR5235 · Montpellier (France)

 Date de prise de poste : 1 janvier 2023


Bio-informatic, biology, genomic, transcriptomic, infectiology, parasitology



  • Candidate with demonstrated experience in Omics data analysis  
  • Minimum 2-year contract, with possible 2-year extension with our collaborators in Marseille
  • Main project: single-cell genomics and transcriptomics of the malaria parasite P. falciparum, from a unique cohort of (a)symptomatic infections from Cameroon




Malaria kills half a million children a year, yet in endemic areas most Plasmodium falciparum infections remain asymptomatic. The goal of our research is to understand the genomic and transcriptomic mechanisms that enable P. falciparum to establish a chronic, asymptomatic, infection in humans. We test in vitro-based hypotheses on field isolates collected in malaria endemic countries. More specifically, we characterise how the parasite escapes the immune system by regularly switching its surface antigens. More details can be found in our recent Trends In Parasitology Opinion (video summary and Open Access copy).



With colleagues at the London School of Hygiene & Tropical Medicine, Crick Institute, Texas Biomed (USA) and at the Sanger Institute (UK), we are sequencing parasite field isolate genomes, transcriptomes and single-cell transcriptomes. Various dry-lab projects are available, the exact research question will be defined based on the candidate expertise:

  • Long-read sequencing data analysis (Nanopore versus PacBio) from P. falciparum clinical isolates
  • Phylogenetic analysis of variant surface antigens (var, rif, stevor) from newly assembled P. falciparum genomes
  • Parasite population genetic diversity in The Gambia and Cameroon.
  • Qualitative and quantitative assessment of variant surface antigen expression from single-cell RNAseq data from symptomatic versus asymptomatic parasite isolates. The ultimate goal is to identify host & parasite biomarkers predicting the outcome of a malaria infection (symptomatic vs asymptomatic).
  • Host antibody characterisation (Wet-lab project, if suitable).

You will interact with our collaborators in the UK/USA, and potentially one trip to Cameroon for teaching at a workshop in bioinformatics. Based on your progress, there is an opportunity for a further 2-year contract with Sandrine Marquet (TAGC, Marseille, France) to analyse PBMC single-cell RNAseq data from the same cohort.



  • Training in biostatistics/bioinformatics, or in molecular biology with demonstrated experience in Omics data analysis
  • Knowledge of population genetics and/or phylogenetics is a plus
  • Able to work independently
  • Great communication skills in English
  • Stay focused on answering a specific biological question, from the initial analysis to publication
  • Passionate about scientific discoveries
  • Other desirable skills: knowledge about malaria biology, willing to occasionally supervise a Master student, participate actively in the lab and institute life, appreciate XKCD humour.



Antoine Claessens (PI) is a malariologist who trained at Edinburgh University, the Sanger Institute, LSHTM and the MRC-Gambia. He joined Montpellier University in 2018 as a “Chargé de Recherche INSERM” and leads an ATIP-Avenir team, currently consisting of three PhD students, one post-doc and one permanent engineer. This position will be funded by the ANR and “MUSE Pre-ERC” funding. 



You will closely interact with mathematicians and computer scientists of the systems biology team from LPHI, with experienced bioinformaticians from the bioinformatics platform and with population geneticists from MIVEGEC. Both ‘UMR’ are very international, with highly competent and friendly scientists. More generally, Montpellier is a large hub for research in Life Sciences, particularly in the field of evolutionary biology. Being able to speak French is not a requirement.

You will join a young and dynamic team. I will try my best to transmit my passion about P. falciparum biology; you might find yourself dreaming about var genes too. You are welcome to bring your own side projects if you wish. If you are planning to stay in academic research, I will help you secure your own funding (e.g. writing a Marie Curie Fellowship application). Perks include Mediterranean climate, food and landscape.  


Procédure : Interested in applying? Please send an email to This position will remain open until a suitable candidate is found. Starting date around the 1st January 2023.

Date limite : 31 décembre 2022


Camille Cohen

Offre publiée le 3 novembre 2022, affichage jusqu'au 31 décembre 2022