Computational Biologist position for single-cell analyses

A Computational Biologist position is available within the laboratory of Dr Mickaël Ménager at the Imagine Institute in Paris, France (

Accélérer la recherche

ATRACTion: Autoimmunity/inflammation Through RNAseq Analysis at the Single-Cell level for Therapeutic Innovation

Our lab is one of the main research team, involved in a big research hospital-university project (RHU), funded by the French national agency of research (ANR). In this project, we are proposing to revisit rare monogenic disorders, characterized by autoimmunity and/or autoinflammation, at the single-cell level. By combining transcriptomic with proteomic and chromatin accessibility analyses performed on cells from the peripheral blood, we are aiming to identify so-called “pathological” cell clusters, mostly enriched of cells from patients as compared to controls. From such “pathological” cluster of cells, we intend to extract new molecular signatures, biomarkers that will help to redefine patients ‘stratification at the molecular level. We are now looking for a very talented and ambitious computational biologist, who will embark with us, on this journey to redefine autoimmunity and autoinflammation at the molecular level.

The Imagine Institute represents a unique setting in which to develop such collaborative project based on human disease related studies, with ample opportunity for collaborations with national and international top-level scientists and clinicians from Imagine, Curie, Pasteur, CEA, INRA and industrial from Sanofi and Ariana Pharma.


Expectations of the current post

The computational Biologist will be expected to set up and optimize pipelines to analyze single-cell multi-omics datasets such as single-cell transcriptomic coupled with barcoded antibodies (CITE-seq), single-cell epigenomics, single-cell spatial transcriptomic, …  In collaboration with the bioinformatic platform and the LabTech Single-Cell@Imagine, he will have to deliver single-cell clustering analyses coupled with differential gene expressions.



We are looking for a highly motivated computational biologist (PhD/engineer diploma or master degree in bioinformatics) with a proven track-record of independent working. The candidate must have first-class skills in mastering open-source packages for single-cell analyses such as SEURAT, Monocle, MNN, Velocyto and others. Candidates with extensive knowledge in programming languages (R, Python, …), and NGS data analysis (STAR, Trinity, picard, samtools, DEseq, EdgeR, CellRanger, Juicebox…) are strongly encouraged to apply. Knowledge of Immunology in general would be ideal.


Salary and length of contract

The contract will start as soon as possible for a period of 3 years. Salary will be established based on experience.


Application details

Applications in English including a letter of motivation, a detailed CV and contacts of appropriate referees should be sent to with the reference Imagine_191.