Job ID: 113905

PhD position, spatial transcriptomics analyses for the inference of ligand-receptor interactions over mouse cerebral cortex development

Position: Ph.D. Student

Deadline: 30 November 2023

Employment Start Date: 1 December 2023

Contract Length: 3 years

City: Marseille

Country: France

Institution: Institut de Neurobiologie de la Méditerrannée, INSERM U1249




We have an opening PhD position in the Cortical development team at INMED (Marseille) to study ligands and receptors that collectively control the stereotypic development of the cerebral cortex. The project is grounded on our own, yet unpublished, single cell RNAseq (scRNA-seq) atlas that infers significant ligand-receptor interactions between all neuronal subtypes over mouse cortical development (17 ages between E11-adulthood), in control and autistic mouse models (Neurod2 KO mice). However, taking in account the position and relative distance between cell type pairs over time remains to be done in order for our atlas to sort the most biologically meaningful ligand-receptor mediated intercellular communications. The project aims at bridging this important gap by integrating MERFISH-based spatial transcriptomics experiments to our already performed scRNA-seq developmental datasets, in control and Neurod2 KO mice. We combine MERFISH, state-of-the-art computational analyses and in vivo “ligand/receptor validations” via in utero electroporations of gain/loss-of-function plasmids or AAV injections.

We are seeking motivated candidates strongly interested in neurodevelopment and with proven expertise in bioinformatics (M2 bioinformatics or equivalent level is a prerequisite). Required skills:

  1. Proficiency in programming languages such as R and Python.
  2. Comprehensive knowledge and/or expertise in analyzing transcriptomics data, including RNA-seq, single-cell RNA-seq, and/or spatial transcriptomics.
  3. Sound understanding of mathematical techniques for analyzing multidimensional data.

The successful candidate shall spend >75% of his time on the dry lab part of the project, analyzing MERFISH/scRNA-seq integrated data. You will work within a multidisciplinary environment made up of experts in bioinformatics and image analysis, as well as neurobiologists. The position is funded by AMiDex Aix-Marseille University for 3 years and is intended to start between October and December 2023.

Our team is part of the Institute of Neurobiology of Méditerranée (INMED), located in the beautiful National Park of Calanques. INMED is a very stimulating scientific environment, with research groups interested in functional and structural organization of neural circuits supporting cognition in healthy or pathological contexts.


Please send formal application (CV, cover letter, 2 references) or questions to The position will remain open until fulfilled.