Host: European Molecular Biology Laboratory (EMBL), DE.

PhD Awarding institution: Heidelberg University (UHEI), DE.

Primary Supervisor: Dr.Yannick Schwab.

Project duration: 36 months.

Project description: The morphome quantitatively describes morphological diversity at multiple scales: At the subcellular level, the set of organelles, their arrangement and associations define functional units that are relevant to cell types (e.g. sarcomeres in muscles, secretory granules in gland cells). The correlation of expression profiles to ultrastructural phenotypes has so far been very difficult. In this project,  will focus on the development of tools to bridge scRNAseq to volume Electron Microscopy (vEM), with the specific goal to identify cell types by their expression profile and target these for detailed sub-cellular description by vEM and subsequent image analysis. Within the consortium, collaborations will lead to the investigation of a few model systems (D.Priapulus, Novocrania, and/or Acanthochitona), with a strong focus on the planula larva of the hydrozoan Clytia, in close collaboration with the group of Evelyn Houliston  (CNRS-IMEV). The PhD candidate will  i) develop correlative in-situ hybridisation and transmission EM workflow to identify cell types and to then ii) further their morphological characterisation by acquiring vEM datasets and iii) performing detailed image analyses (in collaboration the Kreshuk lab). Resulting in a detailed description of the subcellular landscape, iv) parallels will be sought with the corresponding single-cell transcriptomes.

Application deadline: 11th March 2024

How to apply: Candidates shall apply via the EMBL International PhD program at the following link and express their interest in this position within the group of Yannick Schwab.