IBDM is located on the Luminy Campus and comprises about 240 permanent researchers, professors, engineers and technicians and non-permanent staff (CDD, post-docs, PhD students, trainees) working in 21 research teams and 11 technical platforms and services.
IBDM is a joint research unit under the supervision of the CNRS and AMU, which explores the field of developmental biology and associated pathologies.
The activity will be carried out within the team "Computational Biology" directed by Bianca Habermann.
As the team is composed of several nationalities, the practice of English language is essential.
This PhD project is a collaborative effort with an experimental team working on Cerebellar Ataxias (CA), located in Lyon. For the analysis of single-cell RNA-seq data from mouse models of ataxia, the PhD student will implement the ataxiaXplorer tool, based on the mitoXplorer tool developed in the Computational Biology team (http://mitoxplorer.ibdm.univ-mrs.fr ). He/she will extend the functionalities of ataxiaXplorer for the analysis of different cell types, implement new visualization methods for data exploration and new methods for data integration. He/she will then use the tool to mine public data on cerebellar ataxias, as well as data from our collaborative partner.
Data mining to build the ataxia interactome (literature, databases); creation and adaptation of ataxiaXplorer (JavaScript, Python, R programming languages) for single-cell RNA-seq data; data visualization using D3. js or similar libraries; -omics data analysis of RNA-seq and single-cell RNA-seq data from CA mouse models; -omics data integration (RNA-seq, scRNA-seq, metabolomics, phenotype) using ataxiaXplorer and other tools.
Programming in Python, JavaScript, R; statistics; data integration techniques; data visualization techniques; good communication and interpersonal skills to work in an interdisciplinary team of researchers and groups. The working language in our team is English, so good oral and written English skills are mandatory.
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