Recent clinical trials have revealed novel classes of immune-based cancer therapies that target key immune-interacting tumor microenvironment pathways. There is therefore an urgent need to develop reliable patient stratification tools to ensure that only those likely to benefit receive specific treatment.
The incumbent will provide expertise in the application of technologies of all types associated with patient stratification for immuno-oncology treatments. As part of this work, the job holder will use bioinformatics tools to create new analytical pipelines for the analysis of multidimensional datasets. The project involves the analysis of multi-omics (ADNSeq, single-cell RNAseq) and mass cytometry (CyTOF) data from tissue and blood samples. He/she also manages the anonymized clinical database and writes relevant scripts to better organize and manage the patient databases. The post holder will also jointly supervise PhD students and junior research associates with the Associate Professor of Applied Cancer Immunopathology.
This position will be offered on a 12-month fixed-term contract
This is a full-time position – 100% full-time equivalent
• Work on immunological and molecular profiling of patient cells, blood and tissue samples in collaboration with clinical and basic scientists.
• Develop mechanistic knowledge derived from these profiling activities in collaboration with clinical and basic scientists
• Create, implement and use analytical and bioinformatics tools to analyze and interpret multidimensional data, in particular scRNA and CyTOF sequencing.
• Organize and manage patient databases (anonymized) and work closely with clinicians, clinical trial managers, nurses, biobank team and researchers to ensure that the necessary data is collected and that the database is up to date at all times.
• Use and implement new bioinformatics tools for bulk RNA sequence deconvolution, such as Cibersortx or EcoTyper.
The above list of responsibilities may not be exhaustive and the post holder will be required to undertake the duties and responsibilities reasonably expected within the scope and classification of the position.
Skills, knowledge and experience
1. PhD in a relevant field or equivalent
2. Knowledge of relevant platforms and techniques
3. Knowledge of computational biology
4. Working knowledge and expertise in single cell and bulk RNA sequence data analysis.
5. Advanced skills with Microsoft packages such as Word and Excel
6. Computational skills required for statistical analysis of experimental data, including knowledge of a specialized statistical software package (ie SPSS or similar).
7. Ability to analyze data with publicly available and commercial software solutions (e.g. R/Bioconductor, UMAP, viSNE, FlowJo, CytoBank suite)
1. Knowledge of immunology is advantageous
2. Experience working with complex data sets and database management
3. Knowledge/skills in the use of platforms for monitoring the immunological and/or microenvironmental status of patients.