Context: The KATY project, funded from the European Union’s Horizon 2020 Framework Programme, has set out to build a precise personalized medicine system empowered by Artificial Intelligence (AI). The novel AI tool aims to predict the response of kidney cancer to targeted therapies and identify the molecular evidence to support these predictions. Most importantly, the KATY system will offer human interpretable knowledge that clinicians and clinical researchers can trust, adequately evaluate and effectively use in their everyday working routine. To achieve these goals, we will build an infrastructure of biological, clinical and omics data. The data will derive from public resources as well as cohorts profiled by consortium partners. Ethical and privacy concerns will be evaluated to ensure appropriate laws and norms are respected.
Objectives: The objectives on which the recruited bioinformatician will work are threefold: (i) In collaboration with KATY partners, he/she will identify the data collections needed to carry out the project. Biological, clinical, therapeutic response and omics data generated from cell models and normal and tumor tissues will be considered. Homogeneous data reprocessing will be carried out when necessary based on the best bioinformatics practices established with researchers and clinicians from the consortium (ii) Omics data engineering approaches (i.e. feature engineering) will use quantitative measurements of cells building blocks (genes, proteins, metabolites) to model perturbations at higher levels of abstraction. In particular, we will accurately and robustly predict the cellular heterogeneity of the tumor microenvironment and the network-based modeling of molecular deregulations. (iii) Finally, the recruited person will participate in the design and implementation of a Data Lake, making it possible to efficiently host and query these large-scale datasets, and of a Knowledge Graph in collaboration with experts in these fields.
Host laboratory: The research project will take place in the IMAC team, member of the Biology and Biotechnology for Health Laboratory at the Interdisciplinary Research Institute of Grenoble (IRIG), CEA Grenoble.
Research network: The recruited bioinformatician will be integrated into the multi-disciplinary work environment of the KATY consortium, made up of clinicians, biologists, bioinformaticians, developers, and AI experts.
Expected experiences and skills: Engineering or Master degree in bioinformatics / computational biology with at least 2 years of experience.
Good knowledge of biology, oncology and omics data
- cancer biology, cell types, biological pathways, anticancer therapies
- transcriptome, proteome, metabolome
Good experience in bioinformatics
- programming language (Python, R)
- processing, exploration and visualization of omics data
- network / systems biology
- machine learning
- biostatistics
- unix command line
Professional aptitude
- curiosity and willingness to improve one's scientific and technological skills and productivity
- rigor and organization
- ability to work in team and interact with people of different backgrounds
Job contract: The researcher will be recruited on a 2-year work contract financed by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101017453.
To apply: If you want to join this exciting and ambitious research project, please send a curriculum vitae, a cover letter, a letter of recommendation and the name of at least one referent to christophe.battail@cea.fr. The position starts as early as April 2021.
