Mots-Clés

Genomics Transcriptomics Data security: Energy efficiency Workflows

Description

Offer: Master 2 internship - Bioinformatics of cancer genomic data (CEA Grenoble)

Title: Secure and efficient bioinformatic processing of cancer genomic data

Background: Over the past 10 years, technological advances in DNA sequencers have enabled the generation of large amounts of cancer genomic data stored in public repositories with controlled access. The integration of these existing raw genomic data into human health research projects requires taking into account several aspects: their identifying and sensitive properties, their large volumes and the biological and technical biases between cohorts. The evolution of the regulatory context at European level, with the adoption of the General Data Protection Regulation, and the economic context associated with the energy crisis, requires a change of paradigm. It is now a priority that the processing of genomic data integrates strong security components, such as pseudonymization and encryption, and energy efficiency combining speed of calculations and frugality, by hybrid calculation solutions combining CPUs and GPUs.

Objective: This internship will contribute to the development of secure and efficient bioinformatics workflows for processing large cohorts of human genomic and transcriptomic tumor data collected by the European KATY project on personalized medicine (https://katy-project.eu/).

Workplan: At the start of the internship, genomic and transcriptomic data will already have been collected and bioinformatics workflows will already be available. The intern will begin by integrating technological components into these workflows for data security while estimating their impact on the speed of calculations and energy efficiency. He/she will then work on the standardization and normalization of mutation calls and gene expression measurements, ending with the generation of high-level features related to gene network deregulations.

Host laboratory: The intern will be hosted in the “Genetics and Chemogenomics” team of the Interdisciplinary Research Institute of Grenoble (IRIG) of the CEA Grenoble. He/she will be supervised by Christophe Battail, expert in computational analysis and modeling of genomic data, and will evolve in a multidisciplinary research environment composed of bioinformaticians and biologists. The intern will also interact with researchers and developers from the European KATY project.

Candidate profile:

Knowledge and skills in bioinformatics: Genomic and transcriptomic data, unix command line and Python/R programming.

Professional aptitude: curiosity and desire to improve their scientific and technological skills, rigor and organization, and ability to work in a team and interact with other students, engineers and researchers

Job contract:

6-month master's internship starting in February 2023.

Please send a CV, a cover letter and the name of a referee to christophe.battail@cea.fr.