PhD Bioinformatics M/F

Job Description

Thesis Subject

As a referral hospital for France, we have been able to collect a cohort of more than 200 tumors that we have characterized for RNA expression, methylation, whole genome sequencing and single nucleotide polymorphism (SNP) and spatial data.
This cancer is a rare disease that has not yet been documented and we believe that these data will be a major contribution to the understanding of the disease and clinical follow-up. The first results show that we are finding previously unknown subgroups in the pathology that predict the clinical prospects of patients, including survival. The candidate will be able to complement these studies by integrating datasets and determine the response to treatments

The candidate should have experience in omics data analysis and will be working directly within the research team, in close contact with biologists and medical doctors. The candidate should have a diploma in bioinformatics, or in biology with strong skills in bioinformatics/data analysis. The candidate should be able to work within a Unix environment, with the R-software (CRAN/Bioconductor) and ideally be familiar with another scripting language like Bash or Python. A previous experience in analyzing high-throughput sequencing data (RNAseq, exome/genome sequencing) would be greatly appreciated. An experience with single cell or spatial data analyses would also be useful.
The successful candidate should also have strong communication skills to present the results to research partners, through scientific reports or seminars. The candidate will benefit from the technical expertise of the bioinformatics platform and from collaborations. We believe that this innovative project will lead to very good publication opportunities. The duration of the contract is 3 years (start date negotiable, preferably 1st October 2026). The funding has been obtained from the CNRS.

Your Work Environment

The thesis research will be conducted at the Lyon Cancer Center (CRCL, UMR CNRS 5286, Inserm U1052, UCBL, CLB) and aims to understand treatment resistance in intestinal neuroendocrine tumors.
The thesis project is part of one of the research themes of Benjamin Gibert and Thomas Walter's team, titled “Gastroenterology and Health Technologies.”
The candidate (male/female) must hold a Master's degree or an engineering degree.
The research will involve bioinformatics experiments and the integration of biological and medical data.

Constraints and risks

36-month fixed-term contract. The thesis research will be conducted at the Lyon Cancer Research Center (CRCL, UMR CNRS 5286, Inserm U1052, UCBL, CLB), under the scientific supervision of Benjamin GIBERT, Research Director at the CNRS.
The candidate will benefit from an international scientific environment dedicated to cancer research (approximately 550 people), thanks to the presence of 22 research teams and 13 technology platforms on site.
The CRCL is affiliated with four parent organizations: the CNRS, INSERM, Claude Bernard Lyon 1 University, and the “Centre Léon Bérard” oncology hospital.

Compensation and benefits

Compensation

2300 € gross monthly

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

The research professions