Project title:

Processing of the cancer genomic and transcriptomic data

Research environment and project:

Gustave Roussy, the premier European Cancer Centre, recruits an engineer in bioinformatics or computational biology at Institut Hospitalo-Universitaire (IHU) PRISM led by Pr. Fabrice André. IHU PRISM is a joint project of Gustave Roussy, Université Paris-Saclay and other education/research institutions that aims at modeling cancer using integrative patient data for the development of novel precision medicine therapies.

An engineer position in bioinformatics is open in the laboratory of Cancer genomics (headed by Dr Sergey Nikolaev) in the Unit U981 INSERM, Gustave Roussy Cancer Center.

Our goal is to unravel genetic mechanisms leading to metastasis in cancer and discover predicative biomarkers of the disease course and the response to treatment. Our work is based on the whole human genome / exome sequencing and transcriptional profiling. We analyze results utilizing public databases and sophisticated algorithms.

Gustave Roussy provides a dynamic environment with intensive collaborations between bioinformaticians, software engineers, laboratory scientists, and clinicians aiming to produce cutting-edge knowledge on cancer genomics. You will be part of a team focused on implementation and development of the latest methods for analyzing genomics data, building analysis pipelines and algorithms, and validating tools for cancer. 

Responsibilities:

Develop components for cancer NGS data analysis, focusing on genomic / exomic DNA and RNA applications

• Develop and implement tools for accurate somatic variant detection from DNA sequencing
• Update the pipelines and genomic databases
• Implement tools for mutational signature analysis, copy number alterations and structural variant detection

 Qualifications:

• Experience with standard genomics software: BWA, GATK, SAMTools is required
• Experience with genomic analysis of NGS based DNA or RNA assays is required
• Experience developing bioinformatics pipelines and tools for NGS is required
• Advanced degree (PhD) in bioinformatics, genomics, or a related field is a plus
• Experience in cancer genomics is a plus
• Experience with cancer genomics software: Mutect2 etc. is a plus
• Experience of cancer variant detection – mutations, fusions, CNAs, (FACETS, MANTIS, etc)
• Familiarity with cancer databases: Cosmic, TCGA, PCAWG, HARTWIG.

Contract type:

Initial fixed-term 18-month contract, with possible extension. Salary dependents on experience.