Société Française de Bioinformatique

Mots-Clés

Genomics WGS Exome Cancer

Description

Bioinformatics Engineer (M/F) - Cancer Genomics

Immediate position for a 12 months fixed-term contract

Workplace: Teams of Sandrine Roulland "Genomic Instability and Malignant Hemopathies" and Pierre Milpied "Integrative Immunology of B Cells" at the Centre d’Immunologie de Marseille-Luminy (CIML, U1104, Marseille, France)

Description of the teams and the position:

The laboratories of S. Roulland and P. Milpied at the CIML (http://www.ciml.univ-mrs.fr) are pursuing a research program to study the heterogeneity of human hematological malignancies at the single cell level linked to the genetic analysis of these tumors in order to better understand dynamics and mechanisms of tumor evolution, predict treatment response and patient outcomes and identify best therapeutic interventions in those lymphoma patients. The position is for a motivated candidate who will be responsible for developing and conducting the analysis of high-throughput exome sequencing data from a large cohort of human lymphoma samples in the context of the single cell ATLAS program. He/she will work in collaboration with two other bioinformatics data analysts on the project (1 engineer and 1 post-doc) and will benefit from the expertise of CB2M (Computational Biology, Biostatistics and Modeling) of the CIML for the design and development of analysis pipelines and on which he/she will be physically hosted.

Main activities:

• You will conduct bioinformatics analyses involving mainly high-throughput exome sequencing data to gain biological insights on lymphoma genomics and genetic patient stratification
• You will implement tools for quality control, processing and analysis of large-scale exome datasets from patients
• You will implement algorithms for variant prioritization and classification (gain or loss of function), copy number variation (CNV) detection and ploidy estimation tools
• You will develop new bioinformatics tools or analysis methods if required for the project
• You will implement already established computational pipelines for exome sequencing, adapt them to the needs of the project and produce html reports that meet the requirements of the project investigators
• You will analyze with appropriate statistical analysis genomic data linked to clinical data obtained from patients
• You will interact closely with biologists and bioinformaticians to optimize the interpretation of the molecular and cellular impact of the variants
• You will write summary reports and present them orally (English and French) at weekly project meetings

Required Profile and Skills:

• You have a minimum of a BAC+5 (or engineer diploma) in bioinformatics, computational biology, mathematics or equivalent experience, and you have at least 12 months of experience in a similar position
• You master the programming techniques under Linux environment as well as the programming languages Python and R 
• You have a mandatory practical knowledge of exome or whole-genome data processing including annotation of variant effects
• You are familiar with software required for genomic data analysis (Samtools, BWA, GATK, Mutect2/Strelka2/Vardict, VEP/snpEff/Annovar... )
• It would be appreciated if you have an experience in pipeline and automation managers (Snakemake..)
• You are familiar with public genomics databases (NCBI, GenCode, Biomart..)
• Experience in cancer genomics would be a plus
• You are familiar with storage and handling of large data
• You are able to write synthesis reports and present them orally (English and French) during project meetings
• You have excellent communication and interaction skills with multidisciplinary teams (biologists, bioinformaticians, clinicians) and interest in biological issues
• You are fluent in English

Salary according to degree,  experience and INSERM salary rules 

Contact: Send CV, cover letter, and contact details of at least two references by email to Sandrine ROULLAND (roulland@ciml.univ-mrs.fr) and Pierre MILPIED (milpied@ciml.univ-mrs.fr)