[BBC] Bioinformatics Engineer, 36 months contract

[Macha Nikolski]

Job Title : Bioinformatician
Employer : SIRIC BRIO
Location : Bordeaux, France
Reporting to : FX. Mahon, M. Nikolski
Job Family : Bioinformatics Engineer
Duration of Post : 36 months
Salary : dependent on qualification

Main Purpose of Role
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The Bordeaux SIRIC (Site de Recherche Intégrée sur le Cancer) BRIO is seeking a Bioinformatics Engineer to perform next generation sequence (NGS) data processing and analysis in a dynamic and exciting academic environment at the nexus of cancer biology, computer science, statistics and clinical research. The post holder will concentrate on one major SIRIC project at a time, but part of their activity will be dedicated to helping other groups in the SIRIC to solve short-term problems. The work will be performed in a small group atmosphere at the Bordeaux Bioinformatics Center CBiB (approx. 10 members) and the Bergonié Cancer Institute INSERM labs. Analysis will be performed for the benefit of the SIRIC member labs.

Key Duties and Responsibilities
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The job holder will design, develop and operate computational pipelines for the analysis of next generation sequencing data derived from tumors. Work will include both large-scale projects and small custom jobs, and span a wide variety of analysis problems.
- Development of pipelines to process NGS data (for example, for quality control, mapping, SNP and variant calling, and de novo assembly) using public and commercial software or through development of new software tools when appropriate.
- Applying statistical and bioinformatics methods to analyse genomic data (for example, NGS data from DNAseq, RNAseq, CHiP-seq, methylation, exome experiments)
- Accompany non-bioinformaticians in their data processing and analysis needs
- Server administration and next generation data management

Qualification
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PhD or Master’s degree in computer science, bioinformatics, mathematics or a related field, and at least 2 years experience in Bioinformatics software development are required.
- Strong computational/programming skills; including thorough experience with the following: Unix/Linux environment, Cluster computing (SGE, PBS, or LSF familiarity strongly desired), Next-generation analysis toolkits (e.g, BWA, GATK, samtools, etc.);
-   Experience in building and using databases (e.g. SQL);
-   Advanced skills in Perl and Python;
-   Good knowledge of C++, Java and R is preferred.

The candidate should have prior experience of processing NGS data. Experience in constructing web based interfaces, and mathematical and statistical skills would be an advantage.
Good communication skills are a must and proven command of English is essential. The post holder should be able to work independently and interact well within a team of geneticists, oncologists and biologists. Interactions with other SIRIC centers in France will be part of the job.

How to apply
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Please send a mail to Macha Nikolski (macha at labri.fr) and Francois Xavier Mahon (Francois-Xavier.Mahon at u-bordeaux2.fr) containing
- your CV
- a motivation letter
- names of at least two scientists who have agreed to recommend you
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