[Galaxy-france] Engineer position in bioinformatics: structural polymorphism analysis from NGS data

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[Galaxy-france] Engineer position in bioinformatics: structural polymorphism analysis from NGS data

Dave Clements
Hello all,

I saw this posted on the SFBI list.  Cross-posting it to the French Galaxy Community.

Dave C

On Wed, Nov 14, 2012 at 2:38 AM, Johann Joets <[hidden email]> wrote:

Position: Research engineer, CDD. One year with possible extension up to three years
Start: 01/01/2013
City: Gif-sur-Yvette, France
Laboratory: UMR de Génétique Végétale, INRA-Université Paris Sud-CNRS

Contacts:
Johann Joets. [hidden email]
Paul Leadley [hidden email]



Description of the position

The LabEx BASC (Biodiversity, Agroecosystems, Society, Climate), a network of 13 laboratories of the Paris-Saclay Scientific Cluster, is seeking a bioinformatician to analyze Next Generation Sequencing (NGS) data analysis. In the context of a flagship project aiming at understanding and improving the adaptive capacity of agroecosystems it will be critical to establish a link between sequence variation, functional variation, gene/protein expression and phenotypic adaptation. We will gather NGS data in many genotypes of various species, the genomes of which harbor a high level of structural complexity, with copy number variations, insertions-deletions, whole genome and segmental duplications. The successful candidate will be in charge of the detection of polymorphisms including structural variants, of the comparison of multiple and diverse genomes of a same species and of the construction of pan- and core-genomes. These challenging tasks will require bioinformatics developments and implementation of methods for accommodating the high level of repetitiveness of complex genomes. The tools will be integrated into pipelines and made available to end-users through the Galaxy platform. The bioinformatician will therefore also have to provide researchers with advices on their experimental designs in order to ensure compliance of produced datasets with pipelines requirements. He will be hosted by a bioinformatics/informatics team (7 people) (http://moulon.inra.fr/index.php/fr/equipestransversales/atelier-de-bioinformatique) which has computational facilities and expertise in NGS data analysis, and will benefit as well from national and international collaborative networks (Aplibio http://www.renabi.fr/platforms/aplibio/, Transplant http://transplantdb.eu, AMAIZING http://www.amaizing.fr/).

The position requires a doctoral degree (PhD) in bioinformatics with strong expertise in script writing (Python/Perl) and pipeline development.  Experience with NGS data handling will be greatly appreciated. The applicant will have to demonstrate excellent capacity to work in a team and ability to communicate with researchers.

Funding is available for one year and can be extended to three (monthly salary includes health insurance). Applicants should send a CV and the names of 2 referees willing to provide a letter of recommendation to [hidden email].




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