Mots-Clés

évolution, écologie microbienne, bio informatique, génomique, biominéralisation

Description

Engineer in genomics, bioinformatics et evolutionary ecology

24-36 months according to experience

The French Alternative Energies and Atomic Energy Commission (CEA) invites applications for a Bioinformatician position. This full-time fixed term position is for approximately 24 to 36 months (based on applicant experience). The Bioinformatician will report directly to Caroline Monteil (CEA Cadarache, BIAM, BEAMM team), principal investigator of the granted project and David Vallenet (CEA Evry, Génoscope) head of the LabGEM team. The applicant will work with both laboratories in Evry and Saint Paul lez Durance.

The BEAMM team develops research of the biodiversity, ecology and evolution of magnetotactic bacteria and related biomineralizing organisms while the LABGeM extracts biological knowledge from prokaryotic organisms through the development of bioinformatics tools, in the basic research structure of Genoscope  (the national sequencing center), now part of the France Génomique infrastructure. In collaboration with these two teams, the successful applicant will join an interdisciplinary consortium applying microbiology, geochemistry and computational methods in two main project granted by the ANR (CarboMagnet ANR-21-CE01-0010 and SymbioMagnet ANR-21-CE02-0034). The applicant will apply state-of-the-art methods to analyse high throughput sequencing data and will combine:

• Assembling, binning and annotation of genomes from metagenomes and single-cell amplified genomes.
• Generating DNA metabarcoding data.
• Molecular phylogenies reconstruction.
• Interpreting patterns of diversity in an adequate ecological, geochemistry and mineralogical framework.

All together the applicant project will answer to the following questions for the CarboMagnet project:

• What are the specific and functional diversities of magnetotactic bacteria forming intracellular carbonated phases in aquatic habitats (with a special focus on the meromictic lake Pavin)?
• What are the biotic and abiotic factors structuring their distribution in the water column and sediments? What are the syntrophic interactions with the other communities members?
• What are the genes/functions candidates to carbonates formation?

By answering to these questions, the successful applicant will participate to our understanding of the role of some benthic microorganisms in biogeochemical cycles, especially that of inorganic carbon, and to the identification of new models of biomineralizing bacteria.

The applicant project will also be able to participate to the following questions for the SymbioMagnet project:

• What are the specific and functional diversities of magnetotactic holobionts in aquatic habitats ?
• What are the syntrophic interactions between bionts composing magnetotactic holobionts?

By answering to these questions, the successful applicant will participate to our understanding of the role of magnetotaxis in the secondary adaptation of microeukaryotes to anaerobic lifestyle, and to the identification of new models of microbial holobionts.

Summary of additional key responsibilities (job functions include but are not limited to):

• Use of automated bioinformatic pipelines
• Produce a deliverable in time summarizing the different steps
• Generate analysis figures (Heatmaps, barplot, PCA, Tree…)
• Perform differential analysis
• Keep a technological watch in scientific literature  
• Propose new activities or new tools to test

Qualifications / Requirements:

• Msc in a relevant area (Bioinformatics, Evolutionary biology)
• Expertise in the concepts and principles of microbial metabolism, molecular biology and next-generation sequencing
• Practiced understanding and experience of bioinformatic pipelines and tools for microbial metagenomics (assembly, binning, annotation, comparative genomics)
• Fluency with Unix 
• Knowledge of R and Python
• Experience with data management and dataset manipulation
• Good verbal and written communication skills (fluency in French or English is necessary)
• Demonstrated communication, organization, problem solving, and interpersonal skills

PIs : Caroline MONTEIL & David Vallenet

Contact: caroline.monteil@cea.fr; vallenet@genoscope.cns.fr

Host lab : BEAMM team CEA Cadarache, Zone Cité des Énergies BIAM, Bâtiment 1900, 13108 Saint-Paul-lez-Durance, France & LabGEM CEA/Institut de Biologie François Jacob © Genoscope – Centre National de Séquençage, 2 rue Gaston Crémieux CP5706 91057 Evry cedex, France

Starting date : Flexible (October 2022-early 2023)