Institut Méditerranéen d’Océanologie
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Poste de post- doc Bioinformatics : exploring marine plankton genomics (Tara Oceans)

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Bioinformatics : exploring marine plankton genomics (Tara Oceans) in Marseille, France

We invite applications for a 2 year postdoctoral fellowship to explore plankton ecology through data mining of the Tara Oceans environmental genomics datasets. The fellowship is funded by the ANR OCEANOMICS program[1] and the successful applicant will join the Mediterranean Institute of Oceanography (MIO) in Marseille[2].

PROJECT : The Tara Oceans expeditions systematically sampled marine plankton at 210 sites of the world’s ocean, covering the entire ecosystem diversity from viruses and prokaryotes to eukaryotes, including animals (zooplankton)[3]. The project has generated the largest standardised eco-morpho-metaomics dataset available (>40 Terabases), including over 1,000 virus-, prokaryote-, and eukaryote-enriched metagenomes and metatranscriptomes, as well as 4 billion eukaryotic and prokaryotic metabarcodes from 3,000 size-fractionated plankton communities worldwide. This dataset covering global geographic and taxonomic scales represents a unique opportunity to explore the boundaries of a planetary ecosystem at the interface between oceanography, biodiversity, ecology, and evolution. Following the first Tara Oceans global analyses published in Science and Nature in 2015 and 2016[4], the selected candidate will investigate the adaptation of plankton to its marine environment and shed light on the ecological role of specific genes found to be unexpectedly abundant in the ocean.

CANDIDATE : The successful candidate should have i) a PhD in the fields of bioinformatics or environmental genomics, ii) extensive first hand experience in computational analysis of biological sequences (including expertise in as many as possible of the following : similarity searching, phylogeny, variant identification, population genetics, meta-omics mining), iii) proficiency in statistical methods using R, and iv) demonstrated script programming skills in *NIX environments (Perl, python, bash etc.) as well as familiarity with the use of compute farms. Knowledge of numerical ecology approaches (e.g. vegan R package) and/or protein structural biology will be very favourably considered.

ENVIRONMENT : The 200+ staff of the MIO oceanography research laboratory strive to better understand the oceanic system and its evolution in response to global changes. MIO constitutes a center of expertise in marine biology, ecology, biodiversity, genomics, microbiology, halieutics, physics, chemistry, biogeochemistry and sedimentology. Situated in Provence on the outskirts of Marseille close to the sea, in the middle of the Calanques National Parc, MIO is located on the Marseille Luminy scientific campus which hosts several world class research laboratories[5]. The MIO’s new purposely built environmentally friendly 10000m2 buildings provide a modern and attractive work environment.

APPLICATION : Applications and informal queries should be addressed to Pascal Hingamp (<pascal.hingamp@mio.osupytheas.fr> +33(0)634 688 091). Interested candidates should send their CV with a publications list, and a cover letter describing their research interests and motivation. Candidates should also arrange for at least two referees to e-mail recommendation letters directly to <pascal.hingamp@mio.osupytheas.fr> . Review of applications will begin on February 15, 2017 and applications will continue to be accepted until the position is filled.

CONTRACT : The position will start at the earliest possible date, taking into account that drafting the work contract usually takes at least 4 weeks. Initial appointment is for one year and renewable for another year (contingent upon mutual agreement) funded by the ANR OCEANOMICS research program awarded to MIO. The salary will be based on the CNRS salary grid and depends on qualifications and experience. The position is based at MIO in Marseilles, but will involve close national and international collaboration – requiring regular travelling - with partner institutions of the OCEANOMICS and Tara Oceans consortia. The selected candidate will work with Pascal Hingamp, Youri Timsit and Magali Lescot, members of a group of seven bioinformaticians who are part of the MIO Environmental Microbiology and Biotechnology (MEB) team.

REFERENCES :
[1] http://www.oceanomics.eu/
[2] http://www.mio.univ-amu.fr
[3] https://www.embl.de/tara-oceans
[4] Guidi, L. et al. Plankton networks driving carbon export in the oligotrophic ocean. Nature 532, 465-470, doi:10.1038/nature16942 (2016).
Biard, T. et al. In situ imaging reveals the biomass of giant protists in the global ocean. Nature 532, 504-507, doi:10.1038/nature17652 (2016).
Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature, doi:10.1038/nature19366 (2016).
Bork, P. et al. Tara Oceans studies plankton at planetary scale. Science 348, doi:10.1126/science.aac5605 (2015).
[5] http://www.grandluminy.com/en/content/park