2-year position for a bioanalyst specialized in NGS analysis

Type de poste
Niveau d'étude minimal
Dates
Durée du poste
Contrat renouvelable
Contrat non renouvelable
Date de prise de fonction
Date de fin de validité de l'annonce
Localisation
Adresse

place georges teissier
29680 Roscoff
France

Contacts
Laurence Garczarek
Frederic Partensky
Email du/des contacts
laurence.garczarek@sb-roscoff.fr
frederic.partensky@sb-roscoff.fr
Description

Project:

Study of the influence of environmental parameters on ecotypic differentiation and community structure of marine picocyanobacteria using a meta-omic approach (FITNESS)

 

Context

The ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus are the two most abundant photosynthetic microorganisms in the ocean, an ecological success which is partly due to the existence of distinct lineages able to colonize different ecological niches in the environment. These organisms therefore constitute very good biological models to better understand the effect of global change, and in particular the ongoing increase in seawater temperature and the progressive enlargement of nutrient-poor areas, on marine phytoplankton at all organizational scales, from the gene to the global ocean.

In this context, the main objective of the FITNESS project, which is part of several ongoing research projects (ANR CINNAMON 2018-21, ANR EFFICACY 2020-23), will be to better understand the mechanisms of acclimation (i.e., the short-term physiological plasticity) and adaptation (i.e., the long-term genetic plasticity) used by the different lineages to respond to various environmental factors. The project will exploit the numerous genomic, transcriptomic and meta-omic data available for these two genera. From a global point of view, these analyzes should make it possible not only to better understand the role played by these lineages in the current structuring of planktonic communities, but also to predict their respective adaptability and therefore their dynamics and future geographic distribution at different spatio-temporal scales, in the context of global change.

The candidate will work with the ECOMAP team of the Roscoff Biological Station (CNRS and Sorbonne University) under the responsibility of the project manager (Laurence Garczarek) and in close interaction with several team members (2 researchers, 1 postdoc, 3 PhD students, 2 engineers) as well as engineers from the ABIMS bioinformatics platform.

Objectives

The objective of the candidate will be to pursue and finalize the analysis of the numerous NGS data available for these organisms and to integrate these different types of data, notably using network approaches. The data sets currently available include:

  • 150 genomes and nearly 800 SAGs / MAGs which are well representative of the genetic and pigment diversity of these organisms.
  • nearly 360 transcriptomes corresponding to five strains, representative of the dominant lineages of Synechococcus in the natural environment and submitted to various stresses or environmental conditions: high light, UV radiations, high and low temperatures, modulated light simulating the daily variations of light intensity.
  • several hundred meta-genomes and -transcriptomes, notably from the Tara Oceans, Tara Polar circle, Tara Pacific and Malaspina expeditions, which cover fairly well the different ocean regimes present in the marine environment.

In this context, he / she will participate in maintaining and improving existing NGS pipelines and will be have to develop new ones, in particular in order to carry out analyses of nucleotide variants.

He / she will also be required to train and/or support several team members involved in these projects and will be responsible for managing updates to pipelines, databases used in this project and associated documentation.

Methodologies / Skills

  • Good knowledge of R, python, bash languages
  • Previous experience in NGS data analysis
  • Mastery of bioinformatics concepts and tools for the taxonomic and functional analysis of NGS sequencing data (genomes, transcriptomes, metagenomes and metatranscriptomes) and for the realization of statistical analyzes.
  • Knowledge of network analysis (e.g., WGCNA), variant analysis and / or molecular ecology will be appreciated.
  • Good level of English (read, spoken and written)

Diploma

The candidate must have a PhD or engineering degree in Bioinformatics and should have prior experience in the analysis of NGS data.

Required qualities

  • Ability to work in a team and, more particularly in a multidisciplinary environment
  • Autonomy, initiative, organizational capacity, good spirit of analysis and synthesis
  • Interest in biological sciences and more particularly in ecology
  • Mastery of written and oral presentation techniques

Availability

August or September 2020

Type and duration of contract

24 months CDD contract

Keywords

  1. Python, R, bash
  2. NGS, RnaSeq, (meta)genomics and transcriptomics, detection of variants
  3. Git or Mercurial Specialty Bioinformatics

Application procedure:

Please send your application (CV, motivation letter and three references) to: laurence.garczarek@sb-roscoff.fr frederic.partensky@sb-roscoff.fr

Equipe adhérente personne morale SFBI
Equipe Non adhérente