We would be very happy to receive application from a passionate, curious and open-minded researcher at any stage of his/her studies or career: Bachelor, Master students, PhD candidate or PostDoc. Our technics includes bioinformatics (genomics, environemental biology) and experimental lab work (molecular biology, biochemistry, physiology).
Students internships are mostly welcome. Since the number of internship position is limited, please contact us as soon as possible.
The LAGE is affiliated to Université Paris Saclay (Graduate School « Life Sciences and Health » – Doctoral School « Structure and Dynamics of Living Systems »). There are several ways to get a PhD thesis funded (Doctoral School, CEA fellowships, dedicated projects fundings, …). We will offer you help to prepare your fellowship application.
As a post-doc, you will benefit from state-of-the art computing facility have the opportunity to perform wet-lab experiments with our technical support. Unless advertised, we do not have any recurrent funding for postdoc, but we will be happy to discuss funding opportunities and support you in the writing process.
Current Offers
- 6-month Master internship in population genomics starting in january 2025
| Contact : Barbara Porro () |
| Description : Exploring the genetic diversity of a micro-algae in the face of global climate change Introduction, scientific context : Over the last few decades, studies have shown that the decline in plankton biomass is linked to many aspects of climate change. As phytoplankton are primary producers, understanding their ability to respond to their environment is a key factor in understanding climate change. Pelgaomonas calceolata is a photosynthetic cosmopolitan photosynthetic picoeukaryote organism that lives in contrasting environments. Using metagenomics data from water samples collected during the Tara Oceans and Pacific expeditions, the intern will analyse the genetic diversity of P. calceolata using population genetics approaches. This analysis will to estimate the distribution of this diversity and to establish correlations with certain environmental variables. Global warming, ocean acidification and variations in nutrient inputs are significantly affect phytoplankton biomass (Morice et al., 2021; Worden et al., 2012). As an important primary producer in the oceans, the decline in phytoplankton biomass and its geographical distribution are important aspects in understanding the future of marine ecosystems (Cooley et al, 2022). Among phytoplankton, the smallest organisms are sometimes referred to as able to resist environmental variations more effectively than larger organisms (Flombaum et al., 2020). Among these organisms, we are studying laboratory, we are studying the micro-alga, Pelagomonas calceolata (Andersen et al., 1993), which is present in all temperate and tropical oceans (Guérin et al., 2022) but for which we have little information on its genetic diversity. Better understanding of P. calceolata's ability to respond to the environment is therefore a way to understand better the future of phytoplankton in marine ecosystems in a context of global climate change. Research proposal : To explore the adaptive capacities of P. calceolata, the Laboratory of Analyses of Eukaryotes has at its disposal the metagenomes of water samples collected from all the oceans during the Tara Oceans and Tara Pacific expeditions, as well as the reference genome of P. calceolata. Using Tara's metagenomics data and a population genetics approach using a population genetics approach, an initial analysis revealed a structuring between ocean basins into 11 P. calceolata populations. As part internship, the student will initially be required to repeat this analysis of genomic variants using a second strain of P. calceolata as a reference, the genome of which the laboratory sequenced this year. The population structures obtained from the two genomes will be compared to confirm or complete the overall global structuring of P. calceolata. Secondly, the student will establish correlations between genetic variants and environmental parameters in order to identify genes involved in adapting the metabolism of P. calceolata to its environment. Methodologies: The metagenomics data from the Tara samples and the reference genomes are available. The internship will focus on their bioinformatics analysis. The Genoscope provides computing clusters in a Linux environment. You are therefore required to have notions of bash or shell language. Some of the tools used are implemented in R, so a minimum knowledge of this language is also required. Population genetics concepts will be used to interpret the results. Most of the file manipulation will be done using custom scripts or samtools. The identification of genetic variants will be carried out using freebayes and variant quality filters will be done with ad-hoc scripts under R, and bcftools and vcftools software. These tools will also be used to calculate descriptive statistics for the data and population genetics. This will be supplemented by R packages (in particular LEA, poolfstat, adegenet, FactoMineR, vegan). A part of the analysis protocol is still in progress, developments based on the literature may be made before or during the internship, also at the intern's suggestion. |
- Open 2 years post-doctoral position - marine plancton community metabolic modelling
| Contact: Eric Pelletier (eric.pelletier [at] genoscope.fr) |
| Description : Marine plankton encompass highly diverse species assemblages across various environmental conditions, and is pivotal to key ecosystem services, ranging from biological carbon pump, marine food web or impact on major biogeochemical cycles. Throughout more than 15 years of expeditions, the Tara Ocean Consortium gathered a unique collection of samples covering a wide diversity of marine environments to describe composition and biological activities of marine plankton communities, and already contributed to significant breakthroughs in understanding this set of living organisms (cf. Tara Ocean Foundation et al. 2023. Nature Microbiology [https://doi.org/10.1038/s41564-022-01145-5] for recent a review and prospective). What are the biological functions that shape the building of plankton communities? What are the metabolic interactions within a given community? What is the metabolic impact of viral infection? Can we decipher the impact of environmental parameters (e.g. nutrients availability) on biological functions, and vice versa? These are some of the research questions that are addressed in our group. In this context, we propose a 2 years post-doc position at CEA/Genoscope, near Paris (France), to model metabolic interactions within marine plankton communities (from viruses to unicellular eukaryotes) sampled in the context of the Tara Oceans campaigns, and their intertwining with environment. This project will take advantage of a new top-down metabolic modelling system for unicellular phototroph eukaryotes (PhotoEukStein, Burel et al. 2023. BiorXiv) combined with existing methods and resources for prokaryotes, and metabolic niche modelling techniques (Régimbeau et al. 2022. Ecology Letters ; Régimbeau et al. 2023. BiorXiv). Research will take place within the OCean SYstems biology and GENomics (OCSYGEN) group of the Metabolic Genomics research unit at Genoscope (CEA – CNRS – Université Paris Saclay) in Evry, France. Salary ranges from 31 to 33k€ net per year, including health coverage. Position is to start end 2024 |