Bioinformatics Laboratory for Genomics and Biodiversity (Genoscope, CEA) is opening a position for a researcher in bioinformatics and comparative genomics through the funded programme ATLASea “Atlas of marine genomes: from massive data to innovation”. The position is based at Genoscope in Evry, near Paris, France.

Environment

Genoscope (www.genoscope.cns.fr) was founded in 1996 to contribute to the Human genome project and develop genomic programs in France. Genoscope then turned to environmental genomics. Genoscope is part of the CEA (The French Alternative Energies and Atomic Energy Commission, www.cea.fr) and it develops methods and projects for the exploration of biodiversity, in particular with respect to large-scale DNA sequencing and bioinformatics. The projects cover all biodiversity, particularly genomics of plants and fungi and metagenomics of complex ecosystems. Through the investigation and characterisation of biodiversity, Genoscope is committed to contributing to the development of sustainable biological solutions in the field of synthetic chemistry.

Genoscope thus contributes to the sequencing of numerous plant species (orange tree, coffee tree, cacao tree, banana, rapeseed, wheat, etc.) and animal species (european mink, birds, jellyfish, sea urchin, corals), a crucial stage with regard to progress in the field of agronomics and in enhancing our understanding of evolution. Genoscope also contributes to the discovery of unknown microscopic organisms using metagenomics, now feasible thanks to the development of new sequencing technologies and increased bioinformatics data processing capacities. Metagenomics has, for example, been used to study the diversity of the oceans of the world (Mission Tara Oceans, https://fondationtaraocean.org/en/home/).

Genoscope is located in Evry (in the île-de-France region), about thirty kilometers south of Paris. Evry is a hub of innovation and scientific discovery, which has a thriving genomics research community with world-class institutions, such as the Genopole, a renowned biocluster dedicated to genomics and genetics (www.genopole.com).

The lab

The successful candidate will join the Bioinformatics Laboratory for Genomics and Biodiversity (LBGB, www.genoscope.cns.fr/lbgb) at Genoscope, made up of around twenty bioinformaticians. The LBGB is in charge of the management and analysis of the sequencing data produced at Genoscope, with a broad interest in methodological developments and has extensive experience in de novo assembly, gene prediction and comparative genomics of complex genomes and samples. Our lab has been a main actor of several genome projects and has generated and published several eukaryotic reference genomes as well as several bioinformatics tools dedicated to the analysis of genomic data. Since recently, the LBGB has been coordinating a project within the ATLASea programme which aims to produce a high-quality genome for 4,500 marine eukaryotic species.

Sequencing the biodiversity

Initiatives aimed at sequencing biodiversity involve large-scale efforts to decode the genetic information of various species on Earth. These initiatives are crucial for understanding and conserving Earth’s diverse ecosystems. Launched in 2018, Earth BioGenome Project’s goal (EBP, https://www.earthbiogenome.org/) is to sequence the genomes of all known eukaryotic species on Earth, estimated to be around 1.5 million. This ambitious project will provide insights into the diversity of life and inform conservation efforts. In Europe, ERGA consortium (https://www.erga-biodiversity.eu/) and Biodiversity Genomics Europe (BGE, https://biodiversitygenomics.eu/) have the overarching goal of generating high-quality reference genomes for all eukaryotic species in Europe. As an affiliate of EBP, ERGA also serves as an umbrella for national nodes of EBP within Europe (e.g. The ATLASea program in France and the Darwin Tree of Life in the UK).

ATLASea programme and SEQ-Sea project

ATLASea is one of the laureates of the PEPR exploratory programmes, which target emerging scientific or technological sectors where the French government sees a need to identify and structure communities. Co-led by the CNRS and the CEA, the ATLASea programme aims to sequence the genomes of 4,500 marine species, with most species from mainland France, but also including species from overseas territories. The selected species will be sampled by the DIVE-Sea Targeted Project. The samples will be entrusted to the SEQ-Sea Targeted Project teams to produce genome assemblies associated with high-quality structural annotations. The BYTE-Sea Targeted Project will centralize all the genomic data produced by the ATLASea project in a single portal and integrate the genomes of related organisms sequenced by other consortia.
The ATLASea programme will decipher and exploit this colossal wealth of information from marine species on the French coast. It will guarantee the interoperability and security of the data, and facilitate its dissemination and use in accordance with the FAIR and Open Science principles. Funded by a €41.3 million grant over 8 years as part of France 2030, the project will help to understand, study and preserve a broad diversity of marine life forms.

Role and responsibilities

As a Genomic Research Scientist, you will play a pivotal role in advancing our understanding of genetic diversity and evolutionary relationships among species, such as symbiotic interactions. Your work will consist of exploiting the complete genomes obtained through the ATLASea program and more generally the EBP project, using cutting-edge techniques (such as AI-based methods) to deepen comparative studies at the genomic level.

In this role, you will not only analyze and interpret evolutionary relationships and symbiosis from complete genomes extracted from environmental samples but you will also integrate these findings with metagenomic data from the Tara Ocean projects. By doing so, you will contribute to a holistic understanding of marine ecosystems and their complex genomic landscapes.

Your responsibilities will extend beyond analysis to include the supervision of computational tools and pipelines development, ensuring the efficient and accurate analysis of large-scale genomic datasets.

Additionally, you will play a key role in sharing our research findings with the scientific community. This involves contributing to peer-reviewed journal publications and presenting results at scientific conferences, thereby promoting collaboration and knowledge exchange.

As a member of our team, you will stay at the forefront of advancements in genomics, comparative genomics, and related fields. Your commitment to staying informed about the latest developments will play a crucial role in shaping our research strategies.

Qualifications

  • Ph.D. in Genomics, Bioinformatics, Genetics, or a related field with a strong interest in comparative genomics and evolutionary biology
  • Proven experience working with complete and high-quality genomes
  • Proficiency in bioinformatics tools and programming languages commonly used in genomics research (e.g., Python, R, and relevant software packages). Expertise in using high-performance computing clusters and grid resources is a plus
  • A strong interest in AI-based methods would also be an advantage, particularly within the field of genomics.
  • Excellent communication skills and the ability to work collaboratively in a team-oriented environment

Details

Duration of the contract: Open-ended contract
Salary will be commensurate with qualifications and consistent with CEA salary scales
Target start date: Spring/Summer 2024
Location : Evry, 30 kilometers from Paris. Easily accessible by public transport
We provide a highly stimulating environment with state-of-the-art infrastructures.
Flexible working hours and teleworking All applications must be addressed to job-lbgb@genoscope.cns.fr and include:

  • A cover letter
  • A complete CV including contact details
  • Names and contact details of at least two references

More information: https://www.genoscope.cns.fr/externe/lbgb/positions.html

ATLASea Recruitment: Researcher in bioinformatics and comparative genomics (W/M) [CLOSED]
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