We have an opening position for a Bioinformatician through the EU funded project "Biodiversity Genomics Europe (BGE)". BGE is a joint project of ERGA (European Reference Genome Atlas) and BIOSCAN Europe, funded by the EU commission for 3.5 years and involving 33 partner institutions from across Europe.

Environment

Genoscope 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 the genomics of plants and fungi and the 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, 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/).

The lab

The successful candidate will join the Bioinformatics Laboratory for Genomics and Biodiversity (LBGB) at Genoscope, made up of around fifteen 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.

Biodiversity Genomics Europe

Biodiversity Genomics Europe (BGE, https://biodiversitygenomics.eu/) has the overarching goal of accelerating the use of genomic science to enhance understanding of biodiversity, monitor biodiversity changes, and guide interventions to address its decline. The position is part of the ERGA (https://www.erga-biodiversity.eu/) component of BGE, which aims at developing the European node of the Earth BioGenome Project (EBP, https://www.earthbiogenome.org/) to generate 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). Over the course of the project, we estimate that our team will assemble on the order of 100 genomes while building the capacity to sequence thousands in the future. The candidate will work closely with partners at collaborating institutions in Europe who are contributing to the gene prediction and delivery tasks. These tasks will involve extensive communication and exchange with ERGA community members and other project partners as well as active involvement in ERGA committees, in particular the annotation committee.

Role and responsibilities

• Develop bioinformatic workflows to assess the quality of a given gene catalog, based on biological evidence and also on comparative genomics
• Develop gene prediction workflows, for example in the Galaxy environment, designed for gene annotation by non-bioinformaticians but with taxon-specific expertise and data
• Contribute to establishing annotation standards and best practices, together with relevant ERGA partners
• Coordinate the activities of the ERGA annotation committee
• Contribute to relevant ERGA publications

The candidate

The candidate must hold a PhD in Bioinformatics, Genetics, Biology or related discipline or an engineering degree and must demonstrate experience in the field of genomics associated with the development of bioinformatics tools. This position requires fluency in written and spoken English, teamwork, communication within multidisciplinary teams, understanding of scientific questions, rigor and autonomy.

The candidate must have the following technical skills:

• Knowledge of sequencing technologies and methods for gene prediction
• Experience with Unix operating systems, including shell scripts and high performance computing environments
• Proficiency in programming languages such as Python, Perl and R

Details

• Duration of the contract: 18 months, with possibility of extension via the French ATLASea program
• Salary will be commensurate with qualifications and consistent with CEA (https://www.cea.fr) salary scales
• Target start date: March 2023
• 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