General information:
Title:
ATLASea Winter School 2025: From Sampling to Reference Genome Acquisition
Keywords:
Reference Genome – Marine Eukaryotes – Marine Biodiversity – Sampling – Taxonomy -Nucleic Acid Purification – Sequencing – Genome Assembly – Genome Annotation
Course prerequisites:
Basic knowledge in Biology plus knowledge in either Organism Biology, Ecology, Taxonomy, Molecular Biology, Genomics or Bioinformatics.
Dates:
Monday December 8 to Friday December 12, 2025
Number of participants:
16
Coordination:
Stéphanie Bertrand, Stefano Mona
Course objectives and description:
Aims and themes:
Initiatives for obtaining reference genomes for all eukaryotic species have been taken worldwide in recent years. These projects, supported by a broad scientific community, require collaboration between researchers and technical staff from different disciplines, from taxonomy to bioinformatics. ATLASea is one of the laureates of the PEPR exploratory programs, funded by the French government. Co-led by the CNRS and the CEA, the ATLASea program aims to sequence the genomes of 4,500 marine eukaryotic species, with a high coverage of species from metropolitan France, but also including species from overseas territories. The objectives of the ATLASea Thematic School are to allow young scientists and technical staff who are implicated in a reference genome project, who wish to obtain a specific reference genome(s), or who wants to understand how producing reference genomes might be of interest for their particular biological question, to:
- Understand the various stages in the process of obtaining and sharing a high-quality reference genome (Collection, Taxonomy, DNA Extraction, Sequencing, Assembly, Annotation).
- Understand the associated best practices aligned with the FAIR data principles, and the regulatory issues.
- Know the available tools and their characteristics (advantages/limitations).
- Interact with specialists of various fields: taxonomists, molecular biologists, bioinformaticians, evolutionary biologists.
- Explore how reference genomes are used to address questions in various disciplinary fields (Taxonomy, Ecology, Organism biology, Evolution, Genomics, etc.).
- Discover French marine stations and the services they offer.
Organisation:
The course will take place at the Sorbonne University marine station of Banyuls/Mer (France, Department of Pyrenées-Orientales), the “Observatoire Océanologique de Banyuls/Mer”. Participants will be accommodated from Sunday night (7th December) to Saturday morning (13rd December) at the marine station’s accommodation center. They will follow a series of courses and practical or tutorial work in rooms dedicated to teaching activities (see the program). Several seminars by invited speakers, as well as short presentations of their work by the participants, are also scheduled during the week. Common lunches and dinners at the restaurant of the marine station with the speakers and instructors will foster informal discussions.
Program (provisional):
Speakers and Instructors:
Pauline Auffret (Bioinformatics engineer at SeBiMER, Bioinformatics platform of Ifremer, Plouzané)
Didier Aurelle (AMU Associate Professor, ISYEB, Paris)
Jean-Marc Aury (Head of the Bioinformatics Laboratory for Genomics and Biodiversity, CEA/Genoscope)
Stéphanie Bertrand (Associate Professor at Sorbonne University, OOB, Banyuls/Mer)
Sandrine Bodin (Library Manager, OOB, Banyuls/Mer)
Laure Corbari (MNHN Associate Professor, ISYEB, Paris)
Erwan Corre (Scientific manager of the ABiMS platform, IFB, Roscoff)
France Denoeud (Researcher, Bioinformatics Laboratory for Genomics and Biodiversity, CEA/Genoscope)
Stéphane Hourdez (CNRS Research Director, OOB, Banyuls/Mer)
Karine Labadie (Researcher at Sequencing Laboratory, CEA/Genoscope)
Céline Labrune (CNRS Research Engineer, OOB, Banyuls/Mer)
Stefano Mona (Professor at EPHE, ISYEB, Paris)
Nicolas Puillandre (MNHN Associate Professor, ISYEB, Paris)
Janaina Rigonato (Researcher at Sequencing Laboratory, CEA/Genoscope)
Hugues Roest Crollius (CNRS Research Director, IBENS, Paris)
Sarah Samadi (MNHN Professor, ISYEB, Paris)
Mélanie Van Weddingen (MNHN, Direction des collections, ATLASea program, Paris)
Patrick Wincker (Director of the Genoscope, CEA/Genoscope)
How to apply?
Application procedure:
Please register by completing this questionnaire.
In addition, submit a CV and a motivation letter as a single PDF file with the subject header “ATLASea_Training_2025_LASTNAME” to winter_school@atlasea.fr
Application Deadline:
May 31, 2025
Fees and Grants:
The costs of the accommodation and the lunches/dinners from Monday morning to Friday night will be covered by the ATLASea program.