From Bench to Biosphere : Transcriptomics and Environmental Genomics
Master in Life Sciences, ENS – M2
2026-2027 - Semester 1
UNBIO1-067 - From Bench to Biosphere : Transcriptomics and Environmental Genomics
3 ECTS
—2026-2027 program (provisional)—
Level | Semester : M2 | S1
Where : ENS Biology Department, 3rd floor
Duration : 1 week | 30 hours (including personal work)
Dates : September 7-11, 2026
Hours : 09:30-12:30 | 13:30-17:00
Maximum class size : 30 students
Coordination
Lucie Bittner, Sorbonne Université
Léa Swales, École normale supérieure, Paris
Credits
3 ECTS
Keywords
Functional Genomics | Quantitive transcriptomics | Differential Gene Expression | Computational Biology | Environmental Genomics
Course Prerequisites
Computer knowledge : bases in computer programming, practice of Linux command lines and knowledge of R language.
Competency level in Unix : Advanced exploration of the file system, and workspace
Course objectives and description
Aims : This teaching unit provides a comprehensive and practical understanding of functional genomics, from experimental design to biological interpretation. High-throughput transcriptomic data are processed and critically analysed, and differential expression results are connected to functional and environmental contexts.
Themes : This course introduces the theoretical and practical foundations of quantitative transcriptomics, using a marine diatom as an illustrative model to bridge cultured organism biology and environmental genomics. Computer training sessions make use of open-source tools including R/Bioconductor, STAR, IGV, DESeq2 and clusterProfiler, deployed on the IFB cloud platform. The course covers the following fields : experimental design, data quality control, read mapping, count matrix construction, normalisation, differential expression analysis, functional annotation and an introduction to metagenome-assembled genomes (MAGs) and metatranscriptomics.
Organization : The course is organized over one week, combining classroom sessions, computer-training practicals and a free analysis workshop. Mornings are dedicated to active discussion of core concepts, while afternoons consist of hands-on bioinformatics practicals on the IFB cloud platform. Thursday is reserved for independent work on a mini-project, and Friday is devoted to project presentations and a written examination.
Assessment
Students will be evaluated based on a written report at the end of the week.
Course material
The practicals will be conducted on the core cluster of the Institut Français de Bioinformatique. We kindly acknowledge the IFB for supporting this course.
During this course, you will learn some competencies in Unix from levels U5 and U7 (see Competency matrix in unix in bioinformatics)
