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The Genomics of Transposable Elements Unmasking their Complex Contribution to Genome Function and Evolution

Program_TE Genomics

Biology Master, ENS
Bio-Q08_Qlife Winter School | The Genomics of Transposable Elements
Year : 2 (M2)
Semester : 2 (S2)
Duration : 1 week (February 6-10, 2023)
Hours : 50h
Credits : 3 ECTS
Maximum class size : 25 students
This course is open to external students (M2, PhDs, postdocs) and is highly selective.


Patrick Charnay, ENS Department of Biology

Chairman of the scientific committee

Vincent Colot, ENS Department of Biology


Transposable elements, genomics, genome evolution, genetic diversity, GWAS, epigenetics, gene expression, human diseases

Prerequisites for the course

Basic experience in file manipulation under Unix/Linux and coding ability in Python or R. Attendance is competitive (25 participants) and open to M2 and PhD students, postdocs, engineers and junior scientists with backgrounds in life science, physics, computer science and mathematics.

Course objectives and description

Genomics has revealed beyond any doubt that transposable element (TE) activity has significantly shaped the structure and function of extant genomes, ranging from bacteria to humans. Indeed, TE sequences are the main constituent of genomic DNA in many eukaryotic species and they have been co-opted at the macroevolutionary timescale to provide new protein functions as well as sequence motifs involved in the rewiring of gene regulatory networks. Ongoing TE mobilization is also an important generator of genetic diversity, with broad implications for health, disease and adaptation. Moreover, thanks to the epigenetic mechanisms that target them, TE sequences can influence the expression of genes in their vicinity in ways that are distinct from the effects of SNPs and other small size sequence polymorphisms. However, because TE sequences are typically present in large number of copies, which complicate their analysis, we still lack a comprehensive understanding and quantitative assessment of their multiple possible impacts in extant genomes.

The course will assemble world-leading experts from diverse fields to present recent advances in genomics and computational science that make it now possible to study at scale TE sequences and their varied effects. It will constitute a venue for cross-disciplinary discussions, with the goal of catalysing collaborations and of offering a novel conceptual basis for addressing questions on the contribution of TE sequences to organismal biology, disease, adaptation and evolution. The computational workshops will illustrate how robust and quantitative methods based on recently developed computational toolkits can be implemented to unmask and interrogate TE sequences in genomes.

Assessment of M2 students

To be decided later.

Course material (hand-outs, online presentation available,…) :

The course will include introductory lectures, a series of hands-on computational workshops run by experts (each afternoon), and seminars given by international experts on topics complementing those addressed in the lectures and practicals.

Scientific Committee

Chloé-Agathe Azencott, MinesParisTech, Paris
Deborah Bourc’his, Institut Curie, Paris
Patrick Charnay, IBENS, Paris
Vincent Colot, IBENS, Paris
Gaël Cristofari, Université de Nice
Josefa González, Institute of Evolutionary Biology, Barcelona
Felipe Karam Teixeira, University of Cambridge
Helen Rowe, Queen Mary University of London
Denis Thieffry, IBENS, Paris

Application deadline

December 4th, 2022

Registration fees

150 € (fees cover food and lodging from Monday morning to Friday afternoon. Some travel grants will be available).

Registration procedure

Register through the following link : the link will be provided later.
In addition, provide a CV, a 1 page motivation letter (including justification for travel grant if requested) and a supporting letter from a supervisor with “Qlife TE Genomics WS2023_LASTNAME” as subject header to chez

Download the Planning of TE Genomics WS