The updated list of my publications is available through:

And my main tools are available : https://github.com/asfistonlavie

My research focus on the study of the population dynamics and evolution of the transposable elements (TEs), one type of repeats, mainly in insect genomes. I am also particularly interested in the impact of such repetitive elements on genome adaptation. Another interest of my research is to assess the veracity of short and long read sequencing technologies and develop tools for the annotation and analyze of these repeats.

Detection of DNA repeats in assembled and non-assembled data

Transposable elements (TEs). TEs are ubiquitous repetitive elements of genomes representing a large part of genomes. As more and more studies highlight the implication of these elements in the evolution and adaptation of genomes, the annotation of TEs is still a huge challenge. In my research, I developed computational approaches and tools for the detection and annotation of TE insertions in genome sequencing from individuals and pooled data. The accuracy of the detection depends on biologic and technic variables. My current interest is to (1) optimize existing TE detection approaches and (2) assess the impact of repeats on the quality of genome assemblies.

TE dynamics

As TEs may represent a large fraction of genomes, a clear and thorough understanding of how TEs evolve is essential for a full comprehension of genome evolution. In previous work, we showed that most of TE insertions are deleterious and subject to purifying selection. This selection varies predictably with recombination rate, length of individual TEs, and copy number and length of other TEs from the same family. However,  the effect of each factor is not the same for all TE families. To account for the specific biology of each TE family, I am currently investigating their dynamics, focusing on insertion biases and repression mechanisms in several organisms.

Impact of TEs on genome structure and evolution

Another key aspect of my work involves assessing the impact of transposable elements (TEs) on genome structure and evolution. I am particularly interested in understanding how TEs influence genome size evolution and adaptive processes.

preprinted/submitted
  • Manual versus automatic annotation of transposable elements: case studies in Drosophila melanogaster and Aedes albopictus, balancing accuracy and biological relevance. Tomas Carrasco-Valenzuela, Alba Marino, Jessica M. Storer, Iago Bonnici, Camila J. Mazzoni, Michael C. Fontaine, Annabelle Haudry, Matthieu Boulesteix, Anna-Sophie Fiston-Lavier. bioRxiv 2025.01.10.632341; doi: https://doi.org/10.1101/2025.01.10.632341 (submitted)
  • Human pangenome illuminates the dynamics of polymorphic transposable elements. Shadi Shahatit, Jean Monlong, Kateryna D. Makova, Anna-Sophie Fiston-Lavier. (submitted)
  • RF4DEL: A Random Forest approach for accurate deletion detection.
    Xavier R, Fiston-Lavier AS, Alves RCO*, Cherif E*. (* co-last author).
    bioRxiv 2022.03.10.483419; https://doi.org/10.1101/2022.03.10.483419.
Published