My research concerns the study of the role of transposable elements (TEs) in the evolution of eukaryotic genomes using comparative genomics and bioinformatics approaches in different organisms. Since several years, I have developed expertise in the identification of TEs in sequenced genomes, the study of their effects on neighboring genes, but also in the evolutionary analysis of TE sequences.



• Detection of TE copies in whole genome sequences to analyze their dynamics and evolution. For this, we have developed several programs:

  • Genome-wide statistic method to detect horizontally transferred sequences without any a priori  (Modolo et al. 2014) available here.
  • Tool to parse RepeatMasker output file in order to obtain detailed information concerning the TE content in a genome at the family level (Bailly-Bechet et al. 2014) available at One-code-to-find-them-all.
  •  Tool to performe transcriptomic analysis of TEs  (Lerat et al. 2017) available here.
  •  In development: tool to simulate a distribution of polymorphic TE insertions.

• Study of the link between TE insertions, epigenetic modifications and gene expression under various conditions (for example: normal cells vs tumor) in mammals and Drosophila.
•  Influence of TEs on the evolution of duplicated genes .
• Participation in the development of a reference for the annotation of TEs in genomes with several international researchers (Hoen et al. 2015).

Short CV
    • 2005-present : CNRS researcher
    • 2010 : Accreditation to conduct research (HDR)
    • 2004-2005 : Post-doc at the LBBE (FRM funding)
    • 2002-2004 : Post-doc at the University of Arizona (Tucson, USA)
    • 2001-2002 : ATER  at University Lyon 1
    • 1998-2001 : PhD at University Lyon 1

Membership and expertise

  • Member of the "Society for Molecular Biology and Evolution" (SMBE)
  • Member of the French Society of Bioinformatics (SFBI)
  • Associate editor for  "Genome Biology and Evolution" (GBE) since 2008
  • Recommender for PCI Genomics since 2020
  • ResearchGate.

  • Carène Rizzon (lab. Statistics and Genome, Université d’Evry, France)
  • Jocelyn Turpin and Caroline Leroux (UMR 754, INRAe, Univ Lyon)
  • Sandra Duharcourt (Institut Jacques Monod, Paris, France), Linda Sperling (I2BC, Gif sur Yvette, France), Eric Meyer (IBENS, Paris, France)
  • Anne Mey (CarMeN lab, France) et Jacques Samarut (IGFL, ENS Lyon, France)
  • Eric Peyretaillade, Nicolas Parisot, et Pierre Peyret (EA CIDAM, Université d’Auvergne, France)
  • Marc Bailly-Béchet (Institut Sophia Agrobiotech, Univ. Nice Sophia Antipolis)
  • Marie-Pierre Chapuis (Centre de Biologie et de Gestion des Populations, Montpellier)
  • Franck Picard (Lab. Biologie et Modélisation de la Cellule, ENS, Lyon)
  • Claudia Carareto (UNESP, Brazil)
  • Antoine Perasso (Lab. « Chrono-environnement », Université de Franche-Comté, France)
  • Christophe Guyeux (FEMTO-ST institute, Université de France-Comté, France)
  • Josefa Gonzalez (Institut de Biologie Evolutive (CSIC-Universitat Pompeu Fabra) Barcelone, Espagne)
  • Mohamed Makni (Lab. de Génomique des insectes ravageurs de cultures d’intérêt agronomique, Univ Tunis El Manar, Tunisie)
  • Gabriel da Luz Wallau (Department of Entomology, Aggeu Magalhães Institute (IAM), Recife, Brésil)

  • L3: A. Mula (2006), E. Ohanyan (2016 ; co-supervision M Bailly-Béchet)
  • M1: F. Giordano (2006), R. Kahoul (2007), C. Déchaud (2016), A. Benmehdia (2022; co-supervision C. Rizzon), C. Bompard (2022; co-supervision C. Rizzon),
  • M2: B. Cheaib (2007), H. Mortada (2008), L. Modolo (2011), L. Grégoire (2013 ; co-supervision A. Haudry), E. Saulnier (2013 ; co-supervision C. Rizzon), N. Bargues (2015), R. Lannes (2016), C. Déchaud (2017), V. A. Le (2019), M. Le Guet (2019 ; co-supervision G. da Luz Wallau), G. Pozo (2020; co-supervision C. Rizzon), T. Tesseraud (2021 ; co-supervision C. Rizzon).
  • PhD: M. Deloger (2006-2009 ; co-direction C. Vieira et MF Sagot), A. Granzotto (2007-2011 ; co-direction C. Vieira et C. Carrareto), H. Mortada (2008-2011 ; co-direction C. Vieira), L. Modolo (2011-2014), S. Sedghiani (2016), M. Verneret (2022-2025; co-direction J. Turpin).


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