GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Lerat Emmanuelle

Chargée de recherche

CNRS

Address: 69622 VILLEURBANNE cedex
69622 VILLEURBANNE cedex

Tel: 04 72 43 13 44

Email

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.

 

Projects

• 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) (2008-2023)
  • 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), A. Benmehdia (2023; 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).

Publications

Display of 61 to 66 publications on 66 in total

Codon usage by transposable elements and their host genes in five species

E. Lerat, P. Capy, C. Biémont

Journal of Molecular Evolution . 54 : 625-637

Journal article

see the publication

Comparaison de séquences d'éléments transposables et de gènes d'hôte chez cinq espèces : A. thaliana, C. elegans, D. melanogaster, H. sapiens et S. cerevisiae

Emmanuelle Lerat

Thesis

see the publication

Comparaison de séquences d`éléments transposables et de gènes d`hôtes chez cinq espèces : A. Thaliana C. Elegans D. Melanogaster H. Sapiens S. Cerevisiae

E. Lerat

incollection . -- : 347-354

Journal article

see the publication

Codon usage and the origin of P elements

E. Lerat, C. Biémont, P. Capy

Molecular Biology and Evolution . 17 : 467-468

Journal article

see the publication

Retrotransposons and retroviruses: analysis of the envelope gene

E. Lerat, P. Capy

Molecular Biology and Evolution . 16 : 1198-1207

Journal article

see the publication

Is the evolution of transposable elements modular?

E. Lerat, F. Brunet, C. Bazin, P. Capy

Genetica . 107 : 15-25

Journal article

see the publication