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) 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).

Publications

Display of 1 to 30 publications on 59 in total

The era of reference genomes in conservation genomics

Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn...

Trends in Ecology and Evolution . 37 ( 3 ) : 197-202

DOI: 10.1016/j.tree.2021.11.008

Journal article

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The era of reference genomes in conservation genomics

Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn...

Trends in Ecology & Evolution . 37 ( 3 ) : 197-202

DOI: 10.1016/j.tree.2021.11.008

Journal article

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The era of reference genomes in conservation genomics

Florian Maumus, Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely...

Trends in Ecology & Evolution .

DOI: 10.1016/j.tree.2021.11.008

Journal article

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The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality

Margot Correa, Emmanuelle Lerat, Etienne E. Birmelé, Franck Samson, Bérengère Bouillon, Kévin Normand...

Genome Biology and Evolution . 13 ( 5 )

DOI: 10.1093/gbe/evab062

Journal article

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Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

Diamantis Sellis, Frédéric Guérin, Olivier Arnaiz, Walker Pett, Emmanuelle Lerat, Nicole Boggetto...

Plos Biology . 19 ( 7 ) : e3001309

DOI: 10.1371/journal.pbio.3001309

Journal article

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An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice

Tanguy Lallemand, Martin Leduc, Claudine Landès, Carène Rizzon, Emmanuelle Lerat

Genes . 11 ( 9 ) : 1046

DOI: 10.3390/genes11091046

Journal article

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Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?

Romain Lannes, Carène Rizzon, Emmanuelle Lerat

Genes . 10 ( 3 ) : 249

DOI: 10.3390/genes10030249

Journal article

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On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses

Emmanuelle Lerat, Josep Casacuberta, Cristian Chaparro, Cristina Vieira

Genes . 10 ( 4 ) : 258

DOI: 10.3390/genes10040258

Journal article

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Population specific dynamics and selection patterns of transposable element insertions in European natural populations

Emmanuelle Lerat, Clément Goubert, Sara Guirao-Rico, Miriam Merenciano, Anne-Béatrice Dufour, Cristina Vieira...

Molecular Ecology . : 1-17

DOI: 10.1111/mec.14963

Journal article

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Simulation-based estimation of branching models for LTR retrotransposons

Serge Moulin, Nicolas Seux, Stéphane Chrétien, Christophe Guyeux, Emmanuelle Lerat

Bioinformatics . 33 ( 3 ) : 320 - 326

DOI: 10.1093/bioinformatics/btw622

Journal article

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TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

Emmanuelle Lerat, Marie Fablet, Laurent Modolo, Hélène Lopez-Maestre, Cristina Vieira

Nucleic Acids Research . 45 : 13

DOI: 10.1093/nar/gkw953

Journal article

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The transposable element environment of human genes is associated with histone and expression changes in cancer

Laura Grégoire, Annabelle A. Haudry, Emmanuelle Lerat

BMC Genomics . 17 ( 1 )

DOI: 10.1186/s12864-016-2970-1

Journal article

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The Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes

Abdel Belkorchia, Cyrielle Gasc, Valérie Polonais, Nicolas Parisot, Nicolas Gallois, Céline Ribière...

PLoS ONE . 10 ( 9 ) : 1-12

DOI: 10.1371/journal.pone.0139075

Journal article

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A call for benchmarking transposable element annotation methods.

Douglas R Hoen, Glenn Hickey, Guillaume Bourque, Josep Casacuberta, Richard Cordaux, Cédric Feschotte...

Mobile DNA . 6 : 13

DOI: 10.1186/s13100-015-0044-6

Journal article

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Subcellular Localization of ENS-1/ERNI in Chick Embryonic Stem Cells

Sophie Blanc, Florence Ruggiero, Anne-Marie Birot, Hervé Acloque, Didier Decimo, Emmanuelle Lerat...

PLoS ONE . 9 ( 3 ) : e92039

DOI: 10.1371/journal.pone.0092039

Journal article

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Hijacking of Host Cellular Functions by an Intracellular Parasite, the Microsporidian Anncaliia algerae

Johan Panek, Hicham El Alaoui, Anne Mone, Serge Urbach, Edith Demettre, Catherine Texier...

PLoS ONE . 9 ( 6 ) : e100791

DOI: 10.1371/journal.pone.0100791

Journal article

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Microsporidian Genomes Harbor a Diverse Array of Transposable Elements that Demonstrate an Ancestry of Horizontal Exchange with Metazoans.

Nicolas Parisot, Adrian Pelin, Cyrielle Gasc, Valérie Polonais, Abdel Belkorchia, Johan Panek...

Genome Biol Evol . 6 ( 9 ) : 2289-300

DOI: 10.1093/gbe/evu178

Journal article

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Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems

E Peyretaillade, D Boucher, N Parisot, C Gasc, R Butler, J-F Pombert...

Heredity . : 25182222

DOI: 10.1038/hdy.2014.78

Journal article

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“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

Marc Bailly-Bechet, Annabelle Haudry, Emmanuelle Lerat

Mobile DNA . 5 : 13

DOI: 10.1186/1759-8753-5-13

Journal article

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Identification and Analysis of Transposable Elements in Genomic Sequences

Laurent Modolo, Emmanuelle Lerat

Genome analysis, current procedures and applications . 978-1-908230-29-4

Book chapter

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Specific Activation of an I-Like Element in Drosophila Interspecific Hybrids

Elias a G Carnelossi, Emmanuelle Lerat, Hélène Henri, Sonia Martinez, Claudia M A Carareto, Cristina Vieira

Genome Biology and Evolution . 6 : 1806 - 1817

DOI: 10.1093/gbe/evu141

Journal article

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The endogenous retrovirus ENS-1 provides active binding sites for transcription factors in embryonic stem cells that specify extra embryonic tissue

A. Mey, Hervé Acloque, Emmanuelle Lerat, S. Gounel, V. Tribollet, S. Blanc...

Retrovirology . 9 ( 1 ) : 21

DOI: 10.1186/1742-4690-9-21

Journal article

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A comparative analysis of the amounts and dynamics of transposable elements in natural populations of Drosophila melanogaster and Drosophila simulans.

Cristina Vieira, Marie Fablet, Emmanuelle Lerat, Matthieu Boulesteix, Rita Rebollo, Nelly Burlet...

Journal of Environmental Radioactivity . 113 : 83-86

DOI: 10.1016/j.jenvrad.2012.04.001

Journal article

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Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes.

Emmanuelle Lerat, Nelly Burlet, Christian Biémont, Cristina Vieira

Gene . 473 ( 2 ) : 100-9

DOI: 10.1016/j.gene.2010.11.009

Journal article

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