
GECO Evolutionary and Computational Genomics
Bioinformatics, Phylogeny and Evolutionary Genomics Group
Lerat Emmanuelle
Chargée de recherche
CNRS
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
Recent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements
Frontiers in Genetics . 13
Journal article
see the publicationThe era of reference genomes in conservation genomics
Trends in Ecology and Evolution . 37 ( 3 ) : 197-202
Journal article
see the publicationThe era of reference genomes in conservation genomics
Trends in Ecology & Evolution . 37 ( 3 ) : 197-202
Journal article
see the publicationThe era of reference genomes in conservation genomics
Trends in Ecology & Evolution .
Journal article
see the publicationRecent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements
Frontiers in Genetics . 13
Journal article
see the publicationMassive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes
Plos Biology . 19 ( 7 ) : e3001309
Journal article
see the publicationThe Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality
Genome Biology and Evolution . 13 ( 5 )
DOI: 10.1093/gbe/evab062
Journal article
see the publicationTransposable element activity in the transcriptomic analysis of mouse pancreatic tumors
Preprint
see the publicationA new tool to cross and analyze TE and gene annotations
Peer Community in Genomics . : 100010
Other publication
see the publicationAn Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice
Genes . 11 ( 9 ) : 1046
Journal article
see the publicationDoes the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?
Genes . 10 ( 3 ) : 249
Journal article
see the publicationOn the Importance to Acknowledge Transposable Elements in Epigenomic Analyses
Genes . 10 ( 4 ) : 258
Journal article
see the publicationRepeat in genomes: how and why you should consider them in genome analyses
Encyclopedia of Bioinformatics and Computational Biology . 2 : 210-220
Book chapter
see the publicationPopulation specific dynamics and selection patterns of transposable element insertions in European natural populations
Molecular Ecology . : 1-17
DOI: 10.1111/mec.14963
Journal article
see the publicationSimulation-based estimation of branching models for LTR retrotransposons
Bioinformatics . 33 ( 3 ) : 320 - 326
Journal article
see the publicationTEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes
Nucleic Acids Research . 45 : 13
DOI: 10.1093/nar/gkw953
Journal article
see the publicationEvolutionary history of LTR-retrotransposons among 20 Drosophila species
Mobile DNA . 8 : 7
Journal article
see the publicationThe transposable element environment of human genes is associated with histone and expression changes in cancer
BMC Genomics . 17 ( 1 )
Journal article
see the publicationThe Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes
PLoS ONE . 10 ( 9 ) : 1-12
Journal article
see the publicationA call for benchmarking transposable element annotation methods.
Mobile DNA . 6 : 13
Journal article
see the publicationSubcellular Localization of ENS-1/ERNI in Chick Embryonic Stem Cells
PLoS ONE . 9 ( 3 ) : e92039
Journal article
see the publicationHijacking of Host Cellular Functions by an Intracellular Parasite, the Microsporidian Anncaliia algerae
PLoS ONE . 9 ( 6 ) : e100791
Journal article
see the publicationMicrosporidian Genomes Harbor a Diverse Array of Transposable Elements that Demonstrate an Ancestry of Horizontal Exchange with Metazoans.
Genome Biol Evol . 6 ( 9 ) : 2289-300
DOI: 10.1093/gbe/evu178
Journal article
see the publicationExploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems
Heredity . : 25182222
DOI: 10.1038/hdy.2014.78
Journal article
see the publication“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
Mobile DNA . 5 : 13
Journal article
see the publicationIdentification and Analysis of Transposable Elements in Genomic Sequences
Genome analysis, current procedures and applications . 978-1-908230-29-4
Book chapter
see the publicationSpecific Activation of an I-Like Element in Drosophila Interspecific Hybrids
Genome Biology and Evolution . 6 : 1806 - 1817
DOI: 10.1093/gbe/evu141
Journal article
see the publicationThe endogenous retrovirus ENS-1 provides active binding sites for transcription factors in embryonic stem cells that specify extra embryonic tissue
Retrovirology . 9 ( 1 ) : 21
Journal article
see the publicationA comparative analysis of the amounts and dynamics of transposable elements in natural populations of Drosophila melanogaster and Drosophila simulans.
Journal of Environmental Radioactivity . 113 : 83-86
Journal article
see the publicationComparative analysis of transposable elements in the melanogaster subgroup sequenced genomes.
Gene . 473 ( 2 ) : 100-9
Journal article
see the publication