Emmanuelle Lerat

69
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Publications

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Particular sequence characteristics induce bias in the detection of polymorphic transposable element insertions

Marie Verneret , van Anthony Le , Thomas Faraut , Jocelyn Turpin , Emmanuelle Lerat

Peer Community Journal, 2025, 5, pp.e63. ⟨10.24072/pcjournal.570⟩

Article dans une revue hal-05107931v1
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A genome-wide study of ruminants uncovers two endogenous retrovirus families recently active in goats

Marie Verneret , Caroline Leroux , Thomas Faraut , Vincent Navratil , Emmanuelle Lerat et al.

Mobile DNA, 2025, 16 (1), pp.4. ⟨10.1186/s13100-024-00337-6⟩

Article dans une revue hal-04963611v1
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MicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation

Jérémy Tournayre , Valérie Polonais , Ivan Wawrzyniak , Reginald Florian Akossi , Nicolas Parisot et al.

International Journal of Molecular Sciences, 2024, 25 (2), pp.880. ⟨10.3390/ijms25020880⟩

Article dans une revue hal-04427987v1

Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats

Anthony B. Garza , Emmanuelle Lerat , Hani Z. Girgis

Mobile DNA, 2024, 15 (1), pp.8. ⟨10.1186/s13100-024-00317-w⟩

Article dans une revue hal-04706333v1

SMBE Secretary’s Report

Emmanuelle Lerat

Molecular Biology and Evolution, 2024, 41 (6), ⟨10.1093/molbev/msae104⟩

Article dans une revue hal-04706308v1
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How genomics can help biodiversity conservation

Kathrin Theissinger , Carlos Fernandes , Giulio Formenti , Iliana Bista , Paul Berg et al.

Trends in Genetics, 2023, ⟨10.1016/j.tig.2023.01.005⟩

Article dans une revue hal-04082874v1

Recent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements

Emmanuelle Lerat

Frontiers in Genetics, 2022, 13, ⟨10.3389/fgene.2022.891194⟩

Article dans une revue hal-03738345v1
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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 et al.

PLoS Biology, 2021, 19 (7), pp.e3001309. ⟨10.1371/journal.pbio.3001309⟩

Article dans une revue hal-03366429v1
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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 et al.

Genome Biology and Evolution, 2021, 13 (5), ⟨10.1093/gbe/evab062⟩

Article dans une revue hal-03367114v1
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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, 2020, 11 (9), pp.1046. ⟨10.3390/genes11091046⟩

Article dans une revue hal-02977854v1
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On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses

Emmanuelle Lerat , Josep Casacuberta , Cristian Chaparro , Cristina Vieira

Genes, 2019, 10 (4), pp.258. ⟨10.3390/genes10040258⟩

Article dans une revue hal-02093613v1
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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, 2019, 10 (3), pp.249. ⟨10.3390/genes10030249⟩

Article dans une revue hal-02120974v1
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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 et al.

Molecular Ecology, 2018, pp.1-17. ⟨10.1111/mec.14963⟩

Article dans une revue hal-01965027v1
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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, 2017, 45, pp.13. ⟨10.1093/nar/gkw953⟩

Article dans une revue hal-01524877v1

Evolutionary history of LTR-retrotransposons among 20 Drosophila species

N. Bargues , Emmanuelle Lerat

Mobile DNA, 2017, 8, pp.7. ⟨10.1186/s13100-017-0090-3⟩

Article dans une revue hal-02049656v1
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Simulation-based estimation of branching models for LTR retrotransposons

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

Bioinformatics, 2017, 33 (3), pp.320 - 326. ⟨10.1093/bioinformatics/btw622⟩

Article dans une revue hal-02131160v1
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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, 2016, 17 (1), ⟨10.1186/s12864-016-2970-1⟩

Article dans une revue hal-01896846v1
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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 et al.

PLoS ONE, 2015, 10 (9), pp.1-12. ⟨10.1371/journal.pone.0139075⟩

Article dans une revue hal-01247479v1
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A call for benchmarking transposable element annotation methods.

Douglas R Hoen , Glenn Hickey , Guillaume Bourque , Josep Casacuberta , Richard Cordaux et al.

Mobile DNA, 2014, 6, pp.13. ⟨10.1186/s13100-015-0044-6⟩

Article dans une revue hal-01204840v1
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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 et al.

PLoS ONE, 2014, 9 (6), pp.e100791. ⟨10.1371/journal.pone.0100791⟩

Article dans une revue hal-01053924v1
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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, 2014, 5, pp.13. ⟨10.1186/1759-8753-5-13⟩

Article dans une revue hal-01332104v1
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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 et al.

PLoS ONE, 2014, 9 (3), pp.e92039. ⟨10.1371/journal.pone.0092039⟩

Article dans une revue hal-02096948v1
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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 et al.

Genome Biology and Evolution, 2014, 6, pp.1806 - 1817. ⟨10.1093/gbe/evu141⟩

Article dans une revue hal-01526700v1

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 et al.

Heredity, 2014, pp.25182222. ⟨10.1038/hdy.2014.78⟩

Article dans une revue hal-01110134v1
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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 et al.

Genome Biology and Evolution, 2014, 6 (9), pp.2289-300. ⟨10.1093/gbe/evu178⟩

Article dans une revue hal-01071789v1
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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 et al.

Retrovirology, 2012, 9 (1), pp.21. ⟨10.1186/1742-4690-9-21⟩

Article dans une revue hal-02289815v1

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 et al.

Journal of Environmental Radioactivity, 2012, 113, pp.83-86. ⟨10.1016/j.jenvrad.2012.04.001⟩

Article dans une revue hal-00763500v1

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

Emmanuelle Lerat , Nelly Burlet , Christian Biémont , Cristina Vieira

Gene, 2011, 473 (2), pp.100-9. ⟨10.1016/j.gene.2010.11.009⟩

Article dans une revue istex hal-00850380v1

Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species.

Hussein Mortada , Cristina Vieira , Emmanuelle Lerat

Journal of Molecular Evolution, 2010, 71 (3), pp.180-91. ⟨10.1007/s00239-010-9376-5⟩

Article dans une revue istex hal-00850383v1

Genomic environment influences the dynamics of the tirant LTR retrotransposon in Drosophila.

Marie Fablet , Emmanuelle Lerat , Rita Rebollo , Béatrice Horard , Nelly Burlet et al.

FASEB Journal, 2009, 23 (5), pp.1482-9. ⟨10.1096/fj.08-123513⟩

Article dans une revue hal-00850396v1

Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs

E. Lerat

Heredity, 2009, --, pp.1-14

Article dans une revue hal-00539329v1

Genomic environment influences the dynamics of the <i>tirant</i> LTR retrotransposon in <i>Drosophila</i>

M. Fablet , E. Lerat , R. Rebollo , B. Horard , N. Burlet et al.

FASEB Journal, 2009, 23, pp.54-62

Article dans une revue hal-00428323v1

Infra- and Transspecific Clues to Understanding the Dynamics of Transposable Elements

Cristina Vieira , M. Fablet , E. Lerat

genome dyn stab, 2009, --, pp.115-123

Article dans une revue hal-00428338v1

Identification of expressed transposable element insertions in the sequenced genome of <i>Drosophila melanogaster</i>

M. Deloger , F.M.G. Cavalli , E. Lerat , C. Biémont , M.-F. Sagot et al.

Gene, 2009, 439, pp.55-62

Article dans une revue hal-00428351v1

The evolutionary dynamics of the Helena retrotransposon revealed by sequenced Drosophila genomes.

Adriana Granzotto , Fabrício R Lopes , Emmanuelle Lerat , Cristina Vieira , Claudia M A Carareto

BMC Evolutionary Biology, 2009, 9, pp.174. ⟨10.1186/1471-2148-9-174⟩

Article dans une revue hal-00850397v1
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Losing helena: The extinction of a drosophila line-like element

Rita Rebollo , Emmanuelle Lerat , Liliana Lopez Kleine , Christian Biémont , Cristina Vieira

BMC Genomics, 2008, 9, pp.1-11. ⟨10.1186/1471-2164-9-149⟩

Article dans une revue hal-02668006v1

Influence of the transposable element neighborhood on human gene expression in normal and tumor tissues

E. Lerat , M. Sémon

Gene, 2007, 396, pp.303-311

Article dans une revue hal-00434594v1

Maintenance in the chicken genome of the retroviral-like cENS gene family specifically expressed in early embryos

Emmanuelle Lerat , Anne-Marie Birot , Jacques Samarut , Anne Mey

Journal of Molecular Evolution, 2007, 65 (3), pp.215-227. ⟨10.1007/s00239-007-9001-4⟩

Article dans une revue istex hal-02657241v1

Recognizing the pseudogenes in bacterial genomes

E. Lerat , H. Ochman

Nucleic Acids Research, 2005, 33, pp.3125-3132

Article dans une revue hal-00427776v1

Evolutionary origins of genomic repertoires in bacteria

E. Lerat , Vincent Daubin , H. Ochman , N.A. Moran

PLoS Biology, 2005, 3, pp.0807-0814

Article dans une revue hal-00427770v1

A bunch of fun-guys: the whole-genome view of yeast evolution

H. Ochman , Vincent Daubin , E. Lerat

Trends in Genetics, 2005, 21, pp.1-3

Article dans une revue hal-00427798v1

Examining bacterial species under the specter of gene transfer and exchange

H. Ochman , E. Lerat , Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America, 2005, 102, pp.6595-6599

Article dans une revue hal-00427799v1

The evolutionary history of quorum-sensing in bacteria

E. Lerat , N.A. Moran

Molecular Biology and Evolution, 2004, 21, pp.903-913

Article dans une revue hal-00427617v1

$Psi$-$Phi$: Exploring the outer limits of bacterial pseudogenes

E. Lerat , H. Ochman

Genome Research, 2004, 14, pp.2273-2278

Article dans une revue hal-00427616v1

Ψ-Φ: Exploring the outer limits of bacterial pseudogenes

E. Lerat , H. Ochman

Genome Research, 2004, 14, pp.2273--2278

Article dans une revue hal-02379302v1

Hypervariable and highly divergent intron/exon organizations in the chordate <i>Oikopleura dioica</i>

R. Edvardsen , E. Lerat , A.D. Maeland , M. Flat , R. Tewari et al.

Journal of Molecular Biology, 2004, 59, pp.448-457

Article dans une revue hal-00427584v1

Reversing gene erosion: Reconstructing ancestral bacterial genomes from gene-content and order data

J.V. Earnest-Deyoung , E. Lerat , B.M.E. Moret

incollection, 2004, 3240, pp.1-13

Article dans une revue hal-00427561v1
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From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria

Emmanuelle Lerat , Vincent Daubin , Nancy Moran

PLoS Biology, 2003, 1 (1), pp.101-109. ⟨10.1371/journal.pbio.0000019⟩

Article dans une revue hal-00427440v1

Sequence divergence within transposable element families in the Drosophila melanogaster genome

E. Lerat , C. Rizzon , C. Biémont

Genome Research, 2003, 13, pp.1889-1896

Article dans une revue hal-00427441v1

The source of laterally transferred genes in bacterial genomes

Vincent Daubin , E. Lerat , G. Perrière

Genome Biology, 2003, 4, pp.R57.1-R57.12

Article dans une revue hal-00427389v1

The relative abundance of dinucleotides in transposable elements in five species

E. Lerat , P. Capy , C. Biémont

Molecular Biology and Evolution, 2002, 19, pp.964-967

Article dans une revue hal-00427283v1

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

E. Lerat , P. Capy , C. Biémont

Journal of Molecular Evolution, 2002, 54, pp.625-637

Article dans une revue hal-00427284v1

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, 2001, --, pp.347-354

Article dans une revue hal-00427153v1

Codon usage and the origin of P elements

E. Lerat , C. Biémont , P. Capy

Molecular Biology and Evolution, 2000, 17, pp.467-468

Article dans une revue hal-00427091v1

Is the evolution of transposable elements modular?

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

Genetica, 1999, 107, pp.15-25

Article dans une revue hal-00428431v1

Retrotransposons and retroviruses: analysis of the envelope gene

E. Lerat , P. Capy

Molecular Biology and Evolution, 1999, 16, pp.1198-1207

Article dans une revue hal-00428444v1

A first step towards the characterization of endogenous retroviruses’ evolutionary history and impact on small ruminant genomes

Marie Verneret , Caroline Leroux , Vincent Navratil , Thomas Faraut , Emmanuelle Lerat et al.

CNET 2023 : 24th National Congress on Transposable Elements 2023, The French research community working on transposable elements (CNET), Jul 2023, Perpignan, France

Communication dans un congrès hal-04728744v1
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Repeat in genomes: how and why you should consider them in genome analyses

Emmanuelle Lerat

Michael Gribskov; Christian Schonbach; Kenta Nakai; Shoba Ranganathan. Encyclopedia of Bioinformatics and Computational Biology, 2, Elsevier, pp.210-220, 2019, 9780128114148. ⟨10.1016/B978-0-12-809633-8.20227-6⟩

Chapitre d'ouvrage hal-02989096v1

Identification and Analysis of Transposable Elements in Genomic Sequences

Laurent Modolo , Emmanuelle Lerat

Maria S. Poptsova. Genome analysis, current procedures and applications, Caister, Academic Press, 2014, 978-1-908230-29-4

Chapitre d'ouvrage hal-02099541v1