Emmanuelle Lerat

Présentation

Publications

Article dans une revue (56)

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
A genome-wide study of ruminants uncovers two endogenous retrovirus families recently active in goats Marie Verneret,Caroline Leroux,Thomas Faraut,Vincent Navratil,Emmanuelle Leratet al. Mobile DNA, 2025, 16 (1), pp.4. ⟨10.1186/s13100-024-00337-6⟩ Article dans une revue hal-04963611v1
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
MicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation Jérémy Tournayre,Valérie Polonais,Ivan Wawrzyniak,Reginald Florian Akossi,Nicolas Parisotet al. International Journal of Molecular Sciences, 2024, 25 (2), pp.880. ⟨10.3390/ijms25020880⟩ Article dans une revue hal-04427987v1
SMBE Secretary’s Report Emmanuelle Lerat Molecular Biology and Evolution, 2024, 41 (6), ⟨10.1093/molbev/msae104⟩ Article dans une revue hal-04706308v1
How genomics can help biodiversity conservation Kathrin Theissinger,Carlos Fernandes,Giulio Formenti,Iliana Bista,Paul Berget 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
Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes Diamantis Sellis,Frédéric Guérin,Olivier Arnaiz,Walker Pett,Emmanuelle Leratet al. PLoS Biology, 2021, 19 (7), pp.e3001309. ⟨10.1371/journal.pbio.3001309⟩ Article dans une revue hal-03366429v1
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 Bouillonet al. Genome Biology and Evolution, 2021, 13 (5), ⟨10.1093/gbe/evab062⟩ Article dans une revue hal-03367114v1
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
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
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
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 Dufouret al. Molecular Ecology, 2018, pp.1-17. ⟨10.1111/mec.14963⟩ Article dans une revue hal-01965027v1
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
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
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
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 Galloiset al. PLoS ONE, 2015, 10 (9), pp.1-12. ⟨10.1371/journal.pone.0139075⟩ Article dans une revue hal-01247479v1
Specific Activation of an I-Like Element in Drosophila Interspecific Hybrids Elias a G Carnelossi,Emmanuelle Lerat,Hélène Henri,Sonia Martinez,Claudia M A Cararetoet al. Genome Biology and Evolution, 2014, 6, pp.1806 - 1817. ⟨10.1093/gbe/evu141⟩ Article dans une revue hal-01526700v1
Subcellular Localization of ENS-1/ERNI in Chick Embryonic Stem Cells Sophie Blanc,Florence Ruggiero,Anne-Marie Birot,Hervé Acloque,Didier Decimoet al. PLoS ONE, 2014, 9 (3), pp.e92039. ⟨10.1371/journal.pone.0092039⟩ Article dans une revue hal-02096948v1
Hijacking of Host Cellular Functions by an Intracellular Parasite, the Microsporidian Anncaliia algerae Johan Panek,Hicham El Alaoui,Anne Mone,Serge Urbach,Edith Demettreet al. PLoS ONE, 2014, 9 (6), pp.e100791. ⟨10.1371/journal.pone.0100791⟩ Article dans une revue hal-01053924v1
A call for benchmarking transposable element annotation methods. Douglas R Hoen,Glenn Hickey,Guillaume Bourque,Josep Casacuberta,Richard Cordauxet al. Mobile DNA, 2014, 6, pp.13. ⟨10.1186/s13100-015-0044-6⟩ Article dans une revue hal-01204840v1
“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
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 Butleret al. Heredity, 2014, pp.25182222. ⟨10.1038/hdy.2014.78⟩ Article dans une revue hal-01110134v1
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 Belkorchiaet al. Genome Biology and Evolution, 2014, 6 (9), pp.2289-300. ⟨10.1093/gbe/evu178⟩ Article dans une revue hal-01071789v1
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. Tribolletet 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 Rebolloet 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
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 tirant LTR retrotransposon in Drosophila. Marie Fablet,Emmanuelle Lerat,Rita Rebollo,Béatrice Horard,Nelly Burletet al. FASEB Journal, 2009, 23 (5), pp.1482-9. ⟨10.1096/fj.08-123513⟩ Article dans une revue hal-00850396v1
Genomic environment influences the dynamics of the &lt;i&gt;tirant&lt;/i&gt; LTR retrotransposon in &lt;i&gt;Drosophila&lt;/i&gt; M. Fablet,E. Lerat,R. Rebollo,B. Horard,N. Burletet 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 &lt;i&gt;Drosophila melanogaster&lt;/i&gt; M. Deloger,F.M.G. Cavalli,E. Lerat,C. Biémont,M.-F. Sagotet 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
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
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
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
Recognizing the pseudogenes in bacterial genomes E. Lerat,H. Ochman Nucleic Acids Research, 2005, 33, pp.3125-3132 Article dans une revue hal-00427776v1
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
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
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
Hypervariable and highly divergent intron/exon organizations in the chordate &lt;i&gt;Oikopleura dioica&lt;/i&gt; R. Edvardsen,E. Lerat,A.D. Maeland,M. Flat,R. Tewariet 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
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

Communication dans un congrès (1)

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 Leratet 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

Poster de conférence (3)

Exploring endogenous retroviruses in ruminant genomes: They might not be all dead after all Marie Verneret,Caroline Leroux,Thomas Faraut,Vincent Navratil,Emmanuelle Leratet al. Bioinformatics and Evolutionary Genomics (ALPHY = ALignments and PHYlogeny), Feb 2025, Villeurbanne, France Poster de conférence hal-04965269v1
Small ruminants versus endogenous retroviruses: an evolutive showdown still in progress in the domestic goat genome Marie Verneret,Caroline Leroux,Vincent Navratil,Thomas Faraut,Jocelyn Turpinet al. International congress on transposable elements, Apr 2024, Saint Malo, France Poster de conférence hal-04727644v1
OVINE β-ENDOGENOUS RETROVIRUSES : FROM INTEGRATION TO COPY-SPECIFIC TRANSCRIPTION Marie Verneret,Caroline Leroux,Emmanuelle Lerat,Vincent Navratil,Jocelyn Turpin XXVèmes Journées Francophones de Virologie, Apr 2023, Paris, France Poster de conférence hal-04727987v1

Chapitre d'ouvrage (2)

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

Autre publication scientifique (1)

A new tool to cross and analyze TE and gene annotations Emmanuelle Lerat 2021, pp.100010. ⟨10.24072/pci.genomics.100010⟩ Autre publication scientifique hal-03279813v1

Pré-publication, Document de travail (5)

The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons Olivier Arnaiz,Frédéric Guérin,Arnaud Couloux,Caridad Miró-Pina,Guillaume Pellerinet al. 2025 Pré-publication, Document de travail (preprint/prepublication) hal-05355464v1
Particular sequence characteristics induce bias in the detection of polymorphic transposable element insertions Marie Verneret,van Anthony Le,Thomas Faraut,Jocelyn Turpin,Emmanuelle Lerat 2024 Pré-publication, Document de travail hal-04727343v1
A genome-wide study of ruminants reveals two endogenous retrovirus families still active in goats Marie Verneret,Caroline Leroux,Thomas Faraut,Vincent Navratil,Emmanuelle Leratet al. 2024 Pré-publication, Document de travail hal-04706314v1
Look4LTRs: A Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats Anthony Garza,Emmanuelle Lerat,Hani Girgis 2023 Pré-publication, Document de travail hal-04303151v1
Transposable element activity in the transcriptomic analysis of mouse pancreatic tumors Emmanuelle Lerat,Nelly Burlet,Vincent Navratil,Camilles Noûs 2021 Pré-publication, Document de travail hal-03345544v1

Thèse (1)

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 Autre [q-bio.OT]. Université Claude Bernard - Lyon I, 2001. Français. ⟨NNT : ⟩ Thèse tel-00005207v1