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Number of documents

51

cv test

 

2010

Habilitation à Diriger des Recherches (soutenue le 12 juillet 2010)

Depuis 2005

Chargée de Recherche 1ère classe au CNRS (lab. Biométrie et Biologie Evolutive, Université Lyon 1)

2004 - 2005

Post-Doctorante (lab. Biométrie et Biologie Evolutive, Université Lyon 1, financement de la Fondation pour la Recherche Médicale)

2002 - 2004

Chercheur associé, Dep "Ecology and Evolutionary Biology", Université d'Arizona (Tucson, USA)

2001 - 2002

ATER - Université Lyon 1

1998 – 2001

Thèse en bioinformatique soutenue le 26 octobre 2001, mention très honorable

1997 - 1998

DEAAnalyse de Génomes et Modélisation Moléculaire - Université Paris VII

 

Journal articles47 documents

  • Diamantis Sellis, Frédéric Guérin, Olivier Arnaiz, Walker Pett, Emmanuelle Lerat, et al.. Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes. Plos Biology, 2021, 19 (7), pp.e3001309. ⟨10.1371/journal.pbio.3001309⟩. ⟨hal-03366429⟩
  • Margot Correa, Emmanuelle Lerat, Etienne Birmelé, Franck Samson, Bérengère Bouillon, et al.. The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2021, 13 (5), ⟨10.1093/gbe/evab062⟩. ⟨hal-03367114⟩
  • Tanguy Lallemand, Martin Leduc, Claudine Landès, Carène Rizzon, Emmanuelle Lerat. An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice. Genes, MDPI, 2020, 11 (9), pp.1046. ⟨10.3390/genes11091046⟩. ⟨hal-02977854⟩
  • Romain Lannes, Carène Rizzon, Emmanuelle Lerat. Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?. Genes, MDPI, 2019, 10 (3), pp.249. ⟨10.3390/genes10030249⟩. ⟨hal-02120974⟩
  • Emmanuelle Lerat, Josep Casacuberta, Cristian Chaparro, Cristina Vieira. On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses. Genes, MDPI, 2019, 10 (4), pp.258. ⟨10.3390/genes10040258⟩. ⟨hal-02093613⟩
  • Emmanuelle Lerat, Clément Goubert, Sara Guirao-Rico, Miriam Merenciano, Anne-Béatrice Dufour, et al.. Population specific dynamics and selection patterns of transposable element insertions in European natural populations. Molecular Ecology, Wiley, 2018, pp.1-17. ⟨10.1111/mec.14963⟩. ⟨hal-01965027⟩
  • N. Bargues, Emmanuelle Lerat. Evolutionary history of LTR-retrotransposons among 20 Drosophila species. Mobile DNA, BioMed Central, 2017, 8, pp.7. ⟨10.1186/s13100-017-0090-3⟩. ⟨hal-02049656⟩
  • Emmanuelle Lerat, Marie Fablet, Laurent Modolo, Hélène Lopez-Maestre, Cristina Vieira. TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes. Nucleic Acids Research, Oxford University Press, 2017, 45, pp.13. ⟨10.1093/nar/gkw953⟩. ⟨hal-01524877⟩
  • Laura Grégoire, Annabelle Haudry, Emmanuelle Lerat. The transposable element environment of human genes is associated with histone and expression changes in cancer. BMC Genomics, BioMed Central, 2016, 17 (1), ⟨10.1186/s12864-016-2970-1⟩. ⟨hal-01896846⟩
  • Abdel Belkorchia, Cyrielle Gasc, Valérie Polonais, Nicolas Parisot, Nicolas Gallois, et al.. The Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes. PLoS ONE, Public Library of Science, 2015, 10 (9), pp.1-12. ⟨10.1371/journal.pone.0139075⟩. ⟨hal-01247479⟩
  • Marc Bailly-Bechet, Annabelle Haudry, Emmanuelle Lerat. “One code to find them all”: a perl tool to conveniently parse RepeatMasker output files. Mobile DNA, BioMed Central, 2014, 5, pp.13. ⟨10.1186/1759-8753-5-13⟩. ⟨hal-01332104⟩
  • Douglas R Hoen, Glenn Hickey, Guillaume Bourque, Josep Casacuberta, Richard Cordaux, et al.. A call for benchmarking transposable element annotation methods.. Mobile DNA, BioMed Central, 2014, 6, pp.13. ⟨10.1186/s13100-015-0044-6⟩. ⟨hal-01204840⟩
  • E Peyretaillade, D Boucher, N Parisot, C Gasc, R Butler, et al.. Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems. Heredity, Nature Publishing Group, 2014, pp.25182222. ⟨10.1038/hdy.2014.78⟩. ⟨hal-01110134⟩
  • Nicolas Parisot, Adrian Pelin, Cyrielle Gasc, Valérie Polonais, Abdel Belkorchia, et al.. Microsporidian Genomes Harbor a Diverse Array of Transposable Elements that Demonstrate an Ancestry of Horizontal Exchange with Metazoans.. Genome Biol Evol, Oxford University Press, 2014, 6 (9), pp.2289-300. ⟨10.1093/gbe/evu178⟩. ⟨hal-01071789⟩
  • Johan Panek, Hicham El Alaoui, Anne Mone, Serge Urbach, Edith Demettre, et al.. Hijacking of Host Cellular Functions by an Intracellular Parasite, the Microsporidian Anncaliia algerae. PLoS ONE, Public Library of Science, 2014, 9 (6), pp.e100791. ⟨10.1371/journal.pone.0100791⟩. ⟨hal-01053924⟩
  • Sophie Blanc, Florence Ruggiero, Anne-Marie Birot, Hervé Acloque, Didier Decimo, et al.. Subcellular Localization of ENS-1/ERNI in Chick Embryonic Stem Cells. PLoS ONE, Public Library of Science, 2014, 9 (3), pp.e92039. ⟨10.1371/journal.pone.0092039⟩. ⟨hal-02096948⟩
  • Elias Carnelossi, Emmanuelle Lerat, Hélène Henri, Sonia Martinez, Claudia Carareto, et al.. Specific Activation of an I-Like Element in Drosophila Interspecific Hybrids. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2014, 6, pp.1806 - 1817. ⟨10.1093/gbe/evu141⟩. ⟨hal-01526700⟩
  • Cristina Vieira, Marie Fablet, Emmanuelle Lerat, Matthieu Boulesteix, Rita Rebollo, et al.. A comparative analysis of the amounts and dynamics of transposable elements in natural populations of Drosophila melanogaster and Drosophila simulans.. Journal of Environmental Radioactivity, Elsevier, 2012, 113, pp.83-86. ⟨10.1016/j.jenvrad.2012.04.001⟩. ⟨hal-00763500⟩
  • Emmanuelle Lerat, Nelly Burlet, Christian Biémont, Cristina Vieira. Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes.. Gene, Elsevier, 2011, 473 (2), pp.100-9. ⟨10.1016/j.gene.2010.11.009⟩. ⟨hal-00850380⟩
  • Hussein Mortada, Cristina Vieira, Emmanuelle Lerat. Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species.. Journal of Molecular Evolution, Springer Verlag, 2010, 71 (3), pp.180-91. ⟨10.1007/s00239-010-9376-5⟩. ⟨hal-00850383⟩
  • E. Lerat. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity, Nature Publishing Group, 2009, --, pp.1-14. ⟨hal-00539329⟩
  • M. Deloger, F.M.G. Cavalli, E. Lerat, C. Biémont, M.-F. Sagot, et al.. Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster. Gene, Elsevier, 2009, 439, pp.55-62. ⟨hal-00428351⟩
  • Adriana Granzotto, Fabrício R Lopes, Emmanuelle Lerat, Cristina Vieira, Claudia M A Carareto. The evolutionary dynamics of the Helena retrotransposon revealed by sequenced Drosophila genomes.. BMC Evolutionary Biology, BioMed Central, 2009, 9, pp.174. ⟨10.1186/1471-2148-9-174⟩. ⟨hal-00850397⟩
  • Cristina Vieira, M. Fablet, E. Lerat. Infra- and Transspecific Clues to Understanding the Dynamics of Transposable Elements. genome dyn stab, 2009, --, pp.115-123. ⟨hal-00428338⟩
  • M. Fablet, E. Lerat, R. Rebollo, B. Horard, N. Burlet, et al.. Genomic environment influences the dynamics of the tirant LTR retrotransposon in Drosophila. FASEB Journal, Federation of American Society of Experimental Biology, 2009, 23, pp.54-62. ⟨hal-00428323⟩
  • Marie Fablet, Emmanuelle Lerat, Rita Rebollo, Béatrice Horard, Nelly Burlet, et al.. Genomic environment influences the dynamics of the tirant LTR retrotransposon in Drosophila.. FASEB Journal, Federation of American Society of Experimental Biology, 2009, 23 (5), pp.1482-9. ⟨10.1096/fj.08-123513⟩. ⟨hal-00850396⟩
  • Rita Rebollo, Emmanuelle Lerat, Liliana Lopez Kleine, Christian Biémont, Cristina Vieira. Losing helena: The extinction of a drosophila line-like element. BMC Genomics, BioMed Central, 2008, 9, pp.1-11. ⟨10.1186/1471-2164-9-149⟩. ⟨hal-02668006⟩
  • E. Lerat, M. Sémon. Influence of the transposable element neighborhood on human gene expression in normal and tumor tissues. Gene, Elsevier, 2007, 396, pp.303-311. ⟨hal-00434594⟩
  • Emmanuelle Lerat, Anne-Marie Birot, Jacques Samarut, Anne Mey. Maintenance in the chicken genome of the retroviral-like cENS gene family specifically expressed in early embryos. Journal of Molecular Evolution, Springer Verlag, 2007, 65 (3), pp.215-227. ⟨10.1007/s00239-007-9001-4⟩. ⟨hal-02657241⟩
  • H. Ochman, E. Lerat, Vincent Daubin. Examining bacterial species under the specter of gene transfer and exchange. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2005, 102, pp.6595-6599. ⟨hal-00427799⟩
  • E. Lerat, H. Ochman. Recognizing the pseudogenes in bacterial genomes. Nucleic Acids Research, Oxford University Press, 2005, 33, pp.3125-3132. ⟨hal-00427776⟩
  • H. Ochman, Vincent Daubin, E. Lerat. A bunch of fun-guys: the whole-genome view of yeast evolution. Trends in Genetics, Elsevier, 2005, 21, pp.1-3. ⟨hal-00427798⟩
  • E. Lerat, Vincent Daubin, H. Ochman, N.A. Moran. Evolutionary origins of genomic repertoires in bacteria. PLoS Biology, Public Library of Science, 2005, 3, pp.0807-0814. ⟨hal-00427770⟩
  • E. Lerat, H. Ochman. Ψ-Φ: Exploring the outer limits of bacterial pseudogenes. Genome Research, Cold Spring Harbor Laboratory Press, 2004, 14, pp.2273--2278. ⟨hal-02379302⟩
  • R. Edvardsen, E. Lerat, A.D. Maeland, M. Flat, R. Tewari, et al.. Hypervariable and highly divergent intron/exon organizations in the chordate Oikopleura dioica. Journal of Molecular Biology, Elsevier, 2004, 59, pp.448-457. ⟨hal-00427584⟩
  • E. Lerat, H. Ochman. $Psi$-$Phi$: Exploring the outer limits of bacterial pseudogenes. Genome Research, Cold Spring Harbor Laboratory Press, 2004, 14, pp.2273-2278. ⟨hal-00427616⟩
  • E. Lerat, N.A. Moran. The evolutionary history of quorum-sensing in bacteria. Molecular Biology and Evolution, Oxford University Press (OUP), 2004, 21, pp.903-913. ⟨hal-00427617⟩
  • J.V. Earnest-Deyoung, E. Lerat, B.M.E. Moret. Reversing gene erosion: Reconstructing ancestral bacterial genomes from gene-content and order data. incollection, 2004, 3240, pp.1-13. ⟨hal-00427561⟩
  • E. Lerat, Vincent Daubin, N.A. Moran. From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria. PLoS Biology, Public Library of Science, 2003, 1, pp.101-109. ⟨hal-00427440⟩
  • Vincent Daubin, E. Lerat, G. Perrière. The source of laterally transferred genes in bacterial genomes. Genome Biology, BioMed Central, 2003, 4, pp.R57.1-R57.12. ⟨hal-00427389⟩
  • E. Lerat, C. Rizzon, C. Biémont. Sequence divergence within transposable element families in the Drosophila melanogaster genome. Genome Research, Cold Spring Harbor Laboratory Press, 2003, 13, pp.1889-1896. ⟨hal-00427441⟩
  • E. Lerat, P. Capy, C. Biémont. Codon usage by transposable elements and their host genes in five species. Journal of Molecular Evolution, Springer Verlag, 2002, 54, pp.625-637. ⟨hal-00427284⟩
  • E. Lerat, P. Capy, C. Biémont. The relative abundance of dinucleotides in transposable elements in five species. Molecular Biology and Evolution, Oxford University Press (OUP), 2002, 19, pp.964-967. ⟨hal-00427283⟩
  • E. Lerat. Comparaison de séquences d`éléments transposables et de gènes d`hôtes chez cinq espèces : A. Thaliana C. Elegans D. Melanogaster H. Sapiens S. Cerevisiae. incollection, 2001, --, pp.347-354. ⟨hal-00427153⟩
  • E. Lerat, C. Biémont, P. Capy. Codon usage and the origin of P elements. Molecular Biology and Evolution, Oxford University Press (OUP), 2000, 17, pp.467-468. ⟨hal-00427091⟩
  • E. Lerat, F. Brunet, C. Bazin, P. Capy. Is the evolution of transposable elements modular?. Genetica, Springer Verlag, 1999, 107, pp.15-25. ⟨hal-00428431⟩
  • E. Lerat, P. Capy. Retrotransposons and retroviruses: analysis of the envelope gene. Molecular Biology and Evolution, Oxford University Press (OUP), 1999, 16, pp.1198-1207. ⟨hal-00428444⟩

Book sections2 documents

  • Emmanuelle Lerat. Repeat in genomes: how and why you should consider them in genome analyses. 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⟩. ⟨hal-02989096⟩
  • Laurent Modolo, Emmanuelle Lerat. Identification and Analysis of Transposable Elements in Genomic Sequences. Maria S. Poptsova. Genome analysis, current procedures and applications, Caister, Academic Press, 2014, 978-1-908230-29-4. ⟨hal-02099541⟩

Preprints, Working Papers, ...1 document

  • Emmanuelle Lerat, Nelly Burlet, Vincent Navratil, Camilles Noûs. Transposable element activity in the transcriptomic analysis of mouse pancreatic tumors. 2021. ⟨hal-03345544⟩

Theses1 document

  • Emmanuelle Lerat. 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. Autre [q-bio.OT]. Université Claude Bernard - Lyon I, 2001. Français. ⟨tel-00005207⟩