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Emmanuelle Lerat



2010 **Habilitation à Diriger des Recherches** (soutenue le 12 juillet 2010) Depuis 2005 **Chargée de Recherche 1****ère** **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 **DEA****Analyse de Génomes et Modélisation Moléculaire** - Université Paris VII


Recent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements

Emmanuelle Lerat
Frontiers in Genetics, 2022, 13, ⟨10.3389/fgene.2022.891194⟩
Journal articles hal-03738345v1

The era of reference genomes in conservation genomics

Giulio Formenti , Kathrin Theissinger , Carlos Fernandes , Iliana Bista , Aureliano Bombarely
Trends in Ecology & Evolution, 2022, 37 (3), pp.197-202. ⟨10.1016/j.tree.2021.11.008⟩
Journal articles hal-03562293v1

The era of reference genomes in conservation genomics

Giulio Formenti , Kathrin Theissinger , Carlos Fernandes , Iliana Bista , Aureliano Bombarely
Trends in Ecology and Evolution, 2022, 37 (3), pp.197-202. ⟨10.1016/j.tree.2021.11.008⟩
Journal articles hal-03854763v1
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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
PLoS Biology, 2021, 19 (7), pp.e3001309. ⟨10.1371/journal.pbio.3001309⟩
Journal articles 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
Genome Biology and Evolution, 2021, 13 (5), ⟨10.1093/gbe/evab062⟩
Journal articles 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⟩
Journal articles hal-02977854v1
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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⟩
Journal articles hal-02120974v1
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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⟩
Journal articles 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 Dufour
Molecular Ecology, 2018, pp.1-17. ⟨10.1111/mec.14963⟩
Journal articles hal-01965027v1
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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⟩
Journal articles hal-02131160v1

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⟩
Journal articles hal-02049656v1
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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⟩
Journal articles hal-01524877v1
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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⟩
Journal articles 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
PLoS ONE, 2015, 10 (9), pp.1-12. ⟨10.1371/journal.pone.0139075⟩
Journal articles hal-01247479v1

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
Heredity, 2014, pp.25182222. ⟨10.1038/hdy.2014.78⟩
Journal articles hal-01110134v1
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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
PLoS ONE, 2014, 9 (3), pp.e92039. ⟨10.1371/journal.pone.0092039⟩
Journal articles hal-02096948v1
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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⟩
Journal articles hal-01332104v1
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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
Genome Biology and Evolution, 2014, 6, pp.1806 - 1817. ⟨10.1093/gbe/evu141⟩
Journal articles hal-01526700v1

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
Genome Biol Evol, 2014, 6 (9), pp.2289-300. ⟨10.1093/gbe/evu178⟩
Journal articles hal-01071789v1
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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
PLoS ONE, 2014, 9 (6), pp.e100791. ⟨10.1371/journal.pone.0100791⟩
Journal articles hal-01053924v1
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A call for benchmarking transposable element annotation methods.

Douglas R Hoen , Glenn Hickey , Guillaume Bourque , Josep Casacuberta , Richard Cordaux
Mobile DNA, 2014, 6, pp.13. ⟨10.1186/s13100-015-0044-6⟩
Journal articles hal-01204840v1
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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
Retrovirology, 2012, 9 (1), pp.21. ⟨10.1186/1742-4690-9-21⟩
Journal articles 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
Journal of Environmental Radioactivity, 2012, 113, pp.83-86. ⟨10.1016/j.jenvrad.2012.04.001⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles hal-00850383v1

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⟩
Journal articles hal-00850397v1

Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster

M. Deloger , F.M.G. Cavalli , E. Lerat , C. Biémont , M.-F. Sagot
Gene, 2009, 439, pp.55-62
Journal articles hal-00428351v1

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
Journal articles hal-00539329v1

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

Marie Fablet , Emmanuelle Lerat , Rita Rebollo , Béatrice Horard , Nelly Burlet
FASEB Journal, 2009, 23 (5), pp.1482-9. ⟨10.1096/fj.08-123513⟩
Journal articles hal-00850396v1

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

M. Fablet , E. Lerat , R. Rebollo , B. Horard , N. Burlet
FASEB Journal, 2009, 23, pp.54-62
Journal articles 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
Journal articles hal-00428338v1
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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⟩
Journal articles hal-02668006v1

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⟩
Journal articles hal-02657241v1

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
Journal articles hal-00434594v1

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
Journal articles hal-00427799v1

Evolutionary origins of genomic repertoires in bacteria

E. Lerat , Vincent Daubin , H. Ochman , N.A. Moran
PLoS Biology, 2005, 3, pp.0807-0814
Journal articles 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
Journal articles hal-00427798v1

Recognizing the pseudogenes in bacterial genomes

E. Lerat , H. Ochman
Nucleic Acids Research, 2005, 33, pp.3125-3132
Journal articles hal-00427776v1

Ψ-Φ: Exploring the outer limits of bacterial pseudogenes

E. Lerat , H. Ochman
Genome Research, 2004, 14, pp.2273--2278
Journal articles hal-02379302v1

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

E. Lerat , H. Ochman
Genome Research, 2004, 14, pp.2273-2278
Journal articles hal-00427616v1

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
Journal articles hal-00427561v1

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

R. Edvardsen , E. Lerat , A.D. Maeland , M. Flat , R. Tewari
Journal of Molecular Biology, 2004, 59, pp.448-457
Journal articles hal-00427584v1

The evolutionary history of quorum-sensing in bacteria

E. Lerat , N.A. Moran
Molecular Biology and Evolution, 2004, 21, pp.903-913
Journal articles hal-00427617v1

The source of laterally transferred genes in bacterial genomes

Vincent Daubin , E. Lerat , G. Perrière
Genome Biology, 2003, 4, pp.R57.1-R57.12
Journal articles hal-00427389v1

Sequence divergence within transposable element families in the Drosophila melanogaster genome

E. Lerat , C. Rizzon , C. Biémont
Genome Research, 2003, 13, pp.1889-1896
Journal articles hal-00427441v1
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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⟩
Journal articles hal-00427440v1

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
Journal articles hal-00427284v1

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
Journal articles hal-00427283v1

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
Journal articles 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
Journal articles hal-00427091v1

Is the evolution of transposable elements modular?

E. Lerat , F. Brunet , C. Bazin , P. Capy
Genetica, 1999, 107, pp.15-25
Journal articles hal-00428431v1

Retrotransposons and retroviruses: analysis of the envelope gene

E. Lerat , P. Capy
Molecular Biology and Evolution, 1999, 16, pp.1198-1207
Journal articles hal-00428444v1
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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⟩
Book sections 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
Book sections hal-02099541v1