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Anna-Sophie Fiston-Lavier

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TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches

Mourdas Mohamed , François Sabot , Marion Varoqui , Bruno Mugat , Katell Audouin
Genome Biology, 2023, 24 (1), pp.63. ⟨10.1186/s13059-023-02911-2⟩
Journal articles hal-04291760v1
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Structural variation turnovers and defective genomes: key drivers for the in vitro evolution of the large double-stranded DNA koi herpesvirus (KHV)

Nurul Novelia Fuandila , Anne-Sophie Gosselin-Grenet , Marie-Ka Tilak , Sven M Bergmann , Jean-Michel Escoubas
Peer Community Journal, 2022, ⟨10.24072/pcjournal.154⟩
Journal articles hal-03895944v1
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BREC: An R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes

Yasmine Mansour , Annie Chateau , Anna-Sophie Fiston-Lavier
BMC Bioinformatics, 2021, 22 (S6), pp.#396. ⟨10.1186/s12859-021-04233-1⟩
Journal articles lirmm-03475277v1
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Ten simple rules for switching from face-to-face to remote conference: An opportunity to estimate the reduction in GHG emissions

Valentin Guignon , Catherine Breton , Jérôme J. Mariette , Francois Sabot , Julien Fumey
PLoS Computational Biology, 2021, 17 (10), pp.e1009321. ⟨10.1371/journal.pcbi.1009321⟩
Journal articles lirmm-03385026v1
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Genomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses

Martin Kapun , Maite G Barrón , Fabian Staubach , Darren J Obbard , R Axel W. Wiberg
Molecular Biology and Evolution, 2020, 37 (9), pp.2661-2678. ⟨10.1093/molbev/msaa120⟩
Journal articles hal-03014405v1
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Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements.

Rajiv Mccoy , Ryan Taylor , Timothy Blauwkamp , Joanna Kelley , Michael Kertesz
PLoS ONE, 2020, 9 (9), pp.e106689. ⟨10.1371/journal.pone.0106689⟩
Journal articles hal-03024236v1
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Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila.

Gabriel E Rech , María Bogaerts-Márquez , Maite G Barrón , Miriam Merenciano , José Luis Villanueva-Cañas
PLoS Genetics, 2019, 15 (2), pp.e1007900. ⟨10.1371/journal.pgen.1007900⟩
Journal articles hal-02306987v1
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A new species in the major malaria vector complex sheds light on reticulated species evolution

Maite Barrón , Christophe Paupy , Nil Rahola , Ousman Akone-Ella , Marc Ngangue
Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-019-49065-5⟩
Journal articles hal-02958379v1

Stress affects the epigenetic marks added by natural transposable element insertions in Drosophila melanogaster

Lain Guio , Cristina Vieira , Josefa González
Scientific Reports, 2018, 8 (1), pp.1-10. ⟨10.1038/s41598-018-30491-w⟩
Journal articles hal-01965035v1

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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A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits

L. Hibrand Saint-Oyant , T. Ruttink , L. Hamama , I. Kirov , D. Lakhwani
Nature Plants, 2018, 4 (7), pp.473 - 484. ⟨10.1038/s41477-018-0166-1⟩
Journal articles hal-01873309v1
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T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data

Anna-Sophie Fiston-Lavier , Maite G Barrón , Dmitri Petrov , Josefa González
Nucleic Acids Research, 2015, 43 (4), pp.e22-e22. ⟨10.1093/nar/gku1250⟩
Journal articles hal-03035671v1
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Quantification of GC-biased gene conversion in the human genome

Sylvain Glemin , Peter F. Arndt , Messer W. Philip , Petrov M. Dmitri , Nicolas Galtier
Genome Research, 2015, 25 (8), pp.1215 - 1228. ⟨10.1101/gr.185488.114⟩
Journal articles hal-01900676v1

Ancient hybridizations among the ancestral genomes of bread wheat

T. Marcussen , S. Sandve , L. Heier , M. Spannagl , M. Pfeifer
Science, 2014, 345 (6194), pp.1250092-1250092. ⟨10.1126/science.1250092⟩
Journal articles hal-02889053v1

Population Genomics of Transposable Elements in Drosophila

Maite Barrón , Anna-Sophie Fiston-Lavier , Dmitri Petrov , Josefa González
Annual Review of Genetics, 2014, 48 (1), pp.561-581. ⟨10.1146/annurev-genet-120213-092359⟩
Journal articles hal-03041181v1
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Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

T. Rouxel , J. Grandaubert , Jk. Hane , Claire Hoede , Angela P. van de Wouw
Nature Communications, 2011, 2, pp.202. ⟨10.1038/ncomms1189⟩
Journal articles hal-00841751v1
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Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.

E. d'Alençon , H. Sezutsu , Fabrice Legeai , E. Permal , S. Bernard-Samain
Proceedings of the National Academy of Sciences of the United States of America, 2010, 107 (17), pp.7680-5. ⟨10.1073/pnas.0910413107⟩
Journal articles inria-00537908v1
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The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

F. Martin , A. Aerts , D. Ahrén , A. Brun , E. G. J. Danchin
Nature, 2008, 452 (7183), pp.88-93. ⟨10.1038/nature06556⟩
Journal articles halsde-00261893v1

Evolution of genes and genomes on the Drosophila phylogeny

. Drosophila 12 Genomes Consortium , Andrew G Clark , Michael B Eisen , Douglas R Smith , Casey M Bergman
Nature, 2007, 450 (7167), pp.203-18. ⟨10.1038/nature06341⟩
Journal articles hal-02667683v1

Exploring the evolution of Wolbachia compatibility types: a simulation approach

S. Charlat , C. Calmet , Olivier Andrieu , H. Mercot
Genetics, 2005, 170, pp.495-507. ⟨10.1534/genetics.103.015198⟩
Journal articles hal-00427837v1
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Combined evidence annotation of transposable elements in genome sequences

Hadi Quesneville , Casey M. Bergman , Olivier Andrieu , Delphine Autard , Danielle Nouaud
PLoS Computational Biology, 2005, 1 (2), pp.e22. ⟨10.1371/journal.pcbi.0010022⟩
Journal articles hal-00009013v1
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Detection of transposable elements by their compositional bias

Olivier Andrieu , Anna-Sophie Fiston , Dominique Anxolabéhère , Hadi Quesneville
BMC Bioinformatics, 2004, 5 (94), pp.1-13. ⟨10.1186/1471-2105-5-94⟩
Journal articles hal-02682754v1
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Hoppel, a P-like element without introns: a P-element ancestral structure or a retrotranscription derivative?

Daphné Reiss , Hadi Quesneville , Danielle Nouaud , Olivier Andrieu , Dominique Anxolabéhère
Molecular Biology and Evolution, 2003, 20 (6), pp.869-879. ⟨10.1093/molbev/msg090⟩
Journal articles hal-02676873v1

Experience Report: Using Objective Caml to develop safety-critical embedded tool in a certification framework

Bruno Pagano , Olivier Andrieu , Thomas Moniot , Benjamin Canou , Emmanuel Chailloux
The 14th ACM SIGPLAN International Conference on Functional Programming (ICFP 2009), Aug 2009, Edinburgh, United Kingdom. pp.215-220, ⟨10.1145/1596550.1596582⟩
Conference papers hal-00396371v1

Certified development tools implementation in objective caml.

Bruno Pagano , Olivier Andrieu , Benjamin Canou , Emmanuel Chailloux , Jean-Louis Colaço
International Symposium on Practical Aspects of Declarative Languages PADL 08, Jan 2008, San Francisco, United States. pp.1--15
Conference papers hal-00319700v1