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Laurent Duret

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Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans

Florian Bénitière , Anamaria Necsulea , Laurent Duret
eLife, 2024, 13, pp.RP93629. ⟨10.7554/eLife.93629.3⟩
Journal articles hal-04258621v1
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High prevalence of PRDM9-independent recombination hotspots in placental mammals

Julien Joseph , Djivan Prentout , Alexandre Laverré , Théo Tricou , Laurent Duret
Proceedings of the National Academy of Sciences of the United States of America, 2024, 121 (23), pp.e2401973121. ⟨10.1073/pnas.2401973121⟩
Journal articles hal-04604269v1
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GTDrift: a resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes

Florian Bénitière , Laurent Duret , Anamaria Necsulea
NAR Genomics and Bioinformatics, 2024, 6 (2), pp.lqae064. ⟨10.1093/nargab/lqae064⟩
Journal articles hal-04609512v1
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Bridging the gap between the evolutionary dynamics and the molecular mechanisms of meiosis : a model based exploration of the PRDM9 intra-genomic Red Queen

Alice Genestier , Laurent Duret , Nicolas Lartillot
PLoS Genetics, 2023, 20 (5), pp.e1011274. ⟨10.1371/journal.pgen.1011274⟩
Journal articles hal-04272303v2
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Population designations in biomedical research: limitations and perspectives

Caroline Gombault , Guillaume Grenet , Laure Ségurel , Laurent Duret , François Gueyffier
HLA: Immune Response Genetics, 2022, ⟨10.1111/tan.14852⟩
Journal articles hal-03829218v1
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DILS: Demographic inferences with linked selection by using ABC

Christelle Fraïsse , Iva Popovic , Clément Mazoyer , Bruno Spataro , Stephane Delmotte
Molecular Ecology Resources, 2021, ⟨10.1111/1755-0998.13323⟩
Journal articles hal-03156998v1
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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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Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species

Natalia Sawka-Gądek , Alexey Potekhin , Deepankar Pratap Singh , Inessa Grevtseva , Olivier Arnaiz
Genome Biology and Evolution, 2020, evaa258, ⟨10.1093/gbe/evaa258⟩
Journal articles hal-03102341v1
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How consistent is RAD‐seq divergence with DNA‐barcode based clustering in insects?

Marie Cariou , Hélène Henri , Sonia Martinez , Laurent Duret , Sylvain Charlat
Molecular Ecology Resources, 2020, 20 (5), pp.1294-1298. ⟨10.1111/1755-0998.13178⟩
Journal articles hal-03017182v1
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Bedrock radioactivity influences the rate and spectrum of mutation

Nathanaëlle Saclier , Patrick Chardon , Florian Malard , Lara Konecny-Dupré , David Eme
eLife, 2020, 9, pp.e56830. ⟨10.7554/eLife.56830⟩
Journal articles hal-03051267v1
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Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot

Daphné Reiss , Gladys Mialdea , Vincent Miele , Damien M. de Vienne , Jean Peccoud
PLoS Genetics, 2019, 15 (2), pp.e1007965. ⟨10.1371/journal.pgen.1007965⟩
Journal articles hal-02140494v1
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Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest

Georgios Koutsovoulos , Eder Marques , Marie Jeanne Arguel , Laurent Duret , Andressa C. Z. Machado
Evolutionary Applications, 2019, 13, pp.1-16. ⟨10.1111/eva.12881⟩
Journal articles hal-02444457v1
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GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes

Paulina Bolívar , Laurent Guéguen , Laurent Duret , Hans Ellegren , Carina Mugal
Genome Biology, 2019, 20 (1), ⟨10.1186/s13059-018-1613-z⟩
Journal articles hal-02329971v1
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Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints

Florian Massip , Marc Laurent , Caroline Brossas , José miguel Fernández-Justel , Maria Gomez
Nucleic Acids Research, 2019, 47 (10), pp.5114-5125. ⟨10.1093/nar/gkz182⟩
Journal articles hal-02349718v1

Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods

Nathanaëlle Saclier , Clémentine François , Lara Konecny-Dupré , Nicolas Lartillot , Laurent Guéguen
Molecular Biology and Evolution, 2018, 35 (12), pp.2900-2912. ⟨10.1093/molbev/msy184⟩
Journal articles hal-01951580v1
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Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition

Laurent Guéguen , Laurent Duret
Molecular Biology and Evolution, 2018, 35 (3), pp.734-742. ⟨10.1093/molbev/msx308⟩
Journal articles hal-02349724v1
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Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

Nicolas Galtier , Camille Roux , Marjolaine Rousselle , Jonathan Romiguier , Emeric Figuet
Molecular Biology and Evolution, 2018, 35 (5), pp.1092 - 1103. ⟨10.1093/molbev/msy015⟩
Journal articles hal-01806906v1

PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites

Boubou Diagouraga , Julie Clément , L. Duret , Jan Kadlec , Bernard de Massy
Molecular Cell, 2018, 69 (5), pp.853 - 865.e6. ⟨10.1016/j.molcel.2018.01.033⟩
Journal articles hal-01730632v1
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In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

C Grey , Julie a J Clément , J Buard , B Leblanc , I Gut
Genome Research, 2017, 27 (4), pp.580-590. ⟨10.1101/gr.217240.116⟩
Journal articles hal-01505240v1
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The Red Queen model of recombination hot-spot evolution: a theoretical investigation

Thibault Latrille , L. Duret , Nicolas Lartillot
Philosophical Transactions of the Royal Society B: Biological Sciences, 2017, ⟨10.1098/rstb.2016.0463⟩
Journal articles hal-01891448v1
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The fitness cost of mis-splicing is the main determinant of alternative splicing patterns

Baptiste Saudemont , Alexandra Popa , Joanna Parmley , Vincent Rocher , Corinne Blugeon
Genome Biology, 2017, 18, pp.208. ⟨10.1186/s13059-017-1344-6⟩
Journal articles hal-02321589v1
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The global impact of Wolbachia on mitochondrial diversity and evolution

Marie Cariou , Laurent Duret , Sylvain Charlat
Journal of Evolutionary Biology, 2017, 30 (12), pp.2204-2210. ⟨10.1111/jeb.13186⟩
Journal articles hal-02140486v1

Recombination, meiotic expression and human codon usage

F. Pouyet , Dominique Mouchiroud , L. Duret , M. Sémon
eLife, 2017, 6, pp.e27344. ⟨10.7554/eLife.27344.001⟩
Journal articles hal-01943796v1
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Less effective selection leads to larger genomes

Tristan Lefébure , Claire Morvan , Florian Malard , Clémentine François , Lara Konecny-Dupré
Genome Research, 2017, 27, pp.1016-1028. ⟨10.1101/gr.212589.116⟩
Journal articles hal-01544879v2
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How and how much does RAD-seq bias genetic diversity estimates?

M. Cariou , L. Duret , S. Charlat
BMC Evolutionary Biology, 2016, 16, pp.240. ⟨10.1186/s12862-016-0791-0⟩
Journal articles hal-02016409v1

No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes

Clémentine François , L. Duret , Laurent Simon , Florian Mermillod-Blondin , Florian Malard
Molecular Biology and Evolution, 2016, 33 (10), pp.2605-2620. ⟨10.1093/molbev/msw131⟩
Journal articles hal-01370129v1
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GC-Content evolution in bacterial genomes: The biased gene conversion hypothesis expands

Florent Lassalle , Séverine Périan , Thomas Bataillon , Xavier Nesme , L. Duret
PLoS Genetics, 2015, 11 (2), pp.1-20. ⟨10.1371/journal.pgen.1004941⟩
Journal articles hal-01198362v1
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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

Occurrence of a non deleterious gene conversion event in the BRCA1 gene

C. Tessereau , M. Leone , M. Buisson , L. Duret , O. M. Sinilnikova
Genes, Chromosomes & Cancer, 2015, 54, pp.646-52. ⟨10.1002/gcc.22278⟩
Journal articles hal-02018994v1

Optimization of multiplexed RADseq libraries using low-cost adaptors

Hélène Henri , Marie Cariou , Gabriel Terraz , Sonia Martinez , Adil El Filali
Genetica, 2015, 143 (2), pp.139-143. ⟨10.1007/s10709-015-9828-3⟩
Journal articles hal-03225202v1
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Estimation of the RNU2 macrosatellite mutation rate by BRCA1 mutation tracing

C. Tessereau , Yann Lesecque , N. Monnet , M. Buisson , L. Barjhoux
Nucleic Acids Research, 2014, 42 (14), pp.9121-30. ⟨10.1093/nar/gku639⟩
Journal articles hal-02045532v1
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The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells.

Franck Picard , Jean-Charles Cadoret , Benjamin Audit , Alain Arneodo , Adriana A. Alberti
PLoS Genetics, 2014, 10 (5), pp.e1004282. ⟨10.1371/journal.pgen.1004282⟩
Journal articles hal-00995097v1
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The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes

Y Lesecque , S. S. Glemin , N. Lartillot , D. Mouchiroud , L. Duret
PLoS Genetics, 2014, 10, pp.e1004790. ⟨10.1371/journal.pgen.1004790⟩
Journal articles hal-02369480v1

Comparative population genomics in animals uncovers the determinants of genetic diversity

Jonathan Romiguier , P Gayral , M Ballenghien , Arnaud Bernard , V Cahais
Nature, 2014, 515 (7526), pp.261-263. ⟨10.1038/nature13685⟩
Journal articles hal-01313724v1
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Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome

E. M. Kvikstad , L. Duret
Molecular Biology and Evolution, 2014, 31, pp.23-36. ⟨10.1093/molbev/mst185⟩
Journal articles hal-02046828v1

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

S. B. Montgomery , D. L. Goode , E. Kvikstad , C. A. Albers , Z. D. Zhang
Genome Research, 2013, 23, pp.749--61. ⟨10.1101/gr.148718.112⟩
Journal articles hal-02282687v1
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Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

Marie Cariou , Laurent Duret , Sylvain Charlat
Ecology and Evolution, 2013, 3 (4), pp.846-852. ⟨10.1002/ece3.512⟩
Journal articles hal-02140475v1

GC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance

Y. Lesecque , D. Mouchiroud , L. Duret
Molecular Biology and Evolution, 2013, 30, pp.1409--19. ⟨10.1093/molbev/mst056⟩
Journal articles hal-02281861v1

Eloge de l'ADN poubelle

Laurent Duret , Sylvain Charlat
Pour la science, 2013, 81, pp.10--17
Journal articles hal-02140476v1

XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells

C. Vallot , C. Huret , Yann Lesecque , A. Resch , N. Oudrhiri
Nature Genetics, 2013, 45, pp.239--41. ⟨10.1038/ng.2530⟩
Journal articles hal-02446482v1
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Genome-scale coestimation of species and gene trees.

Bastien Boussau , Gergely J Szöllosi , L. Duret , Manolo Gouy , Eric Tannier
Genome Research, 2013, 23 (2), pp.323-330. ⟨10.1101/gr.141978.112⟩
Journal articles hal-00750148v1

Evidence for Widespread GC-biased Gene Conversion in Eukaryotes

Eugénie Pessia , Alexandra Popa , Sylvain Mousset , Clément Rezvoy , Laurent Duret
Genome Biology and Evolution, 2012, 4, pp.787-794. ⟨10.1093/gbe/evs052⟩
Journal articles hal-02282748v1

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences.

Olivier Arnaiz , Nathalie Mathy , Céline Baudry , Sophie Malinsky , Jean-Marc Aury
PLoS Genetics, 2012, 8 (10), pp.e1002984. ⟨10.1371/journal.pgen.1002984⟩
Journal articles hal-00759182v1

High-quality sequence clustering guided by network topology and multiple alignment likelihood.

Vincent Miele , Simon Penel , Vincent Daubin , Franck Picard , Daniel Kahn
Bioinformatics, 2012, 28 (8), pp.1078-85. ⟨10.1093/bioinformatics/bts098⟩
Journal articles hal-00965711v1

Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

Corinne Chureau , Sophie Chantalat , Antonio Romito , Angélique Galvani , Laurent Duret
Human Molecular Genetics, 2011, 20 (4), pp.705-718. ⟨10.1093/hmg/ddq516⟩
Journal articles hal-03030487v1
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Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes.

Brian P. Cusack , Peter F. Arndt , L. Duret , Hugues Roest Crollius
PLoS Genetics, 2011, 7 (10), pp.e1002276. ⟨10.1371/journal.pgen.1002276⟩
Journal articles inserm-00711772v1
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Meiotic recombination favors the spreading of deleterious mutations in human populations

Anamaria Necsulea , L. Duret , Alexandra Popa , David N. Cooper , Peter Stentson
Human Mutation, 2011, 32 (2), pp.198-206. ⟨10.1002/humu.21407⟩
Journal articles hal-00610795v1

Ultra-fast sequence clustering from similarity networks with SiLiX

V. Miele , Simon Penel , L. Duret
BMC Bioinformatics, 2011, 12(116), pp.1-9. ⟨10.1186/1471-2105-12-116⟩
Journal articles hal-00698365v1
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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

Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

C. Chureau , S. Chantalat , A. Romito , A. Galvani , Laurent Duret
Human Molecular Genetics, 2011, 20, pp.705-718. ⟨10.1093/hmg/ddq516⟩
Journal articles hal-02299263v1

Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

J. Beisson , M. Bétermier , M-H. Bré , J. Cohen , S. Duharcourt
Emerging Model Organisms, 2010, 2010, pp.1-55
Journal articles hal-02305011v1

Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

J. Beisson , M. Bétermier , M.-H. Bré , J. Cohen , S. Duharcourt
Emerging Model Organisms, 2010, 2010(1), pp.1-55
Journal articles hal-00539398v1

Detecting positive selection within genomes: the problem of biased gene conversion

A. Ratnakumar , Sylvain Mousset , S. Glémin , J. Berglund , N. Galtier
Philosophical Transactions of the Royal Society B: Biological Sciences, 2010, 365 (1552), pp.2571-2580. ⟨10.1098/rstb.2010.0007⟩
Journal articles hal-00539495v1
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Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia.

Olivier Arnaiz , Jean-François Goût , Mireille Bétermier , Khaled Bouhouche , Jean Cohen
BMC Genomics, 2010, 11 (1), pp.547. ⟨10.1186/1471-2164-11-547⟩
Journal articles inserm-00617225v1
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The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution

Jean-François Gout , Daniel Kahn , Laurent Duret
PLoS Genetics, 2010, 6 (5), pp.e1000944. ⟨10.1371/journal.pgen.1000944⟩
Journal articles hal-00539474v2

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates

N. Galtier , L. Duret , S. Glémin , Vincent Ranwez
Trends in Genetics, 2009, 25(1), pp.1-5
Journal articles hal-00428324v1
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Databases of Homologous Gene Families for Comparative Genomics

Simon Penel , Anne-Muriel Arigon Chifolleau , Jean-François Dufayard , Anne-Sophie Sertier , Vincent Daubin
BMC Bioinformatics, 2009, 10 (Suppl.6) :S3, pp.13. ⟨10.1186/1471-2105-10-S6-S3⟩
Journal articles lirmm-00400099v1

Monoallelic expression and tissue specificity are associated with high crossover rates

A. Necşulea , M. Sémon , L. Duret , L.D. Hurst
Trends in Genetics, 2009, 25(12), pp.519-522
Journal articles hal-00539368v1

Mutation Patterns in the Human Genome:More Variable Than Expected

L. Duret
PLoS Biology, 2009, 7(2) e1000028, pp.803-806
Journal articles hal-00428326v1

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

L. Duret , N. Galtier
Annual Review of Genomics and Human Genetics, 2009, 10, pp.285-311
Journal articles hal-00428399v1

The relationship between DNA replication and human genome organization.

Anamaria Necsulea , Claire Guillet , Jean-Charles Cadoret , Marie-Noëlle Prioleau , L. Duret
Molecular Biology and Evolution, 2009, 26 (4), pp.729-741. ⟨10.1093/molbev/msn303⟩
Journal articles hal-00353551v1

L’évolution des chromosomes sexuels humains

Gabriel Marais , L. Duret
Biofutur, 2009, 304, pp.40-41
Journal articles hal-00539330v1

Differential retention of metabolic genes following whole-genome duplication

Jean-François Gout , Laurent Duret , Daniel Kahn
Molecular Biology and Evolution, 2009, 26 (5), pp.1067-1072. ⟨10.1093/molbev/msp026⟩
Journal articles hal-00428358v2

Comment on “Human-Specific Gain of Function in a Developmental Enhancer”

L. Duret , N. Galtier
Science, 2009, 323(5915), pp.714-715
Journal articles hal-00428327v1

Biased Gene Conversion and its Impact on Human Genome Evolution

N. Galtier , L. Duret
incollection, 2008, --, pp.273-277
Journal articles hal-00428241v1
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Translational control of intron splicing in eukaryotes

Olivier Jaillon , Khaled Bouhouche , Jean-François Gout , Jean-Marc Aury , Benjamin Noel
Nature, 2008, 451 (7176), pp.359-362. ⟨10.1038/nature06495⟩
Journal articles cea-00945555v1
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Genome-wide studies highlight indirect links between human replication origins and gene regulation.

Jean-Charles Cadoret , Françoise Meisch , Vahideh Hassan-Zadeh , Isabelle Luyten , Claire Guillet
Proceedings of the National Academy of Sciences of the United States of America, 2008, 105 (41), pp.15837-42. ⟨10.1073/pnas.0805208105⟩
Journal articles hal-00332341v1

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline

L. Duret , J. Cohen , C. Jubin , P. Dessen , J.-F. Gout
Genome Research, 2008, 18, pp.585-596. ⟨10.1101/gr.074534.107⟩
Journal articles hal-00428190v1

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

A. Studer , Simon Penel , L. Duret , M. Robinson-Rechavi
Genome Research, 2008, 18, pp.1393-1402
Journal articles hal-00428199v1

ISG20L2, a novel vertebrate nucleolar exoribonuclease involved in Ribosome biogenesis.

Yohann Couté , Karine Kindbeiter , Stéphane Belin , Régis Dieckmann , L. Duret
Molecular and Cellular Proteomics, 2008, 7, epub ahead of print. ⟨10.1074/mcp.M700510-MCP200⟩
Journal articles hal-00196384v1

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline.

L. Duret , Jean Cohen , Claire Jubin , Philippe Dessen , Jean-François Goût
Genome Research, 2008, 18 (4), pp.585-96. ⟨10.1101/gr.074534.107⟩
Journal articles hal-00282468v1

The Impact of Recombination on Nucleotide Substitutions in the Human Genome

L. Duret , P.F. Arndt
PLoS Genetics, 2008, 4, pp.1-19
Journal articles hal-00428172v1

Neutral Theory: The Null Hypothesis of Molecular Evolution

L. Duret
Nature Education, 2008, 1 (1), pp.803-806
Journal articles hal-00428242v1

Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution

Nicolas Galtier , L. Duret
Trends in Genetics, 2007, 23 (6), pp.273-277. ⟨10.1016/j.tig.2007.03.011⟩
Journal articles halsde-00424420v1

Unexpected observations after mapping LongSAGE tags to the human genome

C. Keime , M. Sémon , Dominique Mouchiroud , L. Duret , Olivier Gandrillon
BMC Bioinformatics, 2007, 8, pp.1-11
Journal articles hal-00434613v1

Identification and characterization of human Mex-3 proteins, a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies.

Karine Buchet-Poyau , Julien Courchet , Hervé Le Hir , Bertrand Séraphin , Jean-Yves Scoazec
Nucleic Acids Research, 2007, 35 (4), pp.1289-300. ⟨10.1093/nar/gkm016⟩
Journal articles hal-00167447v1

Unexpected observations after mapping LongSAGE tags to the human genome.

Céline Keime , Marie Sémon , Dominique Mouchiroud , Laurent Duret , Olivier Gandrillon
BMC Bioinformatics, 2007, 8, pp.154. ⟨10.1186/1471-2105-8-154⟩
Journal articles hal-00193777v1

GC Content Evolution of the Human and Mouse Genomes : Insights from the Study of Processed Pseudogenes in Regions of Different Recombination Rates.

A. Khelifi , J. Meunier , L. Duret , Dominique Mouchiroud
Journal of Molecular Evolution, 2006, 62, pp.745-752
Journal articles hal-00427980v1

Insights into social insects from the genome of the honeybee Apis mellifera

G.M. Weinstock , G.E. Robinson , R.A. Gibbs , K.C. Worley , J.D. Evans
Nature, 2006, 443, pp.931-949
Journal articles hal-00428044v1

Global trends of whole genome duplications revealed by the genome sequence of the ciliate Paramecium tetraurelia

Jean-Marc Aury , Olivier Jaillon , * Laurent Duret , Benjamin Noel , Claire Jubin
Nature, 2006, 444 (7116), pp.171-178. ⟨10.1038/nature05230⟩
Journal articles hal-00090904v1

The GC Content of Primates and Rodents Genomes Is Not at Equilibrium : a Reply to Antezana

L. Duret
Journal of Molecular Evolution, 2006, --, pp.803-806
Journal articles hal-00427950v1

No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans

M. Sémon , J.R. Lobry , L. Duret
Molecular Biology and Evolution, 2006, 23, pp.523-529
Journal articles hal-00428013v1

The Xist RNA Gene Evolved in Eutherians by Pseudogenization of a Protein-Coding Gene

L. Duret , C. Chureau , S. Samain , J. Weissenbach , P. Avner
Science, 2006, 312, pp.1653-1655
Journal articles hal-00427928v1

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.

Jean-Marc Aury , Olivier Jaillon , L. Duret , Benjamin Noel , Claire Jubin
Nature, 2006, 444 (7116), pp.171-8. ⟨10.1038/nature05230⟩
Journal articles hal-00132091v1

Evolutionary origin and maintenance of coexpressed gene clusters in mammals.

M. Sémon , L. Duret
Molecular Biology and Evolution, 2006, 23, pp.1715-1723
Journal articles hal-00428012v1

A new perspective on isochore evolution

Laurent Duret , Adam Eyre-Walker , Nicolas Galtier
Gene, 2006, 385, pp.71-74. ⟨10.1016/j.gene.2006.04.030⟩
Journal articles halsde-00340990v1

HOPPSIGEN: a database of human and mouse processed pseudogenes.

A. Khelifi , L. Duret , Dominique Mouchiroud
Nucleic Acids Research, 2005, 33 (Database issue), pp.D59-66. ⟨10.1093/nar/gki084⟩
Journal articles hal-00427774v1

Homology-dependent methylation in primate repetitive DNA.

J. Meunier , A. Khelifi , V. Navratil , L. Duret
Proceedings of the National Academy of Sciences of the United States of America, 2005, 102 (15), pp.5471-6. ⟨10.1073/pnas.0408986102⟩
Journal articles hal-00427789v1

Les trésors cachés du génome humain

L. Duret
Pour la science, 2005, --, pp.16-21
Journal articles hal-00427745v1

Natural history of the ERVWE1 endogenous retroviral locus

B. Bonnaud , J. Beliaeff , O. Bouton , G. Oriol , L. Duret
Retrovirology, 2005, 2, pp.1-7
Journal articles hal-00427715v1

Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance

M. Sémon , Dominique Mouchiroud , L. Duret
Human Molecular Genetics, 2005, 14, pp.421-427
Journal articles hal-00427850v1

Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.

Jean-François Dufayard , L. Duret , Simon Penel , Manolo Gouy , F. Rechenmann
Bioinformatics, 2005, 21 (11), pp.2596-603. ⟨10.1093/bioinformatics/bti325⟩
Journal articles hal-00427861v1

Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.

P. Kersey , L. Bower , L. Morris , A. Horne , R. Petryszak
Nucleic Acids Research, 2005, 33 (Database issue), pp.D297-302. ⟨10.1093/nar/gki039⟩
Journal articles hal-00427773v1

Natural history of the ERVWE 1 endogenous retroviral locus.

Bertrand Bonnaud , Jean Beliaeff , Olivier Bouton , Guy Oriol , Laurent Duret
Retrovirology, 2005, 2:57, pp.1 - 7. ⟨10.1186/1742-4692-2-57⟩
Journal articles hal-00021661v1

Bioinformatics with a French accent

L.D. Hurst , L. Duret
Genome Biology, 2005, 6, pp.349.1-349.3
Journal articles hal-00427767v1

Polymorphix: a sequence polymorphism database

E. Bazin , L. Duret , Simon Penel , N. Galtier
Nucleic Acids Research, 2005, 33, pp.481-484
Journal articles hal-00427707v1

Identitag a relational database for SAGE tag identification and interspecies comparison of SAGE libraries

C. Keime , F. Damiola , Dominique Mouchiroud , L. Duret , Olivier Gandrillon
BMC Bioinformatics, 2004, 5, pp.1-12
Journal articles hal-00427517v1

Evidence that functional transcription units cover at least half of the human genome

M. Sémon , L. Duret
Trends in Genetics, 2004, 20, pp.229-232
Journal articles hal-00427647v1

The Decline of Isochores in Mammals: An Assessment of the GC Content Variation Along the Mammalian Phylogeny

E. Belle , L. Duret , N. Galtier , A. Eyre-Walker
Journal of Molecular Evolution, 2004, 58, pp.653-660
Journal articles hal-00427539v1

Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries.

Céline Keime , Francesca Damiola , Dominique Mouchiroud , Laurent Duret , Olivier Gandrillon
BMC Bioinformatics, 2004, 5, pp.143. ⟨10.1186/1471-2105-5-143⟩
Journal articles hal-00193784v1

The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology

Frédéric Mallet , O. Bouton , S. Prudhomme , V. Cheynet , G. Oriol
Proceedings of the National Academy of Sciences of the United States of America, 2004, 101, pp.1731-1736
Journal articles hal-00427686v1
Image document

Grid as a bioinformatic tool

N. Jacq , Christophe Blanchet , C. Combet , E. Cornillot , L. Duret
Parallel Computing, 2004, 30, pp.1093-1107. ⟨10.1016/j.parco.2004.07.013⟩
Journal articles in2p3-00023218v1

Physical and transcript map of the autosomal dominant colobomatous microphthalmia locus on chromosome 15q12-q15 and refinement to a 4.4 Mb region.

Laetitia Michon , Laurette Morlé , Muriel Bozon , L. Duret , Jean-Christophe Zech
European Journal of Human Genetics, 2004, 12 (7), pp.574-8. ⟨10.1038/sj.ejhg.5201197⟩
Journal articles hal-00425119v1

Grid as a bioinformatic tool

N. Jacq , Christophe Blanchet , C. Combet , E. Cornillot , L. Duret
Parallel Computing, 2004, 30, pp.1093-1107
Journal articles hal-00427599v1

ROSO : Research on Optimized Oligonucleotide Probes for Microarrays

N. Reymond , H. Charles , L. Duret , Federica Calevro , G. Beslon
Bioinformatics, 2004, 20, pp.271-273
Journal articles hal-00427641v1

Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries.

C. Keime , F. Damiola , D. Mouchiroud , L. Duret , O. Gandrillon
BMC Bioinformatics, 2004, 5, pp.143
Journal articles hal-00124096v1

Recombination drives the evolution of GC-content in the human genome

J. Meunier , L. Duret
Molecular Biology and Evolution, 2004, 21, pp.984-990
Journal articles hal-00427624v1

Evidence of Selection on the Domesticated ERVWE1 env Retroviral Element Involved in Placentation

B. Bonnaud , O. Bouton , G. Oriol , V. Cheynet , L. Duret
Molecular Biology and Evolution, 2004, 21, pp.1895-1901
Journal articles hal-00427546v1

Physical and transcript map of the autosomal dominant colobomatous microphthalmia locus on chromosome 15q12-q15 and refinement to a 4.4 Mb region.

Laurent Michon , L. Morle , M. Bozon , L. Duret , Zech J. C.
European Journal of Human Genetics, 2004, 12, pp.574-578
Journal articles hal-00161402v1

Grid as a bioinformatic tool

N. Jacq , Christophe Blanchet , C. Combet , E. Cornillot , L. Duret
Parallel Computing, 2004, 30, pp.1093-1107
Journal articles hal-00314551v1

Patterns of selection against transposons inferred from the distribution of Tc1 Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans

C. Rizzon , E. Martin , Gabriel Marais , L. Duret , L. Segalat
Genetics, 2003, 165, pp.1127-1135
Journal articles hal-00427476v1

Placenta-Specific INSL4 Expression Is Mediated by a Human Endogenous Retrovirus Element

I. Bièche , A. Laurent , I. Laurendeau , L. Duret , Y. Giovangrandi
Biology of Reproduction, 2003, 68, pp.1422-1429
Journal articles hal-00427363v1

Neutral effect of recombination on base composition in Drosophila

Gabriel Marais , Dominique Mouchiroud , L. Duret
Genetical Research, 2003, 81, pp.79-89
Journal articles hal-00427447v1

Patterns of selection against transposons inferred from the distribution of Tc1, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans.

Carène Rizzon , Edwige Martin , Gabriel Marais , Laurent Duret , Laurent Ségalat
Genetics, 2003, 165 (3), pp.1127-35
Journal articles hal-00194461v1

Subcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form

O. Assossou , F. Besson , J.P. Rouault , F. Persat , C. Brisson
FEMS Microbiology Letters, 2003, 224, pp.161-168. ⟨10.1016/S0378-1097(03)00479-8⟩
Journal articles hal-00427496v1

Patterns of selection against transposons inferred from the distribution of Tcl, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans.

C. Rizzon , E. Martin , G. Marais , L. Duret , L. Segalat
Genetics, 2003, 165, pp.1127-1135
Journal articles hal-00144031v1

Integrated databanks access and sequence/structure analysis services at the PBIL.

G. Perriere , C. Combet , Simon Penel , Christophe Blanchet , J. Thioulouse
Nucleic Acids Research, 2003, 31 (13), pp.3393-3399. ⟨10.1093/nar/gkg530⟩
Journal articles hal-00313743v1

Subcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form

Jean-Pierre Rouault , Olga Assossou , Franã§oise Besson , Florence Persat , Christine Brisson
FEMS Microbiology Letters, 2003, 224 (2), pp.161-168. ⟨10.1016/S0378-1097(03)00479-8⟩
Journal articles hal-02998536v1

Detecting genomic features under weak selective pressure: the example of codon usage in animals and plants

L. Duret
Bioinformatics, 2002, 18, pp.S91-S91
Journal articles hal-00427268v1

Expected Relationship Between the Silent Substitution Rate and the GC Content: Implications for the Evolution of Isochores

G. Piganeau , Dominique Mouchiroud , L. Duret , Christian Gautier
Journal of Molecular Evolution, 2002, 54, pp.129-133
Journal articles hal-00427292v1

Comparative sequence analysis of the X-inactivation center region in mouse human and bovine

C. Chureau , M. Prissette , A. Bourdet , Valérie Barbe , Laurence Cattolico
Genome Research, 2002, 12, pp.894-908
Journal articles hal-00427257v1

Vanishing GC-Rich Isochores in Mammalian Genomes

L. Duret , M. Sémon , G. Piganeau , Dominique Mouchiroud , N. Galtier
Genetics, 2002, 162, pp.1837-1848
Journal articles hal-00427269v1

Evolution of synonymous codon usage in metazoans

L. Duret
Current Opinion in Genetics and Development, 2002, 12, pp.640-649
Journal articles hal-00427267v1

Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine.

C. Chureau , M. Prissette , A. Bourdet , Valérie Barbe , L. Cattolico
Genome Research, 2002, 12, pp.894-908
Journal articles hal-02672161v1

Why do genes have introns? Recombination might add a new piece to the puzzle

L. Duret
Trends in Genetics, 2001, 17, pp.172-175
Journal articles hal-00427168v1

Organisation Fonctionnement et Evolution des Génomes de Métazoaires : Mais où est donc passée la sélection naturelle ?

L. Duret
incollection, 2001, --, pp.287-289
Journal articles hal-00427170v1

Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes

Gabriel Marais , Dominique Mouchiroud , L. Duret
Proceedings of the National Academy of Sciences of the United States of America, 2001, 98, pp.5688-5692
Journal articles hal-00427184v1

Determinants of CpG islands: expression in early embryo and isochore structure

L. Ponger , L. Duret , Dominique Mouchiroud
Genome Research, 2001, 11, pp.1854-1860
Journal articles hal-00427189v1

The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution

L. Duret , L.D. Hurst
Molecular Biology and Evolution, 2001, 18, pp.757-762
Journal articles hal-00427169v1

Synonymous codon usage accuracy of translation and gene length in Caenorhabditis elegans

Gabriel Marais , L. Duret
Journal of Molecular Evolution, 2001, 52, pp.275-280
Journal articles hal-00427183v1

GC-content evolution in mammalian genomes: the biased gene conversion hypothesis

N. Galtier , G. Piganeau , Dominique Mouchiroud , L. Duret
Genetics, 2001, 159, pp.907-911
Journal articles hal-00427173v1

Plant Physiol.A Medicago truncatula homoglutathione synthetase is derived from glutathione synthetase by gene duplication

P. Frendo , M.J. Jimenez , C. Mathieu , L. Duret , D. Gallesi
Plant Physiology, 2001, 126, pp.1706-1715
Journal articles hal-00427171v1

Nature and structure of human genes that generate retropseudogenes

I. Goncalves , L. Duret , Dominique Mouchiroud
Genome Research, 2000, 10, pp.672-678
Journal articles hal-00427085v1

Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate

L. Duret , Dominique Mouchiroud
Molecular Biology and Evolution, 2000, 17, pp.68-74
Journal articles hal-00427068v1

The covariation between TpA deficiency CpG deficiency and G+C content of human isochores is due to a mathematical artifact

L. Duret , N. Galtier
Molecular Biology and Evolution, 2000, 17, pp.1620-1625
Journal articles hal-00427077v1

HOBACGEN: database system for comparative genomics in bacteria

G. Perrière , L. Duret , Manolo Gouy
Genome Research, 2000, 10, pp.379-385. ⟨10.1101/gr.10.3.379⟩
Journal articles hal-00427099v1

Identification and molecular analysis of BANP

Anne-Marie Birot , Laurent Duret , Laurent Bartholin , Bénédicte Santalucia , Isabelle Tigaud
Gene, 2000, 253 (2), pp.189-196. ⟨10.1016/S0378-1119(00)00244-4⟩
Journal articles hal-02998585v1

tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes

L. Duret
Trends in Genetics, 2000, 16, pp.287-289
Journal articles hal-00427076v1

Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans

L. Duret , Gabriel Marais , C. Biémont
Genetics, 2000, 156, pp.1661-1669
Journal articles hal-00427072v1

Chromosomal distribution and coding capacity of the human endogenous retrovirus HERV-W family

C. Voisset , O. Bouton , F. Bedin , L. Duret , B. Mandrand
AIDS Research and Human Retroviruses, 2000, 16, pp.731-740
Journal articles hal-00427112v1

Use of a TT virus ORF1 recombinant protein to detect anti-TT virus antibodies in human sera

C. Ott , L. Duret , I. Chemin , C. Trepo , B. Mandrand
Journal of General Virology, 2000, 81, pp.2949-2958
Journal articles hal-00427092v1

Multiple alignments for structural functional or phylogenetic analyses of homologous sequences

L. Duret , S. Abdeddaim
incollection, 2000, --, pp.51-76
Journal articles hal-00427048v1

Expression pattern and surprisingly gene length shape codon usage in Caenorhabditis Drosophila and Arabidopsis

L. Duret , Dominique Mouchiroud
Proceedings of the National Academy of Sciences of the United States of America, 1999, 96, pp.4482-4487
Journal articles hal-00428427v1

Molecular characterization and placental expression of HERV-W a new human endogenous retrovirus family

J.L. Blond , F. Beseme , L. Duret , O. Bouton , F. Bedin
Journal of Virology, 1999, 73, pp.1175-1185
Journal articles hal-00428437v1

Regulation of dauer larva development in Caenorhabditis elegans by daf-18, a homologue of the tumour suppressor PTEN

Jean-Pierre Rouault , Patricia Kuwabara , Olga Sinilnikova , Laurent Duret , Danielle Thierry-Mieg
Current Biology - CB, 1999, 9 (6), pp.329-334. ⟨10.1016/S0960-9822(99)80143-2⟩
Journal articles hal-02998593v1

Human and nematode orthologs--lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis elegans

S.J. Wheelan , M.S. Boguski , L. Duret , W. Makalowski
Gene, 1999, 238, pp.163-170
Journal articles hal-00428467v1

Highly conserved RNA sequences that are sensors of environmental stress

A. Spicher , O.M. Guicherit , L. Duret , A. Aslanian , E.M. Sanjines
Molecular and Cellular Biology, 1998, 18, pp.7371-7382
Journal articles hal-00428502v1

New insulin-like proteins with atypical disulfide bond pattern characterized in Caenorhabditis elegans by comparative sequence analysis and homology modeling

L. Duret , N. Guex , M.C. Peitsch , A. Bairoch
Genome Research, 1998, 8, pp.348-353
Journal articles hal-00428485v1

Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata

D. Graur , Manolo Gouy , L. Duret
Molecular Phylogenetics and Evolution, 1997, 7 (2), pp.195-200. ⟨10.1006/mpev.1996.0391⟩
Journal articles hal-00434984v1

Cloning and characterization of a gene encoding a novel immunodominant antigen of Trypanosoma cruzi

M. Lesenechal , L. Duret , M.I. Cano , R.A. Mortara , M. Jolivet
Molecular and Biochemical Parasitology, 1997, 87, pp.193-204
Journal articles hal-00434988v1

Searching for regulatory elements in human noncoding sequences

L. Duret , P. Bucher
Current Opinion in Structural Biology, 1997, 7, pp.399-406
Journal articles hal-00434977v1

Cloning of the mouse BTG3 gene and definition of a new gene family (the BTG family) involved in the negative control of the cell cycle

F Guéhenneux , L. Duret , Mb Callanan , R Bouhas , S Hayette
Leukemia, 1997, 11 (3), pp.370-375. ⟨10.1038/sj.leu.2400599⟩
Journal articles hal-02998613v1

LALNVIEW: a graphical viewer for pairwise sequence alignments

L. Duret , E. Gasteiger , G. Perrière
Computer Applications in the Biosciences, 1996, 12, pp.507-510
Journal articles hal-00435026v1

Phylogenetic position of the order Lagomorpha (rabbits hares and allies)

D. Graur , L. Duret , Manolo Gouy
Nature, 1996, 379, pp.333-335. ⟨10.1038/379333a0⟩
Journal articles hal-00435019v1

Isolation and characterization of a cDNA encoding a chicken actin-like protein

J.J. Michaille , Manolo Gouy , Simon Blanchet , L. Duret
Gene, 1995, 154 (2), pp.205-209. ⟨10.1016/0378-1119(94)00865-P⟩
Journal articles hal-00698055v1

Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores

L. Duret , Dominique Mouchiroud , Christian Gautier
Journal of Molecular Evolution, 1995, 40, pp.308-317
Journal articles hal-00698070v1

Rearrangement of CCND1 (BCL1/PRAD1) 3' untranslated region in mantle-cell lymphomas and t(11q13)-associated leukemias

R. Rimokh , F. Berger , C. Bastard , B. Klein , M. French
Blood, 1994, 83, pp.3689-3696
Journal articles hal-00698183v1

HOVERGEN: a database of homologous vertebrate genes

L. Duret , Dominique Mouchiroud , Manolo Gouy
Nucleic Acids Research, 1994, 22 (12), pp.2360-2365. ⟨10.1093/nar/22.12.2360⟩
Journal articles hal-00698069v1

Sequence analysis reveals that the BTG1 anti-proliferative gene is conserved throughout evolution in its coding and 3' non-coding regions

Jean-Pierre Rouault , J.P. Rouault , C. Samarut , L. Duret , C. Tessa
Gene, 1993, 129 (2), pp.303-306. ⟨10.1016/0378-1119(93)90284-A⟩
Journal articles hal-02998651v1

BTG1, a member of a new family of antiproliferative genes.

Jean-Pierre Rouault , R. Rimokh , C. Tessa , G. Paranhos , M. Ffrench
EMBO Journal, 1992, 11 (4), pp.1663-1670. ⟨10.1002/j.1460-2075.1992.tb05213.x⟩
Journal articles hal-02998663v1
Image document

XACT, a long non-coding transcript coating the active X chromosome in human pluripotent cells

Céline Vallot , Christophe Huret , Yann Lesecque , Alissa Resch , Noufϊssa Oudrhiri
Epigenetics and Chromatin: Interactions and processes, Mar 2013, Boston, MA, United States. pp.O33, ⟨10.1186/1756-8935-6-S1-O33⟩
Conference papers inserm-00801773v1

ROSO: A software to search optimized oligonucleotide probes for microarrays

Hubert Charles , Nancie Reymond , Guillaume Beslon , Laurent Duret , Jean-Michel Fayard
COST853: Agricultural Biomarkers for Array-Technology, Sep 2002, Waedenswill, Switzerland
Conference papers hal-03506465v1

EuGene an eurocaryotic gene finder that combines several sources of evidence

Thomas Schiex , A. Moisan , L. Duret , Pierre Rouzé
Journées ouvertes biologie informatique mathématiques, May 2000, Montpellier, France
Conference papers hal-02770502v1

ROSO: a software to search optimized oligonucleotide probes for microarrays

Nancie Reymond , Hubert Charles , Guillaume Beslon , Laurent Duret , Jean-Michel Fayard
14. Rencontres Régionales de la Recherche, Oct 2003, Saint-Etienne, France
Conference poster hal-03506598v1

ROSO : A Software to Search Optimized Oligonucleotide Probes for Microarrays

Nancie Reymond , Hubert Charles , Guillaume Beslon , Laurent Duret , Jean-Michel Fayard
10. International Conference on Intelligent Systems for Molecular Biology (ISMB), Aug 2002, Edmonton, Canada
Conference poster hal-03506483v1

Modélisation des systèmes biologiques, bioinformatique

Olivier Gascuel , P. Benas , C. Brun , D. Burnouf , Alexandre de Brevern
Rapport de conjoncture 2010 du Comité national de la recherche scientifique, CNRS Editions, chapitre 43, 845-858, 2011, 978-2-271-07263-4
Book sections hal-00799641v1

Evolution Moléculaire

L. Duret , T. Bataillon , N. Bierne , Vincent Daubin , J. Dutheil
sous la direction de Frédéric Thomas; Thierry Lefèvre; Michel Raymond. Biologie évolutive, De Boeck, pp.114-173, 2010, 978-2-8041-0161-9
Book sections hal-00539271v1

HOVERGEN: comparative analysis of homologous vertebrate genes

L. Duret , G. Perrière , Manolo Gouy
Letovsky S. Bioinformatics: databases and systems, Springer, pp.21-35, 1999, 978-0-7923-8573-8. ⟨10.1007/0-306-46903-0_3⟩
Book sections hal-00428428v1