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UMR CNRS 5558 - LBBE "Biométrie et Biologie Évolutive" UCB Lyon 1 - Bât. Grégor Mendel 43 bd du 11 novembre 1918 69622 VILLEURBANNE cedex
- Research
- +Research focus : Evolutionary Genomics & Bioinformatics -Research focus : Evolutionary Genomics & Bioinformatics
Research Interests: "Nothing in a genome makes sense, except in the light of molecular evolution".
My principle research interest is to understand the processes that drive genome evolution. I try to analyze the relative contribution of selection, mutation, drift and biased gene conversion (BGC) to the evolution of genomic features.
During my PhD and my postdoc I studied the evolution of non-coding sequences in vertebrate genomes. I discovered that many vertebrate genes contain long highly conserved sequences in their non-coding regions (Ref,Ref). I also started studying the isochore organization of vertebrate genomes. During the last 10 years, we found strong evidence that the evolution of these peculiar genomic landscapes is the consequence of recombination, via the BGC process (Ref,Ref,Ref). We also discovered that this BGC process interferes with selection, and can drive the fixation of deleterious mutations (Ref,Ref). We also showed that this process can confound the tests that were developed to detect selection within genomes (Ref,Ref).
I am also interested in studying the constraints imposed by gene expression on gene evolution. We notably showed that gene expression level was an important determinant of the rate of protein sequence evolution (Ref). We recently found that the rate of gene losses after whole genome duplications was also strongly dependent on gene expression levels (Ref). We proposed a model, based on the observation that translation is a costly process, that can explain why expression level affects both the selective constraints on gene dosage and on the encoded proteins (Ref). I also contributed to several analyses showing that the cost of expression also imposes constraints on splicing accuracy (Ref), and translation efficiency (Ref,Ref).
I also contributed to understanding the evolution of new genes, e.g. by genome duplication (Ref), or by domestication of viral elements (Ref). I notably discovered that the Xist non-coding RNA, which is involved in X chromosome inactivation in placental mammals, evolved by pseudogenization of a protein-coding gene (Ref)..
Publications
For a list of representative publications (and PDFs), click HERE.
+Publications -Publications
article :
Diagouraga B, Clement JAJ, Duret L, Kadlec J, De Massy B, Baudat F (2018)
PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites, Molecular cell, vol. 69 pp.853-865.
Galtier N, Roux C, Rousselle M, Romiguier J, Figuet E, Glémin S, Bierne N, Duret L (2018)
Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection Effective Population Size and GC-Biased Gene Conversion, Molecular Biology and Evolution, vol. 35 pp.1092-1103.
Guéguen L, Duret L (2018)
Unbiased estimate of synonymous and non-synonymous substitution rates with non-stationary base composition, Molecular biology and evolution, vol. 35 pp.734-742.
Cariou M, Duret L, Charlat S (2017)
The global impact of Wolbachia on mitochondrial diversity and evolution, Journal of Evolutionary Biology, vol. 30 pp.2204-2210.
Grey C, Clement JA, Buard J, Leblanc B, Gut I, Gut M, Duret L, de Massy B (2017)
In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites, Genome research, vol. 27 pp.580-590.
Latrille T, Duret L, Lartillot N (2017)
The Red Queen model of recombination hot-spot evolution: a theoretical investigation, Philosophical transactions of the Royal Society B Biological sciences, vol. 372 pp.20160463-20160463.
Lefebure T, Morvan C, Malard F, Francois C, Konecny-Dupre L, Gueguen L, Weiss-Gayet M, Seguin-Orlando A, Ermini L, Sarkissian C, Charrier N P, Eme D, Mermillod-Blondin F, Duret L, Vieira C, Orlando L, Douady CJ (2017)
Less effective selection leads to larger genomes, Genome research, vol. 27 pp.1016-1028.
Pouyet F, Mouchiroud D, Duret L, Sémon M (2017)
Recombination meiotic expression and human codon usage, eLife, vol. 6 pp.e27344-e27344.
Saudemont B, Popa A, Parmley JL, Rocher V, Blugeon C, Necsulea A, Meyer E, Duret L (2017)
The fitness cost of mis-splicing is the main determinant of alternative splicing patterns, Genome biology, vol. 18 pp.208-208.
Cariou M, Duret L, Charlat S (2016)
How and how much does RAD-seq bias genetic diversity estimates?, BMC evolutionary biology, vol. 16 pp.240-240.
Francois CM, Duret L, Simon L, Mermillod-Blondin F, Malard F, Konecny-Dupre L, Planel R, Penel S, Douady CJ, Lefebure T (2016)
No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes, Molecular Biology and Evolution, vol. 33 pp.2605-20.
Glemin S, Arndt P F, Messer P W, Petrov D, Galtier N, Duret L (2015)
Quantification of GC-biased gene conversion in the human genome, Genome research, vol. 25 pp.1215-28.
Henri H, Cariou M, Terraz G, Martinez S, El Filali A, Veyssiere M, Duret L, Charlat S (2015)
Optimization of multiplexed RADseq libraries using low-cost adaptors, Genetica, vol. 143 pp.139-43.
Lassalle F, Perian S, Bataillon T, Nesme X, Duret L, Daubin V (2015)
GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands, PLoS Genetics, vol. 11 pp.e1004941-e1004941.
Tessereau C, Leone M, Buisson M, Duret L, Sinilnikova OM, Mazoyer S (2015)
Occurrence of a non deleterious gene conversion event in the BRCA1 gene, Genes chromosomes & cancer, vol. 54 pp.646-52.
Kvikstad E M, Duret L (2014)
Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome, Molecular biology and evolution, vol. 31 pp.23-36.
Lesecque Y, Glemin S, Lartillot N, Mouchiroud D, Duret L (2014)
The red queen model of recombination hotspots evolution in the light of archaic and modern human genomes, PLoS genetics, vol. 10 pp.e1004790-e1004790.
Picard F, Cadoret J C, Audit B, Arneodo A, Alberti A, Battail C, Duret L, Prioleau M N (2014)
The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells, PLoS genetics, vol. 10 pp.e1004282-e1004282.
Romiguier J, Gayral P, Ballenghien M, Bernard A, Cahais V, Chenuil A, Chiari Y, Dernat R, Duret L, Faivre N, Loire E, Lourenco J M, Nabholz B, Roux C, Tsagkogeorga G, Weber A A, Weinert L A, Belkhir K, Bierne N, Glemin S, Galtier N (2014)
Comparative population genomics in animals uncovers the determinants of genetic diversity, Nature, vol. 515 pp.261-3.
Tessereau C, Lesecque Y, Monnet N, Buisson M, Barjhoux L, Leone M, Feng B, Goldgar D E, Sinilnikova O M, Mousset S, Duret L, Mazoyer S (2014)
Estimation of the RNU2 macrosatellite mutation rate by BRCA1 mutation tracing, Nucleic Acids Research, vol. 42 pp.9121-30.
Boussau B, Szollosi GJ, Duret L, Gouy M, Tannier E, Daubin V (2013)
Genome-scale coestimation of species and gene trees, Genome Research, vol. 23 pp.323-30.
Cariou M, Duret L, Charlat S (2013)
Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization, Ecology and Evolution, vol. 3 pp.846-852.
Duret L, Charlat S (2013)
Eloge de l’ADN poubelle, Pour la science, vol. 81 pp.10-17.
Lesecque Y, Mouchiroud D, Duret L (2013)
GC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance, Molecular biology and evolution, vol. 30 pp.1409-19.
Montgomery S B, Goode D L, Kvikstad E, Albers C A, Zhang Z D, Mu X J, Ananda G, Howie B, Karczewski K J, Smith K S, Anaya V, Richardson R, Davis J, MacArthur D G, Sidow A, Duret L, Gerstein M, Makova K D, Marchini J, McVean G, Lunter G (2013)
The origin evolution and functional impact of short insertion-deletion variants identified in 179 human genomes, Genome Research, vol. 23 pp.749-61.
Vallot C, Huret C, Lesecque Y, Resch A, Oudrhiri N, Bennaceur-Griscelli A, Duret L, Rougeulle C (2013)
XACT a long noncoding transcript coating the active X chromosome in human pluripotent cells, Nature Genetics, vol. 45 pp.239-41.
Arnaiz O, Mathy N, Baudry C, Malinsky S, Aury JM, Denby Wilkes C, Garnier O, Labadie K, Lauderdale BE, Le Mouël A, Marmignon A, Nowacki M, Poulain J, Prajer M, Wincker P, Meyer E, Duharcourt S, Duret L, Bétermier M, Sperling L (2012)
The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences, PLoS Genetics, vol. 8 pp.e1002984-e1002984.
Miele V, Penel S, Daubin V, Picard F, Kahn D, Duret L (2012)
High-quality sequence clustering guided by network topology and multiple alignment likelihood, Bioinformatics, vol. 28 pp.1078-1085.
Pessia E, Popa A, Mousset S, Rezvoy C, Duret L, Marais G (2012)
Evidence for Widespread GC-biased Gene Conversion in Eukaryotes, Genome Biology and Evolution, vol. 4 pp.787-794.
Chureau C, Chantalat S, Romito A, Galvani A, Duret L, Avner P, Rougeulle C (2011)
Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region, Human Molecular Genetics, vol. 20 pp.705-718.
Cusack BP, Arndt PF, Duret L, Roest Crollius H (2011)
Preventing Dangerous Nonsense: Selection for Robustness to Transcriptional Error in Human Genes, PLoS Genetics, vol. 7 pp.e1002276-e1002276.
Miele V, Penel S, Duret L (2011)
Ultra-fast sequence clustering from similarity networks with SiLiX, BMC Bioinformatics, vol. 12 pp.116-116.
Necşulea A, Popa A, Cooper DN, Stenson PD, Mouchiroud D, Gautier C, Duret L (2011)
Meiotic Recombination favors the spreading of deleterious mutations in human populations, Human Mutation, vol. 32 pp.198-206.
Rouxel T, Grandaubert J, Hane JK, Hoede C, Van de Wouw AP, Couloux A, Dominguez V, Antouhard V, Bally P, Bourras S, Cozijnsen AJ, Ciuffetti LM, Degrave A, Dilmaghani A, Duret L, Fudal I, Goodwin SB, Gout L, Glaser N, Linglin J, GH Keman, Lapalu N, Lawrence CB, May K, Meyer M, Ollivier B, Poulain J, Schoch CL, Simon A, Spatafora JW, Stachoviak A, Turgeon BG, Tyler BM, Vincent D, Weissenbach J, Amselem J, Quesneville H, Oliver RP, Wincker P, Balesdent MH, Howlett BJ (2011)
Effector diversification with in compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations, Nature communications, vol. 2 pp.1-10.
Arnaiz O, Gout J-F, Betermier M, Bouhouche K, Cohen J, Duret L, Kapusta A, Meyer E, Sperling L (2010)
Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia, BMC Genomics, vol. 11 pp.547-547.
Beisson J, Bétermier M, Bré M-H, Cohen J, Duharcourt S, Duret L, Kung C, Malinsky S, Meyer E, Preer Jr JR, Sperling L (2010)
Paramecium tetraurelia: The Renaissance of an Early Unicellular Model, Emerging Model Organisms, vol. 2010 pp.1-55.
Gout J-F, Kahn D, Duret L (2010)
The Relationship among Gene Expression the Evolution of Gene Dosage and the Rate of Protein Evolution, PLoS Genetics, vol. 6 pp.e1000944-e1000944.
Ratnakumar A, Mousset S, Glémin S, Berglund J, Galtier N, Duret L, Webster MT (2010)
Detecting positive selection within genomes: the problem of biased gene conversion, Philosophical transactions of the royal society B-Biological sciences, vol. 365 pp.2571-2580.
Duret L (2009)
Mutation Patterns in the Human Genome:More Variable Than Expected, PLoS Biology, vol. 7(2) e1000028 pp.217-219.
Duret L, Galtier N (2009)
Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes, Annual Review of Genomics and Human Genetics, vol. 10 pp.285-311.
Duret L, Galtier N (2009)
Comment on “Human-Specific Gain of Function in a Developmental Enhancer”, Science, vol. 323(5915) pp.714-715.
Galtier N, Duret L, Glémin S, Ranwez V (2009)
GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates, Trends in Genetics, vol. 25(1) pp.1-5.
Gout J-F, Duret L, Kahn D (2009)
Differential Retention of Metabolic Genes Following Whole-Genome Duplication, Molecular Biology and Evolution, vol. 26(5) pp.1067-1072.
Marais GAB, Duret L (2009)
L’évolution des chromosomes sexuels humains, Biofutur, vol. 304 pp.40-41.
Necşulea A, Guillet C, Cadoret J-C, Prioleau M-N, Duret L (2009)
The Relationship between DNA Replication and Human Genome Organization, Molecular Biology and Evolution, vol. 26(4) pp.729-741.
Necşulea A, Sémon M, Duret L, Hurst LD (2009)
Monoallelic expression and tissue specificity are associated with high crossover rates, Trends in Genetics, vol. 25(12) pp.519-522.
Penel S, Arigon A-M, Dufayard J-F, Sertier A-S, Daubin V, Duret L, Gouy M, Perrière G (2009)
Databases of homologous gene families for comparative genomics, BMC Bioinformatics, vol. 10 pp.s3-s3.
Cadoret J-C, Meisch F, Hassan-Zadeh V, Luyten I, Guillet C, Duret L, Quesneville Q, Prioleau M-N (2008)
Genome-wide studies highlight indirect links between human replication origins and gene regulation, Proceedings of The National Academy of Sciences of The United States of America, vol. 105-41 pp.15837-15842.
Couté Y, Kindbeiter K, Belin S, Dieckmann R, Duret L, Bezin L, Sanchez J-C, Diaz J-J (2008)
ISG20L2 a novel vertebrate nucleolar exoribonuclease involved in ribosome biogenesis, Molecular & cellular proteomics, vol. 7 pp.546-559.
Duret L (2008)
Neutral Theory: The Null Hypothesis of Molecular Evolution, Nature Education, vol. 1 pp.803-806.
Duret L, Arndt PF (2008)
The Impact of Recombination on Nucleotide Substitutions in the Human Genome, PLoS Genetics, vol. 4 pp.1-19.
Duret L, Cohen J, Jubin C, Dessen P, Gout J-F, Mousset S, Aury J-M, Jaillon O, Noël B, Arnaiz O, Bétermier M, Wincker P, Meyer E, Sperling L (2008)
Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline, Genome Research, vol. 18 pp.585-596.
Jaillon O, Bouhouche K, Gout J-F, Aury J-M, Noel B, Saudemont B, Nowacki M, Serrano V, Porcel BM, Ségurens B, Le Mouël A , Lepère G, Schächter V, Bétermier M, Cohen J, Wincker P, Sperling L, Duret L , Meyer E (2008)
Translational control of intron splicing in eukaryotes, Nature, vol. 451 pp.359-362.
Studer A, Penel S, Duret L, Robinson-Rechavi M (2008)
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes, Genome Research, vol. 18 pp.1393-1402.
Buchet-Poyau K, Courchet J, Hir H L, Seraphin B, Scoazec J Y, Duret L, Domon-Dell C, Freund J N, Billaud M (2007)
Identification and characterization of human Mex-3 proteins a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies, Nucleic Acids Research, vol. 35 pp.1289-1300.
Galtier N, Duret L (2007)
Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution, Trends in Genetics, vol. 23 pp.273-277.
Keime C, Sémon M, Mouchiroud D, Duret L, Gandrillon O (2007)
Unexpected observations after mapping LongSAGE tags to the human genome, BMC Bioinformatics, vol. 8 pp.1-11.
Aury J-M, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Segurens B, Daubin V, Anthouard V, Aiach N, Arnaiz O, Billaut A, Beisson J, Blanc I, Bouhouche K, Camara F, Duharcourt S, Guigo R, Gogendeau D, Katinka M, Keller AM, Kissmehl R, Klotz C, Koll F, Le Mouel A, Lepere G, Malinsky S, Nowacki M, Nowak JK, Plattner H, Poulain J, Ruiz F, Serrano V, Zagulski M, Dessen P, Betermier M, Weissenbach J, Scarpelli C, Schachter V, Sperling L, Meyer E, Cohen J, Wincker P (2006)
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia, Nature, vol. 444 pp.171-178.
Duret L (2006)
The GC Content of Primates and Rodents Genomes Is Not at Equilibrium : a Reply to Antezana, Journal of Molecular Evolution, vol. pp.803-806.
Duret L, Chureau C, Samain S, Weissenbach J, Avner P (2006)
The Xist RNA Gene Evolved in Eutherians by Pseudogenization of a Protein-Coding Gene, Science, vol. 312 pp.1653-1655.
Duret L, Eyre-Walker A, Galtier N (2006)
A new perspective on isochore evolution, Gene, vol. pp.71-74.
Khelifi A, Meunier J, Duret L, Mouchiroud D (2006)
GC Content Evolution of the Human and Mouse Genomes : Insights from the Study of Processed Pseudogenes in Regions of Different Recombination Rates., Journal of Molecular Evolution, vol. 62 pp.745-752.
Sémon M, Duret L (2006)
Evolutionary origin and maintenance of coexpressed gene clusters in mammals., Molecular Biology and Evolution, vol. 23 pp.1715-1723.
Sémon M, Lobry JR, Duret L (2006)
No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans, Molecular Biology and Evolution, vol. 23 pp.523-529.
Bazin E, Duret L, Penel S, Galtier N (2005)
Polymorphix: a sequence polymorphism database, Nucleic Acids Research, vol. 33 pp.481-484.
Bonnaud B, Beliaeff J, Bouton O, Oriol G, Duret L, Mallet F (2005)
Natural history of the ERVWE1 endogenous retroviral locus, Retrovirology, vol. 2 pp.57-57.
Dufayard JF, Duret L, Penel S, Gouy M, Rechenmann F, Perrière G (2005)
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases, Bioinformatics, vol. 21 pp.2596-2603.
Duret L (2005)
Les trésors cachés du génome humain, Pour la Science, vol. pp.16-21.
Hurst LD, Duret L (2005)
Bioinformatics with a French accent, Genome Biology, vol. 6 pp.349.1-349.3.
Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I, Gattiker A, Kulikova T, Faruque N, Duggan K, McLaren P, Reimholz B, Duret L, Penel S, Reuter I, Apweiler R (2005)
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes, Nucleic Acids Research, vol. 33 pp.297-302.
Khelifi A, Duret L, Mouchiroud D (2005)
HOPPSIGEN: a database of human and mouse processed pseudogenes, Nucleic Acids Research, vol. 33 pp.59-66.
Meunier J, Khelifi A, Navratil V, Duret L (2005)
Homology-dependent methylation in primate repetitive DNA, Proceedings of The National Academy of Sciences of The United States of America, vol. 102 pp.5471-5476.
Sémon M, Mouchiroud D, Duret L (2005)
Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance, Human Molecular Genetics, vol. 14 pp.421-427.
Belle E, Duret L, Galtier N, Eyre-Walker A (2004)
The Decline of Isochores in Mammals: An Assessment of the GC Content Variation Along the Mammalian Phylogeny, Journal of Molecular Evolution, vol. 58 pp.653-660.
Bonnaud B, Bouton O, Oriol G, Cheynet V, Duret L, Mallet F (2004)
Evidence of Selection on the Domesticated ERVWE1 env Retroviral Element Involved in Placentation, Molecular Biology and Evolution, vol. 21 pp.1895-1901.
Jacq N, Blanchet C, Combet C, Cornillot E, Duret L, Kurata K, Nakamura H, Silvestre T, Breton V (2004)
Grid as a bioinformatic tool, Parallel Computing, vol. 30 pp.1093-1107.
Keime C, Damiola F, Mouchiroud D, Duret L, Gandrillon O (2004)
Identitag a relational database for SAGE tag identification and interspecies comparison of SAGE libraries, BMC Bioinformatics, vol. 5 pp.1-12.
Mallet F, Bouton O, Prudhomme S, Cheynet V, Oriol G, Bonnaud B, Lucotte G, Duret L, Mandrand B (2004)
The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology, Proceedings of The National Academy of Sciences of The United States of America, vol. 101 pp.1731-1736.
Meunier J, Duret L (2004)
Recombination drives the evolution of GC-content in the human genome, Molecular Biology and Evolution, vol. 21 pp.984-990.
Michon L, Morle L, Bozon M, Duret L, Zech JC, Godet J, Plauchu H, Edery P (2004)
Physical and transcript map of the autosomal dominant colobomatous microphthalmia locus on chromosome 15q12-q15 and refinement to a 4.4 Mb region, European Journal of Human Genetics, vol. 12 pp.574-578.
Reymond N, Charles H, Duret L, Calevro F, Beslon G, Fayard J-M (2004)
ROSO : Research on Optimized Oligonucleotide Probes for Microarrays, Bioinformatics, vol. 20 pp.271-273.
Sémon M, Duret L (2004)
Evidence that functional transcription units cover at least half of the human genome, Trends in Genetics, vol. 20 pp.229-232.
Assossou O, Besson F, Rouault JP, Persat F, Brisson C, Duret L, Ferrandiz J, Mayencon M, Peyron F, Picot S (2003)
Subcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form, FEMS Microbiology Letters, vol. 224 pp.161-168..
Bièche I, Laurent A, Laurendeau I, Duret L, Giovangrandi Y, Frendo JL, Olivi M, Fausser JL, Evain-brion D, Vidaud M (2003)
Placenta-Specific INSL4 Expression Is Mediated by a Human Endogenous Retrovirus Element, Biology of Reproduction, vol. 68 pp.1422-1429..
Marais GAB, Mouchiroud D, Duret L (2003)
Neutral effect of recombination on base composition in Drosophila, Genetical Research, vol. 81 pp.79-89.
Perrière G, Combet C, Penel S, Blanchet C, Thioulouse J, Geourjon C, Grassot J, Charavay C, Gouy M, Duret L, Deléage G (2003)
Integrated databanks access and sequence/structure analysis services at the PBIL., Nucleic Acids Research, vol. 31 pp.3393-3399.
Rizzon C, Martin E, Marais GAB, Duret L, Segalat L, Biémont C (2003)
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, Genetics, vol. 165 pp.1127-1135.
Chureau C, Prissette M, Bourdet A, Barbe V, Cattolico L, Jones L, Eggen A, Avner P, Duret L (2002)
Comparative sequence analysis of the X-inactivation center region in mouse human and bovine, Genome Research, vol. 12 pp.894-908..
Duret L (2002)
Detecting genomic features under weak selective pressure: the example of codon usage in animals and plants, Bioinformatics, vol. 18 pp.S91-S91.
Duret L (2002)
Evolution of synonymous codon usage in metazoans, Current Opinion in Genetics and Development, vol. 12 pp.640-649.
Duret L, Sémon M, Piganeau G, Mouchiroud D, Galtier N (2002)
Vanishing GC-Rich Isochores in Mammalian Genomes, Genetics, vol. 162 pp.1837-1848.
Piganeau G, Mouchiroud D, Duret L, Gautier C (2002)
Expected Relationship Between the Silent Substitution Rate and the GC Content: Implications for the Evolution of Isochores, Journal of Molecular Evolution, vol. 54 pp.129-133..
Duret L (2001)
Why do genes have introns? Recombination might add a new piece to the puzzle, Trends in Genetics, vol. 17 pp.172-175.
Duret L, Hurst L D (2001)
The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution, Molecular Biology and Evolution, vol. 18 pp.757-762.
Frendo P, Jimenez M J, Mathieu C, Duret L, Gallesi D, Van de Sype G, Herouart D, Puppo A (2001)
Plant Physiol.A Medicago truncatula homoglutathione synthetase is derived from glutathione synthetase by gene duplication, Plant Physiologie, vol. 126 pp.1706-1715.
Galtier N, Piganeau G, Mouchiroud D, Duret L (2001)
GC-content evolution in mammalian genomes: the biased gene conversion hypothesis, Genetics, vol. 159 pp.907-911.
Marais GAB, Duret L (2001)
Synonymous codon usage accuracy of translation and gene length in Caenorhabditis elegans, Journal of Molecular Evolution, vol. 52 pp.275-280.
Marais GAB, Mouchiroud D, Duret L (2001)
Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes, Proceedings of The National Academy of Sciences of The United States of America, vol. 98 pp.5688-5692.
Ponger L, Duret L, Mouchiroud D (2001)
Determinants of CpG islands: expression in early embryo and isochore structure, Genome Research, vol. 11 pp.1854-1860.
Birot A, Duret L, Bartholin L, Santalucia B, Tigaud I, Magaud J, Rouault J (2000)
Identification and molecular analysis of BANP, Gene, vol. 253 pp.189-196.
Duret L (2000)
tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes, Trends in Genetics, vol. 16 pp.287-289.
Duret L, Galtier N (2000)
The covariation between TpA deficiency CpG deficiency and G+C content of human isochores is due to a mathematical artifact, Molecular Biology and Evolution, vol. 17 pp.1620-1625.
Duret L, Marais GAB, Biémont C (2000)
Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans, Genetics, vol. 156 pp.1661-1669.
Duret L, Mouchiroud D (2000)
Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate, Molecular Biology and Evolution, vol. 17 pp.68-74.
Goncalves I, Duret L, Mouchiroud D (2000)
Nature and structure of human genes that generate retropseudogenes, Genome Research, vol. 10 pp.672-678.
Ott C, Duret L, Chemin I, Trepo C, Mandrand B, Komurian-Pradel F (2000)
Use of a TT virus ORF1 recombinant protein to detect anti-TT virus antibodies in human sera, Journal of General Virology, vol. 81 pp.2949-2958.
Perrière G, Duret L, Gouy M (2000)
HOBACGEN: database system for comparative genomics in bacteria, Genome Research, vol. 10 pp.379-385.
Voisset C, Bouton O, Bedin F, Duret L, Mandrand B, Mallet F, Paranhos-Baccala G (2000)
Chromosomal distribution and coding capacity of the human endogenous retrovirus HERV-W family, AIDS Research and Human Retroviruses, vol. 16 pp.731-740.
Blond JL, Beseme F, Duret L, Bouton O, Bedin F, Perron H, Mandrand B, Mallet F (1999)
Molecular characterization and placental expression of HERV-W a new human endogenous retrovirus family, Journal of Virology, vol. 73 pp.1175-1185.
Duret L, Mouchiroud D (1999)
Expression pattern and surprisingly gene length shape codon usage in Caenorhabditis Drosophila and Arabidopsis, Proceedings of The National Academy of Sciences of The United States of America, vol. 96 pp.4482-4487.
Rouault JP, Kuwabara PE, Sinilnikova OM, Duret L, Thierry-Mieg D, Billaud M (1999)
Regulation of dauer larva development in Caenorhabditis elegans by daf-18 a homologue of the tumour suppressor PTEN, Current Biology, vol. 9 pp.329-332.
Wheelan S J, Boguski M S, Duret L, Makalowski W (1999)
Human and nematode orthologs--lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis elegans, Gene, vol. 238 pp.163-170.
Duret L, Guex N, Peitsch M C, Bairoch A (1998)
New insulin-like proteins with atypical disulfide bond pattern characterized in Caenorhabditis elegans by comparative sequence analysis and homology modeling, Genome Research, vol. 8 pp.348-353.
Spicher A, Guicherit O M, Duret L, Aslanian A, Sanjines E M, Denko N C, Giaccia A J, Blau H M (1998)
Highly conserved RNA sequences that are sensors of environmental stress, Molecular and Cellular Biology, vol. 18 pp.7371-7382.
Duret L, Bucher P (1997)
Searching for regulatory elements in human noncoding sequences, Current Opinion in Structural Biology, vol. 7 pp.399-406.
Graur D, Gouy M, Duret L (1997)
Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata, Molecular Phylogenetics and Evolution, vol. 7 pp.195-200.
Guehenneux F, Duret L, Callanan M B, Bouhas R, Hayette S, Berthet C, Samarut C, Rimokh R, Birot A M, Wang Q, Magaud J P, Rouault J P (1997)
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, Leukemia, vol. 11 pp.370-375.
Lesenechal M, Duret L, Cano M I, Mortara R A, Jolivet M, Camargo M E, da Silveira J F, Paranhos-Baccala G (1997)
Cloning and characterization of a gene encoding a novel immunodominant antigen of Trypanosoma cruzi, Molecular and Biochemical Parasitology, vol. 87 pp.193-204.
Duret L, Gasteiger E, Perrière G (1996)
LALNVIEW: a graphical viewer for pairwise sequence alignments, Computer Applications in the Biosciences, vol. 12 pp.507-510.
Graur D, Duret L, Gouy M (1996)
Phylogenetic position of the order Lagomorpha (rabbits hares and allies), Nature, vol. 379 pp.333-335.
Duret L, Mouchiroud D, Gautier C (1995)
Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores, Journal of Molecular Evolution, vol. 40 pp.308-317.
Michaille J J, Gouy M, Blanchet S, Duret L (1995)
Isolation and characterization of a cDNA encoding a chicken actin-like protein, Gene, vol. 154 pp.205-209.
Duret L, Mouchiroud D, Gouy M (1994)
HOVERGEN: a database of homologous vertebrate genes, Nucleic Acids Research, vol. 22 pp.2360-2365.
Rimokh R, Berger F, Bastard C, Klein B, French M, Archimbaud E, Rouault J P, Santa Lucia B, Duret L, Vuillaume M (1994)
Rearrangement of CCND1 (BCL1/PRAD1) 3` untranslated region in mantle-cell lymphomas and t(11q13)-associated leukemias, Blood, vol. 83 pp.3689-3696.
Duret L, Dorkeld F, Gautier C (1993)
Strong conservation of non-coding sequences during vertebrates evolution: potential involvement in post-transcriptional regulation of gene expression, Nucleic Acids Research, vol. 21 pp.2315-2322.
Rouault JP, Samarut C, Duret L, Tessa C, Samarut J, Magaud J P (1993)
Sequence analysis reveals that the BTG1 anti-proliferative gene is conserved throughout evolution in its coding and 3` non-coding regions, Gene, vol. 129 pp.303-306.
Rouault JP, Rimokh R, Tessa C, Paranhos G, Ffrench M, Duret L, Garoccio M, Germain D, Samarut J, Magaud JP (1992)
BTG1 a member of a new family of antiproliferative genes, EMBO Journal, vol. 11 pp.1663-1670.
inbook :
Duret L, Bataillon T, Bierne N, Daubin V, Dutheil J, Gautier C, Glémin S, Gouy M, Heyer E, Marais G, Mouchiroud D, Pontarroti P, Quintana-Murci L, Robinson-Rechavi M, Galtier N (2010)
Evolution Moléculaire
in: Biologie Evolutive, de Boeck, pp.114-173.
Galtier N, Duret L (2008)
Biased Gene Conversion and its Impact on Human Genome Evolution
in: Encyclopedia of life sciences, , pp.273-277.
Duret L, Abdeddaim S (2000)
Multiple alignments for structural functional or phylogenetic analyses of homologous sequences
in: Bioinformatics a Practical Approach, Oxford University Press, pp.51-76.
Duret L, Perrière G, Gouy M (1999)
HOVERGEN: comparative analysis of homologous vertebrate genes
in: Bioinformatics: databases and systems, Kluwer Academic Publishers, pp.21-35.
phdthesis :
Duret L (2001)
HDR - Organisation Fonctionnement et Evolution des Génomes de Métazoaires : Mais où est donc passée la sélection naturelle ? .
