Selected publications

Last updated: August 2018

L. Guéguen and L. Duret
Unbiased estimate of synonymous and non-synonymous substitution rates with non-stationary base composition
Mol Biol Evol, 2018, 35: 734-742.
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N. Galtier, C. Roux, M. Rousselle, J. Romiguier, E. Figuet, S. Glemin, N. Bierne and L. Duret
Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion
Mol Biol Evol, 2018, 35: 1092-1103.
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B. Diagouraga, J. A. J. Clement, L. Duret, J. Kadlec, B. de Massy and F. Baudat
PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites
Mol Cell, 2018, 69: 853-865 e6.
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B. Saudemont, A. Popa, J. L. Parmley, V. Rocher, C. Blugeon, A. Necsulea, E. Meyer and L. Duret
The fitness cost of mis-splicing is the main determinant of alternative splicing patterns
Genome Biol, 2017, 18: 208.
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F. Pouyet, D. Mouchiroud, L. Duret and M. Semon
Recombination, meiotic expression and human codon usage
Elife, 2017, 6: e27344.
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T. Latrille, L. Duret and N. Lartillot
The Red Queen model of recombination hot-spot evolution: a theoretical investigation
Philos Trans R Soc Lond B Biol Sci, 2017, 372:
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C. Grey, J. A. Clement, J. Buard, B. Leblanc, I. Gut, M. Gut, L. Duret and B. de Massy
In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites
Genome Res, 2017, 27: 580-590.
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M. Cariou, L. Duret and S. Charlat
The global impact of Wolbachia on mitochondrial diversity and evolution
J Evol Biol, 2017, 30: 2204-2210.
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C. M. Francois, L. Duret, L. Simon, F. Mermillod-Blondin, F. Malard, L. Konecny-Dupre, R. Planel, S. Penel, C. J. Douady and T. Lefebure
No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes
Mol Biol Evol, 2016, 33: 2605-20.
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M. Cariou, L. Duret and S. Charlat
How and how much does RAD-seq bias genetic diversity estimates?
BMC Evolutionary Biology, 2016, 16:
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F. Lassalle, S. Perian, T. Bataillon, X. Nesme, L. Duret and V. Daubin
GC-Content evolution in bacterial genomes: the biased gene conversion hypothesis expands
PLoS Genet, 2015, 11: e1004941.
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S. Glemin, P. F. Arndt, P. W. Messer, D. Petrov, N. Galtier and L. Duret
Quantification of GC-biased gene conversion in the human genome
Genome Res, 2015, 25: 1215-28.
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Y. Lesecque, S. Glemin, N. Lartillot, D. Mouchiroud and L. Duret
The red queen model of recombination hotspots evolution in the light of archaic and modern human genomes
PLoS Genet, 2014, 10: e1004790.
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F. Picard, J. C. Cadoret, B. Audit, A. Arneodo, A. Alberti, C. Battail, L. Duret and M. N. Prioleau
The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells
PLoS Genet, 2014, 10: e1004282.
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E. M. Kvikstad and L. Duret
Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome
Mol Biol Evol, 2014, 31: 23-36.
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C. Vallot, C. Huret, Y. Lesecque, A. Resch, N. Oudrhiri, A. Bennaceur-Griscelli, L. Duret and C. Rougeulle
XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells
Nat Genet, 2013, 45: 239-41.
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Y. Lesecque, D. Mouchiroud and L. Duret
GC-biased gene conversion in yeast is specifically associated with crossovers: molecular mechanisms and evolutionary significance
Mol Biol Evol, 2013, 30: 1409-19.
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M. Cariou, L. Duret and S. Charlat
Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization
Ecol Evol, 2013, 3: 846-52.
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E. Pessia, A. Popa, S. Mousset, C. Rezvoy, L. Duret and G. A. Marais
Evidence for Widespread GC-biased Gene Conversion in Eukaryotes
Genome Biol Evol, 2012, 4: 675-82.
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V. Miele, S. Penel, V. Daubin, F. Picard, D. Kahn and L. Duret
High-quality sequence clustering guided by network topology and multiple alignment likelihood
Bioinformatics, 2012, 28: 1078-85.
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V. Miele, S. Penel and L. Duret
Ultra-fast sequence clustering from similarity networks with SiLiX
BMC Bioinformatics, 2011, 12: 116.
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B. P. Cusack, P. F. Arndt, L. Duret and H. R. Crollius
Preventing Dangerous Nonsense: Selection for Robustness to Transcriptional Error in Human Genes
PLoS Genet, 2011, 7: e1002276.
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Necsulea, A., A. Popa, D.N. Cooper, P.D. Stenson, D. Mouchiroud, C. Gautier, and L. Duret
Meiotic recombination favors the spreading of deleterious mutations in human populations.
Hum Mutat, 2011, 32: 198-206.
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Ratnakumar, A., S. Mousset, S. Glemin, J. Berglund, N. Galtier, L. Duret, and M.T. Webster
Detecting positive selection within genomes: the problem of biased gene conversion.
Philos Trans R Soc Lond B Biol Sci, 2010, 365: 2571-2580.
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Gout, J.F., D. Kahn, Paramecium_Post-Genomics_Consortium, and L. Duret
The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution.
PLoS Genet, 2010, 6: e1000944.
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Necsulea, A., M. Semon, L. Duret, and L.D. Hurst
Monoallelic expression and tissue specificity are associated with high crossover rates.
Trends Genet, 2009, 25: 519-522.
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Duret, L. and N. Galtier
Biased gene conversion and the evolution of mammalian genomic landscapes.
Annu Rev Genomics Hum Genet, 2009, 10: 285-311.
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Galtier, N., L. Duret, S. Glemin, and V. Ranwez
GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates.
Trends Genet, 2009, 25: 1-5.
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Duret, L. and N. Galtier
Comment on "Human-specific gain of function in a developmental enhancer".
Science, 2009, 323: 714.
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Penel, S., A.M. Arigon, J.F. Dufayard, A.S. Sertier, V. Daubin, L. Duret, M. Gouy, and G. Perriere
Databases of homologous gene families for comparative genomics.
BMC Bioinformatics, 2009, 10 Suppl 6: S3.
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Necsulea, A., C. Guillet, J.C. Cadoret, M.N. Prioleau, and L. Duret
The relationship between DNA replication and human genome organization.
Mol Biol Evol, 2009, 26: 729-741.
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Gout, J.F., L. Duret, and D. Kahn
Differential retention of metabolic genes following whole-genome duplication.
Mol Biol Evol, 2009, 26: 1067-1072.
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Duret, L. and P.F. Arndt
The impact of recombination on nucleotide substitutions in the human genome.
PLoS Genet, 2008, 4: e1000071.
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Duret, L., J. Cohen, C. Jubin, P. Dessen, J.F. Gout, S. Mousset, J.M. Aury, O. Jaillon, B. Noel, O. Arnaiz, M. Betermier, P. Wincker, E. Meyer, and L. Sperling
Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germ line.
Genome Res, 2008, 18: 585-596.
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Jaillon, O., K. Bouhouche, J.F. Gout, J.M. Aury, B. Noel, B. Saudemont, M. Nowacki, V. Serrano, B.M. Porcel, B. Segurens, A. Le Mouel, G. Lepere, V. Schachter, M. Betermier, J. Cohen, P. Wincker, L. Sperling, L. Duret, and E. Meyer
Translational control of intron splicing in eukaryotes.
Nature, 2008, 451: 359-362.
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Cadoret, J.C., F. Meisch, V. Hassan-Zadeh, I. Luyten, C. Guillet, L. Duret, H. Quesneville, and M.N. Prioleau
Genome-wide studies highlight indirect links between human replication origins and gene regulation.
Proc Natl Acad Sci U S A, 2008, 105: 15837-15842.
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Galtier, N. and L. Duret
Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution.
Trends Genet, 2007, 23: 273-277.
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Aury, J.M., O. Jaillon, L. Duret, B. Noel, C. Jubin, B.M. Porcel, B. Segurens, V. Daubin, V. Anthouard, N. Aiach, O. Arnaiz, A. Billaut, J. Beisson, I. Blanc, K. Bouhouche, F. Camara, S. Duharcourt, R. Guigo, D. Gogendeau, M. Katinka, A.M. Keller, R. Kissmehl, C. Klotz, F. Koll, A. Le Mouel, G. Lepere, S. Malinsky, M. Nowacki, J.K. Nowak, H. Plattner, J. Poulain, F. Ruiz, V. Serrano, M. Zagulski, P. Dessen, M. Betermier, J. Weissenbach, C. Scarpelli, V. Schachter, L. Sperling, E. Meyer, J. Cohen, and P. Wincker
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.
Nature, 2006, 444: 171-178.
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Duret, L., A. Eyre-Walker, and N. Galtier
A new perspective on isochore evolution.
Gene, 2006, 385: 71-74.
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Duret, L., C. Chureau, S. Samain, J. Weissenbach, and P. Avner
The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene.
Science, 2006, 312: 1653-1655.
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Honeybee Genome Sequencing Consortiom [Duret L. co-author]
Insights into social insects from the genome of the honeybee Apis mellifera.
Nature, 2006, 443: 931-949.
PubMed

Semon, M. and L. Duret
Evolutionary origin and maintenance of coexpressed gene clusters in mammals.
Mol Biol Evol, 2006, 23: 1715-1723.
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Semon, M., J.R. Lobry, and L. Duret
No evidence for tissue-specific adaptation of synonymous codon usage in humans.
Mol Biol Evol, 2006, 23: 523-529.
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Dufayard, J.F., L. Duret, S. Penel, M. Gouy, F. Rechenmann, and G. Perriere
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.
Bioinformatics, 2005, 21: 2596-2603.
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Meunier, J., A. Khelifi, V. Navratil, and L. Duret
Homology-dependent methylation in primate repetitive DNA.
Proc Natl Acad Sci U S A, 2005, 102: 5471-5476.
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Semon, M., D. Mouchiroud, and L. Duret
Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance.
Hum Mol Genet, 2005, 14: 421-427.
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Belle, E., L. Duret, N. Galtier, and A. Eyre-walker
The Decline of Isochores in Mammals: An Assessment of the GC Content Variation Along the Mammalian Phylogeny.
J. Mol. Evol., 2004, 58: 653-660.
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Bonnaud, B., O. Bouton, G. Oriol, V. Cheynet, L. Duret, and F. Mallet
Evidence of selection on the domesticated ERVWE1 env retroviral element involved in placentation.
Mol Biol Evol, 2004, 21: 1895-1901.
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Mallet, F., O. Bouton, S. Prudhomme, V. Cheynet, G. Oriol, B. Bonnaud, G. Lucotte, L. Duret, and B. Mandrand
The endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology.
Proc Natl Acad Sci U S A, 2004, 101: 1731-1736.
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Meunier, J. and L. Duret
Recombination drives the evolution of GC-content in the human genome.
Mol Biol Evol, 2004, 21: 984-990.
PubMed PDF [DATASET]

Semon, M. and L. Duret
Evidence that functional transcription units cover at least half of the human genome.
Trends Genet, 2004, 20: 229-232.
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Marais, G., D. Mouchiroud, and L. Duret
Neutral effect of recombination on base composition in Drosophila.
Genet. Res., 2003, 81: 79-89.
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Rizzon, C., E. Martin, G. Marais, L. Duret, L. Segalat, and C. Biemont
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, 2003, 165: 1127-1135.
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Chureau, C., M. Prissette, A. Bourdet, V. Barbe, L. Cattolico, L. Jones, A. Eggen, P. Avner, and L. Duret
Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine.
Genome Res, 2002, 12: 894-908.
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Duret, L.
Evolution of synonymous codon usage in metazoans.
Curr Opin Genet Dev, 2002, 12: 640-649.
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Duret, L., M. Semon, G. Piganeau, D. Mouchiroud, and N. Galtier
Vanishing GC-rich isochores in mammalian genomes.
Genetics, 2002, 162: 1837-1847.
PubMed PDF [DATASET]

Galtier, N., G. Piganeau, D. Mouchiroud, and L. Duret
GC-content evolution in mammalian genomes: the biased gene conversion hypothesis.
Genetics, 2001, 159: 907-911.
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Marais, G. and L. Duret
Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans.
J. Mol. Evol., 2001, 52: 275-280.
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Marais, G., D. Mouchiroud, and L. Duret
Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes.
Proc Natl Acad Sci U S A, 2001, 98: 5688-5692.
PubMed PDF [DATASET]

Ponger, L., L. Duret, and D. Mouchiroud
Determinants of CpG islands: expression in early embryo and isochore structure.
Genome Res, 2001, 11: 1854-1860.
PubMed PDF [DATASET]

Duret, L.
tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes.
Trends Genet, 2000, 16: 287-289.
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Duret, L. and N. Galtier
The covariation between TpA deficiency, CpG deficiency, and G+C content of human isochores is due to a mathematical artifact.
Mol Biol Evol, 2000, 17: 1620-1625.
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Duret, L., G. Marais, and C. Biemont
Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans.
Genetics, 2000, 156: 1661-1169.
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Duret, L. and D. Mouchiroud
Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate.
Mol Biol Evol, 2000, 17: 68-74.
PubMed PDF [DATASET]

Goncalves, I., L. Duret, and D. Mouchiroud
Nature and structure of human genes that generate retropseudogenes.
Genome Res, 2000, 10: 672-678.
PubMed PDF [DATASET]

Perriere, G., L. Duret, and M. Gouy
HOBACGEN: database system for comparative genomics in bacteria.
Genome Res, 2000, 10: 379-385.
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Duret, L. and D. Mouchiroud
Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis.
Proc Natl Acad Sci U S A, 1999, 96: 4482-4487.
PubMed PDF [DATASET]

Duret, L. and P. Bucher
Searching for regulatory elements in human noncoding sequences.
Curr Opin Struct Biol, 1997, 7: 399-406.
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Duret, L., D. Mouchiroud, and C. Gautier
Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores.
J Mol Evol, 1995, 40: 308-317.
PubMed [DATASET]

Duret, L., D. Mouchiroud, and M. Gouy
HOVERGEN: a database of homologous vertebrate genes.
Nucleic Acids Res, 1994, 22: 2360-2365.
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Duret, L., F. Dorkeld, and C. Gautier
Strong conservation of non-coding sequences during vertebrates evolution: potential involvement in post-transcriptional regulation of gene expression.
Nucleic Acids Res, 1993, 21: 2315-2322.
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