Selected publications

Last updated: January 2011

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.
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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.
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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.
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Ponger, L., L. Duret, and D. Mouchiroud
Determinants of CpG islands: expression in early embryo and isochore structure.
Genome Res, 2001, 11: 1854-1860.
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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.
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Goncalves, I., L. Duret, and D. Mouchiroud
Nature and structure of human genes that generate retropseudogenes.
Genome Res, 2000, 10: 672-678.
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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.
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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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