GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Duret Laurent

Directeur de recherche

CNRS

Address: 69622 VILLEURBANNE cedex
69622 VILLEURBANNE cedex

_{Batiment Mendel 2eme étage. Bureau 12.025}

Genomes are the product of various evolutionary processes: certain genomic traits that we observe today reflect functional constraints that currently operate or that have operated in the past; others result from non-adaptive processes. To identify the features of the genome that are important for its functioning, it is necessary to look for features whose mode of evolution deviates from the neutralist model: this is the basic principle of the comparative analysis of genomes, which is at the heart of all my research activity. My work follows a double logic: study the evolution of genomes to better understand how they work - and vice versa, take into account the molecular mechanisms of genome functioning in order to better interpret sequence evolution. We explore genetic diversity at different level, both across species and within species (population genomics). My work is based on bioinformatic and statistical analysis of sequences, but also relies heavily on close collaborations with ‘wet-lab' biologists.
These last years, my main focus has been on exploring the consequences of homologous recombination on genome evolution. In particular, we have discovered that in many species, recombination induces non-Mendelien inheritance, favoring the fixation of GC-alleles (gBGC – for GC-Biased Gene Conversion). This non-adaptive process has a major impact on the evolution of genomic landscapes and also on gene expression processes. We are now trying to understand how and why does gBGC evolve, and how and why do recombination rates vary in space (along chromosomes) and in time (across species).
I am also interested in understanding how the constraints imposed by the cost of gene expression shape genome evolution. We have shown that gene expression level is an important determinant of selective pressures acting on numerous features: on protein sequences, on gene dosage, on splicing accuracy, and on translation efficiency. We are now exploring how variation in the efficacy of selection contributes to the evolution of the complexity of gene expression patterns across species.
I am also working, in collaboration with researchers from Paris and Gif, on the genomics of Paramecia. This unicellular eukaryote displays many very peculiar features that make it a fantastic model to explore various topics (whole genome duplications, proliferation of selfish genetic elements, alternative splicing, transgenerational inheritance of epigenetic modifications, …).

Publications

Display of 91 to 120 publications on 176 in total

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, Betina M. Porcel...

Nature . 444 ( 7116 ) : 171-178

DOI: 10.1038/nature05230

2006

Journal article

see the publication

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

Jean-Marc Aury, Olivier Jaillon, L. Duret, Benjamin Noel, Claire Jubin, Betina M Porcel...

Nature . 444 ( 7116 ) : 171-8

DOI: 10.1038/nature05230

2006

Journal article

see the publication

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

L. Duret

Journal of Molecular Evolution . -- : 803-806

2006

Journal article

see the publication

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

M. Sémon, J.R. Lobry, L. Duret

Molecular Biology and Evolution . 23 : 523-529

2006

Journal article

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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 . 312 : 1653-1655

2006

Journal article

see the publication

Evolutionary origin and maintenance of coexpressed gene clusters in mammals.

M. Sémon, L. Duret

Molecular Biology and Evolution . 23 : 1715-1723

2006

Journal article

see the publication

A new perspective on isochore evolution

Laurent Duret, Adam Eyre-Walker, Nicolas Galtier

Gene . 385 : 71-74

DOI: 10.1016/j.gene.2006.04.030

2006

Journal article

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

M. Sémon, Dominique Mouchiroud, L. Duret

Human Molecular Genetics . 14 : 421-427

2005

Journal article

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HOPPSIGEN: a database of human and mouse processed pseudogenes.

A. Khelifi, L. Duret, Dominique Mouchiroud

Nucleic Acids Research . 33 ( Database issue ) : D59-66

DOI: 10.1093/nar/gki084

2005

Journal article

see the publication

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, G. Perrière

Bioinformatics . 21 ( 11 ) : 2596-603

DOI: 10.1093/bioinformatics/bti325

2005

Journal article

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

P. Kersey, L. Bower, L. Morris, A. Horne, R. Petryszak, C. Kanz...

Nucleic Acids Research . 33 ( Database issue ) : D297-302

DOI: 10.1093/nar/gki039

2005

Journal article

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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 . 102 ( 15 ) : 5471-6

DOI: 10.1073/pnas.0408986102

2005

Journal article

see the publication

Natural history of the ERVWE1 endogenous retroviral locus

B. Bonnaud, J. Beliaeff, O. Bouton, G. Oriol, L. Duret, Frédéric Mallet

Retrovirology . 2 : 1-7

2005

Journal article

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Polymorphix: a sequence polymorphism database

E. Bazin, L. Duret, Simon Penel, N. Galtier

Nucleic Acids Research . 33 : 481-484

2005

Journal article

see the publication

Bioinformatics with a French accent

L.D. Hurst, L. Duret

Genome Biology . 6 : 349.1-349.3

2005

Journal article

see the publication

Natural history of the ERVWE 1 endogenous retroviral locus.

Bertrand Bonnaud, Jean Beliaeff, Olivier Bouton, Guy Oriol, Laurent Duret, François Mallet

Retrovirology . 2:57 : 1 - 7

DOI: 10.1186/1742-4692-2-57

2005

Journal article

see the publication

Les trésors cachés du génome humain

L. Duret

Pour la science . -- : 16-21

2005

Journal article

see the publication

Grid as a bioinformatic tool

N. Jacq, Christophe Blanchet, C. Combet, E. Cornillot, L. Duret, K. Kurata...

Parallel Computing . 30 : 1093-1107

2004

Journal article

see the publication

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 . 5 : 143

DOI: 10.1186/1471-2105-5-143

2004

Journal article

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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, B. Bonnaud...

Proceedings of the National Academy of Sciences of the United States of America . 101 : 1731-1736

2004

Journal article

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

M. Sémon, L. Duret

Trends in Genetics . 20 : 229-232

2004

Journal article

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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 . 58 : 653-660

2004

Journal article

see the publication

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 . 5 : 1-12

2004

Journal article

see the publication

ROSO : Research on Optimized Oligonucleotide Probes for Microarrays

N. Reymond, H. Charles, L. Duret, Federica Calevro, G. Beslon, J.-M. Fayard

Bioinformatics . 20 : 271-273

2004

Journal article

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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, Jacqueline Godet...

European Journal of Human Genetics . 12 ( 7 ) : 574-8

DOI: 10.1038/sj.ejhg.5201197

2004

Journal article

see the publication

Grid as a bioinformatic tool

N. Jacq, Christophe Blanchet, C. Combet, E. Cornillot, L. Duret, K. Kurata...

Parallel Computing . 30 : 1093-1107

2004

Journal article

see the publication

Grid as a bioinformatic tool

N. Jacq, Christophe Blanchet, C. Combet, E. Cornillot, L. Duret, K. Kurata...

Parallel Computing . 30 : 1093-1107

DOI: 10.1016/j.parco.2004.07.013

2004

Journal article

see the publication

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

J. Meunier, L. Duret

Molecular Biology and Evolution . 21 : 984-990

2004

Journal article

see the publication

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

B. Bonnaud, O. Bouton, G. Oriol, V. Cheynet, L. Duret, Frédéric Mallet

Molecular Biology and Evolution . 21 : 1895-1901

2004

Journal article

see the publication

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 . ( 5 ) : 143

2004

Journal article

see the publication

Research Interests: "Nothing in a genome makes sense, except in the light of molecular evolution"...

Publications

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

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

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

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

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

Evolutionary origin and maintenance of coexpressed gene clusters in mammals.

A new perspective on isochore evolution

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

HOPPSIGEN: a database of human and mouse processed pseudogenes.

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

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

Homology-dependent methylation in primate repetitive DNA.

Natural history of the ERVWE1 endogenous retroviral locus

Polymorphix: a sequence polymorphism database

Bioinformatics with a French accent

Natural history of the ERVWE 1 endogenous retroviral locus.

Les trésors cachés du génome humain

Grid as a bioinformatic tool

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

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

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

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

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

ROSO : Research on Optimized Oligonucleotide Probes for Microarrays

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

Grid as a bioinformatic tool

Grid as a bioinformatic tool

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

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

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