GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Duret Laurent

Directeur de recherche

CNRS

Address: 69622 VILLEURBANNE cedex
69622 VILLEURBANNE cedex

Tel: 33 04 72 44 62 97

Email

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 151 to 173 publications on 173 in total

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 . 17 : 1620-1625

Journal article

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

L. Duret, Gabriel Marais, C. Biémont

Genetics . 156 : 1661-1669

Journal article

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

C. Voisset, O. Bouton, F. Bedin, L. Duret, B. Mandrand, Frédéric Mallet...

AIDS Research and Human Retroviruses . 16 : 731-740

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Multiple alignments for structural functional or phylogenetic analyses of homologous sequences

L. Duret, S. Abdeddaim

incollection . -- : 51-76

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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 . 238 : 163-170

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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, H. Perron...

Journal of Virology . 73 : 1175-1185

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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 . 96 : 4482-4487

Journal article

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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, Marc Billaud

Current Biology - CB . 9 ( 6 ) : 329-334

DOI: 10.1016/S0960-9822(99)80143-2

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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 . 8 : 348-353

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Highly conserved RNA sequences that are sensors of environmental stress

A. Spicher, O.M. Guicherit, L. Duret, A. Aslanian, E.M. Sanjines, N.C. Denko...

Molecular and Cellular Biology . 18 : 7371-7382

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Searching for regulatory elements in human noncoding sequences

L. Duret, P. Bucher

Current Opinion in Structural Biology . 7 : 399-406

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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 . 7 ( 2 ) : 195-200

DOI: 10.1006/mpev.1996.0391

Journal article

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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, C Berthet...

Leukemia . 11 ( 3 ) : 370-375

DOI: 10.1038/sj.leu.2400599

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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, M.E. Camargo...

Molecular and Biochemical Parasitology . 87 : 193-204

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

D. Graur, L. Duret, Manolo Gouy

Nature . 379 : 333-335

DOI: 10.1038/379333a0

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LALNVIEW: a graphical viewer for pairwise sequence alignments

L. Duret, E. Gasteiger, G. Perrière

Computer Applications in the Biosciences . 12 : 507-510

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

J.J. Michaille, Manolo Gouy, Simon Blanchet, L. Duret

Gene . 154 ( 2 ) : 205-209

DOI: 10.1016/0378-1119(94)00865-P

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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 . 40 : 308-317

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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, E. Archimbaud...

Blood . 83 : 3689-3696

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HOVERGEN: a database of homologous vertebrate genes

L. Duret, Dominique Mouchiroud, Manolo Gouy

Nucleic Acids Research . 22 ( 12 ) : 2360-2365

DOI: 10.1093/nar/22.12.2360

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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, J. Samarut...

Gene . 129 ( 2 ) : 303-306

DOI: 10.1016/0378-1119(93)90284-A

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