GECO Evolutionary and Computational Genomics
Bioinformatics, Phylogeny and Evolutionary Genomics Group
Duret Laurent
Directeur de recherche
CNRS
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 121 to 150 publications on 173 in total
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 . 165 : 1127-1135
Journal article
see the publicationPatterns of selection against transposons inferred from the distribution of Tcl, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans.
Genetics . ( 165 ) : 1127-1135
Journal article
see the publicationIntegrated databanks access and sequence/structure analysis services at the PBIL.
Nucleic Acids Research . 31 ( 13 ) : 3393-3399
DOI: 10.1093/nar/gkg530
Journal article
see the publicationPatterns 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 . 165 ( 3 ) : 1127-35
Journal article
see the publicationROSO: a software to search optimized oligonucleotide probes for microarrays
14. Rencontres Régionales de la Recherche .
Poster
see the publicationSubcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form
FEMS Microbiology Letters . 224 ( 2 ) : 161-168
Journal article
see the publicationSubcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form
FEMS Microbiology Letters . 224 : 161-168.
Journal article
see the publicationExpected Relationship Between the Silent Substitution Rate and the GC Content: Implications for the Evolution of Isochores
Journal of Molecular Evolution . 54 : 129-133.
Journal article
see the publicationDetecting genomic features under weak selective pressure: the example of codon usage in animals and plants
Bioinformatics . 18 : S91-S91
Journal article
see the publicationROSO: A software to search optimized oligonucleotide probes for microarrays
COST853: Agricultural Biomarkers for Array-Technology .
Conference paper
see the publicationROSO : A Software to Search Optimized Oligonucleotide Probes for Microarrays
10. International Conference on Intelligent Systems for Molecular Biology (ISMB) .
Poster
see the publicationComparative sequence analysis of the X-inactivation center region in mouse, human, and bovine.
Genome Research . 12 : 894-908
Journal article
see the publicationVanishing GC-Rich Isochores in Mammalian Genomes
Genetics . 162 : 1837-1848
Journal article
see the publicationComparative sequence analysis of the X-inactivation center region in mouse human and bovine
Genome Research . 12 : 894-908.
Journal article
see the publicationEvolution of synonymous codon usage in metazoans
Current Opinion in Genetics and Development . 12 : 640-649
Journal article
see the publicationOrganisation Fonctionnement et Evolution des Génomes de Métazoaires : Mais où est donc passée la sélection naturelle ?
incollection . -- : 287-289
Journal article
see the publicationWhy do genes have introns? Recombination might add a new piece to the puzzle
Trends in Genetics . 17 : 172-175
Journal article
see the publicationDeterminants of CpG islands: expression in early embryo and isochore structure
Genome Research . 11 : 1854-1860
Journal article
see the publicationSynonymous codon usage accuracy of translation and gene length in Caenorhabditis elegans
Journal of Molecular Evolution . 52 : 275-280
Journal article
see the publicationGC-content evolution in mammalian genomes: the biased gene conversion hypothesis
Genetics . 159 : 907-911
Journal article
see the publicationPlant Physiol.A Medicago truncatula homoglutathione synthetase is derived from glutathione synthetase by gene duplication
Plant Physiology . 126 : 1706-1715
Journal article
see the publicationThe elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution
Molecular Biology and Evolution . 18 : 757-762
Journal article
see the publicationDoes 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 . 98 : 5688-5692
Journal article
see the publicationThe covariation between TpA deficiency CpG deficiency and G+C content of human isochores is due to a mathematical artifact
Molecular Biology and Evolution . 17 : 1620-1625
Journal article
see the publicationNature and structure of human genes that generate retropseudogenes
Genome Research . 10 : 672-678
Journal article
see the publicationDeterminants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate
Molecular Biology and Evolution . 17 : 68-74
Journal article
see the publicationUse of a TT virus ORF1 recombinant protein to detect anti-TT virus antibodies in human sera
Journal of General Virology . 81 : 2949-2958
Journal article
see the publicationIdentification and molecular analysis of BANP
Gene . 253 ( 2 ) : 189-196
Journal article
see the publicationEuGene an eurocaryotic gene finder that combines several sources of evidence
Journées ouvertes biologie informatique mathématiques .
Conference paper
see the publicationtRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes
Trends in Genetics . 16 : 287-289
Journal article
see the publication