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 91 to 120 publications on 163 in total
Les trésors cachés du génome humain
Pour la science . -- : 16-21
Journal article
see the publicationPolymorphix: a sequence polymorphism database
Nucleic Acids Research . 33 : 481-484
Journal article
see the publicationBioinformatics with a French accent
Genome Biology . 6 : 349.1-349.3
Journal article
see the publicationNatural history of the ERVWE 1 endogenous retroviral locus.
Retrovirology . 2:57 : 1 - 7
Journal article
see the publicationThe endogenous retroviral locus ERVWE1 is a bona fide gene involved in hominoid placental physiology
Proceedings of the National Academy of Sciences of the United States of America . 101 : 1731-1736
Journal article
see the publicationEvidence that functional transcription units cover at least half of the human genome
Trends in Genetics . 20 : 229-232
Journal article
see the publicationThe Decline of Isochores in Mammals: An Assessment of the GC Content Variation Along the Mammalian Phylogeny
Journal of Molecular Evolution . 58 : 653-660
Journal article
see the publicationIdentitag a relational database for SAGE tag identification and interspecies comparison of SAGE libraries
BMC Bioinformatics . 5 : 1-12
Journal article
see the publicationROSO : Research on Optimized Oligonucleotide Probes for Microarrays
Bioinformatics . 20 : 271-273
Journal article
see the publicationGrid as a bioinformatic tool
Parallel Computing . 30 : 1093-1107
Journal article
see the publicationIdentitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries.
BMC Bioinformatics . 5 : 143
Journal article
see the publicationGrid as a bioinformatic tool
Parallel Computing . 30 : 1093-1107
Journal article
see the publicationGrid as a bioinformatic tool
Parallel Computing . 30 : 1093-1107
Journal article
see the publicationRecombination drives the evolution of GC-content in the human genome
Molecular Biology and Evolution . 21 : 984-990
Journal article
see the publicationEvidence of Selection on the Domesticated ERVWE1 env Retroviral Element Involved in Placentation
Molecular Biology and Evolution . 21 : 1895-1901
Journal article
see the publicationIdentitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries.
BMC Bioinformatics . ( 5 ) : 143
Journal article
see the publicationPhysical and transcript map of the autosomal dominant colobomatous microphthalmia locus on chromosome 15q12-q15 and refinement to a 4.4 Mb region.
European Journal of Human Genetics . 12 ( 7 ) : 574-8
Journal article
see the publicationPhysical and transcript map of the autosomal dominant colobomatous microphthalmia locus on chromosome 15q12-q15 and refinement to a 4.4 Mb region.
European Journal of Human Genetics . ( 12 ) : 574-578
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 : 1127-1135
Journal article
see the publicationNeutral effect of recombination on base composition in Drosophila
Genetical Research . 81 : 79-89
Journal article
see the publicationPlacenta-Specific INSL4 Expression Is Mediated by a Human Endogenous Retrovirus Element
Biology of Reproduction . 68 : 1422-1429.
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 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 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 publication