Bioinformatics, Phylogeny and Evolutionary Genomics Group

Members

Our group focuses on two main axes: phylogenomics (i.e. the inference of evolutionary history based on genomics data) and evolutionary genomics (understanding the molecular and population processes that drive genome evolution). We see genomes both as a subject of research (how do genomes evolve, why are they structured the way they are?), but also as a main source of empirical knowledge about the macroevolutionary patterns (what do they tell us about the history of life on Earth?), or about the phenotypes and life-history strategies of organisms. Our works heavily rely on methodological developments (bioinformatics, modeling and statistical inference).

Evolution of genome architecture and expression

Genomes are the result of a long-term evolutionary process, shaped by multiple evolutionary forces. Some genomic features are adaptive (i.e. are beneficial for the fitness of organisms), others result from non-adaptive processes (random drift and biased gene conversion - BGC) or are caused by conflicts between multiple levels of selection (e.g. meiotic drive or the spread of selfish genetic elements). We explore different aspects of genome architecture (base composition landscapes, genome structure and size, impact of transposable elements, …) or functioning (gene expression, lncRNAs, epigenetic landscapes, …), and try to disentangle the relative contribution of adaptive and non-adaptive processes to their evolution. For this purpose, we consider both the molecular mechanisms (mutation, repair, recombination) and the population processes (selection, drift, BGC, …) that shape genetic variation.

Phylogenomics

We are interested in reconstructing the history of life on Earth. This research unfolds along several axes. First, we develop phylogenomic databases of aligned genetic sequences (e.g. BIBI, RiboDB or HOGENOM). Second, we conduct methodological research on how to accurately reconstruct deep phylogenies, infer divergence times, reconstruct ancestral genetic sequences, gene repertoires and life-history traits. This methodological work is translated into publicly available software programs (e.g. SeaView, PhyloBayes, Coevol). Finally, we apply these approaches to several important problems, among which: reconstructing the phylogeny of animals, of archaea, or the global tree of life; using phylogenies and ancestral gene repertoires to investigate the evolution of complex systems and the emergence of molecular and cellular functions in the three domains of life; reconstructing ancestral genetic sequences, a research activity that has industrial and biotechnological applications.

Teaching and outreach

We teach at University Lyon 1 (Master Bioinfo@Lyon), INSA, ENS Lyon, we organize bioinformatics internships. We regularly give conferences on evolution (tree of life, human evolution, genetic diversity, …).
Prospective students and postdocs are invited to apply, as we often welcome visitors for internships or research projects.
 
Keywords: Molecular evolution and Population Genomics; Phylogenomics; Computational Genomics; Comparative genomics; Bioinformatics; Statistical inference.

Publications

Display of 781 to 810 publications on 1006 in total

Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome

C. Rizzon, Gabriel Marais, Manolo Gouy, C. Biémont

Genome Research . 12 : 400-407

DOI: 10.1101/gr.210802

Journal article

see the publication

What is the relevance of obtaining multiple blood samples for culture? A comprehensive model to optimize the strategy for diagnosing bacteremia

B. Lamy, Pascal Roy, G. Carret, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Clinical Infectious Diseases . 35 ( 7 ) : 842-850

DOI: 10.1086/342383

Journal article

see the publication

Modelling the competitive growth of Listeria monocytogenes and Listeria innocua in enrichment broths

Marie Cornu, Martin Kalmokoff, Jean-Pierre Flandrois

International Journal of Food Microbiology . 73 ( 2-3 ) : 261-274

DOI: 10.1016/S0168-1605(01)00658-4

Journal article

see the publication

Archaeal phylogeny based on ribosomal proteins

O. Matte-Tailliez, Céline Brochier-Armanet, Patrick Forterre, H. Philippe

Mol Biol Evol . 19 : 631-639

Journal article

see the publication

Eubacterial phylogeny based on translational apparatus proteins

Céline Brochier, Eric Bapteste, David Moreira, Hervé Philippe

Trends in Genetics . 18 ( 1 ) : 1-5

DOI: 10.1016/s0168-9525(01)02522-7

Journal article

see the publication

Conflicting phylogeographic patterns in rRNA and nifD indicate regionally restricted gene transfer in Bradyrhizobium.

Matthew A. Parker, Benedicte Lafay, Jeremy J. Burdon, Peter van Berkum

Microbiology . 148 ( Pt 8 ) : 2557-65

Journal article

see the publication

ROSO: A software to search optimized oligonucleotide probes for microarrays

Hubert Charles, Nancie Reymond, Guillaume Beslon, Laurent Duret, Jean-Michel Fayard

COST853: Agricultural Biomarkers for Array-Technology .

Conference paper

see the publication

ROSO : A Software to Search Optimized Oligonucleotide Probes for Microarrays

Nancie Reymond, Hubert Charles, Guillaume Beslon, Laurent Duret, Jean-Michel Fayard

10. International Conference on Intelligent Systems for Molecular Biology (ISMB) .

Poster

see the publication

Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine.

C. Chureau, M. Prissette, A. Bourdet, Valérie Barbe, L. Cattolico, L. Jones...

Genome Research . 12 : 894-908

Journal article

see the publication

Vanishing GC-Rich Isochores in Mammalian Genomes

L. Duret, M. Sémon, G. Piganeau, Dominique Mouchiroud, N. Galtier

Genetics . 162 : 1837-1848

Journal article

see the publication

Comparative sequence analysis of the X-inactivation center region in mouse human and bovine

C. Chureau, M. Prissette, A. Bourdet, Valérie Barbe, Laurence Cattolico, L. Jones...

Genome Research . 12 : 894-908.

Journal article

see the publication

Evolution of synonymous codon usage in metazoans

L. Duret

Current Opinion in Genetics and Development . 12 : 640-649

Journal article

see the publication

A mathematical method for determining genome divergence and species delineation using AFLP

Christophe Mougel, J. Thioulouse, G. Perrière, X. Nesme

International Journal of Systematic and Evolutionary Microbiology . 52 : 573-586

DOI: 10.1099/00207713-52-2-573

Journal article

see the publication

A mathematical method for determining genome divergence and species delineation using AFLP

Christophe Mougel, Jean Thioulouse, Guy Perrière, Xavier Nesme

International Journal of Systematic and Evolutionary Microbiology . 52 : 573-586

Journal article

see the publication

NUREBASE: database of nuclear hormone receptors

J. Duarte, G. Perrière, V. Laudet, M. Robinson-Rechavi

Nucleic Acids Research . 30 : 364-368

Journal article

see the publication

Functional and evolutionary analysis of a eukaryotic parasitic genome

Christian Vivarès, Manolo Gouy, F. Thomarat, G. Metenier

Current Opinion in Microbiology . 5 : 499-505

DOI: 10.1016/S1369-5274(02)00356-9

Journal article

see the publication

Modeling the Lag Time of Listeria monocytogenes from Viable Count Enumeration and Optical Density Data

F. Baty, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Applied and Environmental Microbiology . 68 : 5816-5825

Journal article

see the publication

The relative abundance of dinucleotides in transposable elements in five species

E. Lerat, P. Capy, C. Biémont

Molecular Biology and Evolution . 19 : 964-967

Journal article

see the publication

Codon usage by transposable elements and their host genes in five species

E. Lerat, P. Capy, C. Biémont

Journal of Molecular Evolution . 54 : 625-637

Journal article

see the publication

Haplotype tests using coalescent simulations conditional on the number of segregating sites

F. Depaulis, Sylvain Mousset, M. Veuille

Molecular Biology and Evolution . 18 : 1136-1138

Journal article

see the publication

Organisation Fonctionnement et Evolution des Génomes de Métazoaires : Mais où est donc passée la sélection naturelle ?

L. Duret

incollection . -- : 287-289

Journal article

see the publication

Why do genes have introns? Recombination might add a new piece to the puzzle

L. Duret

Trends in Genetics . 17 : 172-175

Journal article

see the publication

Analysis of pFQ31 a 8551-bp cryptic plasmid from the symbiotic nitrogen-fixing actinomycete Frankia

C. Lavire, D. Louis, G. Perrière, J. Briolay, P. Normand, B. Cournoyer

FEMS Microbiology Letters . 197 : 111-116

DOI: 10.1111/j.1574-6968.2001.tb10591.x

Journal article

see the publication

Lipid phosphate phosphatases in Arabidopsis. Regulation of the AtLPP1 gene in response to stress

O. Pierrugues, C. Brutesco, J. Oshiro, Manolo Gouy, Y. Deveaux, G.M. Carman...

Journal of Biological Chemistry . 276 ( 23 ) : 20300-20308

DOI: 10.1074/jbc.M009726200

Journal article

see the publication

Spatial Modeling of Nitrifier Microhabitats in Soil

G. Grundmann, A. Dechesne, F. Bartoli, Jean-Pierre Flandrois, J. Chassé, R. Kizungu

Soil Science Society of America Journal . 65 ( 6 ) : 1709

DOI: 10.2136/sssaj2001.1709

Journal article

see the publication

Comparaison de séquences d'éléments transposables et de gènes d'hôte chez cinq espèces : A. thaliana, C. elegans, D. melanogaster, H. sapiens et S. cerevisiae

Emmanuelle Lerat

Thesis

see the publication

Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes

Gabriel Marais, Dominique Mouchiroud, L. Duret

Proceedings of the National Academy of Sciences of the United States of America . 98 : 5688-5692

Journal article

see the publication

Determinants of CpG islands: expression in early embryo and isochore structure

L. Ponger, L. Duret, Dominique Mouchiroud

Genome Research . 11 : 1854-1860

Journal article

see the publication

Synonymous codon usage accuracy of translation and gene length in Caenorhabditis elegans

Gabriel Marais, L. Duret

Journal of Molecular Evolution . 52 : 275-280

Journal article

see the publication