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 721 to 750 publications on 1006 in total

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

Journal article

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Grid as a bioinformatic tool

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

Parallel Computing . 30 : 1093-1107

Journal article

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Update of NUREBASE: nuclear hormone receptor functional genomics

D. Ruau, J. Duarte, T. Ourjdal, G. Perrière, V. Laudet, M. Robinson-Rechavi

Nucleic Acids Research . 32 : D165-D167

Journal article

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Update of NUREBASE : nuclear hormone receptor functional genomics

D. Ruau, J. Duarte, T. Ourjdal, Guy Perrière, V. Laudet, M. Robinson-Rechavi

Nucleic Acids Research . 32 : D165-D167

Journal article

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Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of microsporidia and reveals a high frequency of fast-evolving genes

F. Thomarat, Christian Vivarès, Manolo Gouy

Journal of Molecular Evolution . 59 : 780-791

DOI: 10.1007/s00239-004-2673-0

Journal article

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A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process

Nicolas Lartillot, Herve Philippe

Molecular Biology and Evolution . 21 ( 6 ) : 1095-1109

DOI: 10.1093/molbev/msh112

Journal article

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The evolutionary history of quorum-sensing in bacteria

E. Lerat, N.A. Moran

Molecular Biology and Evolution . 21 : 903-913

Journal article

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Ψ-Φ: Exploring the outer limits of bacterial pseudogenes

E. Lerat, H. Ochman

Genome Research . 14 : 2273--2278

Journal article

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Hypervariable and highly divergent intron/exon organizations in the chordate Oikopleura dioica

R. Edvardsen, E. Lerat, A.D. Maeland, M. Flat, R. Tewari, M.F. Jensen...

Journal of Molecular Biology . 59 : 448-457

Journal article

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Reversing gene erosion: Reconstructing ancestral bacterial genomes from gene-content and order data

J.V. Earnest-Deyoung, E. Lerat, B.M.E. Moret

incollection . 3240 : 1-13

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

Journal article

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Grid as a bioinformatic tool

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

Parallel Computing . 30 : 1093-1107

Journal article

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

J. Meunier, L. Duret

Molecular Biology and Evolution . 21 : 984-990

Journal article

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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

Journal article

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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

Journal article

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The European ribosomal RNA database

Jan Wuyts, Guy Perrière, Yves van de Peer

Nucleic Acids Research . 32 : D101-D103

DOI: 10.1093/nar/gkh065

Journal article

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Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones.

Aurélien Ginolhac, Cyrille Jarrin, B. Gillet, P. Robe, P. Pujic, K. Tuphile...

Applied and Environmental Microbiology . 70 : 5522-5527

Journal article

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Phylogenetic study and identification of Vibrio splendidus-related strains based on gyrB gene sequences.

Frédérique Le Roux, Mélanie Gay, Christophe Lambert, Jean-Louis Nicolas, Manolo Gouy, Franck Berthe

Diseases of Aquatic Organisms . 58 ( 2-3 ) : 143-150

DOI: 10.3354/dao058143

Journal article

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How does susceptibility prevalence impact on the performance of disk diffusion susceptibility testing?

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

Diagnostic Microbiology and Infectious Disease . 49 : 131-139

Journal article

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Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers

P. Lopez-Garcia, Céline Brochier-Armanet, D. Moreira, F. Rodriguez-Valera

Environmental Microbiology . 6 : 19-34

Journal article

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Molecular analysis of the hypervariable regions in the minicircle of kinetoplastic genome in Trypanosoma cruzi, agent of Chagas'disease

Jenny Telleria, Bénédicte Lafay, Myrna Virreira, Christian Barnabé, Michel Tibayrenc, M. Svoboda

VII INTERNATIONAL MEETING ON MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS OF INFECTIOUS DISEASES (MEEGID VII) .

Conference paper

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Brucella est un ochrobactrum à génome réduit

Corinne Teyssier, Bénédicte Lafay, Agnès Masnou, Estelle Jumas-Bilak, Hélène Marchandin

VI eme Congrès de la Société Française de Microbiologie .

Conference paper

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CAT : Un Modèle Phylogénétique Bayésien permettant de prendre en compte l'Hétérogénéité des Processus de Substitution entre Sites dans les Alignements Protéiques

Nicolas Lartillot, Herve Philippe

Biosystema 22 . 22 : 97-104

Book chapter

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$Psi$-$Phi$: Exploring the outer limits of bacterial pseudogenes

E. Lerat, H. Ochman

Genome Research . 14 : 2273-2278

Journal article

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Invertebrate Data Predict an Early Emergence of Vertebrate Fibrillar Collagen Clades and an Anti-incest Model

Abdel Aouacheria, Caroline Cluzel, Claire Lethias, Manolo Gouy, Robert Garrone, Jean-Yves Exposito

Journal of Biological Chemistry . 279 ( 46 ) : 47711-47719

DOI: 10.1074/jbc.M408950200

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.

Laurent Michon, L. Morle, M. Bozon, L. Duret, Zech J. C., J. Godet...

European Journal of Human Genetics . ( 12 ) : 574-578

Journal article

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Evidence of a high rate of selective sweeps in African Drosophila melanogaster

Sylvain Mousset, L. Brazier, M.L. Cariou, F. Chartois, F. Depaulis, M. Veuille

Genetics . 163 : 599-609

Journal article

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Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach

S. Glinka, L. Ometto, Sylvain Mousset, W. Stephan, D. de Lorenzo

Genetics . 165 : 1269-1278

Journal article

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Power of neutrality tests to detect bottlenecks and hitchhiking

F. Depaulis, Sylvain Mousset, M. Veuille

Journal of Molecular Evolution . 57 : S190-S200

Journal article

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