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 541 to 570 publications on 1006 in total

Happy together: genomic insights into the unique Nanoarchaeum/Ignicoccus association.

Patrick Forterre, Simonetta Gribaldo, Céline Brochier-Armanet

Journal of Biology . 8 ( 1 ) : 7

DOI: 10.1186/jbiol110

Journal article

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Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

Ravi D. Barabote, Gary Xie, David H. Leu, Philippe Normand, Anamaria Necsulea, Vincent Daubin...

Genome Research . ( 19 ) : 1033-1043

DOI: 10.1101/gr.084848.108

Journal article

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Genomic environment influences the dynamics of the tirant LTR retrotransposon in Drosophila

M. Fablet, E. Lerat, R. Rebollo, B. Horard, N. Burlet, S. Martinez...

FASEB Journal . 23 : 54-62

Journal article

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Infra- and Transspecific Clues to Understanding the Dynamics of Transposable Elements

Cristina Vieira, M. Fablet, E. Lerat

genome dyn stab . -- : 115-123

Journal article

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Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster

M. Deloger, F.M.G. Cavalli, E. Lerat, C. Biémont, M.-F. Sagot, Cristina Vieira

Gene . 439 : 55-62

Journal article

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Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs

E. Lerat

Heredity . -- : 1-14

Journal article

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The relationship between DNA replication and human genome organization.

Anamaria Necsulea, Claire Guillet, Jean-Charles Cadoret, Marie-Noëlle Prioleau, L. Duret

Molecular Biology and Evolution . 26 ( 4 ) : 729-741

DOI: 10.1093/molbev/msn303

Journal article

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Fast optimization of statistical potentials for structurally constrained phylogenetic models

Cécile Bonnard, Claudia L. Kleinman, Nicolas Rodrigue, Nicolas Lartillot

BMC Evolutionary Biology . 9 ( 1 ) : 227

DOI: 10.1186/1471-2148-9-227

Journal article

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Comment on “Human-Specific Gain of Function in a Developmental Enhancer”

L. Duret, N. Galtier

Science . 323(5915) : 714-715

Journal article

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Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

L. Duret, N. Galtier

Annual Review of Genomics and Human Genetics . 10 : 285-311

Journal article

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L’évolution des chromosomes sexuels humains

Gabriel Marais, L. Duret

Biofutur . 304 : 40-41

Journal article

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A pharmacologically based multiscale mathematical model of angiogenesis and its use in investigating the efficacy of a new cancer treatment strategy.

Frédérique Billy, Benjamin Ribba, Olivier Saut, Hélène Morre-Trouilhet, Thierry Colin, Didier Bresch...

Journal of Theoretical Biology . 260 ( 4 ) : 545-62

DOI: 10.1016/j.jtbi.2009.06.026

Journal article

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Iron-sulfur (Fe/S) protein biogenesis: phylogenomic and genetic studies of A-type carriers

D. Vinella, Céline Brochier-Armanet, L. Loiseau, E. Talla, F. Barras

PLoS Genetics . 5 : 261-268

Journal article

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Qri7/OSGEPL the mitochondrial version of the universal Kae1/YgjD protein is essential for mitochondrial genome maintenance

J. Oberto, N. Breuil, A. Hecker, F. Farina, Céline Brochier-Armanet, E. Culetto...

Nucleic Acids Research . 37 : 5343-52

Journal article

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Comparison of alignment free string distances for complete genome phylogeny

F. Guyon, Céline Brochier-Armanet, A. Guénoche

Advances in Data Analysis and Classification . 3 : 95-108

Journal article

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Full-Length Genome Characterization of a Novel Simian Immunodeficiency Virus Lineage (SIVolc) from Olive Colobus (Procolobus verus) and New SIVwrcPbb Strains from Western Red Colobus (Piliocolobus badius badius) from the Taï Forest in Ivory Coast

Florian Liegeois, Bénédicte Lafay, Pierre Formenty, Sabrina Locatelli, Valérie Courgnaud, Eric Delaporte...

Journal of Virology . 83 ( 1 ) : 428-439

DOI: 10.1128/JVI.01725-08

Journal article

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Genomic environment influences the dynamics of the tirant LTR retrotransposon in Drosophila.

Marie Fablet, Emmanuelle Lerat, Rita Rebollo, Béatrice Horard, Nelly Burlet, Sonia Martinez...

FASEB Journal . 23 ( 5 ) : 1482-9

DOI: 10.1096/fj.08-123513

Journal article

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The evolutionary dynamics of the Helena retrotransposon revealed by sequenced Drosophila genomes.

Adriana Granzotto, Fabrício R Lopes, Emmanuelle Lerat, Cristina Vieira, Claudia M A Carareto

BMC Evolutionary Biology . 9 : 174

DOI: 10.1186/1471-2148-9-174

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Qri7/OSGEPL, the mitochondrial version of the universal Kae1/YgjD protein, is essential for mitochondrial genome maintenance.

Jacques Oberto, Norman Breuil, Arnaud Hecker, Francesca Farina, Céline Brochier-Armanet, Emmanuel Culetto...

Nucleic Acids Research . : epub ahead of print

DOI: 10.1093/nar/gkp557

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Computational Methods for Evaluating Phylogenetic Models of Coding Sequence Evolution with Dependence between Codons

Nicolas Rodrigue, Claudia L Kleinman, Hervé Philippe, Nicolas Lartillot

Molecular Biology and Evolution . 26 ( 7 ) : 1663 - 1676

DOI: 10.1093/molbev/msp078

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In Retrospect: Lamarck's treatise at 200

Dan Graur, Manolo Gouy, David Wool

Nature . 460 ( 7256 ) : 688-689

DOI: 10.1038/460688a

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Differential retention of metabolic genes following whole-genome duplication

Jean-François Gout, Laurent Duret, Daniel Kahn

Molecular Biology and Evolution . 26 ( 5 ) : 1067-1072

DOI: 10.1093/molbev/msp026

Journal article

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Databases of Homologous Gene Families for Comparative Genomics

Simon Penel, Anne-Muriel Arigon Chifolleau, Jean-François Dufayard, Anne-Sophie Sertier, Vincent Daubin, L. Duret...

BMC Bioinformatics . 10 (Suppl.6) :S3 : 13

DOI: 10.1186/1471-2105-10-S6-S3

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Evolution of the mitochondrial ribosomal proteome

Elie Desmond-Le Quéméner, Celine Brochier-Armanet, Patrick Forterre, Simonetta Gribaldo

16th Annual Meeting of the Society of Molecular Biology and Evolution (SMBE'08) .

Poster

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Dynamic nature of the proximal AZFc region of the human Y chromosome: multiple independent deletion and duplication events revealed by microsatellite analysis.

Patricia Balaresque, Georgina Bowden, Emma Parkin, Ghada Omran, Evelyne Heyer, Lluis Quintana-Murci...

Human Mutation . 29 ( 10 ) : 1171-80

DOI: 10.1002/humu.20757

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Transcription-Induced Mutational Strand Bias and Its Effect on Substitution Rates in Human Genes

Carina Mugal, Hans-Hennig von Grunberg, Martin Peifer

Molecular Biology and Evolution . 26 ( 1 ) : 131-142

DOI: 10.1093/molbev/msn245

Journal article

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Sex-specific genetic structure and social organization in Central Asia: insights from a multi-locus study.

Laure Ségurel, Begoña Martínez-Cruz, Lluis Quintana-Murci, Patricia Balaresque, Myriam Georges, Tatiana Hegay...

PLoS Genetics . 4 ( 9 ) : e1000200

DOI: 10.1371/journal.pgen.1000200

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ISG20L2, a novel vertebrate nucleolar exoribonuclease involved in Ribosome biogenesis.

Yohann Couté, Karine Kindbeiter, Stéphane Belin, Régis Dieckmann, L. Duret, Laurent Bezin...

Molecular and Cellular Proteomics . 7 : epub ahead of print

DOI: 10.1074/mcp.M700510-MCP200

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