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 661 to 690 publications on 1102 in total

Phylogenetic Mixture Models for Proteins

Quang Le Si, Nicolas Lartillot, Olivier Gascuel

Philosophical Transactions of the Royal Society B: Biological Sciences . 363 : 3965-3976

DOI: 10.1098/rstb.2008.0180

Journal article

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Bayesian computation for statistical models with intractable normalizing constants

Yves Atchade, Nicolas Lartillot, Christian Robert

Preprint

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Improvement of Molecular Phylogenetic Inference and the Phylogeny of Bilateria

Nicolas Lartillot, Herve Philippe

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences (1934–1990) . 363 ( 1496 ) : 1463-1472

DOI: 10.1098/rstb.2007.2236

Journal article

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Uniformization for Sampling Realizations of Markov Processes: Applications to Bayesian Implementations of Codon Substitution Models

Nicolas Rodrigue, Herve Philippe, Nicolas Lartillot

Bioinformatics . 24 ( 1 ) : 56-62

DOI: 10.1093/bioinformatics/btm532

Journal article

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Losing helena: The extinction of a drosophila line-like element

Rita Rebollo, Emmanuelle Lerat, Liliana Lopez Kleine, Christian Biémont, Cristina Vieira

BMC Genomics . 9 : 1-11

DOI: 10.1186/1471-2164-9-149

Journal article

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Sequence variability and phylogenetic analyses of the Complement Regulatory Protein expressed by the trypomastigote stage of Trypanosoma cruzi identify a monophyletic group of CRP-like proteins

Françoise Mathieu-Daudé, Bénédicte Lafay, Olivia Touzet, Marie-France Bosseno, Favio Parrado, Ana Maria Rojas...

Xth European Multicolloquium of Parasitology .

Conference paper

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Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

A. Studer, Simon Penel, L. Duret, M. Robinson-Rechavi

Genome Research . 18 : 1393-1402

Journal article

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Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline.

L. Duret, Jean Cohen, Claire Jubin, Philippe Dessen, Jean-François Goût, Sylvain Mousset...

Genome Research . 18 ( 4 ) : 585-96

DOI: 10.1101/gr.074534.107

Journal article

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The Impact of Recombination on Nucleotide Substitutions in the Human Genome

L. Duret, P.F. Arndt

PLoS Genetics . 4 : 1-19

Journal article

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Neutral Theory: The Null Hypothesis of Molecular Evolution

L. Duret

Nature Education . 1 ( 1 ) : 803-806

Journal article

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Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline

L. Duret, J. Cohen, C. Jubin, P. Dessen, J.-F. Gout, Sylvain Mousset...

Genome Research . 18 : 585-596

DOI: 10.1101/gr.074534.107

Journal article

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Démasquage des gènes spécifiques d'une espèce génomique du complexeAgrobacterium tumefaciens par AFLP et multicapteur à ADN

Perrine Portier, Denis Costechareyre, Daniel Muller, David Chapulliot, Christine Oger, Guy Perrière...

7. Colloque national du Bureau des Ressources Génétiques . 7

Conference paper

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Automatic Identification of Large Collections of Protein-Coding or rRNA Sequences

Anne-Muriel Arigon Chifolleau, Guy Perrière, Manolo Gouy

Biochimie . 90 ( 4 ) : 609-614

DOI: 10.1016/j.biochi.2007.08.006

Journal article

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Bioinformatics in the complete genome sequence era

G. Perrière

Biochimie . 90 : 553-554

Journal article

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Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

Bastien Boussau, Laurent Guéguen, Manolo Gouy

BMC Evolutionary Biology . 8 : 272-272

DOI: 10.1186/1471-2148-8-272

Journal article

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A seven-gene multilocus genus-wide approach to the phylogeny of mycobacteria using supertrees

S. Mignard, Jean-Pierre Flandrois

International Journal of Systematic and Evolutionary Microbiology . 58(part 6) : 1432-1441

Journal article

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Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota.

Céline Brochier-Armanet, Bastien Boussau, Simonetta Gribaldo, Patrick Forterre

Nature Reviews Microbiology . 6 ( 3 ) : 245-252

DOI: 10.1038/nrmicro1852

Journal article

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A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya.

Céline Brochier-Armanet, Simonetta Gribaldo, Patrick Forterre

Biol Direct . 3 : 54

DOI: 10.1186/1745-6150-3-54

Journal article

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Les Archaea : évolution et diversité du troisième domaine du vivant

Simonetta Gribaldo, Patrick Forterre, Céline Brochier-Armanet

Bulletin - Société Française de Microbiologie . 23 ( 3 ) : 137-145

Journal article

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Metagenome Annotation Using a Distributed Grid of Undergraduate Students

P. Hingamp, Céline Brochier-Armanet, E. Talla, D. Gautheret, D. Thieffry, C. Herrmann

PLoS Biology . 6 : 239-241

Journal article

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Mating system and recombination affect molecular evolution in four Triticeae species

A. Haudry, A. Cenci, C. Guilhaumon, E. Paux, S. Poirier, S. Santoni...

Genetics Research . 90 : 97-109

Journal article

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Full molecular characterization of a simian immunodeficiency virus, SIVwrcpbt from Temminck's red colobus (Piliocolobus badius temminckii) from Abuko Nature Reserve, The Gambia

Sabrina Locatelli, Bénédicte Lafay, Florian Liegeois, Nelson Ting, Eric Delaporte, Martine Peeters

Virology . 376 ( 1 ) : 90-100

DOI: 10.1016/j.virol.2008.01.049

Journal article

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Prevalence and genetic diversity of simian immunodeficiency virus infection in wild-living red colobus monkeys (Piliocolobus badius badius) from the Taï forest, Côte d'Ivoire SIVwrc in wild-living western red colobus monkeys.

Sabrina Locatelli, Florian Liegeois, Bénédicte Lafay, Amy D Roeder, Michael W Bruford, Pierre Formenty...

Infection, Genetics and Evolution . 8 ( 1 ) : 1-14

DOI: 10.1016/j.meegid.2007.08.004

Journal article

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A Site- and Time-Heterogeneous Model of Amino Acid Replacement

Samuel Blanquart, Nicolas Lartillot

Molecular Biology and Evolution . 25 ( 5 ) : 842-858

DOI: 10.1093/molbev/msn018

Journal article

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Additional molecular support for the new chordate phylogeny.

Frédéric Delsuc, Georgia Tsagkogeorga, Nicolas Lartillot, Herve Philippe

Genesis - The Journal of Genetics and Development . 46 ( 11 ) : 592-604

DOI: 10.1002/dvg.20450

Journal article

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Mating system and recombination affect molecular evolution in four Triticeae species

A. A. Haudry, A. A. Cenci, C C Guilhaumon, Etienne Paux, S. S. Poirier, S. S. Santoni...

Genetics Research . 90 ( 1 ) : 97-109

DOI: 10.1017/S0016672307009032

Journal article

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Parallel Adaptations to High Temperatures in the Archean Eon

Bastien Boussau, Samuel Blanquart, Anamaria Necsulea, Nicolas Lartillot, Manolo Gouy

Nature . 456 ( 7224 ) : 942-945

DOI: 10.1038/nature07393

Journal article

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Analyse et exploitation de la diversité génétique des polykétides synthases de type I dans l'ADN metagénomique d'un sol

Aurélien Ginolhac, Sandrine Demanèche, Cyrille Jarrin, Patrick Robe, Fabrice Lefevre, Renaud Nalin...

7ème colloque national "Ressources génétiques" . : 201-213

Conference paper

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