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 841 to 870 publications on 1006 in total

The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome

Céline Brochier, Hervé Philippe, David Moreira

Trends in Genetics . 16 ( 12 ) : 529-533

DOI: 10.1016/s0168-9525(00)02142-9

Journal article

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Absence of translationally selected synonymous codon usage bias in Helicobacter pylori.

Bénédicte Lafay, John C. Atherton, Paul M. Sharp

Microbiology . 146 ( Pt 4) : 851-60

Journal article

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Molecular Systematics of sponges (Porifera)

Carole Borchiellini, Catherine Chombard, Bénédicte Lafay, Nicole Boury-Esnault

Hydrobiologia . 420 ( 1 ) : 15-27

DOI: 10.1023/A:1003996517083

Journal article

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Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes

N.J. Tourasse, Manolo Gouy

Molecular Phylogenetics and Evolution . 13 : 159-168

DOI: 10.1006/mpev.1999.0675

Journal article

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Characterization of Unexpected Growth of Escherichia coli O157:H7 by Modeling

M. Cornu, Marie Laure Delignette-Muller, Jean-Pierre Flandrois

Applied and Environmental Microbiology . 65 : 5322-5327

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A model describing the relationship between regrowth lag time and mild temperature increase for Listeria monocytogenes

S. Breand, G. Fardel, Jean-Pierre Flandrois, L. Rosso, R. Tomassone

International Journal of Food Microbiology . 46 : 251-261

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Synonymous codon usage variation among Giardia lamblia genes and isolates.

Bénédicte Lafay, Paul M. Sharp

Molecular Biology and Evolution . 16 ( 11 ) : 1484-95

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Retrotransposons and retroviruses: analysis of the envelope gene

E. Lerat, P. Capy

Molecular Biology and Evolution . 16 : 1198-1207

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Regulation of dauer larva development in Caenorhabditis elegans by daf-18, a homologue of the tumour suppressor PTEN

Jean-Pierre Rouault, Patricia Kuwabara, Olga Sinilnikova, Laurent Duret, Danielle Thierry-Mieg, Marc Billaud

Current Biology - CB . 9 ( 6 ) : 329-334

DOI: 10.1016/S0960-9822(99)80143-2

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Human and nematode orthologs--lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis elegans

S.J. Wheelan, M.S. Boguski, L. Duret, W. Makalowski

Gene . 238 : 163-170

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Molecular characterization and placental expression of HERV-W a new human endogenous retrovirus family

J.L. Blond, F. Beseme, L. Duret, O. Bouton, F. Bedin, H. Perron...

Journal of Virology . 73 : 1175-1185

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Expression pattern and surprisingly gene length shape codon usage in Caenorhabditis Drosophila and Arabidopsis

L. Duret, Dominique Mouchiroud

Proceedings of the National Academy of Sciences of the United States of America . 96 : 4482-4487

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JaDis: computing distances between nucleic acid sequences

I. Goncalves, M. Robinson, G. Perrière, Dominique Mouchiroud

Bioinformatics . 15 : 424-425

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Is the evolution of transposable elements modular?

E. Lerat, F. Brunet, C. Bazin, P. Capy

Genetica . 107 : 15-25

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Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases.

Bénédicte Lafay, Andrew T. Lloyd, Michael J. Mclean, Kevin M. Devine, Paul M. Sharp, Kenneth H. Wolfe

Nucleic Acids Research . 27 ( 7 ) : 1642-9

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New insulin-like proteins with atypical disulfide bond pattern characterized in Caenorhabditis elegans by comparative sequence analysis and homology modeling

L. Duret, N. Guex, M.C. Peitsch, A. Bairoch

Genome Research . 8 : 348-353

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Highly conserved RNA sequences that are sensors of environmental stress

A. Spicher, O.M. Guicherit, L. Duret, A. Aslanian, E.M. Sanjines, N.C. Denko...

Molecular and Cellular Biology . 18 : 7371-7382

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Microsporidia amitochondrial protists possess a 70-kDa heat shock protein gene of mitochondrial evolutionary origin

E. Peyretaillade, V. Broussolle, P. Peyret, G. Metenier, Manolo Gouy, Christian Vivarès

Molecular Biology and Evolution . 15 : 683-689

DOI: 10.1093/oxfordjournals.molbev.a025971

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Saccharomyces boulardii Fungemia in a Patient Receiving Ultra‐levure Therapy

Jean-Pierre Flandrois, I. Fredenucci, M. Chomarat, C. Boucaud

Clinical Infectious Diseases . 27 ( 1 ) : 222-223

DOI: 10.1086/517685

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Molecular diversity of rhizobia occurring on native shrubby legumes in southeastern Australia

Bénédicte Lafay, Jeremy J. Burdon

Applied and Environmental Microbiology . 64 ( 10 ) : 3989-97

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What is the state of the art in molecular systematics of marine Porifera ?

Nicole Boury-Esnault, Carole Borchiellini, Catherine Chombard, Bénédicte Lafay

Hydrobiologia .

Conference paper

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The non-redundant Bacillus subtilis (NRSub) database: update 1998

G. Perrière, Manolo Gouy, T. Gojobori

Nucleic Acids Research . 26 ( 1 ) : 60-62

DOI: 10.1093/nar/26.1.60

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Multiple sequence alignment with Clustal X

F. Jeanmougin, J.D. Thompson, Manolo Gouy, D.G. Higgins, T.J. Gibson

Trends in Biochemical Sciences . 23 ( 10 ) : 403-405

DOI: 10.1016/S0968-0004(98)01285-7

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Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis

N. Galtier, Manolo Gouy

Molecular Biology and Evolution . 15 ( 7 ) : 871-879

DOI: 10.1093/oxfordjournals.molbev.a025991

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Microsporidian Encephalitozoon cuniculi a unicellular eukaryote with an unusual chromosomal dispersion of ribosomal genes and a LSU rRNA reduced to the universal core

E. Peyretaillade, C. Biderre, P. Peyret, F. Duffieux, G. Metenier, Manolo Gouy...

Nucleic Acids Research . 26 : 3513-3520

DOI: 10.1093/nar/26.15.3513

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Phylogenetic analysis and genome size of Ostreococcus tauri (Chlorophyta Prasinophyceae)

C. Courties, R. Perasso, M.-J. Chrétiennot-Dinet, Manolo Gouy, Laure Guillou, M. Troussellier

Journal of Phycology . 34 : 844-849

DOI: 10.1046/j.1529-8817.1998.340844.x

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Model of the influence of time and mild temperature on Listeria monocytogenes nonlinear survival curves

S. Breand, G. Fardel, Jean-Pierre Flandrois, L. Rosso, R. Tomassone

International Journal of Food Microbiology . 40 : 185-195

Journal article

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