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 751 to 780 publications on 1095 in total

Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes.

J.R. Lobry, A. Necşulea

Gene . 385 : 128-136

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Revisiting the directionnal mutation pressure theory : The analysis of a particular genomic structure in Leishmania major

A. Necşulea, J.R. Lobry

Gene . 385 : 28-40

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Trypanosoma cruzi: sequence analysis of the variable region of kinetoplast minicircles

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

Experimental Parasitology . 114 ( 4 ) : 279-88

DOI: 10.1016/j.exppara.2006.04.005

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Does lack of recombination enhance asymmetric evolution among duplicate genes? Insights from the Drosophila melanogaster genome

Yves Clément, Raquel Tavares, Gabriel Marais

Gene . 385 : 89-95

DOI: 10.1016/j.gene.2006.05.032

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Recent Origin and Cultural Reversion of a Hunter–Gatherer Group

Hiroki Oota, Brigitte Pakendorf, Günter Weiss, Arndt von Haeseler, Surin Pookajorn, Wannapa Settheetham-Ishida...

PLoS Biology . 3 ( 3 ) : e71

DOI: 10.1371/journal.pbio.0030071

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Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.

Jean-François Dufayard, L. Duret, Simon Penel, Manolo Gouy, F. Rechenmann, G. Perrière

Bioinformatics . 21 ( 11 ) : 2596-603

DOI: 10.1093/bioinformatics/bti325

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Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.

P. Kersey, L. Bower, L. Morris, A. Horne, R. Petryszak, C. Kanz...

Nucleic Acids Research . 33 ( Database issue ) : D297-302

DOI: 10.1093/nar/gki039

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Homology-dependent methylation in primate repetitive DNA.

J. Meunier, A. Khelifi, V. Navratil, L. Duret

Proceedings of the National Academy of Sciences of the United States of America . 102 ( 15 ) : 5471-6

DOI: 10.1073/pnas.0408986102

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Natural history of the ERVWE1 endogenous retroviral locus

B. Bonnaud, J. Beliaeff, O. Bouton, G. Oriol, L. Duret, Frédéric Mallet

Retrovirology . 2 : 1-7

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Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance

M. Sémon, Dominique Mouchiroud, L. Duret

Human Molecular Genetics . 14 : 421-427

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HOPPSIGEN: a database of human and mouse processed pseudogenes.

A. Khelifi, L. Duret, Dominique Mouchiroud

Nucleic Acids Research . 33 ( Database issue ) : D59-66

DOI: 10.1093/nar/gki084

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Phylogenomics of Life-Or-Death Switches in Multicellular Animals: Bcl-2, BH3-Only, and BNip Families of Apoptotic Regulators

A. Aouacheria, F. Brunet, Manolo Gouy

Molecular Biology and Evolution . 22 ( 12 ) : 2395-2416

DOI: 10.1093/molbev/msi234

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[From prevalence to predictive values: considerations on the antimicrobial susceptibility testing dealing with change of susceptibility rates].

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

Annales de Biologie Clinique . 63 ( 5 ) : 493-502

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A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model

G. Devulder, M. Perouse de Montclos, Jean-Pierre Flandrois

International Journal of Systematic and Evolutionary Microbiology . 55 : 293-302

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[Luca: the last universal common ancestor]

Patrick Forterre, Simonetta Gribaldo, Céline Brochier

Médecine/Sciences . 21 ( 10 ) : 860-5

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Multigene Analyses of Bilaterian Animals Corroborate the Monophyly of Ecdysozoa, Lophotrochozoa and Protostomia

Herve Philippe, Nicolas Lartillot, Henner Brinkmann

Molecular Biology and Evolution . 22 ( 5 ) : 1246-1253

DOI: 10.1093/molbev/msi111

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Phylogenomics

Hervé Philippe, Frédéric Delsuc, Henner Brinkmann, Nicolas Lartillot

Annual Review of Ecology, Evolution, and Systematics . 36 : 541-562

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Evolutionary origins of genomic repertoires in bacteria

E. Lerat, Vincent Daubin, H. Ochman, N.A. Moran

PLoS Biology . 3 : 0807-0814

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Recognizing the pseudogenes in bacterial genomes

E. Lerat, H. Ochman

Nucleic Acids Research . 33 : 3125-3132

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Polymorphix: a sequence polymorphism database

E. Bazin, L. Duret, Simon Penel, N. Galtier

Nucleic Acids Research . 33 : 481-484

Journal article

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Les trésors cachés du génome humain

L. Duret

Pour la science . -- : 16-21

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Bioinformatics with a French accent

L.D. Hurst, L. Duret

Genome Biology . 6 : 349.1-349.3

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Natural history of the ERVWE 1 endogenous retroviral locus.

Bertrand Bonnaud, Jean Beliaeff, Olivier Bouton, Guy Oriol, Laurent Duret, François Mallet

Retrovirology . 2:57 : 1 - 7

DOI: 10.1186/1742-4692-2-57

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Online synonymous codon usage analyses with the ade4 and seqinR packages

D. Charif, J. Thioulouse, J.R. Lobry, G. Perrière

Bioinformatics . 21 : 545-547

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MADE4: an R package for multivariate analysis of gene expression data

A.C. Culhane, J. Thioulouse, G. Perrière, D.G. Higgins

Bioinformatics . 21 : 2789-2790

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Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea.

A. Calteau, Manolo Gouy, G. Perrière

Journal of Molecular Evolution . 60 ( 5 ) : 557-65

DOI: 10.1007/s00239-004-0094-8

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Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data

F. Baty, M.P. Bihl, G. Perrière, A.C. Culhane, M.H. Brutsche

BMC Bioinformatics . 6 : 1-12

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