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 961 to 986 publications on 986 in total

Corynebacterium JK: surgical infections in non-immunosuppressed patients

Jean-Pierre Flandrois, A. Lepape, P.Y. Carry, M. Chomarat, J.P. Perdrix, J.M. Grozel...

Intensive Care Medicine . 15 ( 1 )

DOI: 10.1007/bf00255631

Journal article

see the publication

[Use of an expert system as a tool to carry out urinary cyto-bacteriologic tests].

S Comby, G. Carret, Jean-Pierre Flandrois, A. Pavé, M Perouse de Montclos

Annales de Biologie Clinique . 46 ( 8 ) : 669-72

Journal article

see the publication

Early stages of in vitro killing curve of LY146032 and vancomycin for Staphylococcus aureus.

Jean-Pierre Flandrois, Ghislaine Fardel, G. Carret

Antimicrobial Agents and Chemotherapy . 32 ( 4 ) : 454-457

DOI: 10.1128/AAC.32.4.454

Journal article

see the publication

[Effect of subinhibitory concentrations of antibiotics on the growth level of bacteria].

G. Carret, B Charpe, A Cheruy, Jean-Pierre Flandrois, A. Pavé, C Couix

Pathologie Biologie . 35 ( 5 ) : 483-93

Journal article

see the publication

Bacterial growth measurement using an automated system: Mathematical modelling and analysis of growth kinetics

Jean-Pierre Flandrois, A. Corman, G. Carret, A. Pavé, C. Couix

Annales de l'Institut Pasteur / Microbiologie . 137 ( 1 ) : 133-143

DOI: 10.1016/S0769-2609(86)80102-8

Journal article

see the publication

[Evaluation of the Rapid-ATB system for testing the sensitivity of staphylococci to antibiotics. Comparison with the agar dilution reference method].

P Le Noc, G. Carret, C. Couix, Jean-Pierre Flandrois, J Gayral, J. Robert

Pathologie Biologie . 34 ( 5 Pt 2 ) : 600-3

Journal article

see the publication

Gelatin and collagen binding to Staphylococcus aureus strains.

G. Carret, H. Emonard, G. Fardel, M. Druguet, D. Herbage, Jp Flandrois

Ann Inst Pasteur Microbiol . 136A : 241-245

Journal article

see the publication

Evolution of the primate beta-globin gene region. High rate of variation in CpG dinucleotides and in short repeated sequences between man and chimpanzee

P. Savatier, G. Trabuchet, C. Faure, Y. Chebloune, Manolo Gouy, Ghislain Verdier...

Journal of Molecular Biology . 182 ( 1 ) : 21-29

DOI: 10.1016/0022-2836(85)90024-5

Journal article

see the publication

ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage

Manolo Gouy, Christian Gautier, M. Attimonelli, C. Lanave, G. Di Paola

Bioinformatics . 1 : 167-172

DOI: 10.1093/bioinformatics/1.3.167

Journal article

see the publication

Molecular evolution of viruses as seen by nucleic acid sequence study

R. Grantham, T. Greenland, S. Louail, Dominique Mouchiroud, J.-L. Prato, Manolo Gouy...

Bulletin de l'Institut Pasteur . 83 : 95-148

Journal article

see the publication

Prédiction des structures secondaires dans les acides nucléiques: aspects algorithmiques et physiques

Manolo Gouy, P. Marliere, C. Papanicolaou, J. Ninio

Biochimie . 67 ( 5 ) : 523-531

DOI: 10.1016/S0300-9084(85)80272-8

Journal article

see the publication

Evolution of the primate β-globin gene region

P. Savatier, G. Trabuchet, C. Faure, Y. Chebloune, M. Gouy, G. Verdier...

Journal of Molecular Biology . 182 ( 1 ) : 21-29

DOI: 10.1016/0022-2836(85)90024-5

Journal article

see the publication

An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules

C. Papanicolaou, Manolo Gouy, J. Ninio

Nucleic Acids Research . 12 ( 1 ) : 31-44

DOI: 10.1093/nar/12.1Part1.31

Journal article

see the publication

ACNUC: a nucleic acid sequence data base and analysis system

Manolo Gouy, F. Milleret, C. Mugnier, M. Jacobzone, Christian Gautier

Nucleic Acids Research . 12 ( 1 ) : 121-127

DOI: 10.1093/nar/12.1Part1.121

Journal article

see the publication

[Nonparametric approach to the determination of critical diameters. Comparison with conventional methods].

Jean-Pierre Flandrois, G. Carret

Pathologie Biologie . 32 ( 5 Pt 2 ) : 488-91

Journal article

see the publication

Codon usage in bacteria: correlation with gene expressivity

Manolo Gouy, Christian Gautier

Nucleic Acids Research . 10 ( 22 ) : 7055-7074

DOI: 10.1093/nar/10.22.7055

Journal article

see the publication

Codon catalog usage is a genome strategy modulated for gene expressivity

R. Grantham, Christian Gautier, Manolo Gouy, M. Jacobzone, R. Mercier

Nucleic Acids Research . 9 : R43-R74

DOI: 10.1093/nar/9.1.213-b

Journal article

see the publication

Nucleic acid sequences handbook

Christian Gautier, Manolo Gouy, Monique Jacobzone, Richard Grantham

1-2

Book

see the publication

Codon catalog usage and the genome hypothesis

R. Grantham, Christian Gautier, Manolo Gouy, R. Mercier, A. Pave

Nucleic Acids Research . 8 ( 1 ) : R49-R62

DOI: 10.1093/nar/8.1.197-c

Journal article

see the publication

Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type

R. Grantham, Christian Gautier, Manolo Gouy

Nucleic Acids Research . 8 ( 9 ) : 1893-1912

DOI: 10.1093/nar/8.9.1893

Journal article

see the publication

Evolution de la résistance aux antibiotiques des agents infectieux en milieu hospitalier

J Fleurette, S Chassignol, A Moulin, A Biron, Jean-Pierre Flandrois

Bulletin de l'Institut national de la sante et de la recherche medicale . 25 ( 5 ) : 963-92

Journal article

see the publication