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 1051 to 1080 publications on 1085 in total

[Interpretative reading and quality control of an antibiotic sensitivity test using an expert system. Application to the API ATB system and Enterobacteriaceae].

M. Peyret, Jean-Pierre Flandrois, G. Carret, C. Pichat

Pathologie Biologie . 37 ( 5 Pt 2 ) : 624-8

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[Bacteriostatic and bactericidal antibiotics: differences in subinhibitory concentration effects on the growth of Escherichia coli].

S Comby, G. Carret, A. Pavé, Jean-Pierre Flandrois, C. Pichat

Pathologie Biologie . 37 ( 5 ) : 335-40

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Mathematical modelling of growth of Escherichia coli at subinhibitory levels of chloramphenicol or tetracyclines

Jean-Pierre Flandrois, S. Comby, J.P. Flandrois, G. Carret, C. Pichat

Research in Microbiology . 140 ( 3 ) : 243-254

DOI: 10.1016/0923-2508(89)90079-X

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RPA190 the gene coding for the largest subunit of yeast RNA polymerase A

S. Memet, Manolo Gouy, C. Marck, A. Sentenac, J.M. Buhler

Journal of Biological Chemistry . 263 ( 6 ) : 2830-2839

DOI: 10.1016/S0021-9258(18)69144-6

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Mathematical modelling of bacterial growth at subinhibitory levels of aminoglycosides

Jean-Pierre Flandrois, S Comby, G. Carret, C. Pichat

Annales de l'Institut Pasteur / Microbiologie . 139 ( 5 ) : 613-629

DOI: 10.1016/0769-2609(88)90159-7

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[An expert system as an aid to the validation of results of the antibiogram. Feasibility study based on the example of Staphylococcus aureus].

S Comby, Jean-Pierre Flandrois, A. Pavé

Pathologie Biologie . 36 ( 5 ) : 381-5

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[Demonstration of an inoculum effect on the estimation of the minimal inhibitory concentration of LY 146032].

Jean-Pierre Flandrois, G. Carret, M. Peyret, Catherine Pichat

Pathologie Biologie . 36 ( 5 ) : 377-80

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[A mathematical study of the mortality curve of Escherichia coli exposed to aminoglycosides].

Jean-Pierre Flandrois, G. Carret, G. Fardel

Pathologie Biologie . 36 ( 5 ) : 446-51

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Study of staphylococcus aureus teichoic acid immunodominant site by help of synthetic haptens

Michèle Pérouse de Montclos, Paul Boullanger, Jean-Pierre Flandrois

Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectious diseases, virology, parasitology . 267 ( 3 ) : 414-424

DOI: 10.1016/S0176-6724(88)80058-0

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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

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[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

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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

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[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

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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

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[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

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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

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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

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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

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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

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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

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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

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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

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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

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[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

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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

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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

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