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 871 to 900 publications on 1006 in total

NEURAL NETWORKS AS AN ALTERNATIVE METHOD FOR PREDICTING BACTERIAL GROWTH RATE FROM THE BEGINNING OF A GROWTH CURVE

M. Delignette-Muller, Jean-Pierre Flandrois

Industrial Applications of Neural Networks . : 451-457

DOI: 10.1142/9789812816955_0053

Book chapter

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Searching for regulatory elements in human noncoding sequences

L. Duret, P. Bucher

Current Opinion in Structural Biology . 7 : 399-406

Journal article

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The NRSub database: update 1997

G. Perrière, I. Moszer, T. Gojobori

Nucleic Acids Research . 25 : 53-56

Journal article

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Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record

J. Pawlowski, I. Bolivar, J.F. Fahrni, C. de Vargas, Manolo Gouy, L. Zaninetti

Molecular Biology and Evolution . 14 ( 5 ) : 498-505

DOI: 10.1093/oxfordjournals.molbev.a025786

Journal article

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Influence of atmospheric conditions during incubation on the susceptibilities of Streptococcus pneumoniae isolates to five beta- lactam antibiotics

M. Chomarat, L. Chollet, M. Peyret, Jean-Pierre Flandrois

Journal of Antimicrobial Chemotherapy . 40 ( 4 ) : 599-601

DOI: 10.1093/jac/40.4.599

Journal article

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Simple relationship between acid dissociation constant and minimal pH for microbial growth in laboratory medium

Jean-Pierre Flandrois, L. Rosso, E. Zuber, C. Pichat

International Journal of Food Microbiology . 35 ( 1 ) : 75-81

DOI: 10.1016/S0168-1605(96)01231-7

Journal article

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Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata

D. Graur, Manolo Gouy, L. Duret

Molecular Phylogenetics and Evolution . 7 ( 2 ) : 195-200

DOI: 10.1006/mpev.1996.0391

Journal article

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Cloning of the mouse BTG3 gene and definition of a new gene family (the BTG family) involved in the negative control of the cell cycle

F Guéhenneux, L. Duret, Mb Callanan, R Bouhas, S Hayette, C Berthet...

Leukemia . 11 ( 3 ) : 370-375

DOI: 10.1038/sj.leu.2400599

Journal article

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Cloning and characterization of a gene encoding a novel immunodominant antigen of Trypanosoma cruzi

M. Lesenechal, L. Duret, M.I. Cano, R.A. Mortara, M. Jolivet, M.E. Camargo...

Molecular and Biochemical Parasitology . 87 : 193-204

Journal article

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Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony

N.J. Tourasse, Manolo Gouy

Molecular Biology and Evolution . 14 ( 3 ) : 287-298

DOI: 10.1093/oxfordjournals.molbev.a025764

Journal article

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Reappraisal of the effect of temperature on the growth kinetics of Aeromonas salmonicida

V. Guérin-Faublée, Sandrine Charles, M. Chomarat, Jean-Pierre Flandrois

Letters in Applied Microbiology . 25 : 363-366

Journal article

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A model describing the relationship between lag time and mild temperature increase duration

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

International Journal of Food Microbiology . 38 : 157-167

Journal article

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Homogeneous Two-Site Immunometric Assay Kinetics as a Theoretical Tool for Data Analysis

Emmanuel Zuber, Gérard Mathis, Jean-Pierre Flandrois

Analytical Biochemistry . 251 ( 1 ) : 79-88

DOI: 10.1006/abio.1997.2243

Journal article

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A Descriptive Model for the Kinetics of a Homogeneous Fluorometric Immunoassay

Emmanuel Zuber, Laurent Rosso, Bruno Darbouret, Françoise Socquet, Gérard Mathis, Jean-Pierre Flandrois

Journal of Immunoassay and Immunochemistry . 18 ( 1 ) : 21-47

DOI: 10.1080/01971529708005803

Journal article

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The particular behaviour of Listeria monocytogenes under sub-optimal conditions

S. Bajard, L. Rosso, G. Fardel, J.P. Flandrois

International Journal of Food Microbiology . 29 ( 2-3 ) : 201-211

DOI: 10.1016/0168-1605(95)00031-3

Journal article

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Phylogenetic position of the order Lagomorpha (rabbits hares and allies)

D. Graur, L. Duret, Manolo Gouy

Nature . 379 : 333-335

DOI: 10.1038/379333a0

Journal article

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On-line tools for sequence retrieval and multivariate statistics in molecular biology

G. Perrière, J. Thioulouse

Computer Applications in the Biosciences . 12 : 63-69

Journal article

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Application of a modified disc diffusion technique to antimicrobial susceptibility testing of Vibrio anguillarum and Aeromonas salmonicida clinical isolates

V. Guerin-Faublée, Marie Laure Delignette-Muller, M. Vigneulle, Jean-Pierre Flandrois

Veterinary Microbiology . 51 : 137-149

Journal article

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Differential growth of Listeria monocytogenes at 4 and 8°C: Consequences for the Shelf Life of Chilled Products

L. Rosso, S. Bajard, Jean-Pierre Flandrois, C. Lahellec, J. Fournaud, P. Veit

Journal of Food Protection . 59 ( 9 ) : 944-949

DOI: 10.4315/0362-028X-59.9.944

Journal article

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Evaluation of an expert system linked to a rapid antibiotic susceptibility testing system for the detection of β-lactam resistance phenotypes

Jean-Pierre Flandrois, G. Vedel, M. Peyret, J.P. Gayral, Patrick Millot

Research in Microbiology . 147 ( 4 ) : 297-309

DOI: 10.1016/0923-2508(96)81390-8

Journal article

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The particular behaviour of Listeria monocytogenes under sub-optimal conditions

S. Bajard, L. Rosso, G. Fardel, Jean-Pierre Flandrois

International Journal of Food Microbiology . 29 : 201-211

Journal article

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Use of mathematics and statistics in nutrition modelling

G Ciuperca, R Tomassone, Jp Flandrois

Annales de zootechnie . 45 ( Suppl1 ) : 143-152

Journal article

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Correspondence discriminant analysis: a multivariate method for comparing classes of protein and nucleic acid sequences

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

Computer Applications in the Biosciences . 12 : 519-524

Journal article

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LALNVIEW: a graphical viewer for pairwise sequence alignments

L. Duret, E. Gasteiger, G. Perrière

Computer Applications in the Biosciences . 12 : 507-510

Journal article

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NRSub: a non-redundant database for Bacillus subtilis

G. Perrière, I. Moszer, T. Gojobori

Nucleic Acids Research . 24 : 41-45

Journal article

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Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level.

Valérie Cilia, Bénédicte Lafay, Richard Christen

Molecular Biology and Evolution . 13 ( 3 ) : 451-61

Journal article

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An economic approach to the MIC.

M. Delignette-Muller, Jean-Pierre Flandrois, Catherine Chapuis

Zentralblatt fur Bakteriologie : international journal of medical microbiology . 284 ( 1 ) : 67-74

Journal article

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