GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

The main goal of the GECO department is to foster integration and synergies between theoretical and methodological research relevant for the analysis of genomes (computational genomics) and empirical analysis of genomic and multi-omic data (evolutionary and functional genomics). The department is structured in two teams, BAOBAB and BPGE:

BAOBAB is deeply rooted in computer science. Its strengths are in algorithms, models, and mathematical analysis of graphs and networks, with applications to transcriptomics and metabolic networks.

BPGE is oriented towards bioinformatics, phylogenetics and evolutionary genomics. Its research projects cover a broad range of subjects, such as methodological developments for phylogenetic inference, their applications to the reconstruction of the evolutionary history of bacteria and archaea, the role of mobile genetic elements in the evolution of bacteria and of antibioresistance, or the role of recombination, of genomic rearrangements and of transposable elements in the evolution of eukaryotic genomes.

As detailed on their pages, the research conducted in both teams integrates deep and long-ranging theoretical and methodological (algorithmic and computational) developments with data analysis driven by empirical questions. This integration is bi-directional: methodological developments are guided by empirical questions and then used in empirical applications, while theoretical modeling helps clarify the conceptual basis of subsequent empirical analyses.

Publications

Display of 1381 to 1402 publications on 1402 in total

[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