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 1410 publications on 1415 in total

Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data

K.H. Wolfe, Manolo Gouy, Y.W. Yang, P.M. Sharp, W.-H. Li

Proceedings of the National Academy of Sciences of the United States of America . 86 ( 16 ) : 6201-6205

DOI: 10.1073/pnas.86.16.6201

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[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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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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