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 1321 to 1350 publications on 1402 in total

Building large knowledge bases in molecular biology

O. Schmeltzer, C. Medigue, P. Uvietta, F. Rechenmann, F. Dorkeld, G. Perrière...

In Proceedings of the First International Conference on Intelligent Systems for Molecular Biology . 1 : 345-353

Journal article

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Morphological and molecular phylogeny of ophiuroids

Andrew B. Smith, Bénédicte Lafay, Gordon L.J. Paterson

Eigth International Echinoderm Conference .

Conference paper

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An analysis of partial 28S ribosomal RNA sequence suggests early radiations within the phylum Porifera

Bénédicte Lafay, Nicole Boury-Esnault, Jean Vacelet, Richard Christen

4th International Porifera Congress "Sponges in Time and Space" .

Conference paper

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Sequence analysis reveals that the BTG1 anti-proliferative gene is conserved throughout evolution in its coding and 3' non-coding regions

Jean-Pierre Rouault, J.P. Rouault, C. Samarut, L. Duret, C. Tessa, J. Samarut...

Gene . 129 ( 2 ) : 303-306

DOI: 10.1016/0378-1119(93)90284-A

Journal article

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Object-oriented knowledge bases for the analysis of prokaryotic and eukaryotic genomes

G. Perrière, F. Dorkeld, F. Rechenmann, Christian Gautier

In Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology . 1 : 319-327

Journal article

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An unexpected correlation between cardinal temperatures of microbial growth highlighted by a new model

L. Rosso, J.R. Lobry, Jean-Pierre Flandrois

Journal of Theoretical Biology . 162 : 447-463

Journal article

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Actinomyces pyogenes: susceptibility of 103 clinical animal isolates to 22 antimicrobial agents

V Guérin-Faublée, Jp Flandrois, E Broye, F Tupin, Y Richard

Veterinary Research . 24 ( 3 ) : 251-259

Journal article

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Mathematical model for comparison of time-killing curves.

F Guerillot, G. Carret, Jean-Pierre Flandrois

Antimicrobial Agents and Chemotherapy . 37 ( 8 ) : 1685-1689

DOI: 10.1128/AAC.37.8.1685

Journal article

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Antimicrobial susceptibility testing of actinomyces pyogenes: Comparison of disk diffusion test and Api ATB Strep system with the Agar dilution method

Véronique Guérin-Faublée, Jean-Pierre Flandrois, Yves Richard

Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectious diseases, virology, parasitology . 279 ( 3 ) : 377-386

DOI: 10.1016/S0934-8840(11)80370-1

Journal article

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A statistical evaluation of the bactericidal effects of ceftibuten in combination with aminoglycosides and ciprofloxacin

F. Guérillot, G. Carret, Jean-Pierre Flandrois

Journal of Antimicrobial Chemotherapy . 32 ( 5 ) : 685-694

DOI: 10.1093/jac/32.5.685

Journal article

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[Comparative study of two systems for the determination of the sensitivity of yeasts to antifungal agents].

M de Montclos, H. de Montclos, Jean-Pierre Flandrois

Pathologie Biologie . 40 ( 5 ) : 495-9

Journal article

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Gram-positive infections in neutropenic patients: glycopeptide antibiotic choice

Monique Chomarat, Daniel Espinouse, Jean-Pierre Flandrois

Journal of Antimicrobial Chemotherapy . 29 ( 4 ) : 462-463

DOI: 10.1093/jac/29.4.462

Journal article

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Comparative variation of morphological and molecular evolution through geologic time: 28S ribosomal RNA versus morphology in echinoids.

Andrew B. Smith, Bénédicte Lafay, Richard Christen

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences (1934–1990) . 338 ( 1286 ) : 365-82

DOI: 10.1098/rstb.1992.0155

Journal article

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Phylogenetic analysis of the pathogenic anaerobe Clostridium perfringens using the 16S rRNA nucleotide sequence.

Bruno Canard, Thierry Garnier, Bénédicte Lafay, Richard Christen, Stewart T. Cole

International Journal of Systematic Bacteriology . 42 ( 2 ) : 312-4

DOI: 10.1099/00207713-42-2-312

Journal article

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Insect muscle actins differ distinctly from invertebrate and vertebrate cytoplasmic actins

N. Mounier, Manolo Gouy, Dominique Mouchiroud, J.C. Prudhomme

Journal of Molecular Evolution . 34 : 406-415

DOI: 10.1007/BF00162997

Journal article

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Evolution of the primate beta-globin gene region: nucleotide sequence of the delta-beta-globin intergenic region of gorilla and phylogenetic relationships between African apes and man

P. Perrin-Pecontal, Manolo Gouy, V.M. Nigon, G. Trabuchet

Journal of Molecular Evolution . 34 : 17-30

DOI: 10.1007/BF00163849

Journal article

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Monod's bacterial growth model revisited

J.R. Lobry, Jean-Pierre Flandrois, G. Carret, A. Pavé

Bulletin of Mathematical Biology . 54(1) : 117-122

Journal article

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Maintenance requirements of Escherichia coli ATCC 25922 in the presence of sub-inhibitory concentrations of various antibiotics

J.R. Lobry, G. Carret, Jean-Pierre Flandrois

Journal of Antimicrobial Chemotherapy . 29 : 121-127

Journal article

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Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium.

Michel J. Gauthier, Bénédicte Lafay, Richard Christen, Luis Fernandez, M. Acquaviva, Patricia Bonin...

International Journal of Systematic Bacteriology . 42 ( 4 ) : 568-76

Journal article

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An analysis of partial 28S ribosomal RNA sequence suggests early radiations of sponges

Bénédicte Lafay, Nicole Boury-Esnault, Jean Vacelet, Richard Christen

BioSystems . 28 : 139-151

Journal article

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A FORTRAN subroutine for the determination of parameter confidence limits in non-linear Models

J.R. Lobry, L. Rosso, Jean-Pierre Flandrois

Binary . 3 : 86-93

Journal article

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Susceptibility to Aminoglycosides of 63 Strains of Stomatococcus mucilaginosus Isolated from Sputum

Monique Chomarat, Marie-Gabrielle Vital, Jean-Pierre Flandrois

Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectious diseases, virology, parasitology . 276 ( 1 ) : 63-67

DOI: 10.1016/S0934-8840(11)80219-7

Journal article

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[Expert systems and antibiotic sensitivity test].

Jean-Pierre Flandrois, G. Carret

Annales de Biologie Clinique . 49 ( 3 ) : 166-71

Journal article

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Coagulase-negative staphylococci emerging during teicoplanin therapy and problems in the determination of their sensitivity

Monique Chomarat, Daniel Espinouse, Jean-Pierre Flandrois

Journal of Antimicrobial Chemotherapy . 27 ( 4 ) : 475-480

DOI: 10.1093/jac/27.4.475

Journal article

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Identification des organismes et construction de phylogénies moléculaires par comparaison de séquences d'acides nucléiques

Richard Christen, Bénédicte Lafay, Philippe Elbaze, Valérie Boivin, Valérie O. Cilia

Océanis : Série de documents océanographiques . 17 ( 3 ) : 239-256

Journal article

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Regulation of the acetate operon in Escherichia coli: purification and functional characterization of the IclR repressor.

Jc Cortay, D. Negre, A. Galinier, B. Duclos, G. Perriere, Aj Cozzone

EMBO Journal . 10 : 675-679

Journal article

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Primary structure of the intergenic region between aceK and iclR in the Escherichia coli chromosome.

A. Galinier, F. Bleicher, D. Negre, G. Perriere, B. Duclos, Aj Cozzone...

Gene . 97 : 149-150

Journal article

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