GECO Evolutionary and Computational Genomics

A novel method for characterizing the microscale 3D spatial distribution of bacteria in soil

A. Dechesne, C. Pallud, D. Debouzie, J. P. Flandrois, T. M. Vogel, J. P. Gaudet...

Soil Biology and Biochemistry . 35 ( 12 ) : 1537-1546

DOI: 10.1016/S0038-0717(03)00243-8

2003

Journal article

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Y-chromosomal evidence for a strong reduction in male population size of Yakuts

Brigitte Pakendorf, Bharti Morar, Larissa A Tarskaia, Manfred Kayser, Himla Soodyall, Alexander Rodewald...

Human Genetics . 110 ( 2 ) : 198-200

DOI: 10.1007/s00439-001-0664-4

2002

Journal article

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Expected Relationship Between the Silent Substitution Rate and the GC Content: Implications for the Evolution of Isochores

G. Piganeau, Dominique Mouchiroud, L. Duret, Christian Gautier

Journal of Molecular Evolution . 54 : 129-133.

2002

Journal article

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Detecting genomic features under weak selective pressure: the example of codon usage in animals and plants

L. Duret

Bioinformatics . 18 : S91-S91

2002

Journal article

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Further thoughts on the syntenic distance between genomes

N. Pisanti, M.-F. Sagot

Algorithmica . 34 : 157-180

2002

Journal article

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Gene finding in eukaryotes

C. Mathé, Thomas Schiex, Pierre Rouzé, Philippe Blayo, Marie-France Sagot

Cloning and expression technologies . : 27-43

2002

Book chapter

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A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history

Vincent Daubin, Manolo Gouy, G. Perrière

Genome Research . 12 : 1080-1090

DOI: 10.1101/gr.187002

2002

Journal article

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Between-group analysis of microarray data

A.C. Culhane, G. Perrière, E.C. Considine, T.G. Cotter, D.G. Higgins

Bioinformatics . 18 : 1600-1608

2002

Journal article

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Use and misuse of correspondence analysis in codon usage studies

G. Perrière, J. Thioulouse

Nucleic Acids Research . 30 : 4548-4555

2002

Journal article

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Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome

C. Rizzon, Gabriel Marais, Manolo Gouy, C. Biémont

Genome Research . 12 : 400-407

DOI: 10.1101/gr.210802

2002

Journal article

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What is the relevance of obtaining multiple blood samples for culture? A comprehensive model to optimize the strategy for diagnosing bacteremia

B. Lamy, Pascal Roy, G. Carret, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Clinical Infectious Diseases . 35 ( 7 ) : 842-850

DOI: 10.1086/342383

2002

Journal article

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Modelling the competitive growth of Listeria monocytogenes and Listeria innocua in enrichment broths

Marie Cornu, Martin Kalmokoff, Jean-Pierre Flandrois

International Journal of Food Microbiology . 73 ( 2-3 ) : 261-274

DOI: 10.1016/S0168-1605(01)00658-4

2002

Journal article

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Archaeal phylogeny based on ribosomal proteins

O. Matte-Tailliez, Céline Brochier-Armanet, Patrick Forterre, H. Philippe

Mol Biol Evol . 19 : 631-639

2002

Journal article

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Eubacterial phylogeny based on translational apparatus proteins

Céline Brochier, Eric Bapteste, David Moreira, Hervé Philippe

Trends in Genetics . 18 ( 1 ) : 1-5

DOI: 10.1016/s0168-9525(01)02522-7

2002

Journal article

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Conflicting phylogeographic patterns in rRNA and nifD indicate regionally restricted gene transfer in Bradyrhizobium.

Matthew A. Parker, Benedicte Lafay, Jeremy J. Burdon, Peter van Berkum

Microbiology . 148 ( Pt 8 ) : 2557-65

2002

Journal article

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ROSO: A software to search optimized oligonucleotide probes for microarrays

Hubert Charles, Nancie Reymond, Guillaume Beslon, Laurent Duret, Jean-Michel Fayard

COST853: Agricultural Biomarkers for Array-Technology .

2002

Conference paper

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ROSO : A Software to Search Optimized Oligonucleotide Probes for Microarrays

Nancie Reymond, Hubert Charles, Guillaume Beslon, Laurent Duret, Jean-Michel Fayard

10. International Conference on Intelligent Systems for Molecular Biology (ISMB) .

2002

Poster

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Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine.

C. Chureau, M. Prissette, A. Bourdet, Valérie Barbe, L. Cattolico, L. Jones...

Genome Research . 12 : 894-908

2002

Journal article

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Vanishing GC-Rich Isochores in Mammalian Genomes

L. Duret, M. Sémon, G. Piganeau, Dominique Mouchiroud, N. Galtier

Genetics . 162 : 1837-1848

2002

Journal article

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Comparative sequence analysis of the X-inactivation center region in mouse human and bovine

C. Chureau, M. Prissette, A. Bourdet, Valérie Barbe, Laurence Cattolico, L. Jones...

Genome Research . 12 : 894-908.

2002

Journal article

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Evolution of synonymous codon usage in metazoans

L. Duret

Current Opinion in Genetics and Development . 12 : 640-649

2002

Journal article

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A Basis for Repeated Motifs in Pattern Discovery and Text Mining

Nadia Pisanti, Maxime Crochemore, Roberto Grossi, Marie-France Sagot

2002

Report

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Gene finding in eukaryotes

C. Mathé, Thomas Schiex, P. Rouzé, P. Blayo, M.-F. Sagot

incollection . -- : 27-43

2002

Journal article

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Current methods of gene prediction their strengths and weaknesses

C. Mathé, M.-F. Sagot, Thomas Schiex, P. Rouzé

Nucleic Acids Research . 30 : 4103-4117

2002

Journal article

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Occurrence probability of structured motifs in random sequences

S. Robin, J.J. Daudin, H. Richard, M.-F. Sagot, S. Schbath

Journal of Computational Biology . 9 ( 6 ) : 761-773

DOI: 10.1089/10665270260518254

2002

Journal article

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A mathematical method for determining genome divergence and species delineation using AFLP

Christophe Mougel, J. Thioulouse, G. Perrière, X. Nesme

International Journal of Systematic and Evolutionary Microbiology . 52 : 573-586

DOI: 10.1099/00207713-52-2-573

2002

Journal article

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A mathematical method for determining genome divergence and species delineation using AFLP

Christophe Mougel, Jean Thioulouse, Guy Perrière, Xavier Nesme

International Journal of Systematic and Evolutionary Microbiology . 52 : 573-586

2002

Journal article

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NUREBASE: database of nuclear hormone receptors

J. Duarte, G. Perrière, V. Laudet, M. Robinson-Rechavi

Nucleic Acids Research . 30 : 364-368

2002

Journal article

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Automatic RNA secondary structure prediction with a comparative approach

F. Tahi, Manolo Gouy, M. Regnier

Journal of Computational Chemistry . 26 ( 5 ) : 521-530

DOI: 10.1016/S0097-8485(02)00012-8

2002

Journal article

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Functional and evolutionary analysis of a eukaryotic parasitic genome

Christian Vivarès, Manolo Gouy, F. Thomarat, G. Metenier

Current Opinion in Microbiology . 5 : 499-505

DOI: 10.1016/S1369-5274(02)00356-9

2002

Journal article

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GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

A novel method for characterizing the microscale 3D spatial distribution of bacteria in soil

Y-chromosomal evidence for a strong reduction in male population size of Yakuts

Expected Relationship Between the Silent Substitution Rate and the GC Content: Implications for the Evolution of Isochores

Detecting genomic features under weak selective pressure: the example of codon usage in animals and plants

Further thoughts on the syntenic distance between genomes

Gene finding in eukaryotes

A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history

Between-group analysis of microarray data

Use and misuse of correspondence analysis in codon usage studies

Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome

What is the relevance of obtaining multiple blood samples for culture? A comprehensive model to optimize the strategy for diagnosing bacteremia

Modelling the competitive growth of Listeria monocytogenes and Listeria innocua in enrichment broths

Archaeal phylogeny based on ribosomal proteins

Eubacterial phylogeny based on translational apparatus proteins

Conflicting phylogeographic patterns in rRNA and nifD indicate regionally restricted gene transfer in Bradyrhizobium.

ROSO: A software to search optimized oligonucleotide probes for microarrays

ROSO : A Software to Search Optimized Oligonucleotide Probes for Microarrays

Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine.

Vanishing GC-Rich Isochores in Mammalian Genomes

Comparative sequence analysis of the X-inactivation center region in mouse human and bovine

Evolution of synonymous codon usage in metazoans

A Basis for Repeated Motifs in Pattern Discovery and Text Mining

Gene finding in eukaryotes

Current methods of gene prediction their strengths and weaknesses

Occurrence probability of structured motifs in random sequences

A mathematical method for determining genome divergence and species delineation using AFLP

A mathematical method for determining genome divergence and species delineation using AFLP

NUREBASE: database of nuclear hormone receptors

Automatic RNA secondary structure prediction with a comparative approach

Functional and evolutionary analysis of a eukaryotic parasitic genome