GECO Evolutionary and Computational Genomics

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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Modeling the Lag Time of Listeria monocytogenes from Viable Count Enumeration and Optical Density Data

F. Baty, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Applied and Environmental Microbiology . 68 : 5816-5825

2002

Journal article

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The relative abundance of dinucleotides in transposable elements in five species

E. Lerat, P. Capy, C. Biémont

Molecular Biology and Evolution . 19 : 964-967

2002

Journal article

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Codon usage by transposable elements and their host genes in five species

E. Lerat, P. Capy, C. Biémont

Journal of Molecular Evolution . 54 : 625-637

2002

Journal article

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Organisation Fonctionnement et Evolution des Génomes de Métazoaires : Mais où est donc passée la sélection naturelle ?

L. Duret

incollection . -- : 287-289

2001

Journal article

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Why do genes have introns? Recombination might add a new piece to the puzzle

L. Duret

Trends in Genetics . 17 : 172-175

2001

Journal article

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Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification

Laurent Marsan, Marie-France Sagot

Journal of Computational Biology . 7 ( 1 ) : 345-360

2001

Journal article

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Analysis of pFQ31 a 8551-bp cryptic plasmid from the symbiotic nitrogen-fixing actinomycete Frankia

C. Lavire, D. Louis, G. Perrière, J. Briolay, P. Normand, B. Cournoyer

FEMS Microbiology Letters . 197 : 111-116

DOI: 10.1111/j.1574-6968.2001.tb10591.x

2001

Journal article

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Lipid phosphate phosphatases in Arabidopsis. Regulation of the AtLPP1 gene in response to stress

O. Pierrugues, C. Brutesco, J. Oshiro, Manolo Gouy, Y. Deveaux, G.M. Carman...

Journal of Biological Chemistry . 276 ( 23 ) : 20300-20308

DOI: 10.1074/jbc.M009726200

2001

Journal article

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Spatial Modeling of Nitrifier Microhabitats in Soil

G. Grundmann, A. Dechesne, F. Bartoli, Jean-Pierre Flandrois, J. Chassé, R. Kizungu

Soil Science Society of America Journal . 65 ( 6 ) : 1709

DOI: 10.2136/sssaj2001.1709

2001

Journal article

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Comparaison de séquences d'éléments transposables et de gènes d'hôte chez cinq espèces : A. thaliana, C. elegans, D. melanogaster, H. sapiens et S. cerevisiae

Emmanuelle Lerat

2001

Thesis

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Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes

Gabriel Marais, Dominique Mouchiroud, L. Duret

Proceedings of the National Academy of Sciences of the United States of America . 98 : 5688-5692

2001

Journal article

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Determinants of CpG islands: expression in early embryo and isochore structure

L. Ponger, L. Duret, Dominique Mouchiroud

Genome Research . 11 : 1854-1860

2001

Journal article

see the publication

GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

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

Modeling the Lag Time of Listeria monocytogenes from Viable Count Enumeration and Optical Density Data

The relative abundance of dinucleotides in transposable elements in five species

Codon usage by transposable elements and their host genes in five species

Organisation Fonctionnement et Evolution des Génomes de Métazoaires : Mais où est donc passée la sélection naturelle ?

Why do genes have introns? Recombination might add a new piece to the puzzle

Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification

Analysis of pFQ31 a 8551-bp cryptic plasmid from the symbiotic nitrogen-fixing actinomycete Frankia

Lipid phosphate phosphatases in Arabidopsis. Regulation of the AtLPP1 gene in response to stress

Spatial Modeling of Nitrifier Microhabitats in Soil

Comparaison de séquences d'éléments transposables et de gènes d'hôte chez cinq espèces : A. thaliana, C. elegans, D. melanogaster, H. sapiens et S. cerevisiae

Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes

Determinants of CpG islands: expression in early embryo and isochore structure