GECO Evolutionary and Computational Genomics

tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes

L. Duret

Trends in Genetics . 16 : 287-289

2000

Journal article

see the publication

HOBACGEN: database system for comparative genomics in bacteria

G. Perrière, L. Duret, Manolo Gouy

Genome Research . 10 : 379-385

DOI: 10.1101/gr.10.3.379

2000

Journal article

see the publication

The covariation between TpA deficiency CpG deficiency and G+C content of human isochores is due to a mathematical artifact

L. Duret, N. Galtier

Molecular Biology and Evolution . 17 : 1620-1625

2000

Journal article

see the publication

Nature and structure of human genes that generate retropseudogenes

I. Goncalves, L. Duret, Dominique Mouchiroud

Genome Research . 10 : 672-678

2000

Journal article

see the publication

Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate

L. Duret, Dominique Mouchiroud

Molecular Biology and Evolution . 17 : 68-74

2000

Journal article

see the publication

Use of a TT virus ORF1 recombinant protein to detect anti-TT virus antibodies in human sera

C. Ott, L. Duret, I. Chemin, C. Trepo, B. Mandrand, F. Komurian-Pradel

Journal of General Virology . 81 : 2949-2958

2000

Journal article

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Infering regulatory elements from a whole genome. An application to the analysis of genome of $\itemize{Helicobacter Pylori}$ $\sigma_{80}$ family of promoter signals

A. Vanet, Laurent Marsan, A. Labigne, Marie-France Sagot

Journal of Molecular Biology . 297 ( 1 ) : 335-353

2000

Journal article

see the publication

Inferring regulatory elements from a whole genome. An application to the analysis of the genome of Helicobacter pylori sigma 80 family of promoter signals

A. Vanet, L. Marsan, A. Labigne, M.-F. Sagot

Journal of Molecular Biology . 297 : 335-353

2000

Journal article

see the publication

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

L. Marsan, M.-F. Sagot

Journal of Computational Biology . 7 : 345-360

2000

Journal article

see the publication

The Enhanced Microbial Genomes Library

G. Perrière, P. Bessieres, B. Labedan

Nucleic Acids Research . 27 : 63-65

2000

Journal article

see the publication

EMGLib: the enhanced microbial genomes library (update 2000)

G. Perrière, P. Bessieres, B. Labedan

Nucleic Acids Research . 28 ( 1 ) : 68-71

DOI: 10.1093/nar/28.1.68

2000

Journal article

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Phylogenetic analysis of the small subunit ribosomal RNA of Marteilia refringens validates the existence of phylum Paramyxea (Desportes and Perkins 1990)

F.C. Berthe, F. Le Roux, E. Peyretaillade, P. Peyret, D. Rodriguez, Manolo Gouy...

Journal of Eukaryotic Microbiology . 47 ( 3 ) : 288-293

DOI: 10.1111/j.1550-7408.2000.tb00049.x

2000

Journal article

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Codon usage and the origin of P elements

E. Lerat, C. Biémont, P. Capy

Molecular Biology and Evolution . 17 : 467-468

2000

Journal article

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Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans

L. Duret, Gabriel Marais, C. Biémont

Genetics . 156 : 1661-1669

2000

Journal article

see the publication

Chromosomal distribution and coding capacity of the human endogenous retrovirus HERV-W family

C. Voisset, O. Bouton, F. Bedin, L. Duret, B. Mandrand, Frédéric Mallet...

AIDS Research and Human Retroviruses . 16 : 731-740

2000

Journal article

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Multiple alignments for structural functional or phylogenetic analyses of homologous sequences

L. Duret, S. Abdeddaim

incollection . -- : 51-76

2000

Journal article

see the publication

Sequence of the Small Subunit Ribosomal RNA Gene of Perkinsus atlanticus-like Isolated from Carpet Shell Clam in Galicia Spain

A. Figueras, G. Lorenzo, M.C. Ordas, Manolo Gouy, B. Novoa

Marine Biotechnology . 2 : 419-428

DOI: 10.1007/s101260000015

2000

Journal article

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Phylogénies moléculaires et génomes

Céline Brochier-Armanet, H. Philippe

incollection . 206 : 50-53

2000

Journal article

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The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome

Céline Brochier, Hervé Philippe, David Moreira

Trends in Genetics . 16 ( 12 ) : 529-533

DOI: 10.1016/s0168-9525(00)02142-9

2000

Journal article

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Absence of translationally selected synonymous codon usage bias in Helicobacter pylori.

Bénédicte Lafay, John C. Atherton, Paul M. Sharp

Microbiology . 146 ( Pt 4) : 851-60

2000

Journal article

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Molecular Systematics of sponges (Porifera)

Carole Borchiellini, Catherine Chombard, Bénédicte Lafay, Nicole Boury-Esnault

Hydrobiologia . 420 ( 1 ) : 15-27

DOI: 10.1023/A:1003996517083

2000

Journal article

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A nonhyperthermophilic common ancestor to extant life forms

N. Galtier, N. Tourasse, Manolo Gouy

Science . 283 ( 5399 ) : 220-221

DOI: 10.1126/science.283.5399.220

1999

Journal article

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Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes

N.J. Tourasse, Manolo Gouy

Molecular Phylogenetics and Evolution . 13 : 159-168

DOI: 10.1006/mpev.1999.0675

1999

Journal article

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Characterization of Unexpected Growth of Escherichia coli O157:H7 by Modeling

M. Cornu, Marie Laure Delignette-Muller, Jean-Pierre Flandrois

Applied and Environmental Microbiology . 65 : 5322-5327

1999

Journal article

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A model describing the relationship between regrowth lag time and mild temperature increase for Listeria monocytogenes

S. Breand, G. Fardel, Jean-Pierre Flandrois, L. Rosso, R. Tomassone

International Journal of Food Microbiology . 46 : 251-261

1999

Journal article

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Synonymous codon usage variation among Giardia lamblia genes and isolates.

Bénédicte Lafay, Paul M. Sharp

Molecular Biology and Evolution . 16 ( 11 ) : 1484-95

1999

Journal article

see the publication

Retrotransposons and retroviruses: analysis of the envelope gene

E. Lerat, P. Capy

Molecular Biology and Evolution . 16 : 1198-1207

1999

Journal article

see the publication

Regulation of dauer larva development in Caenorhabditis elegans by daf-18, a homologue of the tumour suppressor PTEN

Jean-Pierre Rouault, Patricia Kuwabara, Olga Sinilnikova, Laurent Duret, Danielle Thierry-Mieg, Marc Billaud

Current Biology - CB . 9 ( 6 ) : 329-334

DOI: 10.1016/S0960-9822(99)80143-2

1999

Journal article

see the publication

Human and nematode orthologs--lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis elegans

S.J. Wheelan, M.S. Boguski, L. Duret, W. Makalowski

Gene . 238 : 163-170

1999

Journal article

see the publication

Molecular characterization and placental expression of HERV-W a new human endogenous retrovirus family

J.L. Blond, F. Beseme, L. Duret, O. Bouton, F. Bedin, H. Perron...

Journal of Virology . 73 : 1175-1185

1999

Journal article

see the publication

GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes

HOBACGEN: database system for comparative genomics in bacteria

The covariation between TpA deficiency CpG deficiency and G+C content of human isochores is due to a mathematical artifact

Nature and structure of human genes that generate retropseudogenes

Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate

Use of a TT virus ORF1 recombinant protein to detect anti-TT virus antibodies in human sera

Infering regulatory elements from a whole genome. An application to the analysis of genome of $\itemize{Helicobacter Pylori}$ $\sigma_{80}$ family of promoter signals

Inferring regulatory elements from a whole genome. An application to the analysis of the genome of Helicobacter pylori sigma 80 family of promoter signals

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

The Enhanced Microbial Genomes Library

EMGLib: the enhanced microbial genomes library (update 2000)

Phylogenetic analysis of the small subunit ribosomal RNA of Marteilia refringens validates the existence of phylum Paramyxea (Desportes and Perkins 1990)

Codon usage and the origin of P elements

Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans

Chromosomal distribution and coding capacity of the human endogenous retrovirus HERV-W family

Multiple alignments for structural functional or phylogenetic analyses of homologous sequences

Sequence of the Small Subunit Ribosomal RNA Gene of Perkinsus atlanticus-like Isolated from Carpet Shell Clam in Galicia Spain

Phylogénies moléculaires et génomes

The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome

Absence of translationally selected synonymous codon usage bias in Helicobacter pylori.

Molecular Systematics of sponges (Porifera)

A nonhyperthermophilic common ancestor to extant life forms

Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes

Characterization of Unexpected Growth of Escherichia coli O157:H7 by Modeling

A model describing the relationship between regrowth lag time and mild temperature increase for Listeria monocytogenes

Synonymous codon usage variation among Giardia lamblia genes and isolates.

Retrotransposons and retroviruses: analysis of the envelope gene

Regulation of dauer larva development in Caenorhabditis elegans by daf-18, a homologue of the tumour suppressor PTEN

Human and nematode orthologs--lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis elegans

Molecular characterization and placental expression of HERV-W a new human endogenous retrovirus family