GECO Evolutionary and Computational Genomics

Synonymous codon usage accuracy of translation and gene length in Caenorhabditis elegans

Gabriel Marais, L. Duret

Journal of Molecular Evolution . 52 : 275-280

2001

Journal article

see the publication

GC-content evolution in mammalian genomes: the biased gene conversion hypothesis

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

Genetics . 159 : 907-911

2001

Journal article

see the publication

Plant Physiol.A Medicago truncatula homoglutathione synthetase is derived from glutathione synthetase by gene duplication

P. Frendo, M.J. Jimenez, C. Mathieu, L. Duret, D. Gallesi, G. van de Sype...

Plant Physiology . 126 : 1706-1715

2001

Journal article

see the publication

The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution

L. Duret, L.D. Hurst

Molecular Biology and Evolution . 18 : 757-762

2001

Journal article

see the publication

Some approximation results for the maximum agreement forest problem

E. M. Rodrigues, Marie-France Sagot, Y. Wakabayashi

Approximation, Randomization and Combinatorial Optimization: Algorithms and Techniques (APPROX RANDOM 2001) . 2129 : 159-169

2001

Conference paper

see the publication

Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes

Stéphane Guindon, G. Perrière

Molecular Biology and Evolution . 18 ( 9 ) : 1838-1840

DOI: 10.1093/oxfordjournals.molbev.a003972

2001

Journal article

see the publication

Nrh, a human homologue of Nr-13 associates with Bcl-Xs and is an inhibitor of apoptosis

A. Aouacheria, Estelle Arnaud, S. Venet, P. Lalle, M. Gouy, D. Rigal...

Oncogene . 20 : 5846-5855

DOI: 10.1038/sj.onc.1204740

2001

Journal article

see the publication

Molecular evidence for the existence of two species of Marteilia in Europe

F. Le Roux, G. Lorenzo, P. Peyret, C. Audemard, A. Figueras, C. Vivares...

Journal of Eukaryotic Microbiology . 48 ( 4 ) : 449-454

DOI: 10.1111/j.1550-7408.2001.tb00178.x

2001

Journal article

see the publication

Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi

M.D. Katinka, S. Duprat, E. Cornillot, G. Metenier, F. Thomarat, G. Prensier...

Nature . 414 : 450-453

DOI: 10.1038/35106579

2001

Journal article

see the publication

A mathematical model describing the thermal virus inactivation

C. Noel, Sandrine Charles, A. Francon, Jean-Pierre Flandrois

Vaccine . 19 : 3575-3582

2001

Journal article

see the publication

Comparaison de séquences d`éléments transposables et de gènes d`hôtes chez cinq espèces : A. Thaliana C. Elegans D. Melanogaster H. Sapiens S. Cerevisiae

E. Lerat

incollection . -- : 347-354

2001

Journal article

see the publication

Small-subunit rRNA genotyping of rhizobia nodulating Australian Acacia spp.

Bénédicte Lafay, Jeremy J. Burdon

Applied and Environmental Microbiology . 67 ( 1 ) : 396-402

DOI: 10.1128/AEM.67.1.396-402.2001

2001

Journal article

see the publication

Fitness and competitive growth advantage of new gentamicin-susceptible MRSA clones spreading in French hospitals

Jean-Pierre Flandrois, F. Laurent

Journal of Antimicrobial Chemotherapy . 47 ( 3 ) : 277-283

DOI: 10.1093/jac/47.3.277

2001

Journal article

see the publication

Identification and molecular analysis of BANP

Anne-Marie Birot, Laurent Duret, Laurent Bartholin, Bénédicte Santalucia, Isabelle Tigaud, Jean-Pierre Magaud...

Gene . 253 ( 2 ) : 189-196

DOI: 10.1016/S0378-1119(00)00244-4

2000

Journal article

see the publication

EuGene an eurocaryotic gene finder that combines several sources of evidence

Thomas Schiex, A. Moisan, L. Duret, Pierre Rouzé

Journées ouvertes biologie informatique mathématiques .

2000

Conference paper

see the publication

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

see the publication

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

see the publication

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

see the publication

Codon usage and the origin of P elements

E. Lerat, C. Biémont, P. Capy

Molecular Biology and Evolution . 17 : 467-468

2000

Journal article

see the publication

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

see the publication

GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Synonymous codon usage accuracy of translation and gene length in Caenorhabditis elegans

GC-content evolution in mammalian genomes: the biased gene conversion hypothesis

Plant Physiol.A Medicago truncatula homoglutathione synthetase is derived from glutathione synthetase by gene duplication

The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution

Some approximation results for the maximum agreement forest problem

Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes

Nrh, a human homologue of Nr-13 associates with Bcl-Xs and is an inhibitor of apoptosis

Molecular evidence for the existence of two species of Marteilia in Europe

Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi

A mathematical model describing the thermal virus inactivation

Comparaison de séquences d`éléments transposables et de gènes d`hôtes chez cinq espèces : A. Thaliana C. Elegans D. Melanogaster H. Sapiens S. Cerevisiae

Small-subunit rRNA genotyping of rhizobia nodulating Australian Acacia spp.

Fitness and competitive growth advantage of new gentamicin-susceptible MRSA clones spreading in French hospitals

Identification and molecular analysis of BANP

EuGene an eurocaryotic gene finder that combines several sources of evidence

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