GECO Evolutionary and Computational Genomics

A parallel algorithm for the extraction of structured motifs

A. Carvalho, A.T. Freitas, A.L. Oliveira, M.-F. Sagot

ACM Symposium on Applied Computing . -- : 147-153

2004

Conference paper

see the publication

The at-most $k$-deep factor tree

Julien Allali, Marie-France Sagot

2004

Report

see the publication

Motifs in Sequences: Localization and Extraction

Maxime Crochemore, Marie-France Sagot

Compact Handbook of Computational Biology . : 47-97

2004

Book chapter

see the publication

Update of NUREBASE: nuclear hormone receptor functional genomics

D. Ruau, J. Duarte, T. Ourjdal, G. Perrière, V. Laudet, M. Robinson-Rechavi

Nucleic Acids Research . 32 : D165-D167

2004

Journal article

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Update of NUREBASE : nuclear hormone receptor functional genomics

D. Ruau, J. Duarte, T. Ourjdal, Guy Perrière, V. Laudet, M. Robinson-Rechavi

Nucleic Acids Research . 32 : D165-D167

2004

Journal article

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Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of microsporidia and reveals a high frequency of fast-evolving genes

F. Thomarat, Christian Vivarès, Manolo Gouy

Journal of Molecular Evolution . 59 : 780-791

DOI: 10.1007/s00239-004-2673-0

2004

Journal article

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A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process

Nicolas Lartillot, Herve Philippe

Molecular Biology and Evolution . 21 ( 6 ) : 1095-1109

DOI: 10.1093/molbev/msh112

2004

Journal article

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The evolutionary history of quorum-sensing in bacteria

E. Lerat, N.A. Moran

Molecular Biology and Evolution . 21 : 903-913

2004

Journal article

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Ψ-Φ: Exploring the outer limits of bacterial pseudogenes

E. Lerat, H. Ochman

Genome Research . 14 : 2273--2278

2004

Journal article

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Hypervariable and highly divergent intron/exon organizations in the chordate Oikopleura dioica

R. Edvardsen, E. Lerat, A.D. Maeland, M. Flat, R. Tewari, M.F. Jensen...

Journal of Molecular Biology . 59 : 448-457

2004

Journal article

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Reversing gene erosion: Reconstructing ancestral bacterial genomes from gene-content and order data

J.V. Earnest-Deyoung, E. Lerat, B.M.E. Moret

incollection . 3240 : 1-13

2004

Journal article

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Novel tree edit operations for RNA secondary structure comparison

Julien Allali, Marie-France Sagot

Workshop on Algorithms in Bioinformatics 2004 . 3240 : 412--425

DOI: 10.1007/978-3-540-30219-3_35

2004

Conference paper

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Physical and transcript map of the autosomal dominant colobomatous microphthalmia locus on chromosome 15q12-q15 and refinement to a 4.4 Mb region.

Laetitia Michon, Laurette Morlé, Muriel Bozon, L. Duret, Jean-Christophe Zech, Jacqueline Godet...

European Journal of Human Genetics . 12 ( 7 ) : 574-8

DOI: 10.1038/sj.ejhg.5201197

2004

Journal article

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Grid as a bioinformatic tool

N. Jacq, Christophe Blanchet, C. Combet, E. Cornillot, L. Duret, K. Kurata...

Parallel Computing . 30 : 1093-1107

2004

Journal article

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Grid as a bioinformatic tool

N. Jacq, Christophe Blanchet, C. Combet, E. Cornillot, L. Duret, K. Kurata...

Parallel Computing . 30 : 1093-1107

DOI: 10.1016/j.parco.2004.07.013

2004

Journal article

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Recombination drives the evolution of GC-content in the human genome

J. Meunier, L. Duret

Molecular Biology and Evolution . 21 : 984-990

2004

Journal article

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Evidence of Selection on the Domesticated ERVWE1 env Retroviral Element Involved in Placentation

B. Bonnaud, O. Bouton, G. Oriol, V. Cheynet, L. Duret, Frédéric Mallet

Molecular Biology and Evolution . 21 : 1895-1901

2004

Journal article

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Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries.

C. Keime, F. Damiola, D. Mouchiroud, L. Duret, O. Gandrillon

BMC Bioinformatics . ( 5 ) : 143

2004

Journal article

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Longest Motifs with a Functionally Equivalent Central Block

Maxime Crochemore, Raffaele Giancarlo, Marie-France Sagot

SPIRE'2004 . 3246 : 298-309

DOI: 10.1007/978-3-540-30213-1_42

2004

Conference paper

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Sorting by reversals in subquadratic time

Eric Tannier, M.-F. Sagot

Annual Symposium on Combinatorial Pattern Matching (CPM) . 3109 : 1-13

DOI: 10.1007/978-3-540-27801-6_1

2004

Conference paper

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Sorting by reversals in subquadratic time

Eric Tannier, Marie-France Sagot

2004

Report

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Longest repeated motif with a block of don't cares

Maxime Crochemore, Costas S. Iliopoulos, Manal Mohamed, Marie-France Sagot

6th Latin American Theoretical Informatics (LATIN'04) . 2976 : 271-278

DOI: 10.1007/978-3-540-24698-5_31

2004

Conference paper

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The European ribosomal RNA database

Jan Wuyts, Guy Perrière, Yves van de Peer

Nucleic Acids Research . 32 : D101-D103

DOI: 10.1093/nar/gkh065

2004

Journal article

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Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones.

Aurélien Ginolhac, Cyrille Jarrin, B. Gillet, P. Robe, P. Pujic, K. Tuphile...

Applied and Environmental Microbiology . 70 : 5522-5527

2004

Journal article

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Phylogenetic study and identification of Vibrio splendidus-related strains based on gyrB gene sequences.

Frédérique Le Roux, Mélanie Gay, Christophe Lambert, Jean-Louis Nicolas, Manolo Gouy, Franck Berthe

Diseases of Aquatic Organisms . 58 ( 2-3 ) : 143-150

DOI: 10.3354/dao058143

2004

Journal article

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How does susceptibility prevalence impact on the performance of disk diffusion susceptibility testing?

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

Diagnostic Microbiology and Infectious Disease . 49 : 131-139

2004

Journal article

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Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers

P. Lopez-Garcia, Céline Brochier-Armanet, D. Moreira, F. Rodriguez-Valera

Environmental Microbiology . 6 : 19-34

2004

Journal article

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Molecular analysis of the hypervariable regions in the minicircle of kinetoplastic genome in Trypanosoma cruzi, agent of Chagas'disease

Jenny Telleria, Bénédicte Lafay, Myrna Virreira, Christian Barnabé, Michel Tibayrenc, M. Svoboda

VII INTERNATIONAL MEETING ON MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS OF INFECTIOUS DISEASES (MEEGID VII) .

2004

Conference paper

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Brucella est un ochrobactrum à génome réduit

Corinne Teyssier, Bénédicte Lafay, Agnès Masnou, Estelle Jumas-Bilak, Hélène Marchandin

VI eme Congrès de la Société Française de Microbiologie .

2004

Conference paper

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CAT : Un Modèle Phylogénétique Bayésien permettant de prendre en compte l'Hétérogénéité des Processus de Substitution entre Sites dans les Alignements Protéiques

Nicolas Lartillot, Herve Philippe

Biosystema 22 . 22 : 97-104

2004

Book chapter

see the publication

GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

A parallel algorithm for the extraction of structured motifs

The at-most $k$-deep factor tree

Motifs in Sequences: Localization and Extraction

Update of NUREBASE: nuclear hormone receptor functional genomics

Update of NUREBASE : nuclear hormone receptor functional genomics

Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of microsporidia and reveals a high frequency of fast-evolving genes

A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process

The evolutionary history of quorum-sensing in bacteria

Ψ-Φ: Exploring the outer limits of bacterial pseudogenes

Hypervariable and highly divergent intron/exon organizations in the chordate Oikopleura dioica

Reversing gene erosion: Reconstructing ancestral bacterial genomes from gene-content and order data

Novel tree edit operations for RNA secondary structure comparison

Physical and transcript map of the autosomal dominant colobomatous microphthalmia locus on chromosome 15q12-q15 and refinement to a 4.4 Mb region.

Grid as a bioinformatic tool

Grid as a bioinformatic tool

Recombination drives the evolution of GC-content in the human genome

Evidence of Selection on the Domesticated ERVWE1 env Retroviral Element Involved in Placentation

Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries.

Longest Motifs with a Functionally Equivalent Central Block

Sorting by reversals in subquadratic time

Sorting by reversals in subquadratic time

Longest repeated motif with a block of don't cares

The European ribosomal RNA database

Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones.

Phylogenetic study and identification of Vibrio splendidus-related strains based on gyrB gene sequences.

How does susceptibility prevalence impact on the performance of disk diffusion susceptibility testing?

Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers

Molecular analysis of the hypervariable regions in the minicircle of kinetoplastic genome in Trypanosoma cruzi, agent of Chagas'disease

Brucella est un ochrobactrum à génome réduit

CAT : Un Modèle Phylogénétique Bayésien permettant de prendre en compte l'Hétérogénéité des Processus de Substitution entre Sites dans les Alignements Protéiques