GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

The main goal of the GECO department is to foster integration and synergies between theoretical and methodological research relevant for the analysis of genomes (computational genomics) and empirical analysis of genomic and multi-omic data (evolutionary and functional genomics). The department is structured in two teams, BAOBAB and BPGE:

BAOBAB is deeply rooted in computer science. Its strengths are in algorithms, models, and mathematical analysis of graphs and networks, with applications to transcriptomics and metabolic networks.

BPGE is oriented towards bioinformatics, phylogenetics and evolutionary genomics. Its research projects cover a broad range of subjects, such as methodological developments for phylogenetic inference, their applications to the reconstruction of the evolutionary history of bacteria and archaea, the role of mobile genetic elements in the evolution of bacteria and of antibioresistance, or the role of recombination, of genomic rearrangements and of transposable elements in the evolution of eukaryotic genomes.

As detailed on their pages, the research conducted in both teams integrates deep and long-ranging theoretical and methodological (algorithmic and computational) developments with data analysis driven by empirical questions. This integration is bi-directional: methodological developments are guided by empirical questions and then used in empirical applications, while theoretical modeling helps clarify the conceptual basis of subsequent empirical analyses.

Publications

Display of 1201 to 1230 publications on 1408 in total

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

Journal article

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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

Conference paper

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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A mathematical model describing the thermal virus inactivation

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

Vaccine . 19 : 3575-3582

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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Gene flow in a facultative apomictic poacea the savanna grass Hyparrhenia diplandra

J. Durand, L. Garnier, I. Dajoz, Sylvain Mousset, M. Veuille

Genetics . 156 : 823-831

Journal article

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Selective sweep near the In(2L)t inversion breakpoint in an African population of Drosophila melanogaster

F. Depaulis, L. Brazier, Sylvain Mousset, A. Turbe, M. Veuille

Genetical Research . 76 : 149-158

Journal article

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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

Journal article

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EuGene an eurocaryotic gene finder that combines several sources of evidence

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

Journées ouvertes biologie informatique mathématiques .

Conference paper

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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

Journal article

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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

Journal article

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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

Journal article

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Nature and structure of human genes that generate retropseudogenes

I. Goncalves, L. Duret, Dominique Mouchiroud

Genome Research . 10 : 672-678

Journal article

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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

Journal article

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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

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

Journal article

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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

Journal article

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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

Journal article

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The Enhanced Microbial Genomes Library

G. Perrière, P. Bessieres, B. Labedan

Nucleic Acids Research . 27 : 63-65

Journal article

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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

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

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

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

Journal article

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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

Journal article

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Multiple alignments for structural functional or phylogenetic analyses of homologous sequences

L. Duret, S. Abdeddaim

incollection . -- : 51-76

Journal article

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