GECO Evolutionary and Computational Genomics

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 1111 to 1140 publications on 1402 in total

Invertebrate Data Predict an Early Emergence of Vertebrate Fibrillar Collagen Clades and an Anti-incest Model

Abdel Aouacheria, Caroline Cluzel, Claire Lethias, Manolo Gouy, Robert Garrone, Jean-Yves Exposito

Journal of Biological Chemistry . 279 ( 46 ) : 47711-47719

DOI: 10.1074/jbc.M408950200

2004

Journal article

see the publication

Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana

Gabriel Marais, B. Charlesworth, S.I. Wright

Genome Biology . 5 : R45.1-R45.9

2004

Journal article

see the publication

Correlated evolution of synonymous and nonsynonymous sites in Drosophila

Gabriel Marais, T. Domazet-Loso, D. Tautz, B. Charlesworth

Journal of Molecular Evolution . 59 : 771-779

2004

Journal article

see the publication

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

Laurent Michon, L. Morle, M. Bozon, L. Duret, Zech J. C., J. Godet...

European Journal of Human Genetics . ( 12 ) : 574-578

2004

Journal article

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Contribution of Computational Tree Logic to Biological Regulatory Networks: Example from Pseudomonas Aeruginosa

Sabine Peres, Comet Jean-Paul

Lecture Notes in Computer Sciences . 2602 : 47-56

DOI: 10.1007/3-540-36481-1_5

2003

Journal article

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Evidence of a high rate of selective sweeps in African Drosophila melanogaster

Sylvain Mousset, L. Brazier, M.L. Cariou, F. Chartois, F. Depaulis, M. Veuille

Genetics . 163 : 599-609

2003

Journal article

see the publication

Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach

S. Glinka, L. Ometto, Sylvain Mousset, W. Stephan, D. de Lorenzo

Genetics . 165 : 1269-1278

2003

Journal article

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Power of neutrality tests to detect bottlenecks and hitchhiking

F. Depaulis, Sylvain Mousset, M. Veuille

Journal of Molecular Evolution . 57 : S190-S200

2003

Journal article

see the publication

Mitochondrial DNA evidence for admixed origins of central Siberian populations

Brigitte Pakendorf, Victor Wiebe, Larissa Tarskaia, Victor Spitsyn, Himla Soodyall, Alexander Rodewald...

American Journal of Physical Anthropology . 120 ( 3 ) : 211-224

DOI: 10.1002/ajpa.10145

2003

Journal article

see the publication

Neutral effect of recombination on base composition in Drosophila

Gabriel Marais, Dominique Mouchiroud, L. Duret

Genetical Research . 81 : 79-89

2003

Journal article

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Placenta-Specific INSL4 Expression Is Mediated by a Human Endogenous Retrovirus Element

I. Bièche, A. Laurent, I. Laurendeau, L. Duret, Y. Giovangrandi, J.L. Frendo...

Biology of Reproduction . 68 : 1422-1429.

2003

Journal article

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Patterns of selection against transposons inferred from the distribution of Tc1 Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans

C. Rizzon, E. Martin, Gabriel Marais, L. Duret, L. Segalat, C. Biémont

Genetics . 165 : 1127-1135

2003

Journal article

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A basis of tiling motifs for generating repeated patterns and its complexity for higher quorum

Nadia Pisanti, Maxime Crochemore, Roberto Grossi, Marie-France Sagot

International Symposium on Mathematical Foundations of Computer Science 2003 . 2747 : 622-632

DOI: 10.1007/978-3-540-45138-9_56

2003

Conference paper

see the publication

G+C3 structuring along the genome: a common feature in prokaryotes

Vincent Daubin, G. Perrière

Molecular Biology and Evolution . 20 : 471-483

2003

Journal article

see the publication

The source of laterally transferred genes in bacterial genomes

Vincent Daubin, E. Lerat, G. Perrière

Genome Biology . 4 : R57.1-R57.12

2003

Journal article

see the publication

RTKdb: database of Receptor Tyrosine Kinase

J. Grassot, G. Mouchiroud, G. Perrière

Nucleic Acids Research . 31 : 353-358

2003

Journal article

see the publication

Quelques problèmes statistiques rencontrés dans l`estimation de la température minimale de croissance de Listeria monocytogenes

S. Charles-Bajard, Jean-Pierre Flandrois, R. Tomassone

Revue de Statistique Appliquée . LI : 59-71

2003

Journal article

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MgtC as a horizontally-acquired virulence factor of intracellular bacterial pathogens: evidence from molecular phylogeny and comparative genomics.

Anne-Béatrice Blanc-Potard, Bénédicte Lafay

Journal of Molecular Evolution . 57 ( 4 ) : 479-86

DOI: 10.1007/s00239-003-2496-4

2003

Journal article

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From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria

Emmanuelle Lerat, Vincent Daubin, Nancy Moran

PLoS Biology . 1 ( 1 ) : 101-109

DOI: 10.1371/journal.pbio.0000019

2003

Journal article

see the publication

Sequence divergence within transposable element families in the Drosophila melanogaster genome

E. Lerat, C. Rizzon, C. Biémont

Genome Research . 13 : 1889-1896

2003

Journal article

see the publication

Integrated databanks access and sequence/structure analysis services at the PBIL.

G. Perriere, C. Combet, Simon Penel, Christophe Blanchet, J. Thioulouse, C. Geourjon...

Nucleic Acids Research . 31 ( 13 ) : 3393-3399

DOI: 10.1093/nar/gkg530

2003

Journal article

see the publication

Patterns of selection against transposons inferred from the distribution of Tc1, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans.

Carène Rizzon, Edwige Martin, Gabriel Marais, Laurent Duret, Laurent Ségalat, Christian Biémont

Genetics . 165 ( 3 ) : 1127-35

2003

Journal article

see the publication

ROSO: a software to search optimized oligonucleotide probes for microarrays

Nancie Reymond, Hubert Charles, Guillaume Beslon, Laurent Duret, Jean-Michel Fayard

14. Rencontres Régionales de la Recherche .

2003

Poster

see the publication

Subcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form

Jean-Pierre Rouault, Olga Assossou, Franã§oise Besson, Florence Persat, Christine Brisson, Laurent Duret...

FEMS Microbiology Letters . 224 ( 2 ) : 161-168

DOI: 10.1016/S0378-1097(03)00479-8

2003

Journal article

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Subcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form

O. Assossou, F. Besson, J.P. Rouault, F. Persat, C. Brisson, L. Duret...

FEMS Microbiology Letters . 224 : 161-168.

DOI: 10.1016/S0378-1097(03)00479-8

2003

Journal article

see the publication

Patterns of selection against transposons inferred from the distribution of Tcl, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans.

C. Rizzon, E. Martin, G. Marais, L. Duret, L. Segalat, C. Biemont

Genetics . ( 165 ) : 1127-1135

2003

Journal article

see the publication

Orphan gene finding - An exon assembly approach

Philippe Blayo, Pierre Rouzé, Marie-France Sagot

Theoretical Computer Science . 290 ( 1 ) : 1407-1431

2003

Journal article

see the publication

Pattern inference under many guises

M.-F. Sagot, Y. Wakabayashi

incollection . -- : 245-288

2003

Journal article

see the publication

Use of Correspondence Discriminant Analysis to predict the subcellular location of bacterial proteins

G. Perrière, J. Thioulouse

Computer Methods and Programs in Biomedicine . 70 : 99-105

2003

Journal article

see the publication

Cross-platform comparison and visualisation of gene expression data using co-inertia analysis

A.C. Culhane, G. Perrière, D.G. Higgins

BMC Bioinformatics . 4 : 1-15

2003

Journal article

see the publication

GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Invertebrate Data Predict an Early Emergence of Vertebrate Fibrillar Collagen Clades and an Anti-incest Model

Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana

Correlated evolution of synonymous and nonsynonymous sites in Drosophila

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

Contribution of Computational Tree Logic to Biological Regulatory Networks: Example from Pseudomonas Aeruginosa

Evidence of a high rate of selective sweeps in African Drosophila melanogaster

Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach

Power of neutrality tests to detect bottlenecks and hitchhiking

Mitochondrial DNA evidence for admixed origins of central Siberian populations

Neutral effect of recombination on base composition in Drosophila

Placenta-Specific INSL4 Expression Is Mediated by a Human Endogenous Retrovirus Element

Patterns of selection against transposons inferred from the distribution of Tc1 Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans

A basis of tiling motifs for generating repeated patterns and its complexity for higher quorum

G+C3 structuring along the genome: a common feature in prokaryotes

The source of laterally transferred genes in bacterial genomes

RTKdb: database of Receptor Tyrosine Kinase

Quelques problèmes statistiques rencontrés dans l`estimation de la température minimale de croissance de Listeria monocytogenes

MgtC as a horizontally-acquired virulence factor of intracellular bacterial pathogens: evidence from molecular phylogeny and comparative genomics.

From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria

Sequence divergence within transposable element families in the Drosophila melanogaster genome

Integrated databanks access and sequence/structure analysis services at the PBIL.

Patterns of selection against transposons inferred from the distribution of Tc1, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans.

ROSO: a software to search optimized oligonucleotide probes for microarrays

Subcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form

Subcellular localization of 14-3-3 proteins in Toxoplasma gondii tachyzoites and evidence for a lipid raft-associated form

Patterns of selection against transposons inferred from the distribution of Tcl, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans.

Orphan gene finding - An exon assembly approach

Pattern inference under many guises

Use of Correspondence Discriminant Analysis to predict the subcellular location of bacterial proteins

Cross-platform comparison and visualisation of gene expression data using co-inertia analysis