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 811 to 840 publications on 1415 in total

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.

Ludovic Cottret, David Wildridge, Florence Vinson, Michael P Barrett, Hubert Charles, Marie-France Sagot...

Nucleic Acids Research . 38 ( Web Server issue ) : W132-7

DOI: 10.1093/nar/gkq312

Journal article

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Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata.

Ludovic Cottret, Paulo Vieira Milreu, Vicente Acuña, Alberto Marchetti-Spaccamela, Leen Stougie, Hubert Charles...

PLoS Computational Biology . 6 ( 9 ) : epub ahead of print

DOI: 10.1371/journal.pcbi.1000904

Journal article

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The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution

Jean-François Gout, Daniel Kahn, Laurent Duret

PLoS Genetics . 6 ( 5 ) : e1000944

DOI: 10.1371/journal.pgen.1000944

Journal article

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Evolution of the ribosome: testing eukaryotic origins

Elie Desmond-Le Quéméner, Celine Brochier-Armanet, Patrick Forterre, Simonetta Gribaldo

Archaea and the tree of life .

Conference paper

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Genetic Admixture History of Eastern Indonesia as Revealed by Y-Chromosome and Mitochondrial DNA Analysis

S. Mona, K. Grunz, S. Brauer, Brigitte Pakendorf, L. Castri, H. Sudoyo...

Molecular Biology and Evolution . 26 ( 8 ) : 1865-1877

DOI: 10.1093/molbev/msp097

Journal article

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Genetic diversity and the emergence of ethnic groups in Central Asia

Evelyne Heyer, Patricia Balaresque, Mark Jobling, Lluis Quintana-Murci, Raphaelle Chaix, Laure Segurel...

BMC Genetics . 10 ( 1 ) : 49

DOI: 10.1186/1471-2156-10-49

Journal article

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Mutation Patterns in the Human Genome:More Variable Than Expected

L. Duret

PLoS Biology . 7(2) e1000028 : 803-806

Journal article

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Monoallelic expression and tissue specificity are associated with high crossover rates

A. Necşulea, M. Sémon, L. Duret, L.D. Hurst

Trends in Genetics . 25(12) : 519-522

Journal article

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GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates

N. Galtier, L. Duret, S. Glémin, Vincent Ranwez

Trends in Genetics . 25(1) : 1-5

Journal article

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Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum.

Lilia Brinza, José Viñuelas, Ludovic Cottret, Federica Calevro, Yvan Rahbé, Gérard Febvay...

Comptes Rendus. Biologies . 332 ( 11 ) : 1034-49

DOI: 10.1016/j.crvi.2009.09.007

Journal article

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The Acyrthosiphon pisum Cyc database (AcypiCyc) created using a novel BioCyc Annotation Database System (CycADS): a useful tool to explore and study the pea aphid metabolism

Stefano Colella, A. Vellozo, Ludovic Cottret, Gérard Febvay, Federica Calevro, Yvan Rahbé...

5th Meeting of the International Aphid Genomics Consortium "Pea Aphid Genome Annotation Workshop 2, Barcelona, Espagne, juin 2009 .

Conference paper

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Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes

Claire Lemaitre, Marília D.V. Braga, Christian Gautier, M.-F. Sagot, Eric Tannier, Gabriel Marais

Genome Biology and Evolution . 1(1) : 56-66

Journal article

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Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster

M. Deloger, F.M.G. Cavalli, E. Lerat, C. Biémont, M.-F. Sagot, Cristina Vieira

Gene . 439 : 55-62

Journal article

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Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

Claire Lemaitre, Lamia Zaghloul, Marie-France Sagot, Christian Gautier, Alain Arneodo, Eric Tannier...

BMC Genomics . 10 ( 1 ) : 335

DOI: 10.1186/1471-2164-10-335

Journal article

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A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies

Bastien Boussau, Laurent Guéguen, Manolo Gouy

Evolutionary Bioinformatics . 5 : 67-79

DOI: 10.4137/EBO.S2242

Journal article

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Phylogeny of prokaryotes: does it exist and why should we care?

Simonetta Gribaldo, Céline Brochier-Armanet

Research in Microbiology . 160 : 513-21

Journal article

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Happy together: genomic insights into the unique Nanoarchaeum/Ignicoccus association.

Patrick Forterre, Simonetta Gribaldo, Céline Brochier-Armanet

Journal of Biology . 8 ( 1 ) : 7

DOI: 10.1186/jbiol110

Journal article

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Genomic environment influences the dynamics of the tirant LTR retrotransposon in Drosophila

M. Fablet, E. Lerat, R. Rebollo, B. Horard, N. Burlet, S. Martinez...

FASEB Journal . 23 : 54-62

Journal article

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Infra- and Transspecific Clues to Understanding the Dynamics of Transposable Elements

Cristina Vieira, M. Fablet, E. Lerat

genome dyn stab . -- : 115-123

Journal article

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Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs

E. Lerat

Heredity . -- : 1-14

Journal article

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The relationship between DNA replication and human genome organization.

Anamaria Necsulea, Claire Guillet, Jean-Charles Cadoret, Marie-Noëlle Prioleau, L. Duret

Molecular Biology and Evolution . 26 ( 4 ) : 729-741

DOI: 10.1093/molbev/msn303

Journal article

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Multiple alignment of biological networks: A flexible approach

Yves-Pol Deniélou, Frédéric Boyer, Alain Viari, Marie-France Sagot

Combinatorial Pattern Matching (CPM) . 5577 : 263-273

DOI: 10.1007/978-3-642-02441-2_23

Conference paper

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Assessing the exceptionality of coloured motifs in networks

Sophie S. Schbath, Vincent Lacroix, Marie-France Sagot

EURASIP Journal on Bioinformatics and Systems Biology . 2009 : 9 pages on line

DOI: 10.1155/2009/616234

Journal article

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Fast optimization of statistical potentials for structurally constrained phylogenetic models

Cécile Bonnard, Claudia L. Kleinman, Nicolas Rodrigue, Nicolas Lartillot

BMC Evolutionary Biology . 9 ( 1 ) : 227

DOI: 10.1186/1471-2148-9-227

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Comment on “Human-Specific Gain of Function in a Developmental Enhancer”

L. Duret, N. Galtier

Science . 323(5915) : 714-715

Journal article

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Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

L. Duret, N. Galtier

Annual Review of Genomics and Human Genetics . 10 : 285-311

Journal article

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L’évolution des chromosomes sexuels humains

Gabriel Marais, L. Duret

Biofutur . 304 : 40-41

Journal article

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Current tools for the identification of miRNA genes and their targets

N.D. Mendes, A.T. Freitas, M.-F. Sagot

Nucleic Acids Research . 2009 : 2419-2433

Journal article

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Lossless filter for multiple repeats with bounded edit distance

Pierre Peterlongo, Gustavo Akio Tominaga Sacomoto, Alair Pereira Do Lago, Nadia Pisanti, Marie-France Sagot

Algorithms for Molecular Biology . 4 ( 1 ) : 3

DOI: 10.1186/1748-7188-4-3

Journal article

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An asymmetric approach to preserve common intervals while sorting by reversals

Marília D.V. Braga, Christian Gautier, Marie-France Sagot

Algorithms for Molecular Biology . 4 ( 1 ) : 16

DOI: 10.1186/1748-7188-4-16

Journal article

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