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 751 to 780 publications on 1415 in total

Comparative high-throughput transcriptome sequencing and development of SiESTa, the \textitSilene EST annotation database

N. Blavet, D. Charif, C. Oger-Desfeux, Gabriel Marais, A. Widmer

BMC Genomics . 12 : 1-11

DOI: 10.1186/1471-2164-12-376

Journal article

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Absence of a core metabolic network common to symbiotic bacteria

Cecilia Coimbra Klein, Ludovic Cottret, Hubert Charles, Christian Gautier, Ana Tereza Ribeiro de Vasconcelos, Vincent Lacroix...

6. Meeting GDRE-RA Comparative genomics . : 33 diapositives

Conference paper

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CycADS: an annotation database system to ease the development and update of BioCyc databases.

Augusto F Vellozo, Amélie S Véron, Patrice Baa-Puyoulet, Jaime Huerta-Cepas, Ludovic Cottret, Gérard Febvay...

Database - The journal of Biological Databases and Curation . 2011 : bar008

DOI: 10.1093/database/bar008

Journal article

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Bacterial syntenies: an exact approach with gene quorum.

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

BMC Bioinformatics . 12 : 193

DOI: 10.1186/1471-2105-12-193

Journal article

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BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks

Stéphanie Rialle, Liza Felicori, Camila Dias-Lopes, Sabine Peres, Sanaâ El Atia, Alain Thierry...

Bioinformatics . 26 ( 18 ) : 2298-2304

DOI: 10.1093/bioinformatics/btq409

Journal article

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Computing biological functions using BioΨ, a formal description of biological processes based on elementary bricks of actions

Sabine Peres, Liza Felicori, Stéphanie Rialle, Elodie Jobard, Franck Molina

Bioinformatics . 26 ( 12 ) : 1542-1547

DOI: 10.1093/bioinformatics/btq169

Journal article

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An efficient method to find potentially universal population genetic markers applied to metazoans

A. Chenuil, Thierry B. Hoareau, E. Egea, G. Penant, C. Rocher, D. Aurelle...

BMC Evolutionary Biology . 10 ( 276 ) : 1-17

DOI: 10.1186/1471-2148-10-276

Journal article

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Genetic perspectives on forager-farmer interaction in the Luangwa Valley of Zambia

Cesare de Filippo, Patricia Heyn, Lawrence Barham, Mark Stoneking, Brigitte Pakendorf

American Journal of Physical Anthropology . 141 ( 3 ) : 382-394

DOI: 10.1002/ajpa.21155

Journal article

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Conservation of Neutral Substitution Rate and Substitutional Asymmetries in Mammalian Genes

Carina Mugal, J. Wolf, H. von Grünberg, H. Ellegren

Genome Biology and Evolution . 2 : 19-28

DOI: 10.1093/gbe/evp056

Journal article

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Molecular evolution of genes in avian genomes

Ki Woong Nam, Carina Mugal, Benoit Nabholz, Holger Schielzeth, Jochen B W Wolf, Niclas Backström...

Genome Biology . 11 ( 6 ) : 17 p.

DOI: 10.1186/gb-2010-11-6-r68

Journal article

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Phylogénie moléculaire

Samuel Blanquart, Alexis Criscuolo, Christophe J Douady, Emmanuel Douzery, Nicolas Lartillot, Herve Philippe...

Biologie évolutive . 9782804101619

Book chapter

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Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Cécile Fleury, Marie Francoise M. F. Gautier, Pierre Larmande, Sabine Pérès, Frédéric F. de Lamotte, Franck Molina...

JOBIM2010 .

Conference paper

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Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Cécile Fleury, Marie Francoise M. F. Gautier, Pierre Larmande, Sabine Pérès, Frédéric F. de Lamotte, Franck Molina...

18. Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) .

Conference paper

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Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Cécile Fleury, Marie Francoise M. F. Gautier, Pierre Larmande, Sabine Pérès, Frédéric F. de Lamotte, Franck Molina...

Séminaire Génomique Végétale .

Conference paper

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Géographie des interfaces. Une nouvelle vision du territoire

C. Lampin-Maillet, Sabine Pérès, J.P. Ferrier, P. Allard

978-2-7592-0857-9 : 168

Book

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In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations

Evelyne Heyer, Begoña Martínez-Cruz, Renaud Vitalis, Laure Ségurel, Frédéric Austerlitz, Myriam Georges...

European Journal of Human Genetics .

DOI: 10.1038/ejhg.2010.153

Journal article

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Mode de vie et diversité génétique dans les populations humaines d'Asie Centrale

Laure Ségurel

Thesis

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Frequency of the AGT Pro11Leu polymorphism in humans: Does diet matter?

Laure Ségurel, Sophie Lafosse, Evelyne Heyer, Renaud Vitalis

Annals of Human Genetics . 74 ( 1 ) : 57-64

DOI: 10.1111/j.1469-1809.2009.00549.x

Journal article

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Looking for signatures of sex-specific demography and local adaptation on the X chromosome.

Evelyne Heyer, Laure Segurel

Genome Biology . 11 ( 1 ) : 203

DOI: 10.1186/gb-2010-11-1-203

Journal article

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Evolution Moléculaire

L. Duret, T. Bataillon, N. Bierne, Vincent Daubin, J. Dutheil, Christian Gautier...

Biologie évolutive . 978-2-8041-0161-9 : 114-173

Book chapter

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Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

J. Beisson, M. Bétermier, M.-H. Bré, J. Cohen, S. Duharcourt, L. Duret...

Emerging Model Organisms . 2010(1) : 1-55

Journal article

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Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia.

Olivier Arnaiz, Jean-François Goût, Mireille Bétermier, Khaled Bouhouche, Jean Cohen, L. Duret...

BMC Genomics . 11 ( 1 ) : 547

DOI: 10.1186/1471-2164-11-547

Journal article

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Mod/Resc Parsimony Inference

Igor Nor, Danny Hermelin, Sylvain Charlat, Jan Engelstadter, Max Reuter, Olivier Duron...

Combinatorial Pattern Matching . 6129 : 202--213

DOI: 10.1007/978-3-642-13509-5_19

Conference paper

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A tale of genome, annotations, metabolism and phylogenomics: the pea aphid genome resources

Fabrice Legeai, Stefano Colella, Jaime Huerta-Cepas, Jean-Pierre Gauthier, Augusto Vellozo, Patrice Baa-Puyoulet...

10. Cold Spring Harbor Laboratory / Wellcome Trust conference on Genome Informatics . : 1 p.

Poster

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

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

JOBIM 2010 . : 1 p.

Poster

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A note on the complexity of finding and enumerating elementary modes.

Vicente Acuña, Alberto Marchetti-Spaccamela, Marie-France Sagot, Leen Stougie

BioSystems . 99 ( 3 ) : 210-4

DOI: 10.1016/j.biosystems.2009.11.004

Journal article

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Concepts et méthodes en phylogénie moléculaire

G. Perrière, Céline Brochier-Armanet

Springer . 978-2-287-99047-2

Book

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Concepts et méchodes en phylogénie moléculaire

G. Perrière, C. Brochier-Armanet

incollection . -- : 63-65

Journal article

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Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

Sophie S. Abby, Eric Tannier, Manolo Gouy, Vincent Daubin

BMC Bioinformatics . 11 ( 324 ) : 13

DOI: 10.1186/1471-2105-11-324

Journal article

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Species identification of staphylococci by amplification and sequencing of the gene compared to the gene and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry

M. Bergeron, O. Dauwalder, M. Gouy, A.-M. Freydiere, M. Bes, H. Meugnier...

European Journal of Clinical Microbiology and Infectious Diseases . : 343-354

DOI: 10.1007/s10096-010-1091-z

Journal article

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