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 1402 in total

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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Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea.

Valérie de Crécy-Lagard, Céline Brochier-Armanet, Jaunius Urbonavicius, Bernard Fernandez, Gabriela Phillips, Benjamin Lyons...

Molecular Biology and Evolution . 27 ( 9 ) : 2062-77

DOI: 10.1093/molbev/msq096

Journal article

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The Pseudomonas aeruginosa patatin-like protein PlpD is the archetype of a novel Type V secretion system

R. Salacha, F. Kovacic, Céline Brochier-Armanet, S. Wilhelm, J. Tommassen, A. Filloux...

Environmental Microbiology . 12 ( 6 ) : 1498-512

DOI: 10.1111/j.1462-2920.2010.02174.x

Journal article

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Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms

Paulo Vieira Milreu, Vicente Acuña, Etienne E. Birmelé, Pierluigi Crescenzi, Alberto Marchetti-Spaccamela, Marie-France Sagot...

Algorithms in Bioinformatics . 6293 : 226-237

DOI: 10.1007/978-3-642-15294-8_19

Conference paper

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Using the “CycADS” annotation management system to develop a BioCyc metabolic network database for sequenced arthropods genomes: first steps towards “ArthropodsCyc”

Augusto Vellozo, Patrice Baa-Puyoulet, Jaime Huerta-Cepas, Gérard Febvay, Federica Calevro, Yvan Rahbé...

4. Annual Arthropod Genomics Symposium on “Arthropod Genomics: New Approaches and Outcomes” . : 45 p.

Poster

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AN INTEGRATIVE TEST OF THE DEAD-END HYPOTHESIS OF SELFING EVOLUTION IN TRITICEAE (POACEAE)

Juan Escobar, Alberto Cenci, Jeremy Bolognini, Annabelle A. Haudry, Stefan Laurent, Jacques David...

Evolution - International Journal of Organic Evolution . 64 ( 10 ) : no - no

DOI: 10.1111/j.1558-5646.2010.01045.x

Journal article

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Statistical Potentials for Improved Structurally Constrained Evolutionary Models

Claudia L Kleinman, Nicolas Rodrigue, Nicolas Lartillot, Hervé Philippe

Molecular Biology and Evolution . 27 ( 7 ) : 1546 - 1560

DOI: 10.1093/molbev/msq047

Journal article

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Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species.

Hussein Mortada, Cristina Vieira, Emmanuelle Lerat

Journal of Molecular Evolution . 71 ( 3 ) : 180-91

DOI: 10.1007/s00239-010-9376-5

Journal article

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Detecting positive selection within genomes: the problem of biased gene conversion

A. Ratnakumar, Sylvain Mousset, S. Glémin, J. Berglund, N. Galtier, L. Duret...

Philosophical Transactions of the Royal Society B: Biological Sciences . 365 ( 1552 ) : 2571-2580

DOI: 10.1098/rstb.2010.0007

Journal article

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Paramecium tetraurelia: The Renaissance of an Early Unicellular Model

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

Emerging Model Organisms . 2010 : 1-55

Journal article

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Identifying SNPs without a reference genome by comparing raw reads

Pierre Peterlongo, Nicolas Schnel, Nadia Pisanti, Marie-France Sagot, Vincent Lacroix

String Processing and Information Retrieval . 6393 : 147-158

DOI: 10.1007/978-3-642-16321-0_14

Conference paper

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Cassis: detection of genomic rearrangement breakpoints.

Christian Baudet, Claire Lemaitre, Zanoni Dias, Christian Gautier, Eric Tannier, Marie-France Sagot

Bioinformatics . 26 ( 15 ) : 1897-8

DOI: 10.1093/bioinformatics/btq301

Journal article

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Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Iagc The International Aphid Genomics Consortium, Federica Calevro, Hubert Charles, Stefano Colella, Gérard Febvay, Caroline Anselme...

PLoS Biology . 8 ( 2 ) : e1000313

DOI: 10.1371/journal.pbio.1000313

Journal article

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Repetition-free longest common subsequence

S.S Adi, M. Braga, C.G. Fernandes, C.E. Ferreira, F.V. Martinez, M.-F. Sagot...

Discrete Applied Mathematics . 158 ( 12 ) : 1315-1324

DOI: 10.1016/j.dam.2009.04.023

Journal article

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Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi

Nuno Mendes, Ana Freitas, Ana Vasconcelos, Marie-France Sagot

BMC Genomics . 11 ( 1 ) : 529

DOI: 10.1186/1471-2164-11-529

Journal article

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