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 781 to 810 publications on 1415 in total

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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SeaView Version 4: a Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

Manolo Gouy, Stéphane Guindon, Olivier Gascuel

Molecular Biology and Evolution . 27 : 221-224

DOI: 10.1093/molbev/msp259

Journal article

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The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

Simonetta Gribaldo, Anthony M. Poole, Vincent Daubin, Patrick Forterre, C. Brochier-Armanet

Nature Reviews Microbiology . 8 ( 10 ) : 743-753

DOI: 10.1038/nrmicro2426

Journal article

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Distinct gene set in two different lineages of ammoniaoxidizing archaea supports the phylum Thaumarchaeota

A. Spang, R. Hatzenpichler, Céline Brochier-Armanet, T. Rattei, P. Tischler, E. Spieck...

Trends Microbiol . 18(8) : 331-40

Journal article

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Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

C.B. Walker, J.R. La Torre, M.G. Klotz, H. Urakawa, N. Pinel, D.J. Arp...

Proceedings of the National Academy of Sciences of the United States of America . 107 ( 19 ) : 8818-23

DOI: 10.1073/pnas.0913533107

Journal article

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Structure, function, and evolution of the Thiomonas spp. genome.

Florence Arsène-Ploetze, Sandrine Koechler, Marie Marchal, Jean-Yves Coppée, Michael Chandler, Violaine Bonnefoy...

PLoS Genetics . 6 ( 2 ) : e1000859

DOI: 10.1371/journal.pgen.1000859

Journal article

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RECONSTRUCTING ORIGINS OF LOSS OF SELF-INCOMPATIBILITY AND SELFING IN NORTH AMERICAN ARABIDOPSIS LYRATA: A POPULATION GENETIC CONTEXT

John Paul Foxe, Marc Stift, Andrew Tedder, Annabelle A. Haudry, Stephen Wright, Barbara Mable

Evolution - International Journal of Organic Evolution . 64 ( 12 ) : 3495 - 3510

DOI: 10.1111/j.1558-5646.2010.01094.x

Journal article

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Reconstructing origins of loss of self-incompatibility and selfing in North American Arabidopsis lyrata: a population genetic context

John Paul Foxe, Marc Stift, Andrew Tedder, Annabelle A. Haudry, Stephen Wright, Barbara Mable

Evolution - International Journal of Organic Evolution . 64 : 3495-3510

DOI: 10.1111/j.1558-5646.2010.01094.x

Journal article

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A Phylogenetic Model for Investigating Correlated Evolution of Substitution Rates and Continuous Phenotypic Characters

Nicolas Lartillot, Raphaël Poujol

Molecular Biology and Evolution . 28 ( 1 ) : 729 - 744

DOI: 10.1093/molbev/msq244

Journal article

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A Dirichlet Process Covarion Mixture Model and Its Assessments Using Posterior Predictive Discrepancy Tests

Yan Zhou, Henner Brinkmann, Nicolas Rodrigue, Nicolas Lartillot, Herve Philippe

Molecular Biology and Evolution . 27 ( 2 ) : 371-384

DOI: 10.1093/molbev/msp248

Journal article

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Proposals for classification methods dedicated to biological data

Anne-Muriel Arigon Chifolleau, Guy Perrière, Manolo Gouy

International Journal of Biomedical Engineering and Technology (IJBET) . 3 ( 1/2 ) : 4-21

DOI: 10.1504/IJBET.2010.029649

Journal article

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Specialization of a Drosophila capping protein essential for the protection of sperm telomeres.

Raphaëlle Dubruille, Guillermo A Orsi, Lætitia Delabaere, Elisabeth Cortier, Pierre Couble, Gabriel A.B. Marais...

Current Biology . 20 ( 23 ) : 2090-9

DOI: 10.1016/j.cub.2010.11.013

Journal article

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Can Intra-Y Gene Conversion Oppose the Degeneration of the Human Y Chromosome? A Simulation Study

Gabriel Marais, P.R.A. Campos, I. Gordo

Genome Biology and Evolution . 2 : 347-357

Journal article

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Structure and evolution of Apetala3 a sex-linked gene in Silene latifolia

R. Cegan, Gabriel Marais, H. Kubekova, N. Blavet, A. Widmer, B. Vyskot...

BMC Plant Biology . 10 : 1-10

Journal article

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Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome

Y.E. Zhang, M.D. Vibranovski, P. Landback, Gabriel Marais, M. Long

PLoS Biology . 8 ( 10 ) : 1-13

DOI: 10.1371/journal.pbio.1000494

Journal article

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Specialization of a Drosophila Capping Protein Essential for the Protection of Sperm Telomeres

R. Dubruille, G.A. Orsi, L. Delabaere, E. Cortier, P. Couble, Gabriel Marais...

Current Biology . 20 : 1-10

DOI: 10.1016/j.cub.2010.11.013

Journal article

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