GECO Génomique Computationnelle et Evolutive

Monte Carlo algorithms for Brownian phylogenetic models

Benjamin Horvilleur, Nicolas Lartillot

Bioinformatics . 30 ( 21 ) : 3020-3028

DOI: 10.1093/bioinformatics/btu485

2014

Article dans une revue

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A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data

Nicolas Lartillot

Bioinformatics . 30 ( 4 ) : 488-96

DOI: 10.1093/bioinformatics/btt707

2014

Article dans une revue

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Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package

N. Rodrigue, Nicolas Lartillot

Bioinformatics . 30 ( 7 ) : 1020-1

DOI: 10.1093/bioinformatics/btt729

2014

Article dans une revue

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Hijacking of Host Cellular Functions by an Intracellular Parasite, the Microsporidian Anncaliia algerae

Johan Panek, Hicham El Alaoui, Anne Mone, Serge Urbach, Edith Demettre, Catherine Texier...

PLoS ONE . 9 ( 6 ) : e100791

DOI: 10.1371/journal.pone.0100791

2014

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Microsporidian Genomes Harbor a Diverse Array of Transposable Elements that Demonstrate an Ancestry of Horizontal Exchange with Metazoans.

Nicolas Parisot, Adrian Pelin, Cyrielle Gasc, Valérie Polonais, Abdel Belkorchia, Johan Panek...

Genome Biology and Evolution . 6 ( 9 ) : 2289-300

DOI: 10.1093/gbe/evu178

2014

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Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems

E Peyretaillade, D Boucher, N Parisot, C Gasc, R Butler, J-F Pombert...

Heredity . : 25182222

DOI: 10.1038/hdy.2014.78

2014

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An angiosperm-wide analysis of the gynodioecy-dioecy pathway.

Mathilde Dufaÿ, P. Champelovier, J Käfer, Jean-Pierre Henry, Sylvain Mousset, Gabriel A.B. Marais

Annals of Botany . 114 : 539-548

DOI: 10.1093/aob/mcu134

2014

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Comparative population genomics in animals uncovers the determinants of genetic diversity

Jonathan Romiguier, P Gayral, M Ballenghien, Arnaud Bernard, V Cahais, Anne Chenuil...

Nature . 515 ( 7526 ) : 261-263

DOI: 10.1038/nature13685

2014

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Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes

Nc. Rochette, Céline Brochier-Armanet, M. Gouy

Molecular Biology and Evolution . 31 ( 4 ) : 832-45

DOI: 10.1093/molbev/mst272

2014

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Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

Pierre P. Gladieux, Jeanne Ropars, Helene Badouin, Antoine Branca, Gabriela G. Aguileta, Damien M. de Vienne...

Molecular Ecology . 23 ( 4 ) : 753-773

DOI: 10.1111/mec.12631

2014

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Navigating in a Sea of Repeats in RNA-seq without Drowning

Gustavo Sacomoto, Blerina Sinaimeri, Camille Marchet, Vincent Miele, Marie-France Sagot, Vincent Lacroix

WABI 2014 - 14th International Workshop on Algorithms in Bioinformatics . 8701 : 82-96

DOI: 10.1007/978-3-662-44753-6_7

2014

Acte de congrès

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Efficiently listing bounded length st-paths

Romeo Rizzi, Gustavo Sacomoto, Marie-France Sagot

Twenty-Fifth International Workshop on Combinatorial Algorithms (IWOCA 2014) . : in press

2014

Acte de congrès

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Rime: Repeat identification

Maria Federico, Pierre Peterlongo, Nadia Pisanti, Marie-France Sagot

Discrete Applied Mathematics . 163 ( 3 ) : 275–286

DOI: 10.1016/j.dam.2013.02.016

2014

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Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure

Paulo Vieira Milreu, Cecilia Coimbra Klein, Ludovic Cottret, Vicente Acuña, Etienne E. Birmelé, Michele Borassi...

Bioinformatics . 30 ( 1 ) : 61-70

DOI: 10.1093/bioinformatics/btt597

2014

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Optimization of the reactional medium and a food impact study for a colorimetric in situ Salmonella spp. detection method

L. Morand, D. Michel, Jean-Pierre Flandrois, T. Junillon, D. Mosticon, B. Mallen...

International Journal of Food Microbiology . 181 : 48-52

2014

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Enhanced tetrazolium violet reduction of Salmonella spp. by magnesium addition to the culture media

T. Junillon, L. Morand, Jean-Pierre Flandrois

Food Microbiology . 42 : 132-135

2014

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Ribosomal proteins: Toward a next generation standard for prokaryotic systematics?

Hemalatha Golaconda Ramulu, Mathieu Groussin, Emmanuel Talla, Rémi Planel, Vincent Daubin, Céline Brochier-Armanet

Molecular Phylogenetics and Evolution . 75 : 103 - 117

DOI: 10.1016/j.ympev.2014.02.013

2014

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Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon, Archaeoglobus fulgidus.

Nadia Khelifi, Oulfat Amin Ali, Philippe Roche, Vincent Grossi, Céline Brochier-Armanet, Odile Valette...

The International Society of Microbiologial Ecology Journal . : 18

DOI: 10.1038/ismej.2014.58

2014

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Halomonas olivaria sp. nov., a moderately halophilic bacterium isolated from olive-processing effluents

A. Amouric, Pierre-Pol Liebgott, M. Joseph, Céline Brochier-Armanet, J. Lorquin

International Journal of Systematic and Evolutionary Microbiology . 64 ( Pt 1 ) : 46 - 54

DOI: 10.1099/ijs.0.049007-0

2014

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Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea.

Kasie Raymann, Patrick Forterre, Céline Brochier-Armanet, Simonetta Gribaldo

Genome Biology and Evolution . 6 ( 1 ) : 192-212

DOI: 10.1093/gbe/evu004

2014

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“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

Marc Bailly-Bechet, Annabelle Haudry, Emmanuelle Lerat

Mobile DNA . 5 : 13

DOI: 10.1186/1759-8753-5-13

2014

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Dioecy is associated with higher diversification rates in flowering plants

Jos Käfer, Hugo J de Boer, Sylvain Mousset, Anneleen Kool, Mathilde Dufaÿ, Gabriel A.B. Marais

Journal of Evolutionary Biology . 27 : 1478-1490

DOI: 10.1111/jeb.12385

2014

Article dans une revue

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Identification and Analysis of Transposable Elements in Genomic Sequences

Laurent Modolo, Emmanuelle Lerat

Genome analysis, current procedures and applications . 978-1-908230-29-4

2014

Chapitre d'ouvrage

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Formation of chromosome in bacteria

Olivier Poirion, Bénédicte Lafay

FEBS-EMBO 2014 Conference .

2014

Acte de congrès

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Amortized Õ(|V|) -Delay Algorithm for Listing Chordless Cycles in Undirected Graphs

Rui Ferreira, Roberto Grossi, Romeo Rizzi, Gustavo Sacomoto, Marie-France Sagot

22th Annual European Symposium on Algorithms . 8737 : 418-429

DOI: 10.1007/978-3-662-44777-2_35

2014

Acte de congrès

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Specific Activation of an I-Like Element in Drosophila Interspecific Hybrids

Elias a G Carnelossi, Emmanuelle Lerat, Hélène Henri, Sonia Martinez, Claudia M A Carareto, Cristina Vieira

Genome Biology and Evolution . 6 : 1806 - 1817

DOI: 10.1093/gbe/evu141

2014

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GC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance

Y. Lesecque, D. Mouchiroud, L. Duret

Molecular Biology and Evolution . 30 : 1409--19

DOI: 10.1093/molbev/mst056

2013

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XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells

C. Vallot, C. Huret, Yann Lesecque, A. Resch, N. Oudrhiri, A. Bennaceur-Griscelli...

Nature Genetics . 45 : 239--41

DOI: 10.1038/ng.2530

2013

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The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

S. B. Montgomery, D. L. Goode, E. Kvikstad, C. A. Albers, Z. D. Zhang, X. J. Mu...

Genome Research . 23 : 749--61

DOI: 10.1101/gr.148718.112

2013

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PCR survey of 50 introns in animals: Cross-amplification of homologous EPIC loci in eight non-bilaterian, protostome and deuterostome phyla

K. Gerard, E. Guilloton, S. Arnaud-Haond, Didier Aurelle, R. Bastrop, Pierre Chevaldonné...

Marine Genomics . 12 : 1-8

DOI: 10.1016/j.margen.2013.10.001

2013

Article dans une revue

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Publications

Monte Carlo algorithms for Brownian phylogenetic models

A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data

Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package

Hijacking of Host Cellular Functions by an Intracellular Parasite, the Microsporidian Anncaliia algerae

Microsporidian Genomes Harbor a Diverse Array of Transposable Elements that Demonstrate an Ancestry of Horizontal Exchange with Metazoans.

Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems

An angiosperm-wide analysis of the gynodioecy-dioecy pathway.

Comparative population genomics in animals uncovers the determinants of genetic diversity

Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes

Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

Navigating in a Sea of Repeats in RNA-seq without Drowning

Efficiently listing bounded length st-paths

Rime: Repeat identification

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure

Optimization of the reactional medium and a food impact study for a colorimetric in situ Salmonella spp. detection method

Enhanced tetrazolium violet reduction of Salmonella spp. by magnesium addition to the culture media

Ribosomal proteins: Toward a next generation standard for prokaryotic systematics?

Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon, Archaeoglobus fulgidus.

Halomonas olivaria sp. nov., a moderately halophilic bacterium isolated from olive-processing effluents

Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea.

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

Dioecy is associated with higher diversification rates in flowering plants

Identification and Analysis of Transposable Elements in Genomic Sequences

Formation of chromosome in bacteria

Amortized Õ(|V|) -Delay Algorithm for Listing Chordless Cycles in Undirected Graphs

Specific Activation of an I-Like Element in Drosophila Interspecific Hybrids

GC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance

XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

PCR survey of 50 introns in animals: Cross-amplification of homologous EPIC loci in eight non-bilaterian, protostome and deuterostome phyla