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 541 to 570 publications on 1415 in total

MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis.

Jean-Pierre Flandrois, Gérard Lina, Oana Dumitrescu

BMC Bioinformatics . 15 ( 1 ) : 107

DOI: 10.1186/1471-2105-15-107

Journal article

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Mycobacterium Species Related to M. leprae and M. lepromatosis from Cows with Bovine Nodular Thelitis

D. Pin, V. Guerin-Faublee, V. Garreau, F. Breysse, Oana Dumitrescu, Jean-Pierre Flandrois...

Emerging Infectious Diseases . 20 : 2111-4

DOI: 10.3201/eid2012.140184

Journal article

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Reference-free detection of isolated SNPs

Raluca Uricaru, Guillaume Rizk, Vincent Lacroix, Elsa Quillery, Olivier Plantard, Rayan Chikhi...

Nucleic Acids Research . 43 ( 2 ) : e11

DOI: 10.1093/nar/gku1187

Journal article

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Promiscuous Nickel Import in Human Pathogens: Structure, Thermodynamics, and Evolution of Extracytoplasmic Nickel-Binding Proteins

Hugo Lebrette, Céline Brochier-Armanet, Barbara Zambelli, Hilde de Reuse, Elise Borezée-Durant, Stéfano Ciurli...

Structure . 22 ( 10 ) : 1421-1432

DOI: 10.1016/j.str.2014.07.012

Journal article

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Protein SYCP2 Is an Ancient Component of the Metazoan Synaptonemal Complex

J. Fraune, M. Alsheimer, J. Redolfi, Céline Brochier-Armanet, R. Benavente

Cytogenetic and genome research . 144 : 299-305

DOI: 10.1159/000381080

Journal article

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Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family

R. Zallot, Céline Brochier-Armanet, K. W. Gaston, F. Forouhar, P. A. Limbach, J. F. Hunt...

ACS Chemical Biology . 9 ( 8 ) : 1812-1825

DOI: 10.1021/cb500278k

Journal article

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Ail and PagC-Related Proteins in the Entomopathogenic Bacteria of Photorhabdus Genus

Annabelle Mouammine, Anne Lanois, Sylvie Pages, Bénédicte Lafay, Virginie Molle, Marc Canova...

PLoS ONE . 9 ( 10 ) : e110060

DOI: 10.1371/journal.pone.0110060

Journal article

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Contribution of graphs to the analysis of bacterial genome architecture

Olivier Poirion, Bénédicte Lafay

BioNetVisA workshop, ECCB'14, the 13th European Conference on Computational Biology .

Conference paper

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Structuration of the bacterial replicon space

Olivier Poirion, Bénédicte Lafay

ECCB'14 . CD

Conference paper

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Chromosome formation in bacteria

Olivier Poirion, Bénédicte Lafay

EMBO Conference "Microbiology after the genomics revolution : Genomes 2014" .

Conference paper

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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

Journal article

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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

Journal article

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Standard Sister Clade Comparison Fails when Testing Derived Character States

Jos Käfer, S. Mousset

Systematic Biology . 63 ( 4 ) : 601-609

DOI: 10.1093/sysbio/syu024

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

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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

Conference paper

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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

Conference paper

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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