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 691 to 720 publications on 1402 in total

Modélisation des systèmes biologiques, bioinformatique

Olivier Gascuel, P. Benas, C. Brun, D. Burnouf, Alexandre de Brevern, A. Denise...

Rapport de conjoncture 2010 du Comité national de la recherche scientifique . 978-2-271-07263-4 : chapitre 43, 845-858

Book chapter

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RNA-seq without a reference genome: a comparison of the mapping and the assembly approaches

M.-C. Carpentier, J. Charif, Vincent Lacroix, Marie-France Sagot, Fabrice Vavre

JOBIM .

Conference paper

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kisSplice, détection d'évènements d'épissages alternatifs dans les données RNA-seq

Gustavo Akio Tominaga Sacomoto, J. Kielbassa, Pavlos Antoniou, Rayan Chikhi, Raluca Uricaru, Marie-France Sagot...

: 12

Report

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Metabolic network comparison of bacteria in the context of symbiosis

Cecilia C. Klein, Ludovic Cottret, Hubert Charles, Christian Gautier, Ana T Vasconcelos, Vincent Lacroix...

Otto Warburg International Summer School and Research Symposium on Evolutionary Genomics .

Conference paper

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Telling Stories

Vicente Acuña, Etienne Birmele, Ludovic Cottret, Pierluigi Crescenzi, Fabien Jourdan, Vincent Lacroix...

ICALP 2011 satellite workshop: Graph Algorithms and Applications (GA) .

DOI: 10.1016/j.tcs.2012.07.023

Conference paper

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Bioinformatics developments for NGS data analysis at PRABI

F. Picard, Guy Perrière

EMBNet.journal . 17 : 12

Journal article

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

Marie Bergeron, Olivier Dauwalder, Manolo Gouy, Anne-Marie Freydiere, Michèle Bes, Hélène Meugnier...

European Journal of Clinical Microbiology and Infectious Diseases . 30 ( 3 ) : 343-54

DOI: 10.1007/s10096-010-1091-z

Journal article

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Species-driven interpretation guidelines in case of a single-sampling strategy for blood culture

D. Leyssene, S. Gardes, P. Vilquin, Jp. Flandrois, Gérard Carret, B. Lamy

European Journal of Clinical Microbiology and Infectious Diseases . 30 : 1537-1541

DOI: 10.1007/s10096-011-1257-3

Journal article

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Phylogeny and evolution of the Archaea: one hundred genomes later.

Celine Brochier-Armanet, Patrick Forterre, Simonetta Gribaldo

Current Opinion in Microbiology . : epub ahead of print

DOI: 10.1016/j.mib.2011.04.015

Journal article

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Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite.

France Denoeud, Michaël Roussel, Benjamin Noel, Ivan Wawrzyniak, Corinne da Silva, Marie Diogon...

Genome Biology . 12 ( 3 ) : R29

DOI: 10.1186/gb-2011-12-3-r29

Journal article

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Cultivation of the first mesophilic representative ("mesotoga") within the order Thermotogales

Wajdi Ben Hania, Ramzi Ghodbane, Anne Postec, Celine Brochier-Armanet, Moktar Hamdi, Marie Laure Fardeau...

Systematic and Applied Microbiology . 34 : 581-585

DOI: 10.1016/j.syapm.2011.04.001

Journal article

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The GTPase Function of YvcJ and Its Subcellular Relocalization Are Dependent on Growth Conditions in Bacillus subtilis

F. Pompeo, J. Luciano, Céline Brochier-Armanet, A. Galinier

Journal of Molecular Microbiology and Biotechnology . 20 : 156-67

Journal article

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Survival of extremely and moderately halophilic isolates of Tunisian solar salterns after UV-B or oxidative stress

H. Trigui, Salma Masmoudi, Céline Brochier-Armanet, S. Maalej, S. Dukan

Canadian Journal of Microbiology . 57(11) : 923-33

Journal article

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The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes

L. Eme, A. Trilles, D. Moreira, Céline Brochier-Armanet

BMC Evolutionary Biology . 11 : 923-33

DOI: 10.1186/1471-2148-11-265

Journal article

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The Assembly Mode of the Pseudopilus: a hallmark to distinguish a novel secretion system subtype

E. Durand, S. Alphonse, Céline Brochier-Armanet, G. Ball, Badreddine Douzi, A. Filloux...

Journal of Biological Chemistry . 286 ( 27 ) : 24407-24416

DOI: 10.1074/jbc.M111.234278

Journal article

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Multiple Nuclear Gene Phylogenetic Analysis of the Evolution of Dioecy and Sex Chromosomes in the Genus Silene

Gabriel Marais, A. Forrest, E. Kamau, Jos Käfer, Vincent Daubin, D. Charlesworth

PLoS ONE . 6 : e21915

DOI: 10.1371/journal.pone.0021915

Journal article

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Taxonomie et phylogénie des procaryotes. Chapitre 6

Pierre Caumette, Céline Brochier-Armanet, Philippe Normand

Ecologie Microbienne : Microbiologie des milieux naturels et anthropisés . 2-35311-022-3 9782353110223 : 1004 p.

Book chapter

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Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

C. Chureau, S. Chantalat, A. Romito, A. Galvani, Laurent Duret, P. Avner...

Human Molecular Genetics . 20 : 705-718

DOI: 10.1093/hmg/ddq516

Journal article

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Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

Thierry Rouxel, J. Grandaubert, Jk. Hane, Claire Hoede, Angela P. van de Wouw, A. Couloux...

Nature Communications . 2 : 202

DOI: 10.1038/ncomms1189

Journal article

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Wolbachia detection: an assessment of standard PCR protocols.

P. M. Simões, G. Mialdea, D. Reiss, Marie-France Sagot, S. Charlat

Molecular Ecology Resources . 11 ( 3 ) : 567-72

DOI: 10.1111/j.1755-0998.2010.02955.x

Journal article

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Finding Long and Multiple Repeats with Edit Distance

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

The Prague Stringology Conference 2011 .

Conference paper

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ArthropodaCyc: a BioCyc database powered by CycADS to study and compare the metabolism of arthropods

Patrice Baa-Puyoulet, Augusto F Vellozo, Jaime Huerta-Cepas, Gérard Febvay, T. Gabaldon, Marie-France Sagot...

5th Annual Arthropod Genomics Symposium "Arthropod Genomics 2011: Exploring Diversity, Relating Similarity" .

Conference paper

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Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny

Amélie Véron, Claire Lemaitre, Christian Gautier, Vincent Lacroix, Marie-France Sagot

BMC Genomics . 12 ( 1 ) : 303

DOI: 10.1186/1471-2164-12-303

Journal article

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Initial metabolic reconstruction of Klebsiella pneumoniae Kp13, a multidrug resistant pathogen involved in nosocomial outbreaks in Brazil

P. Ivan, Cecilia C. Klein, Ludovic Cottret, Ana T Vasconcelos, Ac Gales, Marie-France Sagot...

X-meeting .

Conference paper

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Tpms: a Tree Pattern-matching Utility for Querying Gene Trees Collections

Thomas Bigot, Vincent Daubin, G. Perrière

Journées Ouvertes Biologie Informatique Mathématiques (JOBIM) . : 111-112

Conference paper

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Apport des nouvelles générations de séquençage pour accéder à la diversité des communautés microbiennes du sol : nécessité d’un ‘pipeline’ bio-informatique pour les biologistes

Sébastien Terrat, Richard Christen, Samuel S. Dequiedt, Pierre-Alain Maron, Christophe Mougel, Guy Perriere...

1ères Rencontres bioinformaticiens et statisticiens de l’INRA . : 1 p.

Conference paper

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Adaptation to Environmental Temperature Is a Major Determinant of Molecular Evolutionary Rates in Archaea

M. Groussin, Manolo Gouy

Molecular Biology and Evolution . 28 : 2661-2674

DOI: 10.1093/molbev/msr098

Journal article

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Pendant trois milliards d'années les micro-organismes sont les seuls habitants de la terre

J.C. Bertrand, Céline Brochier-Armanet, Manolo Gouy, F. Westall

incollection . 2-35311-022-3 9782353110223 : 94-U259

Book chapter

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NGS without a reference genome, comparison and visualisation of non assembled data

Vincent Lacroix

Statistical Methods for Post-Genomic Data (SMPGD) .

Conference paper

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