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 331 to 360 publications on 1415 in total

Exploring and Visualising Spaces of Tree Reconciliations

Katharina Huber, Vincent Moulton, Marie-France Sagot, Blerina Sinaimeri

Systematic Biology . : 1-36

DOI: 10.1093/sysbio/syy075

Journal article

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Pierce's Disease of Grapevines: A Review of Control Strategies and an Outline of an Epidemiological Model

Ifigeneia Kyrkou, Taneli Pusa, Lea Ellegaard-Jensen, Marie-France Sagot, Lars Hestbjerg Hansen

Frontiers in Microbiology . 9 : 1-23

DOI: 10.3389/fmicb.2018.02141

Journal article

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Hydrogen peroxide production and myo-inositol metabolism as important traits for virulence of Mycoplasma hyopneumoniae

Mariana G. Ferrarini, Scheila Gabriele Mucha, Delphine Parrot, Guillaume Meiffren, José Fernando Ruggiero Bachega, Gilles Comte...

Molecular Microbiology . : 1-45

DOI: 10.1111/mmi.13957

Journal article

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A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events

Magali Jaillard, Leandro Lima, Maud Tournoud, Pierre Mahé, Alex van Belkum, Vincent Lacroix...

PLoS Genetics . 14 ( 11 ) : 1-28

DOI: 10.1371/journal.pgen.1007758

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Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data

Clara Benoit-Pilven, Camille Marchet, Emilie Chautard, Leandro Lima, Marie-Pierre Lambert, Gustavo Sacomoto...

Scientific Reports . 8 ( 1 )

DOI: 10.1038/s41598-018-21770-7

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PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae

L. Zucchini, C. Mercy, Ps. Garcia, C. Cluzel, V. Gueguen-Chaignon, F. Galisson...

Nature Microbiology . 3 ( 2 ) : 197-209

DOI: 10.1038/s41564-017-0069-3

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Obligate sugar oxidation in Mesotoga spp., phylum Thermotogae , in the presence of either elemental sulfur or hydrogenotrophic sulfate-reducers as electron acceptor

Khaled Fadhlaoui, Wagdi Ben Hania, Fabrice Armougom, Manon Joseph, Marie-Laure Fardeau, Gaël Erauso...

Environmental Microbiology . 20 ( 1 ) : 281-292

DOI: 10.1111/1462-2920.13995

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Loss-of-Function Mutations in UNC45A Cause a Syndrome Associating Cholestasis, Diarrhea, Impaired Hearing, and Bone Fragility

Clothilde Esteve, Ludmila Francescatto, Perciliz Tan, Aurélie Bourchany, Cécile de Leusse, Evelyne Marinier...

American Journal of Human Genetics . 102 ( 3 ) : 364 - 374

DOI: 10.1016/j.ajhg.2018.01.009

Journal article

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Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation–Selection Models

Simon Laurin-Lemay, Nicolas Rodrigue, Nicolas Lartillot, Herve Philippe

Molecular Biology and Evolution . 35 ( 11 ) : 2819-2834

DOI: 10.1093/molbev/msy173

Journal article

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Population specific dynamics and selection patterns of transposable element insertions in European natural populations

Emmanuelle Lerat, Clément Goubert, Sara Guirao-Rico, Miriam Merenciano, Anne-Béatrice Dufour, Cristina Vieira...

Molecular Ecology . : 1-17

DOI: 10.1111/mec.14963

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Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods

Nathanaëlle Saclier, Clémentine François, Lara Konecny-Dupré, Nicolas Lartillot, Laurent Guéguen, L. Duret...

Molecular Biology and Evolution . 35 ( 12 ) : 2900-2912

DOI: 10.1093/molbev/msy184

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PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites

Boubou Diagouraga, Julie Clément, L. Duret, Jan Kadlec, Bernard de Massy, Frédéric Baudat

Molecular Cell . 69 ( 5 ) : 853 - 865.e6

DOI: 10.1016/j.molcel.2018.01.033

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Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

Nicolas Galtier, Camille Roux, Marjolaine Rousselle, Jonathan Romiguier, Emeric Figuet, Sylvain Glemin...

Molecular Biology and Evolution . 35 ( 5 ) : 1092 - 1103

DOI: 10.1093/molbev/msy015

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Geometric medians in reconciliation spaces

Katharina Huber, Vincent Moulton, Marie-France Sagot, Blerina Sinaimeri

Information Processing Letters . 136 : 96 - 101

DOI: 10.1016/j.ipl.2018.04.001

Journal article

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Reconfiguration of graphs with connectivity constraints

Nicolas Bousquet, Arnaud Mary

WAOA 2018 - International Workshop on Approximation and Online Algorithms . 11312 : 295-309

DOI: 10.1007/978-3-030-04693-4_18

Conference paper

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Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis

Caroline Monteil, Guy Perrière, Nicolas Menguy, Nicolas Ginet, Béatrice Alonso, Nicolas Waisbord...

Environmental Microbiology .

DOI: 10.1111/1462-2920.14364

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Extreme halophilic archaea derive from two distinct methanogen Class II lineages

Monique Aouad, Najwa Taïb, Anne Oudart, Michel Lecocq, Manolo Gouy, Céline Brochier-Armanet

Molecular Phylogenetics and Evolution . 127 : 46-54

DOI: 10.1016/j.ympev.2018.04.011

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Highly Reduced Genome of the New Species Mycobacterium uberis, the Causative Agent of Nodular Thelitis and Tuberculoid Scrotitis in Livestock and a Close Relative of the Leprosy Bacilli

Andrej Benjak, Charlotte Avanzi, Yvonne Benito, Franck Breysse, Christophe Chartier, Maria-Laura Boschiroli...

MSphere . 3 ( 5 ) : e00405-18

DOI: 10.1128/mSphere.00405-18

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Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France

Maxime Barbier, Oana Dumitrescu, Catherine Pichat, Gérard Carret, Anne-Sophie Ronnaux-Baron, Ghislaine Blasquez...

Scientific Reports . 8 ( 1 ) : 5855

DOI: 10.1038/s41598-018-24034-6

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Tsunami sedimentary deposits of Crete records climate during the ‘Minoan Warming Period’ (≈3350 yr BP)

Christophe Lécuyer, François Atrops, Romain Amiot, Delphine Angst, Valérie Daux, Jean-Pierre Flandrois...

The Holocene .

DOI: 10.1177/0959683617752840

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Helena and BS: two travellers between the genera Drosophila and Zaprionus

M C Simão, Annabelle A. Haudry, A Granzotto, N de Setta, C M A Carareto

Genome Biology and Evolution .

DOI: 10.1093/gbe/evy184

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Multiple convergent supergene evolution events in mating-type chromosomes

Sara E Branco, Fantin E Carpentier, Ricardo Rodriguez de La Vega, Hélène Badouin, Alodie Snirc, Stéphanie Le Prieur...

Nature Communications . 9 ( 1 ) : 2000

DOI: 10.1038/s41467-018-04380-9

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The sunflower genome provides insights into Asterid evolution and relationships between paleoploidization and the genetic architecture of a major breeding trait

Hélène E Badouin

Second Joint Congress on Evolutionary Biology .

Conference paper

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The Rosa genome provides new insights into the domestication of modern roses

Olivier Raymond, Jerome Gouzy, Jérémy Just, Hélène Badouin, Marion Verdenaud, Arnaud Lemainque...

Nature Genetics . 50 ( 6 ) : 772-777

DOI: 10.1038/s41588-018-0110-3

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Sex gap in aging and longevity: can sex chromosomes play a role?

Gabriel A.B. Marais, Jean-Michel Gaillard, Cristina Vieira, Ingrid Plotton, Damien Sanlaville, François Gueyffier...

Biology of Sex Differences . 9 ( 1 ) : 1-14

DOI: 10.1186/s13293-018-0181-y

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Amphioxus functional genomics and the origins of vertebrate gene regulation

Ferdinand Marletaz, Panos N. Firbas, Ignacio Maeso, Juan J. Tena, Ozren Bogdanovic, Malcolm Perry...

Nature . 564 ( 7734 ) : 64-70

DOI: 10.1038/s41586-018-0734-6

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A Survey and a Positive Psychology Intervention on French PhD Student Well-being

Gabriel Marais, Rebecca Shankland, Pascale Haag, Robin Fiault, Briget Juniper

International Journal of Doctoral Studies . 13 : 109-138

DOI: 10.28945/3948

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Fast-SG: an alignment-free algorithm for hybrid assembly

Alex Di Genova, Gonzalo A Ruz, Marie-France Sagot, Alejandro Maass

GigaScience . 7 ( 5 ) : 1 - 15

DOI: 10.1093/gigascience/giy048

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Genomic imprinting mediates dosage compensation in a young plant XY system

Aline Muyle, Niklaus Zemp, Cécile Fruchard, Radim Cegan, Jan Vrána, Clothilde Deschamps...

Nature Plants . 4 ( 9 ) : 677-680

DOI: 10.1038/s41477-018-0221-y

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Integrative Mobilizable Element (IMEs): a reservoir of antibiotic resistance genes in the zoonotic pathogen Streptococcus suis

Virginie Libante, Nombre Yves, Charles Coluzzi, Gérard Guédon, Marcelo Gottschalk, Nahuel Fittipaldi...

GDR 3546 - Les elements mobiles du mécanisme aux populations, une approche intégrative .

Conference paper

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