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 271 to 300 publications on 1403 in total

Structure, Function, and Evolution of the Pseudomonas aeruginosa Lysine Decarboxylase LdcA

Eaazhisai Kandiah, Diego Carriel, Pierre Simon Garcia, Jan Felix, Manuel Banzhaf, George Kritikos...

Structure .

DOI: 10.1016/j.str.2019.10.003

Journal article

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The bacterial MrpORP is a novel Mrp/NBP35 protein involved in iron-sulfur biogenesis

Romain Pardoux, Anouchka Fiévet, Cíntia Carreira, Céline Brochier-Armanet, Odile Valette, Zorah Dermoun...

Scientific Reports . 9 ( 1 ) : 360-373

DOI: 10.1038/s41598-018-37021-8

Journal article

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Description Osteo-Oto-Hepato-Enteric (O2HE) syndrome, a new recessive autosomal syndrome secondary to loss of function mutations in the UNC45A gene

L. Faivre, Clothilde Esteve, L. Francescatto, P. L. Tan, A. Bourchany, C. Delafoulhouze...

European Journal of Human Genetics . 27 ( 1 ) : 795-796

Journal article

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On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses

Emmanuelle Lerat, Josep Casacuberta, Cristian Chaparro, Cristina Vieira

Genes . 10 ( 4 ) : 258

DOI: 10.3390/genes10040258

Journal article

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Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?

Romain Lannes, Carène Rizzon, Emmanuelle Lerat

Genes . 10 ( 3 ) : 249

DOI: 10.3390/genes10030249

Journal article

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Homme/femme, mâle/femelle : la détermination du sexe dans l’espèce humaine et le reste du vivant

Gabriel Marais, Jos Käfer

Sexe & genre: De la biologie à la sociologie .

Book chapter

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Metapopulation ecology links antibiotic resistance, consumption and patient transfers in a network of hospital wards.

Julie Teresa Shapiro, Gilles Leboucher, Anne-Florence Myard-Dury, Pascale Girardo, Anatole Luzatti, Mélissa Mary...

DOI: 10.1101/771790

Preprint

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P2857 Quantifying drivers of antimicrobial resistance in a large network of hospital wards: a meta-population approach.

Julie Teresa Shapiro, Leboucher Gilles, Anatole Luzzati, Jean Francois Sauzon, Olivier Dauwalder, Pascale Girardo...

29TH ECCMID .

Conference paper

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GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes

Paulina Bolívar, Laurent Guéguen, Laurent Duret, Hans Ellegren, Carina Mugal

Genome Biology . 20 ( 1 )

DOI: 10.1186/s13059-018-1613-z

Journal article

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Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints

Florian Massip, Marc Laurent, Caroline Brossas, José miguel Fernández-Justel, Maria Gomez, Marie-Noëlle Prioleau...

Nucleic Acids Research . 47 ( 10 ) : 5114-5125

DOI: 10.1093/nar/gkz182

Journal article

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On Bubble Generators in Directed Graphs

Vicente Acuña, Roberto Grossi, Giuseppe F. Italiano, Leandro Lima, Romeo Rizzi, Gustavo Sacomoto...

Algorithmica . : 1-19

DOI: 10.1007/s00453-019-00619-z

Journal article

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Efficient enumeration of solutions produced by closure operations

Arnaud Mary, Yann Strozecki

Discrete Mathematics and Theoretical Computer Science . : 1-30

DOI: 10.23638/DMTCS-21-3-22

Journal article

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The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

Alexandre Duprey, Najwa Taïb, Simon Leonard, Tiffany Garin, Jean-Pierre Flandrois, William Nasser...

Environmental Microbiology . 21 ( 8 ) : 2809-2835

DOI: 10.1111/1462-2920.14627

Journal article

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New insights into minor splicing-a transcriptomic analysis of cells derived from TALS patients

Audric Cologne, Clara Benoit-Pilven, Alicia Besson, Audrey Putoux, Amandine Campan-Fournier, Michael B Bober...

RNA . : 1-21

DOI: 10.1261/rna.071423.119

Journal article

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Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing

Usama Ashraf, Clara Benoit-Pilven, Vincent Lacroix, Vincent Navratil, Nadia Naffakh

Trends in Microbiology . 27 ( 3 ) : 268-281

DOI: 10.1016/j.tim.2018.11.004

Journal article

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Francisella tularensis: FupA mutation contributes tofluoroquinolone resistance by increasing vesicle secretion and biofilm formation

Claire Siebert, Helena Lindgren, Sabrina Ferré, Corinne Villers, Sandrine Boisset, Julien Pérard...

Emerging microbes & infections . 8 ( 1 ) : 808-822

DOI: 10.1080/22221751.2019.1615848

Journal article

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Comparative genomics and proteogenomics highlight key molecular players involved in Frankia sporulation

Lorine Bethencourt, Hasna Boubakri, Najwa Taïb, Philippe Normand, J. Armengaud, Pascale P Fournier...

Research in Microbiology . 170 ( 4-5 ) : 202-213

DOI: 10.1016/j.resmic.2019.04.002

Journal article

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Evolutionary placement of Methanonatronarchaeia

Monique Aouad, Guillaume Borrel, Céline Brochier-Armanet, Simonetta Gribaldo

Nature Microbiology .

DOI: 10.1038/s41564-019-0359-z

Journal article

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GeneSpy, a user-friendly and flexible genomic context visualizer

Pierre Simon Garcia, Frédéric Jauffrit, Christophe Grangeasse, Céline Brochier-Armanet

Bioinformatics . 35 ( 2 ) : 329-331

DOI: 10.1093/bioinformatics/bty459

Journal article

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Article 5. L’émergence des eucaryotes : une mosaïque d’ADN

Dominique D. Joly, Celine Brochier-Armanet

101 secrets de l’ADN. CNRS Éditions, Paris, pp 39-41 . : 39-41

Book chapter

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Dynamic Interactions Between the Genome and an Endogenous Retrovirus: Tirant in Drosophila simulans Wild-Type Strains

Marie Fablet, Angelo Jacquet, Rita Rebollo, Annabelle A. Haudry, Carine Rey, Judit Salces-Ortiz...

G3 . 9 ( 3 ) : 855-865

DOI: 10.1534/g3.118.200789

Journal article

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Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis annua

Paris Veltsos, Kate Ridout, Melissa Toups, Santiago González-Martínez, Aline Muyle, Olivier Emery...

Genetics . 212 ( 3 ) : 815-835

DOI: 10.1534/genetics.119.302045

Journal article

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Detecting adaptive convergent amino acid evolution

Carine Rey, Vincent Lanore, Philippe Veber, Laurent Guéguen, Nicolas Lartillot, Marie Sémon...

Philosophical Transactions of the Royal Society B: Biological Sciences . 374 ( 1777 ) : 1-11

DOI: 10.1098/rstb.2018.0234

Journal article

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Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

Camille Sessegolo, Corinne Cruaud, Corinne da Silva, Audric Cologne, Marion Dubarry, Thomas Derrien...

Scientific Reports . 9 ( 1 ) : 14908

DOI: 10.1038/s41598-019-51470-9

Journal article

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Evolution of Young Sex Chromosomes in Two Dioecious Sister Plant Species with Distinct Sex Determination Systems

Hélène Martin, Fantin E Carpentier, Sophie Gallina, Cécile Godé, Eric Schmitt, Aline Muyle...

Genome Biology and Evolution . 11 ( 2 ) : 350-361

DOI: 10.1093/gbe/evz001

Journal article

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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...

DOI: 10.1101/179044

Preprint

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Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia

Nguyen Thuy Duong, Enrico Macholdt, Nguyen Dang Ton, Leonardo Arias, Roland Schröder, Nguyen van Phong...

Scientific Reports . 8 ( 1 )

DOI: 10.1038/s41598-018-29989-0

Journal article

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