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 421 to 450 publications on 1402 in total

Evolutionary history of the mammalian synaptonemal complex

J. Fraune, Céline Brochier-Armanet, M. Alsheimer, J. N. Volff, K. Schucker, R. Benavente

Chromosoma . 125 : 355-60

DOI: 10.1007/s00412-016-0583-8

Journal article

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Closing the gap between rocks and clocks using total-evidence dating

F. Ronquist, Nicolas Lartillot, M.J. Phillips

Philosophical Transactions of the Royal Society B: Biological Sciences . 371 : 20150136

DOI: 10.1098/rstb.2015.0136

Journal article

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Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl

Gabriela G. Aguileta, Helene Badouin, Michael E Hood, Anders Pape Møller, Stephanie Le Prieur, Alodie Snirc...

Molecular Ecology . 25 ( 14 ) : 3370-83

DOI: 10.1111/mec.13675

Journal article

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The changing view of eukaryogenesis - fossils, cells, lineages and how they all come together

J. B. Dacks, M. C. Field, R. Buick, L. Eme, Simonetta Gribaldo, A. J. Roger...

Journal of Cell Science . 129 ( 20 ) : 3695-3703

DOI: 10.1242/jcs.178566

Journal article

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A mixed relaxed clock model

Nicolas Lartillot, M. J. Phillips, F. Ronquist

Philosophical Transactions of the Royal Society B: Biological Sciences . 371 : 20150132

DOI: 10.1098/rstb.2015.0132

Journal article

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Polymorphic Microsatellite Markers for the Tetrapolar Anther-Smut Fungus Microbotryum saponariae Based on Genome Sequencing

Taiadjana M. Fortuna, Alodie Snirc, Hélène Badouin, Jerome Gouzy, Sophie Siguenza, Diane Esquerre...

PLoS ONE . 11 ( 11 ) : e0165656

DOI: 10.1371/journal.pone.0165656

Journal article

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SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

Hélène Lopez-Maestre, Lilia Brinza, Camille Marchet, Janice Kielbassa, Sylvère Bastien, Mathilde Boutigny...

Nucleic Acids Research .

DOI: 10.1093/nar/gkw655

Journal article

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Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling

Mariana G. Ferrarini, Franciele M. Siqueira, Scheila G. Mucha, Tony Lionel Palama, Elodie Jobard, Bénédicte Elena-Herrmann...

BMC Genomics . 17 ( 1 ) : 353

DOI: 10.1186/s12864-016-2644-z

Journal article

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DegreeCox – a network-based regularization method for survival analysis

André Veríssimo, Arlindo Limede Oliveira, Marie-France Sagot, Susana Vinga

BMC Bioinformatics . 17 ( Suppl 16 ) : 109-121

DOI: 10.1186/s12859-016-1310-4

Journal article

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Enumeration of minimal stoichiometric precursor sets in metabolic networks

Ricardo Andrade, Martin Wannagat, Cecilia C. Klein, Vicente Acuña, Alberto Marchetti-Spaccamela, Paulo V. Milreu...

Algorithms for Molecular Biology . 11 ( 1 ) : 25

DOI: 10.1186/s13015-016-0087-3

Journal article

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Robustness of the Parsimonious Reconciliation Method in Cophylogeny

Laura Urbini, Blerina Sinaimeri, Catherine Matias, Marie-France Sagot

Lecture Notes in Computer Science . 9702 : 12

DOI: 10.1007/978-3-319-38827-4_10

Journal article

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Computing and Listing st-Paths in Subway Networks

Kateřina Böhmová, Matúš Mihalák, Tobias Pröger, Gustavo Sacomoto, Marie-France Sagot, Peter Widmayer

CSR 2016 - 11th International Computer Science Symposium in Russia . 9691 : 102-116

DOI: 10.1007/978-3-319-34171-2_8

Conference paper

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Introduction to the Special Theme - Tackling Big Data in the Life Sciences

Roeland M.H. Merks, Marie-France Sagot

Other publication

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Qualité des données NGS : de la séquence aux bases de données

Pierre Peyret, Julie Aubert, Vincent Breton, François Enault, Line Le Gall, Denis Le Paslier...

La génomique environnementale . 978-1-78405-151-8 : 180 p.

Book chapter

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Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated

Mathieu Groussin, Bastien Boussau, Gergely J Szollosi, Laura Eme, Manolo Gouy, Céline Brochier-Armanet...

Molecular Biology and Evolution . 33 ( 2 ) : 305 - 310

DOI: 10.1093/molbev/msv249

Journal article

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RiboDB database: a comprehensive resource for prokaryotic systematics

Frédéric Jauffrit, Simon Penel, Stéphane Delmotte, Carine Rey, Damien M de Vienne, Manolo Gouy...

Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172

DOI: 10.1093/molbev/msw088

Journal article

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Combined Genotypic, Phylogenetic, and Epidemiologic Analyses of Mycobacterium tuberculosis Genetic Diversity in the Rhône Alpes Region, France

Catherine Pichat, David Couvin, Gérard Carret, Isabelle Frédénucci, Véronique Jacomo, Anne Carricajo...

PLoS ONE . 11 ( 4 ) : e0153580

DOI: 10.1371/journal.pone.0153580

Journal article

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Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy

Fernande Freyermuth, Frédérique Rau, Yosuke Kokunai, Thomas Linke, Chantal Sellier, Masayuki Nakamori...

Nature Communications . 7 : 11067

DOI: 10.1038/ncomms11067

Journal article

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Silencing of natural transformation by an RNA chaperone and a multitarget small RNA

Laetitia Attaiech, Aïda Boughammoura, Céline Brochier-Armanet, Omran Allatif, Flora Peillard-Fiorente, Ross A. Edwards...

Proceedings of the National Academy of Sciences of the United States of America . 113 ( 31 ) : 8813-8818

DOI: 10.1073/pnas.1601626113

Journal article

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Transcriptional start site turnover in the evolution of bacterial paralogous genes - the pelE-pelD virulence genes in Dickeya

Alexandre Duprey, William Nasser, Simon Leonard, Céline Brochier-Armanet, Sylvie Reverchon

FEBS Journal . 283 ( 22 ) : 4192-4207

Journal article

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Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies

Camille Sessegolo, Nelly Burlet, Annabelle A. Haudry

Biology Letters . 12 ( 8 )

DOI: 10.1098/rsbl.2016.0407

Journal article

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SEX-DETector: a probabilistic approach to study sex chromosomes in non-model organisms

A. Muyle, Jos Käfer, N. Zemp, S. Mousset, Franck Picard, Gabriel Marais

Genome Biology and Evolution . 8 : 2530-2543

DOI: 10.1093/gbe/evw172

Journal article

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Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes.

Luisa Cs Antunes, Daniel Poppleton, Andreas Klingl, Alexis Criscuolo, Bruno Dupuy, Céline Brochier-Armanet...

eLife . 5 : e14589

DOI: 10.7554/eLife.14589.020

Journal article

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Cell division of Streptococcus pneumoniae: think positive!

P. S. Garcia, J. P. Simorre, Céline Brochier-Armanet, C. Grangeasse

Current Opinion in Microbiology . 34 : 18-23

DOI: 10.1016/j.mib.2016.07.014

Journal article

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MultiPus: Conception de communautés microbiennes pour la production de composés d'intérêt

A Julien-Laferrière, Laurent Bulteau, D Parrot, A Marchetti-Spaccamela, L Stougie, S Vinga...

Jobim .

Poster

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Reply to Halanych et al.

Davide Pisani, Walker Pett, Martin Dohrmann, Roberto Feuda, Omar Rota-Stabelli, Herve Philippe...

Proceedings of the National Academy of Sciences of the United States of America . 113 ( 8 ) : E948-E949

DOI: 10.1073/pnas.1525718113

Journal article

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RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

S. Hohna, M. J. Landis, T. A. Heath, Bastien Boussau, Nicolas Lartillot, B. R. Moore...

Systematic Biology . 65 : 726-36

DOI: 10.1093/sysbio/syw021

Journal article

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The transposable element environment of human genes is associated with histone and expression changes in cancer

Laura Grégoire, Annabelle A. Haudry, Emmanuelle Lerat

BMC Genomics . 17 ( 1 )

DOI: 10.1186/s12864-016-2970-1

Journal article

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Life Histories, Axes of Variation in

Aline Muyle, Gabriel Marais

The Encyclopedia of Evolutionary Biology . 2 : 480-492

Book chapter

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Efficient Enumeration of Solutions Produced by Closure Operations

Arnaud Mary, Yann Strozecki

33rd Symposium on Theoretical Aspects of Computer Science, STACS 2016 . 47

DOI: 10.4230/LIPIcs.STACS.2016.52

Conference paper

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