GECO Génomique Computationnelle et Evolutive

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

2016

Article dans une revue

voir la publication

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

2016

Acte de congrès

voir la publication

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

Roeland M.H. Merks, Marie-France Sagot

2016

Autre publication

voir la publication

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.

2016

Chapitre d'ouvrage

voir la publication

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

2016

Article dans une revue

voir la publication

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

2016

Article dans une revue

voir la publication

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

2016

Article dans une revue

voir la publication

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

2016

Article dans une revue

voir la publication

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

2016

Article dans une revue

voir la publication

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, S. Reverchon

FEBS Journal . 283 ( 22 ) : 4192-4207

2016

Article dans une revue

voir la publication

Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape

R. Schep, A. Necsulea, E. Rodriguez-Carballo, I. Guerreiro, G. Andrey, T.H. Nguyen Huynh...

Proceedings of the National Academy of Sciences of the United States of America . 113 ( 48 ) : e7720-e7729

DOI: 10.1073/pnas.1617141113

2016

Article dans une revue

voir la publication

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

2016

Article dans une revue

voir la publication

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

2016

Article dans une revue

voir la publication

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 .

2016

Poster

voir la publication

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

2016

Article dans une revue

voir la publication

Hotair Is Dispensible for Mouse Development

Ar. Amandio, A. Necsulea, E. Joye, B. Mascrez, D. Duboule

PLoS Genetics . 12 : e1006232

DOI: 10.1371/journal.pgen.1006232

2016

Article dans une revue

voir la publication

A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus

L. Beccari, N. Yakushiji-Kaminatsui, J. M. Woltering, A. Necsulea, N. Lonfat, E. Rodriguez-Carballo...

Genes and Development . 30 : 1172-86

DOI: 10.1101/gad.281055.116

2016

Article dans une revue

voir la publication

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

2016

Article dans une revue

voir la publication

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

2016

Article dans une revue

voir la publication

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

2016

Acte de congrès

voir la publication

On Maximal Chain Subgraphs and Covers of Bipartite Graphs

Tiziana Calamoneri, Mattia Gastaldello, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri

Combinatorial Algorithms - 27th International Workshop, IWOCA 2016 . 9843 : 137-150

DOI: 10.1007/978-3-319-44543-4_11

2016

Acte de congrès

voir la publication

Mycoplasma non-coding RNA: identification of small RNAs and targets

Franciele Maboni Siqueira, Guilherme Loss de Morais, Susan Higashi, Laura Scherer Beier, Gabriela Merker Breyer, Caio Padoan de Sá Godinho...

BMC Genomics . 23 : 1289 - 26

DOI: 10.1186/s12864-016-3061-z

2016

Article dans une revue

voir la publication

No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes

Clémentine François, L. Duret, Laurent Simon, Florian Mermillod-Blondin, Florian Malard, Lara Konecny-Dupré...

Molecular Biology and Evolution . 33 ( 10 ) : 2605–2620

DOI: 10.1093/molbev/msw131

2016

Article dans une revue

voir la publication

Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill–Robertson Interference, in an Avian System

Paulina Bolívar, Carina Mugal, Alexander Nater, Hans Ellegren

Molecular Biology and Evolution . 33 ( 1 ) : 216-227

DOI: 10.1093/molbev/msv214

2015

Article dans une revue

voir la publication

GC‐biased gene conversion links the recombination landscape and demography to genomic base composition

Carina Mugal, Claudia Weber, Hans Ellegren

BioEssays . 37 ( 12 ) : 1317-1326

DOI: 10.1002/bies.201500058

2015

Article dans une revue

voir la publication

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers

Reto Burri, Alexander Nater, Takeshi Kawakami, Carina Mugal, Pall Olason, Linnea Smeds...

Genome Research . 25 ( 11 ) : 1656-1665

DOI: 10.1101/gr.196485.115

2015

Article dans une revue

voir la publication

Evolutionary Consequences of DNA Methylation on the GC Content in Vertebrate Genomes

Carina Mugal, Peter Arndt, Lena Holm, Hans Ellegren

G3 . 5 ( 3 ) : 441-447

DOI: 10.1534/g3.114.015545

2015

Article dans une revue

voir la publication

Cell cycle progression is regulated by intertwined redox oscillators

Jorgelindo da Veiga Moreira, Sabine Pérès, Jean-Marc Steyaert, Erwan Bigan, Loïc Paulevé, Marcel Levy Nogeira...

Theoretical Biology and Medical Modelling . 12 ( 1 ) : 10

DOI: 10.1186/s12976-015-0005-2

2015

Article dans une revue

voir la publication

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence

Elise R Morton, Joshua Lynch, Alain Froment, Sophie Lafosse, Evelyne Heyer, Molly M. Przeworski...

PLoS Genetics . 11 ( 11 ) : e1005658

DOI: 10.1371/journal.pgen.1005658

2015

Article dans une revue

voir la publication

Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci

Qiong Rao, Pierre-Antoine Rollat-Farnier, Dan-Tong Zhu, Diego Santos-Garcia, Francisco J Silva, Andrés Moya...

BMC Genomics . 16 : 226

DOI: 10.1186/s12864-015-1379-6

2015

Article dans une revue

voir la publication

GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Publications

Robustness of the Parsimonious Reconciliation Method in Cophylogeny

Computing and Listing st-Paths in Subway Networks

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

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

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

RiboDB database: a comprehensive resource for prokaryotic systematics

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

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

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

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

Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape

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

Cell division of Streptococcus pneumoniae: think positive!

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

Reply to Halanych et al.

Hotair Is Dispensible for Mouse Development

A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus

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

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

Efficient Enumeration of Solutions Produced by Closure Operations

On Maximal Chain Subgraphs and Covers of Bipartite Graphs

Mycoplasma non-coding RNA: identification of small RNAs and targets

No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes

Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill–Robertson Interference, in an Avian System

GC‐biased gene conversion links the recombination landscape and demography to genomic base composition

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers

Evolutionary Consequences of DNA Methylation on the GC Content in Vertebrate Genomes

Cell cycle progression is regulated by intertwined redox oscillators

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence

Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci