GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Display of 361 to 390 publications on 1251 in total

MeDuSa: A multi-draft based scaffolder.

Emanuele Bosi, Beatrice Donati, Marco Galardini, Sara Brunetti, Marie-France Sagot, Pietro Lió...

Bioinformatics . : pii: btv171 [Epub ahead of print]

DOI: 10.1093/bioinformatics/btv171

Journal article

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A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs

Gustavo Sacomoto, Vincent Lacroix, Marie‑france Sagot

Algorithms for Molecular Biology . : 10

DOI: 10.1186/s13015-015-0046-4

Journal article

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Mitochondrial respiration and genomic analysis provide insight into the influence of the symbiotic bacterium on host trypanosomatid oxygen consumption.

Allan C. Azevedo-Martins, A. C. L. Machado, Cecilia Coimbra Klein, L. Ciapina, Luiz Gonzaga, Ana Tereza Ribeiro Vasconcelos...

Parasitology . 142 ( 2 ) : 352-362

DOI: 10.1017/S0031182014001139

Journal article

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Polynomial Delay Algorithm for Listing Minimal Edge Dominating Sets in Graphs

Mamadou Moustapha Kanté, Vincent Limouzy, Arnaud Mary, Lhouari Nourine, Takeaki Uno

Algorithms and Data Structures (WADS) . 9214 : 446-457

Conference paper

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Assessment of polycarbonate filter in a molecular analytical system for the microbiological quality monitoring of recycled waters onboard ISS

Anne-Laure Bechy-Loizeau, Jean-Pierre Flandrois, Hafid Abaibou

Life Sciences in Space Research . 6 : 29-35

DOI: 10.1016/j.lssr.2015.06.002

Journal article

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Nontuberculous Mycobacteria: An Underestimated Cause of Bioprosthetic Valve Infective Endocarditis

C. Bouchiat, J. Saison, S. Boisset, Jean-Pierre Flandrois, B. Issartel, O. Dauwalder...

Open Forum Infectious Diseases . 2 ( 2 )

DOI: 10.1093/ofid/ofv047

Journal article

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Adaptation in toxic environments: arsenic Genomic Islands in the bacterial genus $Thiomonas$

Kelle Freel, Martin Krueger, Julien Farasin, Céline Brochier-Armanet, Valérie Barbe, Jérémy Andres...

PLoS ONE . 10 ( 9 ) : 0139011

DOI: 10.1371/journal.pone.0139011

Journal article

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GC-Content evolution in bacterial genomes: The biased gene conversion hypothesis expands

Florent Lassalle, Séverine Périan, Thomas Bataillon, Xavier Nesme, L. Duret, Vincent Daubin

PLoS Genetics . 11 ( 2 ) : 1-20

DOI: 10.1371/journal.pgen.1004941

Journal article

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Quantification of GC-biased gene conversion in the human genome

Sylvain Glemin, Peter F. Arndt, Messer W. Philip, Petrov M. Dmitri, Nicolas Galtier, L. Duret

Genome Research . 25 ( 8 ) : 1215 - 1228

DOI: 10.1101/gr.185488.114

Journal article

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Optimization of multiplexed RADseq libraries using low-cost adaptors

Hélène Henri, Marie Cariou, Gabriel Terraz, Sonia Martinez, Adil El Filali, Marine Veyssière...

Genetica . 143 ( 2 ) : 139-143

DOI: 10.1007/s10709-015-9828-3

Journal article

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Incremental complexity of a bi-objective hypergraph transversal problem

Ricardo Andrade, Etienne E. Birmelé, Arnaud Mary, Thomas Picchetti, Marie-France Sagot

Fundamentals of Computation Theory (FCT2015) . 9210 : 202-213

DOI: 10.1007/978-3-319-22177-9_16

Conference paper

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EUCALYPT: efficient tree reconciliation enumerator

Beatrice Donati, Christian Baudet, Blerina Sinaimeri, Pierluigi Crescenzi, Marie-France Sagot

Algorithms for Molecular Biology . 10 ( 1 ) : 11

DOI: 10.1186/s13015-014-0031-3

Journal article

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Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data

Susan Higashi, Cyril Fournier, Christian Gautier, Christine Gaspin, Marie-France Sagot

BMC Bioinformatics . 16 ( 1 ) : 179

DOI: 10.1186/s12859-015-0594-0

Journal article

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Cophylogeny Reconstruction via an Approximate Bayesian Computation

Christian Baudet, Béatrice Donati, Blerina Sinaimeri, Pierluigi Crescenzi, Christian Gautier, Catherine Matias...

Systematic Biology . 64 ( 3 ) : 416-431

DOI: 10.1093/sysbio/syu129

Journal article

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An average study of hypergraphs and their minimal transversals

Julien David, Loïck Lhote, Arnaud Mary, François Rioult

Theoretical Computer Science . 596 : 124-141

DOI: 10.1016/j.tcs.2015.06.052

Journal article

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Analyse de 32 souches de Legionella pneumophila de sévérités variables afin d'identifier les déterminants de la pathogénicité

Amandine Campan-Fournier, Christine Oger, Christophe Ginevra, Vincent Navratil, Anne-Gaëlle Ranc, G. Perrière...

JOBIM 2015 - 16èmes Journées Ouvertes en BIologie, Informatique et Mathématiques .

Poster

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Evolutionary history of phosphatidylinositol- 3-kinases: ancestral origin in eukaryotes and complex duplication patterns

H. Philippon, Céline Brochier-Armanet, G. Perriere

BMC Evolutionary Biology . 15 : 226

DOI: 10.1186/s12862-015-0498-7

Journal article

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Molecular and functional evolution of the fungal diterpene synthase genes

Marc Fischer, Camille Rustenhloz, Véronique Leh-Louis, Guy Perrière

BMC Microbiology . 15 ( 1 ) : 221

DOI: 10.1186/s12866-015-0564-8

Journal article

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leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences

Jean-Pierre Flandrois, G. Perrière, Manolo Gouy

BMC Bioinformatics . 16 ( 1 ) : 251

DOI: 10.1186/s12859-015-0692-z

Journal article

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A Toolbox for Nonlinear Regression in R: The Package nistools

F. Baty, C. Ritz, Sandrine Charles, M. Brutsche, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Journal of Statistical Software . 66 : 1-21

Journal article

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Evolution of Helicobacter: Acquisition by Gastric Species of Two Histidine-Rich Proteins Essential for Colonization

Daniel Vinella, Frédéric Fischer, Egor Vorontsov, Julien Gallaud, Christian Malosse, Valérie Michel...

PLoS Pathogens . 11 ( 12 ) : e1005312

DOI: 10.1371/journal.ppat.1005312

Journal article

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Exploration of Frankia genomes to identify genetic determinants involved in sporogenesis: Towards promising tracks to understand in plant sporuration

Lorine Bethencourt, N. Taib, J. Briolay, P. Fournier, M.P. Fernandez, Céline Brochier-Armanet...

18th International Meeting on Frankia and Actinorhizal plants .

Poster

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Evolution and Design Governing Signal Precision and Amplification in a Bacterial Chemosensory Pathway

Mathilde Guzzo, Rym Agrebi, Leon Espinosa, Gregory Baronian, Virginie Molle, Emilia M. F. Mauriello...

PLoS Genetics . 11 ( 8 ) : e1005460

DOI: 10.1371/journal.pgen.1005460

Journal article

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Taxonomy and Phylogeny of Prokaryotes

Pierre Caumette, Céline Brochier-Armanet, Philippe Normand

Environmental Microbiology: Fundamentals and Applications . 978-94-017-9118-2 : 145-190

DOI: 10.1007/978-94-017-9118-2_6

Book chapter

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Draft genome sequence of Mesotoga strain PhosAC3, a mesophilic member of the bacterial order Thermotogales, isolated from a digestor treating phosphogypsum in Tunisia

Wajdi Ben Hania, Khaled Fadhlaoui, Céline Brochier-Armanet, Cecile Persillon, Anne Postec, Moktar Hamdi...

Standards in Genomic Sciences . 10

DOI: 10.1186/1944-3277-10-12

Journal article

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Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum

Stéphanie Borland, Anne Oudart, Claire Prigent-Combaret, Céline Brochier-Armanet, Florence Wisniewski-Dyé

BMC Genomics . 16 : 833

DOI: 10.1186/s12864-015-1962-x

Journal article

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Extending the conserved phylogenetic core of \textitarchaea disentangles the evolution of the third domain of life

C. Petitjean, P. Deschamps, P. Lopez-Garcia, D. Moreira, Céline Brochier-Armanet

Molecular Biology and Evolution . 32 : 1242-54

Journal article

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Constitutive arsenite oxidase expression detected in arsenic-hypertolerant Pseudomonas xanthomarina S11

S. Koechler, F. Arsene-Ploetze, Céline Brochier-Armanet, F. Goulhen-Chollet, A. Heinrich-Salmeron, B. Jost...

Research in Microbiology . 166 : 205-14

Journal article

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Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi

Eric Fontanillas, Michael E Hood, Hélène Badouin, Elsa Petit, Valérie Barbe, Jerome Gouzy...

Molecular Biology and Evolution . 32 ( 4 ) : 928-943

DOI: 10.1093/molbev/msu396

Journal article

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Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae

Hélène Badouin, Michael E Hood, Jerome Gouzy, Gabriela Aguileta, Sophie Siguenza, Michael H Perlin...

Genetics . 200 ( 4 ) : 1275-1284

DOI: 10.1534/genetics.115.177709

Journal article

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