GECO Evolutionary and Computational Genomics

Structural, functional and evolutionary analysis of the unusually large stilbene synthase gene family in grapevine (Vitis vinifera)

C. Parage, R. Tavares, S. Réty, R. Baltenweck-Guyot, A. Poutaraud, L. Renault...

Plant Physiology . 160 : 1407-1419

2012

Journal article

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Lateral gene transfer as a support for the tree of life.

Sophie S Abby, Eric Tannier, Manolo Gouy, Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America . 109 ( 13 ) : 4962-4967

DOI: 10.1073/pnas.1116871109

2012

Journal article

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High-quality sequence clustering guided by network topology and multiple alignment likelihood.

Vincent Miele, Simon Penel, Vincent Daubin, Franck Picard, Daniel Kahn, L. Duret

Bioinformatics . 28 ( 8 ) : 1078-85

DOI: 10.1093/bioinformatics/bts098

2012

Journal article

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High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences.

Ivan Nasidze, Anna Schönberg, Christoph Theunert, Mingkun Li, Mark Stoneking

European Journal of Human Genetics .

DOI: 10.1038/ejhg.2011.62

2011

Journal article

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Y-Chromosomal Variation in Sub-Saharan Africa: Insights Into the History of Niger-Congo Groups

C. de Filippo, C. Barbieri, M. Whitten, S. Mpoloka, E. Gunnarsdottir, K. Bostoen...

Molecular Biology and Evolution . 28 ( 3 ) : 1255-1269

DOI: 10.1093/molbev/msq312

2011

Journal article

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Larger mitochondrial DNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra

Ellen Dröfn Gunnarsdóttir, Madhusudan Nandineni, Mingkun Li, Sean Myles, David Gil, Brigitte Pakendorf...

Nature Communications . 2 : 228

DOI: 10.1038/ncomms1235

2011

Journal article

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Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content

Carina Mugal, Hans Ellegren

Genome Biology . 12 ( 6 ) : R58

DOI: 10.1186/gb-2011-12-6-r58

2011

Journal article

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Analysis of the variability of human normal urine by 2D-GE reveals a "public" and a "private" proteome

Laurence Molina, Nicolas Salvetat, Randa Ben Ameur, Sabine Pérès, Nicolas Sommerer, Faycal Jarraya...

Journal of Proteomics . 75 ( 1 ) : 70 - 80

DOI: 10.1016/j.jprot.2011.06.031

2011

Journal article

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ACoM: A classification method for elementary flux modes based on motif finding

Sabine Pérès, Francois Vallee, Marie M. Beurton-Aimar, Jean-Pierre Mazat

BioSystems . 103 ( 3 ) : 410-419

2011

Journal article

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Lactase persistence in central Asia: phenotype, genotype, and evolution.

Evelyne Heyer, Lionel Brazier, Laure Ségurel, Tatiana Hegay, Frédéric Austerlitz, Lluis Quintana-Murci...

Human Biology . 83 ( 3 ) : 379-92

DOI: 10.3378/027.083.0304

2011

Journal article

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The Case of the Fickle Fingers: How the PRDM9 Zinc Finger Protein Specifies Meiotic Recombination Hotspots in Humans

Laure Ségurel, Ellen Miranda Leffler, Molly M. Przeworski

PLoS Biology . 9 ( 12 ) : e1001211

DOI: 10.1371/journal.pbio.1001211

2011

Journal article

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“ArthropodaCyc”: a BioCyc database powered by CycADS to study and compare the metabolism of arthropods

Patrice Baa-Puyoulet, Augusto Vellozo, Jaime Huerta-Cepas, Gérard Febvay, Toni Gabaldon, Marie-France Sagot...

5. Annual Arthropod Genomics Symposium “Arthropod Genomics 2011: Exploring Diversity, Relating Similarity” . : 33 p.

2011

Poster

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Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes.

Brian P. Cusack, Peter F. Arndt, L. Duret, Hugues Roest Crollius

PLoS Genetics . 7 ( 10 ) : e1002276

DOI: 10.1371/journal.pgen.1002276

2011

Journal article

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Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

Corinne Chureau, Sophie Chantalat, Antonio Romito, Angélique Galvani, Laurent Duret, Philip Avner...

Human Molecular Genetics . 20 ( 4 ) : 705-718

DOI: 10.1093/hmg/ddq516

2011

Journal article

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Meiotic recombination favors the spreading of deleterious mutations in human populations

Anamaria Necsulea, L. Duret, Alexandra Popa, David N. Cooper, Peter Stentson, Dominique Mouchiroud...

Human Mutation . 32 ( 2 ) : 198-206

DOI: 10.1002/humu.21407

2011

Journal article

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Modélisation des systèmes biologiques, bioinformatique

Olivier Gascuel, P. Benas, C. Brun, D. Burnouf, Alexandre de Brevern, A. Denise...

Rapport de conjoncture 2010 du Comité national de la recherche scientifique . 978-2-271-07263-4 : chapitre 43, 845-858

2011

Book chapter

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RNA-seq without a reference genome: a comparison of the mapping and the assembly approaches

M.-C. Carpentier, J. Charif, Vincent Lacroix, Marie-France Sagot, Fabrice Vavre

JOBIM .

2011

Conference paper

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kisSplice, détection d'évènements d'épissages alternatifs dans les données RNA-seq

Gustavo Akio Tominaga Sacomoto, J. Kielbassa, Pavlos Antoniou, Rayan Chikhi, Raluca Uricaru, Marie-France Sagot...

: 12

2011

Report

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Metabolic network comparison of bacteria in the context of symbiosis

Cecilia C. Klein, Ludovic Cottret, Hubert Charles, Christian Gautier, Ana T Vasconcelos, Vincent Lacroix...

Otto Warburg International Summer School and Research Symposium on Evolutionary Genomics .

2011

Conference paper

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Telling Stories

Vicente Acuña, Etienne Birmele, Ludovic Cottret, Pierluigi Crescenzi, Fabien Jourdan, Vincent Lacroix...

ICALP 2011 satellite workshop: Graph Algorithms and Applications (GA) .

DOI: 10.1016/j.tcs.2012.07.023

2011

Conference paper

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Bioinformatics developments for NGS data analysis at PRABI

F. Picard, Guy Perrière

EMBNet.journal . 17 : 12

2011

Journal article

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Species identification of staphylococci by amplification and sequencing of the tuf gene compared to the gap gene and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Marie Bergeron, Olivier Dauwalder, Manolo Gouy, Anne-Marie Freydiere, Michèle Bes, Hélène Meugnier...

European Journal of Clinical Microbiology and Infectious Diseases . 30 ( 3 ) : 343-54

DOI: 10.1007/s10096-010-1091-z

2011

Journal article

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Species-driven interpretation guidelines in case of a single-sampling strategy for blood culture

D. Leyssene, S. Gardes, P. Vilquin, Jp. Flandrois, Gérard Carret, B. Lamy

European Journal of Clinical Microbiology and Infectious Diseases . 30 : 1537-1541

DOI: 10.1007/s10096-011-1257-3

2011

Journal article

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Phylogeny and evolution of the Archaea: one hundred genomes later.

Celine Brochier-Armanet, Patrick Forterre, Simonetta Gribaldo

Current Opinion in Microbiology . : epub ahead of print

DOI: 10.1016/j.mib.2011.04.015

2011

Journal article

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Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite.

France Denoeud, Michaël Roussel, Benjamin Noel, Ivan Wawrzyniak, Corinne da Silva, Marie Diogon...

Genome Biology . 12 ( 3 ) : R29

DOI: 10.1186/gb-2011-12-3-r29

2011

Journal article

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Cultivation of the first mesophilic representative ("mesotoga") within the order Thermotogales

Wajdi Ben Hania, Ramzi Ghodbane, Anne Postec, Celine Brochier-Armanet, Moktar Hamdi, Marie Laure Fardeau...

Systematic and Applied Microbiology . 34 : 581-585

DOI: 10.1016/j.syapm.2011.04.001

2011

Journal article

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The GTPase Function of YvcJ and Its Subcellular Relocalization Are Dependent on Growth Conditions in Bacillus subtilis

F. Pompeo, J. Luciano, Céline Brochier-Armanet, A. Galinier

Journal of Molecular Microbiology and Biotechnology . 20 : 156-67

2011

Journal article

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Survival of extremely and moderately halophilic isolates of Tunisian solar salterns after UV-B or oxidative stress

H. Trigui, Salma Masmoudi, Céline Brochier-Armanet, S. Maalej, S. Dukan

Canadian Journal of Microbiology . 57(11) : 923-33

2011

Journal article

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The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes

L. Eme, A. Trilles, D. Moreira, Céline Brochier-Armanet

BMC Evolutionary Biology . 11 : 923-33

DOI: 10.1186/1471-2148-11-265

2011

Journal article

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The Assembly Mode of the Pseudopilus: a hallmark to distinguish a novel secretion system subtype

E. Durand, S. Alphonse, Céline Brochier-Armanet, G. Ball, Badreddine Douzi, A. Filloux...

Journal of Biological Chemistry . 286 ( 27 ) : 24407-24416

DOI: 10.1074/jbc.M111.234278

2011

Journal article

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GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Structural, functional and evolutionary analysis of the unusually large stilbene synthase gene family in grapevine (Vitis vinifera)

Lateral gene transfer as a support for the tree of life.

High-quality sequence clustering guided by network topology and multiple alignment likelihood.

High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences.

Y-Chromosomal Variation in Sub-Saharan Africa: Insights Into the History of Niger-Congo Groups

Larger mitochondrial DNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra

Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content

Analysis of the variability of human normal urine by 2D-GE reveals a "public" and a "private" proteome

ACoM: A classification method for elementary flux modes based on motif finding

Lactase persistence in central Asia: phenotype, genotype, and evolution.

The Case of the Fickle Fingers: How the PRDM9 Zinc Finger Protein Specifies Meiotic Recombination Hotspots in Humans

“ArthropodaCyc”: a BioCyc database powered by CycADS to study and compare the metabolism of arthropods

Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes.

Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

Meiotic recombination favors the spreading of deleterious mutations in human populations

Modélisation des systèmes biologiques, bioinformatique

RNA-seq without a reference genome: a comparison of the mapping and the assembly approaches

kisSplice, détection d'évènements d'épissages alternatifs dans les données RNA-seq

Metabolic network comparison of bacteria in the context of symbiosis

Telling Stories

Bioinformatics developments for NGS data analysis at PRABI

Species identification of staphylococci by amplification and sequencing of the tuf gene compared to the gap gene and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Species-driven interpretation guidelines in case of a single-sampling strategy for blood culture

Phylogeny and evolution of the Archaea: one hundred genomes later.

Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite.

Cultivation of the first mesophilic representative ("mesotoga") within the order Thermotogales

The GTPase Function of YvcJ and Its Subcellular Relocalization Are Dependent on Growth Conditions in Bacillus subtilis

Survival of extremely and moderately halophilic isolates of Tunisian solar salterns after UV-B or oxidative stress

The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes

The Assembly Mode of the Pseudopilus: a hallmark to distinguish a novel secretion system subtype