GECO Génomique Computationnelle et Evolutive

Les défis de la systématique face au monde microbien

Céline Brochier-Armanet, Simonetta Gribaldo

incollection . 328 : 49-52

2012

Article dans une revue

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Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage

V. de Crécy-Lagard, F. Forouhar, Céline Brochier-Armanet, L. Tong, Jf. Hunt

Biology Direct . 7 : 1--13

DOI: 10.1186/1745-6150-7-32

2012

Article dans une revue

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A comparative analysis of the amounts and dynamics of transposable elements in natural populations of Drosophila melanogaster and Drosophila simulans.

Cristina Vieira, Marie Fablet, Emmanuelle Lerat, Matthieu Boulesteix, Rita Rebollo, Nelly Burlet...

Journal of Environmental Radioactivity . 113 : 83-86

DOI: 10.1016/j.jenvrad.2012.04.001

2012

Article dans une revue

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The CycADS annotation database system to support the development and update of enriched BioCyc databases. Development of ad hoc BioCyc DB : AcypiCyc, ArthopodaCyc

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

5. Réunion Réseau BAPOA .

2012

Poster

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Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches.

Nuno D Mendes, Steffen Heyne, Ana T Freitas, Marie-France Sagot, Rolf Backofen

Bioinformatics . 28 ( 23 ) : 3034-3041

DOI: 10.1093/bioinformatics/bts574

2012

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Analysis of RNA Transcripts by High-Throughput RNA Sequencing

Paolo Ribeca, Vincent Lacroix, Michael Sammeth, Roderic Guigó

Alternative pre-mRNA Splicing: Theory and Protocols . 9783527636778

DOI: 10.1002/9783527636778.ch50

2012

Chapitre d'ouvrage

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Molecular organization, biochemical function, cellular role and evolution of NfuA, an atypical Fe-S carrier.

Béatrice Py, Catherine Gerez, Sandra Angelini, Rémy Planel, Daniel Vinella, Laurent Loiseau...

Molecular Microbiology . 86 ( 1 ) : 155-71

DOI: 10.1111/j.1365-2958.2012.08181.x

2012

Article dans une revue

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Spotlight on the Thaumarchaeota

C. Brochier-Armanet, Simonetta Gribaldo, Patrick Forterre

The International Society of Microbiologial Ecology Journal . 6 : 227-230

DOI: 10.1038/ismej.2011.145

2012

Article dans une revue

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The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences.

Olivier Arnaiz, Nathalie Mathy, Céline Baudry, Sophie Malinsky, Jean-Marc Aury, Cyril Denby Wilkes...

PLoS Genetics . 8 ( 10 ) : e1002984

DOI: 10.1371/journal.pgen.1002984

2012

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Mod/Resc Parsimony Inference: Theory and application

Igor Nor, Danny Hermelin, Sylvain Charlat, Jan Engelstadter, Max Reuter, Olivier Duron...

Information and Computation . 213 : 23-32

DOI: 10.1016/j.ic.2011.03.008

2012

Article dans une revue

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Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks.

Vicente Acuña, Paulo Vieira Milreu, Ludovic Cottret, Alberto Marchetti-Spaccamela, Leen Stougie, Marie-France Sagot

Bioinformatics . 28 ( 19 ) : 2474-2483

DOI: 10.1093/bioinformatics/bts423

2012

Article dans une revue

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The CycADS annotation database system to support the development and update of enriched BioCyc databases. Development of ad hoc BioCyc DB : AcypiCyc, ArthopodaCyc

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

13. Journées Ouvertes en Biologie, Informatique et Mathématiques . 978-2-7261-1301-1 : Pagination multiple

2012

Acte de congrès

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Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets

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

Theoretical Computer Science . 457 : 1--9

DOI: 10.1016/j.tcs.2012.07.023

2012

Article dans une revue

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Exploration of the core metabolism of symbiotic bacteria

Cecilia Coimbra Klein, Ludovic Cottret, Janice Kielbassa, Hubert Charles, Christian Gautier, Ana Tereza Ribeiro de Vasconcelos...

BMC Genomics . 13 ( 1 ) : 438

DOI: 10.1186/1471-2164-13-438

2012

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ReNaBi-IFB : The French Bioinformatics Infrastructure

Guy Perrière

EMBNet.journal . 18 : 12-13

DOI: 10.14806/ej.18.1.502

2012

Article dans une revue

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What genomes have to say about the evolution of the Earth

Bastien Boussau, Manolo Gouy

Gondwana Research . 21 : 483-494

DOI: 10.1016/j.gr.2011.08.002

2012

Article dans une revue

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ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.

Milana Frenkel-Morgenstern, Alessandro Gorohovski, Vincent Lacroix, Mark Rogers, Kristina Ibanez, Cesar Boullosa...

Nucleic Acids Research . 41 ( D1 ) : D142-D151

DOI: 10.1093/nar/gks1041

2012

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Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.

Milana Frenkel-Morgenstern, Vincent Lacroix, Iakes Ezkurdia, Yishai Levin, Alexandra Gabashvili, Jaime Prilusky...

Genome Research . 22 ( 7 ) : 1231-1242

DOI: 10.1101/gr.130062.111

2012

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Evidence for transcript networks composed of chimeric RNAs in human cells

Sarah Djebali, Julien Lagarde, Philipp Kapranov, Vincent Lacroix, Christelle Borel, Jonathan M. Mudge...

PLoS ONE . 7 ( 1 ) : Non paginé

DOI: 10.1371/journal.pone.0028213

2012

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Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

Sarah Djebali, Julien Lagarde, Philipp Kapranov, Vincent Lacroix, Christelle Borel, Jonathan M. Mudge...

PLoS ONE . 7 : 1-22

2012

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Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archea

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

BMC Evolutionary Biology . 12 : 226

DOI: 10.1186/1471-2148-12-226

2012

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Primate evolutionary history contribution to the deciphering of SIV/HIV origin and diversification

Bénédicte Lafay

Evolution Ottawa - 1th Joint Congress on Evolutionary Biology .

2012

Acte de congrès

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De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities.

Priya Narasingarao, Sheila Podell, Juan A Ugalde, Céline Brochier-Armanet, Joanne B Emerson, Jochen J Brocks...

The International Society of Microbiologial Ecology Journal . 6 ( 1 ) : 81-93

DOI: 10.1038/ismej.2011.78

2012

Article dans une revue

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Interaction between Selection and Biased Gene Conversion in Mammalian Protein-Coding Sequence Evolution Revealed by a Phylogenetic Covariance Analysis

Nicolas Lartillot

Molecular Biology and Evolution . 30 : 356 - 368

DOI: 10.1093/molbev/mss231

2012

Article dans une revue

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Rapport du groupe de travail sur la gestion et le partage des données

Christine Gaspin, Dominique Pontier, Laurence Colinet, Frédéric Dardel, Alain Franc, Odile Hologne...

2012

Rapport

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Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia a Plant with Young Sex Chromosomes

A. Muyle, N. Zemp, C. Deschamps, Sylvain Mousset, A. Wildmer, Gabriel Marais

PLoS Biology . 10 ( 4 ) : e1001308

DOI: 10.1371/journal.pbio.1001308

2012

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Repeated evolution of testis-specific new genes: the case of telomere-capping genes in Drosophila.

Raphaëlle Dubruille, Gabriel A.B. Marais, Benjamin Loppin

Int J Evol Biol . 2012 : 708980

DOI: 10.1155/2012/708980

2012

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Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome

E. Pessia, T. Makino, M. Bailly-Bechet, A. Mclysaght, Gabriel Marais

Proceedings of the National Academy of Sciences of the United States of America . 109 ( 14 ) : 5346-5351

DOI: 10.1073/pnas.1116763109

2012

Article dans une revue

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Structural and dynamical analysis of biological networks.

Cecilia C. Klein, Andrea Marino, Marie-France Sagot, Paulo Vieira Milreu, Matteo Brilli

Briefings in Functional Genomics and Proteomics . 14 : 309

DOI: 10.1093/bfgp/els030

2012

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BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms

Julien Allali, Cédric Saule, Cedric Chauve, Yves d'Aubenton-Carafa, Alain Denise, Christine Drevet...

Advances in Bioinformatics . 2012 : 1-5

DOI: 10.1155/2012/893048

2012

Article dans une revue

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Publications

Les défis de la systématique face au monde microbien

Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage

A comparative analysis of the amounts and dynamics of transposable elements in natural populations of Drosophila melanogaster and Drosophila simulans.

The CycADS annotation database system to support the development and update of enriched BioCyc databases. Development of ad hoc BioCyc DB : AcypiCyc, ArthopodaCyc

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches.

Analysis of RNA Transcripts by High-Throughput RNA Sequencing

Molecular organization, biochemical function, cellular role and evolution of NfuA, an atypical Fe-S carrier.

Spotlight on the Thaumarchaeota

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences.

Mod/Resc Parsimony Inference: Theory and application

Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks.

The CycADS annotation database system to support the development and update of enriched BioCyc databases. Development of ad hoc BioCyc DB : AcypiCyc, ArthopodaCyc

Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets

Exploration of the core metabolism of symbiotic bacteria

ReNaBi-IFB : The French Bioinformatics Infrastructure

What genomes have to say about the evolution of the Earth

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.

Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.

Evidence for transcript networks composed of chimeric RNAs in human cells

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archea

Primate evolutionary history contribution to the deciphering of SIV/HIV origin and diversification

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities.

Interaction between Selection and Biased Gene Conversion in Mammalian Protein-Coding Sequence Evolution Revealed by a Phylogenetic Covariance Analysis

Rapport du groupe de travail sur la gestion et le partage des données

Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia a Plant with Young Sex Chromosomes

Repeated evolution of testis-specific new genes: the case of telomere-capping genes in Drosophila.

Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome

Structural and dynamical analysis of biological networks.

BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms