GECO Evolutionary and Computational Genomics

Baobab Group

Sagot Marie-France

Directrice de recherche

INRIA

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

Tel: 33 04 72 44 82 38

Email

Publications

Display of 91 to 120 publications on 210 in total

Wolbachia detection: an assessment of standard PCR protocols.

P. M. Simões, G. Mialdea, D. Reiss, Marie-France Sagot, S. Charlat

Molecular Ecology Resources . 11 ( 3 ) : 567-72

DOI: 10.1111/j.1755-0998.2010.02955.x

Journal article

see the publication

Initial metabolic reconstruction of Klebsiella pneumoniae Kp13, a multidrug resistant pathogen involved in nosocomial outbreaks in Brazil

P. Ivan, Cecilia C. Klein, Ludovic Cottret, Ana T Vasconcelos, Ac Gales, Marie-France Sagot...

X-meeting .

Conference paper

see the publication

Using the “CycADS” annotation management system to develop a BioCyc metabolic network database for sequenced arthropods genomes: first steps towards “ArthropodsCyc”

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

Rencontres bioinformaticiens et statisticiens de l’INRA . : 1 p.

Poster

see the publication

Absence of a core metabolic network common to symbiotic bacteria

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

6. Meeting GDRE-RA Comparative genomics . : 33 diapositives

Conference paper

see the publication

CycADS: an annotation database system to ease the development and update of BioCyc databases.

Augusto F Vellozo, Amélie S Véron, Patrice Baa-Puyoulet, Jaime Huerta-Cepas, Ludovic Cottret, Gérard Febvay...

Database - The journal of Biological Databases and Curation . 2011 : bar008

DOI: 10.1093/database/bar008

Journal article

see the publication

Bacterial syntenies: an exact approach with gene quorum.

Yves-Pol Deniélou, Marie-France Sagot, Frédéric Boyer, Alain Viari

BMC Bioinformatics . 12 : 193

DOI: 10.1186/1471-2105-12-193

Journal article

see the publication

Mod/Resc Parsimony Inference

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

Combinatorial Pattern Matching . 6129 : 202--213

DOI: 10.1007/978-3-642-13509-5_19

Conference paper

see the publication

A note on the complexity of finding and enumerating elementary modes.

Vicente Acuña, Alberto Marchetti-Spaccamela, Marie-France Sagot, Leen Stougie

BioSystems . 99 ( 3 ) : 210-4

DOI: 10.1016/j.biosystems.2009.11.004

Journal article

see the publication

A tale of genome, annotations, metabolism and phylogenomics: the pea aphid genome resources

Fabrice Legeai, Stefano Colella, Jaime Huerta-Cepas, Jean-Pierre Gauthier, Augusto Vellozo, Patrice Baa-Puyoulet...

10. Cold Spring Harbor Laboratory / Wellcome Trust conference on Genome Informatics . : 1 p.

Poster

see the publication

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

Ludovic Cottret, David Wildridge, Florence Vinson, Michael P. Barrett, Marie-France Sagot, Hubert Charles...

JOBIM 2010 . : 1 p.

Poster

see the publication

Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms

Paulo Vieira Milreu, Vicente Acuña, Etienne E. Birmelé, Pierluigi Crescenzi, Alberto Marchetti-Spaccamela, Marie-France Sagot...

Algorithms in Bioinformatics . 6293 : 226-237

DOI: 10.1007/978-3-642-15294-8_19

Conference paper

see the publication

Using the “CycADS” annotation management system to develop a BioCyc metabolic network database for sequenced arthropods genomes: first steps towards “ArthropodsCyc”

Augusto Vellozo, Patrice Baa-Puyoulet, Jaime Huerta-Cepas, Gérard Febvay, Federica Calevro, Yvan Rahbé...

4. Annual Arthropod Genomics Symposium on “Arthropod Genomics: New Approaches and Outcomes” . : 45 p.

Poster

see the publication

Cassis: detection of genomic rearrangement breakpoints.

Christian Baudet, Claire Lemaitre, Zanoni Dias, Christian Gautier, Eric Tannier, Marie-France Sagot

Bioinformatics . 26 ( 15 ) : 1897-8

DOI: 10.1093/bioinformatics/btq301

Journal article

see the publication

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Iagc The International Aphid Genomics Consortium, Federica Calevro, Hubert Charles, Stefano Colella, Gérard Febvay, Caroline Anselme...

PLoS Biology . 8 ( 2 ) : e1000313

DOI: 10.1371/journal.pbio.1000313

Journal article

see the publication

Repetition-free longest common subsequence

S.S Adi, M. Braga, C.G. Fernandes, C.E. Ferreira, F.V. Martinez, M.-F. Sagot...

Discrete Applied Mathematics . 158 ( 12 ) : 1315-1324

DOI: 10.1016/j.dam.2009.04.023

Journal article

see the publication

Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi

Nuno Mendes, Ana Freitas, Ana Vasconcelos, Marie-France Sagot

BMC Genomics . 11 ( 1 ) : 529

DOI: 10.1186/1471-2164-11-529

Journal article

see the publication

Identifying SNPs without a reference genome by comparing raw reads

Pierre Peterlongo, Nicolas Schnel, Nadia Pisanti, Marie-France Sagot, Vincent Lacroix

String Processing and Information Retrieval . 6393 : 147-158

DOI: 10.1007/978-3-642-16321-0_14

Conference paper

see the publication

Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata.

Ludovic Cottret, Paulo Vieira Milreu, Vicente Acuña, Alberto Marchetti-Spaccamela, Leen Stougie, Hubert Charles...

PLoS Computational Biology . 6 ( 9 ) : epub ahead of print

DOI: 10.1371/journal.pcbi.1000904

Journal article

see the publication

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.

Ludovic Cottret, David Wildridge, Florence Vinson, Michael P Barrett, Hubert Charles, Marie-France Sagot...

Nucleic Acids Research . 38 ( Web Server issue ) : W132-7

DOI: 10.1093/nar/gkq312

Journal article

see the publication

Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum.

Lilia Brinza, José Viñuelas, Ludovic Cottret, Federica Calevro, Yvan Rahbé, Gérard Febvay...

Comptes Rendus Biologies . 332 ( 11 ) : 1034-49

DOI: 10.1016/j.crvi.2009.09.007

Journal article

see the publication

The Acyrthosiphon pisum Cyc database (AcypiCyc) created using a novel BioCyc Annotation Database System (CycADS): a useful tool to explore and study the pea aphid metabolism

Stefano Colella, A. Vellozo, Ludovic Cottret, Gérard Febvay, Federica Calevro, Yvan Rahbé...

5th Meeting of the International Aphid Genomics Consortium "Pea Aphid Genome Annotation Workshop 2, Barcelona, Espagne, juin 2009 .

Conference paper

see the publication

Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes

Claire Lemaitre, Marília D.V. Braga, Christian Gautier, M.-F. Sagot, Eric Tannier, Gabriel Marais

Genome Biology and Evolution . 1(1) : 56-66

Journal article

see the publication

Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster

M. Deloger, F.M.G. Cavalli, E. Lerat, C. Biémont, M.-F. Sagot, Cristina Vieira

Gene . 439 : 55-62

Journal article

see the publication

Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

Claire Lemaitre, Lamia Zaghloul, Marie-France Sagot, Christian Gautier, Alain Arneodo, Eric Tannier...

BMC Genomics . 10 ( 1 ) : 335

DOI: 10.1186/1471-2164-10-335

Journal article

see the publication

Assessing the exceptionality of coloured motifs in networks

Sophie S. Schbath, Vincent Lacroix, Marie-France Sagot

EURASIP Journal on Bioinformatics and Systems Biology . 2009 : 9 pages on line

DOI: 10.1155/2009/616234

Journal article

see the publication

Multiple alignment of biological networks: A flexible approach

Yves-Pol Deniélou, Frédéric Boyer, Alain Viari, Marie-France Sagot

Combinatorial Pattern Matching (CPM) . 5577 : 263-273

DOI: 10.1007/978-3-642-02441-2_23

Conference paper

see the publication

Current tools for the identification of miRNA genes and their targets

N.D. Mendes, A.T. Freitas, M.-F. Sagot

Nucleic Acids Research . 2009 : 2419-2433

Journal article

see the publication

Lossless filter for multiple repeats with bounded edit distance

Pierre Peterlongo, Gustavo Akio Tominaga Sacomoto, Alair Pereira Do Lago, Nadia Pisanti, Marie-France Sagot

Algorithms for Molecular Biology . 4 ( 1 ) : 3

DOI: 10.1186/1748-7188-4-3

Journal article

see the publication

An asymmetric approach to preserve common intervals while sorting by reversals

Marília D.V. Braga, Christian Gautier, Marie-France Sagot

Algorithms for Molecular Biology . 4 ( 1 ) : 16

DOI: 10.1186/1748-7188-4-16

Journal article

see the publication

AcypiCyc (Acyrthosiphon pisum Cyc database) and CycADS (Cyc Annotation Database System): moving from genome sequence annotation to metabolic network analyses

Stefano Colella, A. Vellozo, L. Cottret, G. Febvay, Federica Calevro, Yvan Rahbé...

8th International Symposium on Aphids (8 ISA 2009) . : 1-1

Conference paper

see the publication