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Motif representation and discovery

A.M. Carvalho
Bioinformatics [q-bio.QM]. Universidade técnica de Lisboa Instituto superior técnico, 2011. English. ⟨NNT : ⟩
Theses tel-00755042v1
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Identification of metabolic network models from incomplete high-throughput datasets

Sara Berthoumieux , Matteo Brilli , Hidde De Jong , Daniel Kahn , Eugenio Cinquemani et al.
Bioinformatics, 2011, 27 (13), pp.i186-i195. ⟨10.1093/bioinformatics/btr225⟩
Journal articles hal-00793039v1
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Etude structurelle des réseaux : modèles aléatoires, motifs et cycles.

Etienne Birmele
Bio-informatique [q-bio.QM]. Université d'Evry-Val d'Essonne, 2011
Habilitation à diriger des recherches tel-00750375v1
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Absence of a core metabolic network common to symbiotic bacteria

Cecilia Coimbra Klein , Ludovic Cottret , Hubert Charles , Christian Gautier , Ana Tereza Ribeiro de Vasconcelos et al.
6. Meeting GDRE-RA Comparative genomics, Nov 2011, Lyon, France. 33 diapositives
Conference papers hal-02806316v1
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Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia

Veasna Duong , Cameron Simmons , Laurent Gavotte , Alain Viari , Sivuth Ong et al.
Infection, Genetics and Evolution, 2011, N/A (N/A), pp.N/A. ⟨10.1016/j.meegid.2011.06.019⟩
Journal articles pasteur-00805484v1
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Expression et évolution du phénotype étendu dans une association parasitoïde-virus

Julien Martinez
Sciences agricoles. Université Claude Bernard - Lyon I, 2011. Français. ⟨NNT : 2011LYO10329⟩
Theses tel-00751985v1
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The evolution of recombination and genomic structures: a modeling approach.

Alexandra Popa
Bioinformatics [q-bio.QM]. Université Claude Bernard - Lyon I, 2011. English. ⟨NNT : ⟩
Theses tel-00750370v1
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A genomic reappraisal of symbiotic function in the aphid/buchnera symbiosis: reduced transporter sets and variable membrane organisations.

Hubert Charles , Severine Balmand , Araceli Lamelas , Ludovic Cottret , Vicente Pérez-Brocal et al.
PLoS ONE, 2011, 6 (12), pp.e29096. ⟨10.1371/journal.pone.0029096⟩
Journal articles hal-00659506v1
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Structure and dynamics of the operon map of Buchnera aphidicola sp. strain APS.

Lilia Brinza , Federica Calevro , Gabrielle Duport , Karen Gaget , Christian Gautier et al.
BMC Genomics, 2010, 11 (666), pp.666. ⟨10.1186/1471-2164-11-666⟩
Journal articles hal-00632959v1
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Multichromosomal median and halving problems under different genomic distances

Eric Tannier , Chunfang Zheng , David Sankoff
BMC Bioinformatics, 2009, 10 (1), pp.120. ⟨10.1186/1471-2105-10-120⟩
Journal articles hal-00784456v1
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Lossless filter for multiple repeats with bounded edit distance

Pierre Peterlongo , Gustavo Akio Tominaga Sacomoto , Alair Pereira Do Lago , Nadia Pisanti , Marie-France Sagot et al.
Algorithms for Molecular Biology, 2009, 4 (1), pp.3. ⟨10.1186/1748-7188-4-3⟩
Journal articles hal-00784457v1
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Characterization of partenogenetic embryo development in the context of symbiosis using transcriptome analysis in the pea aphid model

Andréane Rabatel , Gérard Febvay , Karen Gaget , Marie-Gabrielle Duport , Yvan Rahbé et al.
EMBO Workshop on Systems Biology of Development, EMBO. Heidelberg, DEU., Aug 2010, Ascona, Switzerland. 1 p
Conference papers hal-01231279v1
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Exploration et inférence du réseau de régulation de la transcription de la bactérie symbiotique intracellulaire à génome réduit Buchnera aphidicola

Lilia Brinza
Bio-informatique [q-bio.QM]. INSA de Lyon, 2010. Français. ⟨NNT : ⟩
Theses tel-00750363v1
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Efficient algorithms for the identification of miRNA motifs in DNA sequences

Nuno D Mendes
Bioinformatics [q-bio.QM]. UNIVERSIDADE TECNICA DE LISBOA INSTITUTO SUPERIOR TECNICO, 2011. English. ⟨NNT : ⟩
Theses tel-00750693v1
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Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms

Paulo Vieira Milreu , Vicente Acuña , Etienne E. Birmelé , Pierluigi Crescenzi , Alberto Marchetti-Spaccamela et al.
Workshop on Algorithms in Bioinformatics (WABI), Sep 2010, Liverpool, United Kingdom. pp.226-237, ⟨10.1007/978-3-642-15294-8_19⟩
Conference papers hal-00751339v1
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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 et al.
10. Cold Spring Harbor Laboratory / Wellcome Trust conference on Genome Informatics, Sep 2010, Hinxton, United Kingdom. 1 p., 2010
Conference poster hal-01231276v1
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Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays

Cyril Dégletagne , Céline Keime , Benjamin Rey , Marc de Dinechin , Fabien Forcheron et al.
BMC Genomics, 2010, 11, pp.344. ⟨10.1186/1471-2164-11-344⟩
Journal articles hal-00851240v1
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Bacterial syntenies: an exact approach with gene quorum.

Yves-Pol Deniélou , Marie-France Sagot , Frédéric Boyer , Alain Viari
BMC Bioinformatics, 2011, 12, pp.193. ⟨10.1186/1471-2105-12-193⟩
Journal articles hal-00746864v1
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Identification of metabolic network models from incomplete high-throughput datasets

Sara Berthoumieux , Matteo Brilli , Hidde de Jong , Kahn Daniel , Eugenio Cinquemani et al.
[Research Report] RR-7524, INRIA. 2011
Reports inria-00561999v1
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Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Iagc The International Aphid Genomics Consortium , Federica Calevro , Hubert Charles , Stefano Colella , Gérard Febvay et al.
PLoS Biology, 2010, 8 (2), pp.e1000313. ⟨10.1371/journal.pbio.1000313⟩
Journal articles hal-00459970v1
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Models and algorithms for metabolic networks: elementary modes and precursor sets

Vicente Acuña
Algorithme et structure de données [cs.DS]. Université Claude Bernard - Lyon I, 2010. Français. ⟨NNT : ⟩
Theses tel-00850705v1
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The auxin signalling network translates dynamic input into robust patterning at the shoot apex

Teva Vernoux , Géraldine Brunoud , Etienne Farcot , Valérie Morin , Hilde van Den Daele et al.
Molecular Systems Biology, 2011, 7 (508), ⟨10.1038/msb.2011.39⟩
Journal articles hal-00828880v1
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Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny

Amélie Véron , Claire Lemaitre , Christian Gautier , Vincent Lacroix , Marie-France Sagot et al.
BMC Genomics, 2011, 12 (1), pp.303. ⟨10.1186/1471-2164-12-303⟩
Journal articles hal-00784423v1
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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, 2010, 11 (1), pp.529. ⟨10.1186/1471-2164-11-529⟩
Journal articles hal-00784432v1
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MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.

Ludovic Cottret , David Wildridge , Florence Vinson , Michael P Barrett , Hubert Charles et al.
Nucleic Acids Research, 2010, 38 (Web Server issue), pp.W132-7. ⟨10.1093/nar/gkq312⟩
Journal articles hal-00690651v1
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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 et al.
PLoS Computational Biology, 2010, 6 (9), epub ahead of print. ⟨10.1371/journal.pcbi.1000904⟩
Journal articles hal-00690650v1
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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 et al.
[Research Report] RR-7852, INRIA. 2011, pp.12
Reports hal-00654249v2
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Global analysis of DNA methylation and transcription of human repetitive sequences.

Béatrice Horard , Angéline Eymery , Geneviève Fourel , Nikita Vassetzky , Jacques Puechberty et al.
Epigenetics, 2009, 4 (5), pp.339-50. ⟨10.4161/epi.4.5.9284⟩
Journal articles hal-00851248v1
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Overexpression of transcription factor Sp1 leads to gene expression perturbations and cell cycle inhibition.

Emmanuelle Deniaud , Joël Baguet , Roxane Chalard , Bariza Blanquier , Lilia Brinza et al.
PLoS ONE, 2009, 4 (9), pp.e7035. ⟨10.1371/journal.pone.0007035⟩
Journal articles hal-00851247v1
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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 et al.
Database - The journal of Biological Databases and Curation, 2011, 2011, pp.bar008. ⟨10.1093/database/bar008⟩
Journal articles hal-00632965v1