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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
HDR tel-00750375v1
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A snapshot of histone modifications within transposable elements in Drosophila wild type strains.

 Rita Rebollo , Béatrice Horard , Flora Begeot , Marion Delattre , Eric Gilson , et al.
PLoS ONE, 2012, 7 (9), pp.1-7. ⟨10.1371/journal.pone.0044253⟩
Article dans une revue hal-00850321v1

Integration of metabolic pathways and host regulation in symbiosis: tyrosine and cuticular protein biosynthesis during the pea aphid embryonic development

 Andréane Rabatel , Gérard Febvay , Karen Gaget , Gabrielle Duport , Nadia Bendridi , et al.
Sixth International Symposium on Molecular Insect Science, 2011, Amsterdam, Netherlands
Communication dans un congrès hal-00748785v1
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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
Communication dans un congrès hal-02806316v1
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Tyrosine pathway regulation is host-mediated in the pea aphid symbiosis during late embryonic and early larval development

 Andréane Rabatel , Gérard Febvay , Karen Gaget , Gabrielle Duport , Patrice Baa-Puyoulet , et al.
BMC Genomics, 2013, 14 (1), pp.235. ⟨10.1186/1471-2164-14-235⟩
Article dans une revue hal-00824527v1

Reconciliation of metabolites and biochemical reactions for metabolic networks.

 Thomas Bernard , Alan Bridge , Anne Morgat , Sébastien Moretti , Ioannis Xenarios , et al.
Briefings in Bioinformatics, 2012, 15 (1), pp.123-135. ⟨10.1093/bib/bbs058⟩
Article dans une revue hal-00764412v1
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Genomic regions harboring insecticide resistance-associated Cyp genes are enriched by transposable element fragments carrying putative transcription factor binding sites in two sibling Drosophila species

 Claudia M A Carareto , Eric H Hernandez , Cristina Vieira
Gene, 2014, 537 (1), pp.93-99. ⟨10.1016/j.gene.2013.11.080⟩
Article dans une revue hal-00922703v1

Intragenomic conflict in populations infected by Parthenogenesis Inducing Wolbachia ends with irreversible loss of sexual reproduction.

 Richard Stouthamer , James E Russell , Fabrice Vavre , Leonard Nunney
BMC Evolutionary Biology, 2010, 10, pp.229. ⟨10.1186/1471-2148-10-229⟩
Article dans une revue hal-00850399v1
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Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses

 Cecilia C Klein , João M P Alves , Myrna G Serrano , Gregory A Buck , Ana Tereza R Vasconcelos , et al.
PLoS ONE, 2013, 8 (11), pp.e79786. ⟨10.1371/journal.pone.0079786⟩
Article dans une revue hal-00922587v1

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data

 Gustavo Akio Tominaga Sacomoto , Vincent Lacroix , Marie-France Sagot
Workshop on Algorithms in Bioinformatics (WABI), Sep 2013, Nice, France
Communication dans un congrès hal-00842982v1

Does a parthenogenesis-inducing Wolbachia induce vestigial cytoplasmic incompatibility?

 Ken Kraaijeveld , Barbara M Reumer , Laurence Mouton , Natacha Kremer , Fabrice Vavre , et al.
The Science of Nature Naturwissenschaften, 2011, 98 (3), pp.175-80. ⟨10.1007/s00114-010-0756-x⟩
Article dans une revue hal-00746858v1
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Using cascading Bloom filters to improve the memory usage for de Brujin graphs

 Kamil Salikhov , Gustavo Sacomoto , Gregory Kucherov
Algorithms for Molecular Biology, 2014, 9 (1), pp.2. ⟨10.1186/1748-7188-9-2⟩
Article dans une revue hal-00971576v1
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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
Bioinformatics, 2011, 27 (13), pp.i186-i195. ⟨10.1093/bioinformatics/btr225⟩
Article dans une revue hal-00793039v1

Spatial modelling of plant diversity from high-throughput environmental dna sequence data

 Angelika Studeny , Florence Forbes , Eric Coissac , Alain Viari , Celine Mercier , et al.
45èmes Journées de Statistique, Société Française de Statistique, May 2013, Toulouse, France
Communication dans un congrès hal-00933699v1

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 , et al.
Comptes Rendus Biologies, 2009, 332 (11), pp.1034-49. ⟨10.1016/j.crvi.2009.09.007⟩
Article dans une revue istex hal-00445861v1

The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes

 Valentina Baldazzi , Delphine Ropers , Yves Markowicz , Daniel Kahn , Hans Geiselmann , et al.
Actes des Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM 2010), 2010, Montpellier, France. pp.11-12
Communication dans un congrès hal-00793021v1

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

 Patrice Baa-Puyoulet , Augusto F Vellozo , Jaime Huerta-Cepas , Gérard Febvay , T. Gabaldon , et al.
5th Annual Arthropod Genomics Symposium "Arthropod Genomics 2011: Exploring Diversity, Relating Similarity", Jun 2011, Kansas City, United States
Communication dans un congrès hal-00748601v1

Joint segmentation of multivariate Gaussian processes using mixed linear models

 Franck F. Picard , E. Lebarbier , E. E. Budinska , Stephane S. Robin
Computational Statistics and Data Analysis, 2011, 55 (2), pp.1160 - 1170. ⟨10.1016/j.csda.2010.09.015⟩
Article dans une revue hal-01001452v1
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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, Oct 2010, Los Cabos, Mexico. pp.147-158, ⟨10.1007/978-3-642-16321-0_14⟩
Communication dans un congrès inria-00514887v1
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Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers

 João Alves , Cecilia Klein , Flávia Maia da Silva , André Costa-Martins , Myrna Serrano , et al.
BMC Evolutionary Biology, 2013, 13 (1), pp.190. ⟨10.1186/1471-2148-13-190⟩
Article dans une revue hal-00868763v1

Efficiently listing bounded length st-paths

 Romeo Rizzi , Gustavo Sacomoto , Marie-France Sagot
Twenty-Fifth International Workshop on Combinatorial Algorithms (IWOCA 2014), Sep 2014, Duluth, Minnesota, France. in press
Communication dans un congrès hal-01091924v1

Binding properties of the N-acetylglucosamine and high-mannose N-glycan PP2-A1 phloem lectin in Arabidopsis.

 Julie Beneteau , Denis Renard , Laurent Marché , Elise Douville , Laurence Lavenant , et al.
Plant Physiology, 2010, 153 (3), pp.1345-61. ⟨10.1104/pp.110.153882⟩
Article dans une revue hal-00850393v1

The evolutionary dynamics of the Helena retrotransposon revealed by sequenced Drosophila genomes.

 Adriana Granzotto , Fabrício R Lopes , Emmanuelle Lerat , Cristina Vieira , Claudia M A Carareto
BMC Evolutionary Biology, 2009, 9, pp.174. ⟨10.1186/1471-2148-9-174⟩
Article dans une revue hal-00850397v1
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Genomic analysis of the regulatory elements and links with intrinsic DNA structural properties in the shrunken genome of Buchnera

 Lilia Brinza , Federica Calevro , Hubert Charles
BMC Genomics, 2013, 14 (1), pp.73. ⟨10.1186/1471-2164-14-73⟩
Article dans une revue hal-00788161v1

Making (good) use of Wolbachia: what the models say.

 Fabrice Vavre , Sylvain Charlat
Current Opinion in Microbiology, 2012, 15 (3), pp.263-8. ⟨10.1016/j.mib.2012.03.005⟩
Article dans une revue istex hal-00763517v1
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Alignement Multiple de Données Génomiques et Post-Génomiques : Approches Algorithmiques

 Yves-Pol Denielou
Autre [cs.OH]. Université de Grenoble, 2010. Français. ⟨NNT : ⟩
Thèse tel-00610419v1

Ongoing and future developments at the Universal Protein Resource.

 Anne Morgat , Rolf Apweiler , Maria-Jesus Martin , C. O'Donovan , M. Magrane , et al.
Nucleic Acids Research, 2011, 39 (Database issue), pp.D214-9. ⟨10.1093/nar/gkq1020⟩
Article dans une revue hal-00746843v1

Comparative genomics of VirR regulons in Clostridium perfringens strains

 A. Frandi , A. Mengoni , M. Brilli
BMC Evolutionary Biology, 2010, 10, pp.1-20. ⟨10.1186/1471-2180-10-65⟩
Article dans une revue hal-00539448v1
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Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure

 Paulo Vieira Milreu , Cecilia Coimbra Klein , Ludovic Cottret , Vicente Acuña , Etienne E. Birmelé , et al.
Bioinformatics, 2014, 30 (1), pp.61-70. ⟨10.1093/bioinformatics/btt597⟩
Article dans une revue hal-00922567v1
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The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis.

 Matteo Brilli , Marco Fondi , Renato Fani , Alessio Mengoni , Lorenzo Ferri , et al.
BMC Systems Biology, 2010, 4, pp.52. ⟨10.1186/1752-0509-4-52⟩
Article dans une revue hal-00682798v1
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