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Finding Long and Multiple Repeats with Edit Distance

Maria Federico , Pierre Peterlongo , Nadia Pisanti , Marie-France Sagot
The Prague Stringology Conference 2011, Aug 2011, Prague, Czech Republic
Conference papers inria-00608208v1

Structural and dynamical analysis of biological networks.

Cecilia C. Klein , Andrea Marino , Marie-France Sagot , Paulo Vieira Milreu , Matteo Brilli et al.
Briefings in Functional Genomics and Proteomics, 2012, 14, pp.309. ⟨10.1093/bfgp/els030⟩
Journal articles hal-00737455v1

NGS without a reference genome, comparison and visualisation of non assembled data

Vincent Lacroix
Statistical Methods for Post-Genomic Data (SMPGD), 2011, Paris, France
Conference papers hal-00748787v1

The DivJ, CbrA and PleC system controls DivK phosphorylation and symbiosis in Sinorhizobium meliloti

Francesco Pini , Benjamin Frage , Lorenzo Ferri , Nicole J. de Nisco , Saswat S. Mohapatra et al.
Molecular Microbiology, 2013, 90 (1), pp.54 - 71. ⟨10.1111/mmi.12347⟩
Journal articles hal-02646296v1

Wolbachia detection: an assessment of standard PCR protocols.

P. M. Simões , G. Mialdea , D. Reiss , Marie-France Sagot , S. Charlat et al.
Molecular Ecology Resources, 2011, 11 (3), pp.567-72. ⟨10.1111/j.1755-0998.2010.02955.x⟩
Journal articles istex hal-00746848v1

Intraspecific specialization of the generalist parasitoid Cotesia sesamiae revealed by polyDNAvirus polymorphism and associated with different Wolbachia infection.

Antoine Branca , Bruno Pierre Le Ru , Fabrice Vavre , Jean-François Silvain , Stéphane Dupas et al.
Molecular Ecology, 2011, 20 (5), pp.959-71. ⟨10.1111/j.1365-294X.2010.04977.x⟩
Journal articles istex hal-00746863v1

Transposon proliferation in an asexual parasitoid.

Ken Kraaijeveld , Brechtje Zwanenburg , Benjamin Hubert , Cristina Vieira , Sylvia de Pater et al.
Molecular Ecology, 2012, 21 (16), pp.3898-3906. ⟨10.1111/j.1365-294X.2012.5582.x⟩
Journal articles istex hal-00850325v1

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

Patrice Baa-Puyoulet , Augusto Vellozo , Jaime Huerta-Cepas , Gérard Febvay , Federica Calevro et al.
8. Meeting of the International Aphid Genomics Consortium, Jan 2013, Harpenden, United Kingdom
Conference poster hal-03506707v1

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 et al.
13. Journées Ouvertes en Biologie, Informatique et Mathématiques, Institut National de Recherche en Informatique et en Automatique (INRIA). Rennes, FRA., Jul 2012, Rennes, France. Pagination multiple
Conference papers hal-02747415v1

tirant, a newly discovered active endogenous retrovirus in Drosophila simulans.

Abdou Akkouche , Rita Rebollo , Nelly Burlet , Caroline Esnault , Sonia Martinez et al.
Journal of Virology, 2012, 86 (7), pp.3675-3681. ⟨10.1128/JVI.07146-11⟩
Journal articles hal-00763499v1

Mod/Resc Parsimony Inference: Theory and application

Igor Nor , Danny Hermelin , Sylvain Charlat , Jan Engelstadter , Max Reuter et al.
Information and Computation, 2012, 213, pp.23-32. ⟨10.1016/j.ic.2011.03.008⟩
Journal articles hal-00763405v1

Maternally deposited germline piRNAs silence the tirant retrotransposon in somatic cells

Abdou Akkouche , Thomas Grentzinger , Marie Fablet , Claudia Armenise , Nelly Burlet et al.
EMBO Reports, 2013, 14 (5), pp.458-64. ⟨10.1038/embor.2013.38⟩
Journal articles hal-00850319v1

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
Conference papers hal-00933699v1

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
Conference papers hal-00842982v1

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⟩
Journal articles hal-00764412v1

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⟩
Journal articles hal-00746858v1

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
Conference papers hal-00748785v1

Using cascading Bloom filters to improve the memory usage for de Brujin graphs

Kamil Salikhov , Gustavo Sacomoto , Gregory Kucherov
Workshop on Algorithms in Bioinformatics, Sep 2013, Sophia Antipolis, France. 13p
Conference papers hal-00824697v1

Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks.

Steven M Kelk , Brett G Olivier , Leen Stougie , Frank J Bruggeman
Scientific Reports, 2012, 2, pp.580. ⟨10.1038/srep00580⟩
Journal articles hal-00763439v1

Brief Announcement: Flooding in Dynamic Graphs with Arbitrary Degree Sequence

Hervé Baumann , Pierluigi Crescenzi , Pierre Fraigniaud
26th International Symposium on Distributed Computing, 2012, Salvador, Brazil. pp.417-419
Conference papers hal-00763446v1

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti.

Marco Galardini , Alessio Mengoni , Matteo Brilli , Francesco Pini , Antonella Fioravanti et al.
BMC Genomics, 2011, 12, pp.235. ⟨10.1186/1471-2164-12-235⟩
Journal articles hal-00746865v1

Partial enumeration of solutions traces for the problem of sorting by signed reversals

Christian Baudet , Zanoni Dias
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine, Aug 2011, Chicago, United States. pp.505--507, ⟨10.1145/2147805.2147884⟩
Conference papers hal-00748607v1

A dynamic programming algorithm for the tree mapping problem

C.E. Ferreira , A. S. Freire , G. A. Puglia
Electronic Notes in Discrete Mathematics, 2011, pp.147-152
Journal articles hal-00748779v1

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 et al.
X-meeting, 2011, Florianópolis, Brazil
Conference papers hal-00748781v1

[Big Data in biology].

Alain Viari
médecine/sciences, 2012, 28 (12), pp.1027-8. ⟨10.1051/medsci/20122812001⟩
Journal articles hal-00851569v1

Vertical inheritance and bursts of transposition have shaped the evolution of the BS non-LTR retrotransposon in Drosophila.

Adriana Granzotto , Fabrício R Lopes , Cristina Vieira , Claudia M A Carareto
Molecular Genetics and Genomics, 2011, 286 (1), pp.57-66. ⟨10.1007/s00438-011-0629-9⟩
Journal articles istex hal-00850379v1

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

Milana Frenkel-Morgenstern , Vincent Lacroix , Iakes Ezkurdia , Yishai Levin , Alexandra Gabashvili et al.
Genome Research, 2012, 22 (7), pp.1231-1242. ⟨10.1101/gr.130062.111⟩
Journal articles hal-00744761v1

The sex-specific impact of meiotic recombination on nucleotide composition.

Alexandra Popa , Paul Samollow , Christian Gautier , Dominique Mouchiroud
Genome Biology and Evolution, 2012, 4 (3), pp.412-422. ⟨10.1093/gbe/evs023⟩
Journal articles hal-00851234v1

PhEVER: a database for the global exploration of virus-host evolutionary relationships.

Leonor Palmeira , Simon Penel , Vincent Lotteau , Chantal Rabourdin-Combe , Christian Gautier et al.
Nucleic Acids Research, 2011, 39 (Database issue), pp.D569-75. ⟨10.1093/nar/gkq1013⟩
Journal articles hal-00562509v1

Analysis of RNA Transcripts by High-Throughput RNA Sequencing

Paolo Ribeca , Vincent Lacroix , Michael Sammeth , Roderic Guigó
Stefan Stamm, Christopher W. J. Smith, Reinhard Lührmann. Alternative pre-mRNA Splicing: Theory and Protocols, Wiley-VCH Verlag GmbH & Co. KGaA, 2012, 9783527636778. ⟨10.1002/9783527636778.ch50⟩
Book sections hal-00850866v1