EN FR
EN FR
BAMBOO - 2011
BAMBOO - 2011


Team Bamboo


Members
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
Partnerships and Cooperations
Dissemination
Bibliography


Team Bamboo


Members
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
Partnerships and Cooperations
Dissemination
Bibliography




Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 1E. Birmelé.

    Etude structurelle des réseaux: modèles aléatoires, motifs et cycles, Université d'Évry Val d'Essonne, 2011, Habilitation, Ph. D. Thesis.
  • 2A. Carvalho.

    Motif representation and discovery, Instituto Superior Técnico Lisbon, 2011, Supervisors: A. Oliveira and M.-F. Sagot.
  • 3N. Mendes.

    Efficient algorithms for the identification of miRNA motifs in DNA sequences, Université Lyon 1 and Instituto Superior Técnico Lisbon, 2011, Supervisors: M.-F. Sagot and A. T. Freitas.
  • 4A. Popa.

    The evolution of recombination and genomic structures: a modeling approach, Université Lyon 1, 2011, Supervisors: C. Gautier and D. Mouchiroud.

Articles in International Peer-Reviewed Journal

  • 5R. Alcántara, K. B. Axelsen, A. Morgat, E. Belda, E. Coudert, A. Bridge, H. Cao, P. de Matos, M. Ennis, S. Turner, G. Owen, L. Bougueleret, I. Xenarios, C. Steinbeck.

    Rhea–a manually curated resource of biochemical reactions, in: Nucleic Acids Res, Dec 2011.
  • 6S. Berthoumieux, M. Brilli, H. de Jong, D. Kahn, E. Cinquemani.

    Identification of metabolic network models from incomplete high-throughput datasets, in: Bioinformatics, 2011, vol. 27, no 13, p. I186-I195, 19th Annual International Conference on Intelligent Systems for Molecular Biology/10th European Conference on Computational Biology. [ DOI : 10.1093/bioinformatics/btr225 ]
  • 7A. Branca, B. P. Le Ru, F. Vavre, J.-F. Silvain, S. Dupas.

    Intraspecific specialization of the generalist parasitoid Cotesia sesamiae revealed by polyDNAvirus polymorphism and associated with different Wolbachia infection, in: Molecular Ecology, 2011, vol. 20, no 5, p. 959-971. [ DOI : 10.1111/j.1365-294X.2010.04977.x ]
  • 8Y.-P. Denielou, M.-F. Sagot, F. Boyer, A. Viari.

    Bacterial syntenies: an exact approach with gene quorum, in: BMC Bioinformatics, 2011, vol. 12. [ DOI : 10.1186/1471-2105-12-193 ]
  • 9S. Djebali, J. Lagarde, P. Kapranov, V. Lacroix, J. Mudge, C. Ucla, S. Foissac, C. Howald, J. Chrast, P. Ribeca, D. Martin, R. Murray, X. Yang, L. Ghamsari, C. Lin, I. Bell, E. Dumais, J. Drenkow, N. Van Berkum, B. Lajoie, M. Vidal, J. Stamatoyannopoulos, J. Harrow, T. Hubbard, J. Dekker, A. Frankish, K. Salehi-Ashtiani, A. Reymond, S. Antonarakis, R. Guigó, T. Gingeras.

    Evidence for Transcript Networks composed of chimeric RNAs in human cells, in: PLoS One, 2011, to appear.
  • 10V. Duong, C. Simmons, L. Gavotte, A. Viari, S. Ong, N. Chantha, N. J. Lennon, B. W. Birren, S. Vong, J. J. Farrar, M. R. Henn, V. Deubel, R. Frutos, P. Buchy.

    Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia, in: Infect Genet Evol, Jul 2011.
  • 11J. Ferrari, F. Vavre.

    Bacterial symbionts in insects or the story of communities affecting communities, in: Philosophical Transactions of the Royal Society B-Biological Sciences, 2011, vol. 366, no 1569, p. 1389-1400. [ DOI : 10.1098/rstb.2010.0226 ]
  • 12M. Galardini, A. Mengoni, M. Brilli, F. Pini, A. Fioravanti, S. Lucas, A. Lapidus, J.-F. Cheng, L. Goodwin, S. Pitluck, M. Land, L. Hauser, T. Woike, N. Mikhailova, N. Ivanova, H. Daligault, D. Bruce, C. Detter, R. Tapia, C. Han, H. Teshima, S. Mocali, M. Bazzicalupo, E. G. Biondi.

    Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti, in: BMC Genomics, 2011, vol. 12. [ DOI : 10.1186/1471-2164-12-235 ]
  • 13R. A. Gutiérrez, A. Viari, B. Godelle, R. Frutos, P. Buchy.

    Biased mutational pattern and quasispecies hypothesis in H5N1 virus, in: Infect Genet Evol, Oct 2011.
  • 14K. Kraaijeveld, B. M. Reumer, L. Mouton, N. Kremer, F. Vavre, J. J. M. van Alphen.

    Does a parthenogenesis-inducing Wolbachia induce vestigial cytoplasmic incompatibility?, in: Naturwissenschaften, 2011, vol. 98, no 3, p. 175-180. [ DOI : 10.1007/s00114-010-0756-x ]
  • 15E. Lerat, N. Burlet, C. Biemont, C. Vieira.

    Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes, in: Gene, 2011, vol. 473, no 2, p. 100-109. [ DOI : 10.1016/j.gene.2010.11.009 ]
  • 16A. Morgat, E. Coissac, E. Coudert, K. B. Axelsen, G. Keller, A. Bairoch, A. Bridge, L. Bougueleret, I. Xenarios, A. Viari.

    UniPathway: a resource for the exploration and annotation of metabolic pathways, in: Nucleic Acids Res, Nov 2011.
  • 17A. Necsulea, A. Popa, D. N. Cooper, P. D. Stenson, D. Mouchiroud, C. Gautier, L. Duret.

    Meiotic Recombination Favors the Spreading of Deleterious Mutations in Human Populations, in: Human Mutation, 2011, vol. 32, no 2, p. 198-206. [ DOI : 10.1002/humu.21407 ]
  • 18L. Palmeira, S. Penel, V. Lotteau, C. Rabourdin-Combe, C. Gautier.

    PhEVER: a database for the global exploration of virus-host evolutionary relationships, in: Nucleic Acids Research, 2011, vol. 39, no Database issue, p. D569-75. [ DOI : 10.1093/nar/gkq1013 ]

    http://hal.inria.fr/hal-00562509/en
  • 19T. Riaz, W. Shehzad, A. Viari, F. Pompanon, P. Taberlet, E. Coissac.

    ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis, in: Nucleic Acids Res, Nov 2011, vol. 39, no 21, e145 p.
  • 20P. M. Simões, G. Mialdea, D. Reiss, M.-F. Sagot, S. Charlat.

    Wolbachia detection: an assessment of standard PCR Protocols, in: Molecular Ecology Resources, 2011, vol. 11, no 3, p. 567-572. [ DOI : 10.1111/j.1755-0998.2010.02955.x ]
  • 21 UniProt Consortium.

    Ongoing and future developments at the Universal Protein Resource, in: Nucleic Acids Res, Jan 2011, vol. 39, no Database issue, p. D214-9.
  • 22A. F. Vellozo, A. S. Véron, P. Baa-Puyoulet, J. Huerta-Cepas, L. Cottret, G. Febvay, F. Calevro, Y. Rahbé, A. E. Douglas, T. Gabaldón, M.-F. Sagot, H. Charles, S. Colella.

    CycADS: an annotation database system to ease the development and update of BioCyc databases, in: Database (Oxford), 2011, vol. 2011, bar008 p. [ DOI : 10.1093/database/bar008 ]

    http://hal.inria.fr/hal-00632965/en
  • 23J. Viñuelas, G. Febvay, G. Duport, S. Colella, J.-M. Fayard, H. Charles, Y. Rahbé, F. Calevro.

    Multimodal dynamic response of the Buchnera aphidicola pLeu plasmid to variations in leucine demand of its host, the pea aphid Acyrthosiphon pisum, in: Molecular Microbiology, 2011, vol. 81, no 5, p. 1271-1285. [ DOI : 10.1111/j.1365-2958.2011.07760.x ]
  • 24A. Véron, C. Lemaitre, C. Gautier, V. Lacroix, M.-F. Sagot.

    Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny, in: BMC Genomics, 2011, vol. 12, no 1, 303 p. [ DOI : 10.1186/1471-2164-12-303 ]

    http://hal.inria.fr/inserm-00617206/en

International Conferences with Proceedings

  • 25M. Federico, P. Peterlongo, N. Pisanti, M.-F. Sagot.

    Finding Long and Multiple Repeats with Edit Distance, in: The Prague Stringology Conference 2011, Prague, Czech Republic, 2011.

    http://hal.inria.fr/inria-00608208/en
  • 26T. Sacomoto, G. Akio, A. Pereira do Lago.

    A New Algorithm for Sparse Suffix Trees, in: Brazilian Symposium on Bioinformatics, O. Norberto de Souza, G. Telles, M. Palakal (editors), Lecture Notes in Computer Science, Springer, 2011, vol. 6832, p. 34-41.

Conferences without Proceedings

  • 27V. Acuña, E. Birmelé, L. Cottret, P. Crescenzi, F. Jourdan, V. Lacroix, A. Marchetti-Spaccamela, A. Marino, P. Vieira Milreu, M.-F. Sagot, L. Stougie.

    Telling Stories, in: ICALP 2011 satellite workshop: Graph Algorithms and Applications (GA), 2011, Talk.
  • 28P. Baa-Puyoulet, A. F. Vellozo, J. Huerta-Cepas, G. Febvay, T. Gabaldon, M.-F. Sagot, H. Charles, S. Colella.

    ArthropodaCyc: a BioCyc database powered by CycADS to study and compare the metabolism of arthropods, in: 5th Annual Arthropod Genomics Symposium “Arthropod Genomics 2011: Exploring Diversity, Relating Similarity”, 2011, Poster.
  • 29C. Baudet, Z. Dias.

    Partial Enumeration of Traces of Solutions for the Problem of Sorting by Signed Reversals, in: ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2011, Poster.
  • 30M.-C. Carpentier, J. Charif, V. Lacroix, M.-F. Sagot, F. Vavre.

    RNA-seq without a reference genome: a comparison of the mapping and the assembly approaches, in: JOBIM, 2011, Poster.
  • 31C. E. Ferreira, A. S. Freire, G. A. Puglia.

    A dynamic programming algorithm for the tree mapping problem, in: VI Latin-America Graphs and Algorithms Sysmposium (LAGOS), 2011, Talk.
  • 32P. Ivan, C. Klein, L. Cottret, A. T. Vasconcelos, A. Gales, M.-F. Sagot, M. Nicolás.

    Initial metabolic reconstruction of Klebsiella pneumoniae Kp13, a multidrug resistant pathogen involved in nosocomial outbreaks in Brazil, in: X-Meeting, 2011, Poster.
  • 33C. Klein, L. Cottret, H. Charles, C. Gautier, A. T. Vasconcelos, V. Lacroix, M.-F. Sagot.

    Metabolic network comparison of bacteria in the context of symbiosis, in: Otto Warburg International Summer School and Research Symposium on Evolutionary Genomics, 2011, Poster.
  • 34V. Lacroix.

    KisSplice : de-novo calling alternative splicing events from RNA-seq data, in: Groupement De Recherche Européen - Arc Rhône Alpin (GDRE-RA), 2011.

    http://gdrera.univ-lyon1.fr/
  • 35V. Lacroix.

    NGS without a reference genome, comparison and visualisation of non assembled data, in: Statistical Methods for Post-Genomic Data (SMPGD), 2011.

    http://smpgd2011.curie.fr/
  • 36A. Rabatel, G. Febvay, K. Gaget, G. Duport, N. Bendridi, Y. Rahbé, P. Baa-Puyoulet, H. Charles, F. Calevro, S. Colella.

    Integration of metabolic pathways and host regulation in symbiosis: tyrosine and cuticular protein biosynthesis during the pea aphid embryonic development, in: Sixth International Symposium on Molecular Insect Science, 2011, Poster.