Team Bamboo

Overall Objectives

Team Bamboo

Overall Objectives


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 ]

  • 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 ]

  • 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 ]


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.

  • 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.

  • 35V. Lacroix.

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

  • 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.