EN FR
EN FR
BAMBOO - 2012
BAMBOO - 2012




Project-Team Bamboo
Members
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
Partnerships and Cooperations
Dissemination
Bibliography




Project-Team Bamboo
Members
Overall Objectives
Scientific Foundations
Application Domains
Software
New Results
Partnerships and Cooperations
Dissemination
Bibliography


previous Previous | up Home


Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

  • 1S. S. Abby, E. Tannier, M. Gouy, V. Daubin.

    Lateral gene transfer as a support for the tree of life., in: Proceedings of the National Academy of Sciences, March 2012, vol. 109, no 13, p. 4962-7. [ DOI : 10.1073/pnas.1116871109 ]

    http://hal.inria.fr/hal-00752055
  • 2V. Acuña, E. Birmelé, L. Cottret, P. Crescenzi, F. Jourdan, V. Lacroix, A. Marchetti-Spaccamela, A. Marino, P. V. Milreu, M.-F. Sagot, L. Stougie.

    Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets, in: Theoretical Computer Science (TCS), 2012, vol. 457, p. 1–9. [ DOI : 10.1016/j.tcs.2012.07.023 ]

    http://hal.inria.fr/hal-00764025
  • 3V. Acuña, P. V. Milreu, L. Cottret, A. Marchetti-Spaccamela, L. Stougie, M.-F. Sagot.

    Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks., in: Bioinformatics, October 2012, vol. 28, no 19, p. 2474-2483. [ DOI : 10.1093/bioinformatics/bts423 ]

    http://hal.inria.fr/hal-00751715
  • 4A. Akkouche, R. Rebollo, N. Burlet, C. Esnault, S. Martinez, B. Viginier, C. Terzian, C. Vieira, M. Fablet.

    tirant, a newly discovered active endogenous retrovirus in Drosophila simulans., in: J Virol, April 2012, vol. 86, no 7, p. 3675-81. [ DOI : 10.1128/JVI.07146-11 ]

    http://hal.inria.fr/hal-00763499
  • 5R. Alcântara, 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 Research, January 2012, vol. 40, no Database issue, p. D754-60. [ DOI : 10.1093/nar/gkr1126 ]

    http://hal.inria.fr/hal-00746861
  • 6J. Allali, C. Saule, C. Chauve, Y. D'Aubenton-Carafa, A. Denise, C. Drevet, P. Ferraro, D. Gautheret, C. Herrbach, F. Leclerc, A. De Monte, A. Ouangraoua, M.-F. Sagot, M. Termier, C. Thermes, H. Touzet.

    BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms, in: Advances in Bioinformatics, 2012.

    http://hal.inria.fr/hal-00647725
  • 7C. Baudet, Z. Dias, M.-F. Sagot.

    Sampling Solution Traces for the Problem of Sorting Permutations by Signed Reversals., in: Algorithms for Molecular Biology, June 2012, vol. 7, no 1, 18 p. [ DOI : 10.1186/1748-7188-7-18 ]

    http://hal.inria.fr/hal-00739414
  • 8T. Bernard, A. Bridge, A. Morgat, S. Moretti, I. Xenarios, M. Pagni.

    Reconciliation of metabolites and biochemical reactions for metabolic networks., in: Briefings in Bioinformatics, December 2012. [ DOI : 10.1093/bib/bbs058 ]

    http://hal.inria.fr/hal-00764412
  • 9S. Berthoumieux, M. Brilli, D. Kahn, H. De Jong, E. Cinquemani.

    On the identifiability of metabolic network models, in: Journal of Mathematical Biology, November 2012. [ DOI : 10.1007/s00285-012-0614-x ]

    http://hal.inria.fr/hal-00762620
  • 10S. Djebali, J. Lagarde, P. Kapranov, V. Lacroix, C. Borel, J. M. Mudge, C. Howald, S. Foissac, C. Ucla, J. Chrast, P. Ribeca, D. Martin, R. R. Murray, X. Yang, L. Ghamsari, C. Lin, I. Bell, E. Dumais, J. Drenkow, M. L. Tress, J. L. Gelpi, M. Orozco, A. Valencia, N. L. Van Berkum, B. R. Lajoie, M. Vidal, J. Stamatoyannopoulos, P. Batut, A. Dobin, J. Harrow, T. Hubbard, J. Dekker, A. Frankish, K. Salehi-Ashtiani, A. Reymond, S. E. Antonarakis, R. Guigó, T. R. Gingeras.

    Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells, in: PLoS ONE, 2012, vol. 7, p. 1-22.

    http://hal.inria.fr/hal-00698428
  • 11V. Duong, M. R. Henn, C. Simmons, C. Ngan, Y. Bunthin, L. Gavotte, A. Viari, S. Ong, R. Huy, N. J. Lennon, S. Ly, S. Vong, B. W. Birren, J. J. Farrar, V. Deubel, R. Frutos, P. Buchy.

    Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters., in: Infection, Genetics and Evolution, June 2012. [ DOI : 10.1016/j.meegid.2012.05.012 ]

    http://hal.inria.fr/hal-00763498
  • 12M. Frenkel-Morgenstern, A. Gorohovski, V. Lacroix, M. Rogers, K. Ibanez, C. Boullosa, E. Andres Leon, A. Ben-Hur, A. Valencia.

    ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data., in: Nucleic Acids Research, November 2012. [ DOI : 10.1093/nar/gks1041 ]

    http://hal.inria.fr/hal-00756097
  • 13M. Frenkel-Morgenstern, V. Lacroix, I. Ezkurdia, Y. Levin, A. Gabashvili, J. Prilusky, A. Del Pozo, M. L. Tress, R. Johnson, R. Guigó, A. Valencia.

    Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts., in: Genome Research, July 2012, vol. 22, no 7, p. 1231-42. [ DOI : 10.1101/gr.130062.111 ]

    http://hal.inria.fr/hal-00744761
  • 14T. Griebel, B. Zacher, P. Ribeca, E. Raineri, V. Lacroix, R. Guigó, M. Sammeth.

    Modelling and simulating generic RNA-Seq experiments with the flux simulator., in: Nucleic Acids Research, September 2012. [ DOI : 10.1093/nar/gks666 ]

    http://hal.inria.fr/hal-00744755
  • 15S. Kelk, B. G. Olivier, L. Stougie, F. J. Bruggeman.

    Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks., in: Nature Scientific Reports, 2012, vol. 2, 580 p. [ DOI : 10.1038/srep00580 ]

    http://hal.inria.fr/hal-00763439
  • 16S. Kelk, L. van Iersel, N. Lekic, S. Linz, C. Scornavacca, L. Stougie.

    Cycle killer... qu'est-ce que c'est? On the comparative approximability of hybridization number and directed feedback vertex set, in: Siam Journal on Discrete Mathematics, 2012, vol. 26, no 4, p. 1635-1656.

    http://hal.inria.fr/hal-00765019
  • 17C. Klein, L. Cottret, J. Kielbassa, H. Charles, C. Gautier, A. T. Vasconcelos, V. Lacroix, M.-F. Sagot.

    Exploration of the core metabolism of symbiotic bacteria., in: BMC Genomics, 2012, vol. 13, no 1. [ DOI : 10.1186/1471-2164-13-438 ]

    http://hal.inria.fr/hal-00737452
  • 18C. Klein, A. Marino, M.-F. Sagot, P. Vieira Milreu, M. Brilli.

    Structural and dynamical analysis of biological networks., in: Briefings in Functional Genomics, 2012. [ DOI : 10.1093/bfgp/els030 ]

    http://hal.inria.fr/hal-00737455
  • 19N. Kremer, D. Charif, H. Henri, F. Gavory, P. Wincker, P. Mavingui, F. Vavre.

    Influence of Wolbachia on host gene expression in an obligatory symbiosis., in: BMC Microbiology, January 2012, vol. 12 Suppl 1, S7 p. [ DOI : 10.1186/1471-2180-12-S1-S7 ]

    http://hal.inria.fr/hal-00763438
  • 20J. Martinez, A. Duplouy, M. Woolfit, F. Vavre, S. L. O'Neill, J. Varaldi.

    Influence of the virus LbFV and of Wolbachia in a host-parasitoid interaction., in: PLoS ONE, 2012, vol. 7, no 4, e35081. [ DOI : 10.1371/journal.pone.0035081 ]

    http://hal.inria.fr/hal-00763437
  • 21N. D. Mendes, S. Heyne, A. T. Freitas, M.-F. Sagot, R. Backofen.

    Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches., in: Bioinformatics, October 2012. [ DOI : 10.1093/bioinformatics/bts574 ]

    http://hal.inria.fr/hal-00752408
  • 22A. 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 Research, January 2012, vol. 40, no Database issue, D761-9. [ DOI : 10.1093/nar/gkr1023 ]

    http://hal.inria.fr/hal-00746856
  • 23I. Nor, D. Hermelin, S. Charlat, J. Engelstadter, M. Reuter, O. Duron, M.-F. Sagot.

    Mod/Resc Parsimony Inference: Theory and application, in: Information and Computation, 2012, vol. 213, p. 23-32. [ DOI : 10.1016/j.ic.2011.03.008 ]

    http://hal.inria.fr/hal-00763405
  • 24G. A. T. Sacomoto, J. Kielbassa, R. Chikhi, R. Uricaru, P. Antoniou, M.-F. Sagot, P. Peterlongo, V. Lacroix.

    KisSplice: de-novo calling alternative splicing events from RNA-seq data, in: BMC Bioinformatics, March 2012.

    http://hal.inria.fr/hal-00681995
  • 25D. Santos-Garcia, P.-A. Farnier, F. Beitia, E. Zchori-Fein, F. Vavre, L. Mouton, A. Moya, A. Latorre, F. J. Silva.

    Complete Genome Sequence of "Candidatus Portiera aleyrodidarum" BT-QVLC, an Obligate Symbiont That Supplies Amino Acids and Carotenoids to Bemisia tabaci., in: J Bacteriol, December 2012, vol. 194, no 23, p. 6654-6655. [ DOI : 10.1128/JB.01793-12 ]

    http://hal.inria.fr/hal-00763436
  • 26A. A. T. Smith, E. Belda, A. Viari, C. Medigue, D. Vallenet.

    The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes., in: PLoS Computational Biology, May 2012, vol. 8, no 5, e1002540. [ DOI : 10.1371/journal.pcbi.1002540 ]

    http://hal.inria.fr/hal-00763496
  • 27S. Sorn, T. Sok, S. Ly, S. Rith, N. Tung, A. Viari, L. Gavotte, D. Holl, H. Seng, N. Asgari, B. Richner, D. Laurent, N. Chea, V. Duong, T. Toyoda, C. Y. Yasuda, P. Kitsutani, P. Zhou, S. Bing, V. Deubel, R. Donis, R. Frutos, P. Buchy.

    Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade., in: Infection, Genetics and Evolution, June 2012. [ DOI : 10.1016/j.meegid.2012.05.013 ]

    http://hal.inria.fr/hal-00763497
  • 28F. Vavre, S. Charlat.

    Making (good) use of Wolbachia: what the models say., in: Curr Opin Microbiol, June 2012, vol. 15, no 3, p. 263-8. [ DOI : 10.1016/j.mib.2012.03.005 ]

    http://hal.inria.fr/hal-00763517
  • 29C. Vieira, M. Fablet, E. Lerat, M. Boulesteix, R. Rebollo, N. Burlet, A. Akkouche, B. Hubert, H. Mortada, C. Biémont.

    A comparative analysis of the amounts and dynamics of transposable elements in natural populations of Drosophila melanogaster and Drosophila simulans., in: Journal of Environmental Radioactivity, November 2012, vol. 113, p. 83-6. [ DOI : 10.1016/j.jenvrad.2012.04.001 ]

    http://hal.inria.fr/hal-00763500

International Conferences with Proceedings

  • 30H. Baumann, P. Crescenzi, P. Fraigniaud.

    Brief Announcement: Flooding in Dynamic Graphs with Arbitrary Degree Sequence, in: 26th International Symposium on Distributed Computing, Salvador, Brésil, 2012, p. 417-419.

    http://hal.inria.fr/hal-00763446
  • 31E. Birmelé, P. Crescenzi, R. Ferreira, R. Grossi, V. Lacroix, A. Marino, N. Pisanti, G. A. T. Sacomoto, M.-F. Sagot.

    Efficient Bubble Enumeration in Directed Graphs, in: SPIRE, Cartagena, Colombie, Lecture Notes in Computer Science, 2012, vol. 7608, p. 118-129. [ DOI : 10.1007/978-3-642-34109-0_13 ]

    http://hal.inria.fr/hal-00738927
  • 32S. Canzar, M. El-Kebir, R. Pool, K. M. Elbassioni, A. K. Malde, A. E. Mark, D. P. Geerke, L. Stougie, G. W. Klau.

    Charge Group Partitioning in Biomolecular Simulation, in: RECOMB, Lecture Notes in Computer Science, Springer, 2012, vol. 7262, p. 29-43.
  • 33P. Crescenzi, R. Grossi, L. Lanzi, A. Marino.

    On Computing the Diameter of Real-World Directed (Weighted) Graphs, in: 11th International Symposium on Experimental Algorithms, Bordeaux, France, 2012, p. 99-110.

    http://hal.inria.fr/hal-00763452
  • 34A. D. S. Freire, V. Acuña, P. Crescenzi, C. E. Ferreira, V. Lacroix, P. V. Milreu, E. Moreno, M.-F. Sagot.

    Minimum ratio cover of matrix columns by extreme rays of its induced cone, in: Proceedings of the Second international conference on Combinatorial Optimization, Athens, Grèce, Lecture Notes in Computer Science, Springer-Verlag, 2012, vol. 7422, p. 165–177. [ DOI : 10.1007/978-3-642-32147-4_16 ]

    http://hal.inria.fr/hal-00763455

Scientific Books (or Scientific Book chapters)

  • 35P. Ribeca, V. Lacroix, M. Sammeth, R. Guigó.

    Analysis of RNA Transcripts by High-Throughput RNA Sequencing, Wiley-VCH Verlag GmbH & Co. KGaA, 2012, p. 544–554. [ DOI : 10.1002/9783527636778.ch50 ]

    http://hal.inria.fr/hal-00750967


previous Previous | up Home