2011.bib

@comment{{This file has been generated by bib2bib 1.97}}
@comment{{Command line: bib2bib -oc cite2011 -ob 2011.bib 2011.bib}}
@article{giraud:2011:hal-00623404:1,
  author = {Giraud, Mathieu and Varr{\'e}, Jean-St{\'e}phane},
  title = {{Parallel Position Weight Matrices Algorithms}},
  journal = {{Parallel Computing}},
  volume = {37},
  pages = {466-478},
  year = {2011},
  doi = {10.1016/j.parco.2010.10.001},
  x-international-audience = {yes},
  x-editorial-board = {yes},
  url = {http://hal.inria.fr/hal-00623404/en},
  x-id-hal = {hal-00623404}
}
@article{gambin:2011:inria-00609791:1,
  author = {Gambin, Anna and Lasota, Slawomir and Startek, Michal and Sykulski, Maciej and No{\'e}, Laurent and Kucherov, Gregory},
  x-pays = {PL},
  title = {{Subset seed extension to Protein BLAST}},
  journal = {{Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2011)}},
  publisher = {SciTePress},
  pages = {149-158},
  year = {2011},
  doi = {10.5220/0003147601490158},
  x-international-audience = {yes},
  x-editorial-board = {yes},
  url = {http://hal.inria.fr/inria-00609791/en},
  x-id-hal = {inria-00609791}
}
@article{thomas:2011:inria-00635003:1,
  author = {Thomas, Antoine and Varr{\'e}, Jean-St{\'e}phane and Ouangraoua, A{\"\i}da},
  title = {{Genome Dedoubling by DCJ and Reversal}},
  journal = {{BMC Bioinformatics}},
  publisher = {BioMed Central},
  volume = {12},
  number = {Suppl 9},
  pages = {S20},
  year = {2011},
  note = {Proceedings of the Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics},
  x-international-audience = {yes},
  x-editorial-board = {yes},
  url = {http://hal.inria.fr/inria-00635003/en},
  x-id-hal = {inria-00635003},
  doi = {10.1186/1471-2105-12-S9-S20}
}
@article{ouangraoua:2011:inria-00635016:1,
  author = {Ouangraoua, A{\"\i}da and Tannier, Eric and Chauve, Cedric},
  x-pays = {CA},
  title = {{Reconstructing the architecture of the ancestral amniote genome.}},
  journal = {{Bioinformatics}},
  publisher = {Oxford University Press},
  volume = {27},
  number = {19},
  pages = {2664-2671},
  year = {2011},
  doi = {10.1093/bioinformatics/btr461},
  x-international-audience = {yes},
  x-editorial-board = {yes},
  url = {http://hal.inria.fr/inria-00635016/en},
  x-id-hal = {inria-00635016}
}
@article{ouangraoua:2011:inria-00635025:1,
  author = {Ouangraoua, A{\"\i}da and Swenson, Krister and Chauve, Cedric},
  x-pays = {CA},
  title = {{A 2-Approximation for the Minimum Duplication Speciation Problem}},
  journal = {{Journal of Computational Biology}},
  publisher = {Mary Ann Lieber},
  volume = {18},
  number = {9},
  pages = {1041-1053},
  year = {2011},
  doi = {10.1089/cmb.2011.0108},
  x-international-audience = {yes},
  x-editorial-board = {yes},
  url = {http://hal.inria.fr/inria-00635025/en},
  x-id-hal = {inria-00635025}
}
@article{ouangraoua:2011:inria-00635033:1,
  author = {Ouangraoua, A{\"\i}da and Bergeron, Anne and Swenson, Krister},
  x-pays = {CA},
  title = {{Theory and practice of ultra-perfection}},
  journal = {{Journal of Computational Biology}},
  publisher = {Mary Ann Liebert},
  volume = {18},
  number = {9},
  pages = {1219-1230},
  year = {2011},
  doi = {10.1089/cmb.2011.0086},
  x-international-audience = {yes},
  x-editorial-board = {yes},
  url = {http://hal.inria.fr/inria-00635033/en},
  x-id-hal = {inria-00635033}
}
@article{ouangraoua:2011:inria-00635043:1,
  author = {Ouangraoua, A{\"\i}da and Guignon, Valentin  and Hamel, Sylvie and Chauve, Cedric},
  x-pays = {CA},
  title = {{A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes}},
  journal = {{Theoretical Computer Science}},
  publisher = {Elsevier},
  volume = {412},
  number = {8-10},
  pages = {753-764},
  year = {2011},
  doi = {10.1016/j.tcs.2010.11.020},
  x-international-audience = {yes},
  x-editorial-board = {yes},
  url = {http://hal.inria.fr/inria-00635043/en},
  x-id-hal = {inria-00635043}
}
@article{leonard:2011:inria-00636066:1,
  author = {L{\'e}onard, Martine and Mouchard, Laurent and Salson, Mika{\"e}l},
  title = {{On the number of elements to reorder when updating a suffix array}},
  journal = {{Journal of Discrete Algorithms}},
  publisher = {Elsevier},
  year = {2011},
  month = jan,
  doi = {10.1016/j.jda.2011.01.002},
  x-international-audience = {yes},
  x-editorial-board = {yes},
  url = {http://hal.inria.fr/inria-00636066/en},
  x-id-hal = {inria-00636066}
}
@article{blanquart:2011:inria-00636084:1,
  author = {Blanquart, Samuel and Gascuel, Olivier},
  title = {{Mitochondrial genes support a common origin of Plasmodium falciparum and relatives with rodent malaria parasites.}},
  journal = {{BMC Evolutionary Biology}},
  publisher = {BMC},
  year = {2011},
  month = mar,
  x-international-audience = {yes},
  x-editorial-board = {yes},
  url = {http://hal.inria.fr/inria-00636084/en},
  doi = {10.1186/1471-2148-11-70},
  x-id-hal = {inria-00636084}
}
@inproceedings{leve:2011:hal-00636058:1,
  author = {Lev{\'e}, Florence and Groult, Richard and Arnaud, Guillaume and S{\'e}guin, Cyril and Gaymay, R{\'e}mi and Giraud, Mathieu},
  title = {{Rhythm extraction from polyphonic symbolic music}},
  booktitle = {{12th International Society for Music Information Retrieval Conference (ISMIR 2011)}},
  year = {2011},
  pages = {375-380},
  address = {United States},
  x-international-audience = {yes},
  x-proceedings = {yes},
  url = {http://hal.inria.fr/hal-00636058/en},
  x-id-hal = {hal-00636058}
}
@inproceedings{giraud:2011:inria-00623390:1,
  author = {Giraud, Mathieu and Janot, St{\'e}phane and Berthelot, Jean-Fr{\'e}d{\'e}ric and Deltel, Charles and Jourdan, Laetitia and Lavenier, Dominique and Touzet, Helene and Varr{\'e}, Jean-St{\'e}phane},
  title = {{Biomanycores, open-source parallel code for many-core bioinformatics}},
  booktitle = {{Bioinformatics Open Source Conference (BOSC 2011)}},
  year = {2011},
  address = {Vienne, Austria},
  x-international-audience = {yes},
  x-proceedings = {no},
  url = {http://hal.inria.fr/inria-00623390/en},
  x-id-hal = {inria-00623390}
}
@inproceedings{tran:2011:inria-00637227:1,
  author = {Tran, Tuan Tu and Giraud, Mathieu and Varr{\'e}, Jean-St{\'e}phane},
  title = {{Bit-Parallel Multiple Pattern Matching}},
  booktitle = {{Parallel Processing and Applied Mathematics / Parallel Biocomputing Conference (PPAM / PBC 11)}},
  year = {2011},
  address = {Torun, Poland},
  doi = {10.1007/978-3-642-31500-8_30},
  x-international-audience = {yes},
  x-proceedings = {yes},
  url = {http://hal.inria.fr/inria-00637227/en},
  x-id-hal = {inria-00637227}
}
@inproceedings{berthelot:2011:hal-00637847:1,
  author = {Berthelot, Jean-Fr{\'e}d{\'e}ric and Deltel, Charles and Giraud, Mathieu and Janot, St{\'e}phane and Jourdan, Laetitia and Lavenier, Dominique and Touzet, Helene and Varr{\'e}, Jean-St{\'e}phane},
  title = {{biomanycores.org: a repository of interoperable open-source code for many-core bioinformatics}},
  year = {2011},
  month = jul,
  booktitle = {{JOBIM 2011}},
  address = {Paris, France},
  x-international-audience = {no},
  x-proceedings = {no},
  url = {http://hal.inria.fr/hal-00637847/en},
  x-id-hal = {hal-00637847}
}
@incollection{varre:2011:hal-00563408:1,
  author = {Varr{\'e}, Jean-St{\'e}phane and Schmidt, Bertil and Janot, St{\'e}phane and Giraud, Mathieu},
  x-pays = {SG},
  title = {{Manycore high-performance computing in bioinformatics}},
  year = {2011},
  booktitle = {{Advances in Genomic Sequence Analysis and Pattern Discovery}},
  editor = {Laura Elnitski and Helen Piontkivska and Lonnie R Welch},
  publisher = {World Scientific},
  pages = {chapter 8},
  x-international-audience = {yes},
  url = {http://hal.inria.fr/hal-00563408/en},
  x-id-hal = {hal-00563408}
}
@article{philippe:2011:lirmm-00632958:1,
  author = {Philippe, Nicolas and Salson, Mika{\"e}l and Lecroq, Thierry and L{\'e}onard, Martine and Commes, Th{\'e}r{\`e}se and Rivals, Eric},
  title = {{Querying Large Read Collections in Main Memory: A Versatile data Structure}},
  journal = {{BMC Bioinformatics}},
  volume = {12},
  pages = {242+},
  year = {2011},
  month = {June},
  doi = {10.1186/1471-2105-12-242},
  x-international-audience = {yes},
  x-editorial-board = {yes},
  url = {http://hal.inria.fr/lirmm-00632958/en},
  x-id-hal = {lirmm-00632958}
}
@article{touzet:2011:RNAspace,
  author = {Cros, Marie-Jos{\'e}e and de Monte, Antoine and Mariette, J{\'e}r{\oe}me and Bardou, Philippe and Grenier-Boley, Benjamin and Gautheret, Daniel and Touzet, Helene and Gaspin, Christine},
  title = {{RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA}},
  journal = {{RNA}},
  volume = {17},
  pages = {1947-1956},
  year = {2011},
  month = {September},
  x-international-audience = {yes},
  x-editorial-board = {yes},
  url = {http://rnajournal.cshlp.org/content/17/11/1947.long},
  doi = {10.1261/rna.2844911}
}
@phdthesis{saffarian:tel-00832700,
  hal_id = {tel-00832700},
  url = {http://tel.archives-ouvertes.fr/tel-00832700},
  title = {{Algorithmes de pr{\'e}diction et de recherche de multi-structures d'ARN}},
  author = {Saffarian, Azadeh},
  affiliation = {Laboratoire d'Informatique Fondamentale de Lille - LIFL , BONSAI - INRIA Lille - Nord Europe},
  school = {Universit{\'e} Lille 1},
  type = {THESE},
  year = {2011},
  month = nov,
  pdf = {http://tel.archives-ouvertes.fr/tel-00832700/PDF/phd-azadeh-saffarian.pdf}
}

This file was generated by bibtex2html 1.97.