@comment{{This file has been generated by bib2bib 1.94}}
@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}
}
@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},
number = {19},
pages = {2664-2671},
year = {2011},
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},
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},
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},
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},
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},
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/no},
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 = {Jun},
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}
}
@phdthesis{SaffarianPhD11,
author = {Saffarian, Azadeh},
title = {{A}lgorithmes de pr\'ediction et de recherche de multi-structures d'{ARN}},
school = {Universit\'e Lille 1},
year = {2011}
}
This file was generated by bibtex2html 1.94.