2007.bib

@comment{{This file has been generated by bib2bib 1.97}}
@comment{{Command line: bib2bib -oc cite2007 -ob 2007.bib 2007.bib}}
@article{TouzetVarreAMB07,
  author = {Touzet, H. and Varr\'e, J.-S.},
  title = {Efficient and accurate P-value computation for Position 
Weight Matrices},
  journal = {Algorithms for Molecular Biology},
  year = {2007},
  volume = {2},
  number = {15},
  doi = {10.1186/1748-7188-2-15},
  url = {http://www.almob.org/content/2/1/15},
  pdf = {http://www.almob.org/content/pdf/1748-7188-2-15.pdf},
  aeres = {ACL},
  selectif = {oui},
  labo = {dans},
  inria = {SEQUOIA}
}
@article{DidierDebomyPupinBMCBioinformatics07,
  title = {Comparing sequences without using alignments: application to 
{HIV}/{SIV} subtyping},
  author = {Didier, G. and Debomy, L. and Pupin, M. and Zhang, M. and 
Grossmann, A. and Devauchelle, C. and Laprevotte, I.},
  journal = {{BMC} Bioinformatics},
  year = {2007},
  volume = {8},
  number = {1},
  doi = {doi:10.1186/1471-2105-8-1},
  url = {http://www.biomedcentral.com/1471-2105/8/1},
  pdf = {http://www.biomedcentral.com/content/pdf/1471-2105-8-1.pdf},
  aeres = {ACL},
  selectif = {oui},
  labo = {dans},
  inria = {SEQUOIA}
}
@article{TouzetJDA07,
  author = {Touzet, H.},
  title = {Comparing similar ordered trees in linear-time},
  journal = {Journal of Discrete Algorithms},
  volume = {5},
  number = {4},
  pages = {696-705},
  year = {2007},
  doi = {10.1016/j.jda.2006.07.002},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S1570866706000700},
  aeres = {ACL},
  selectif = {oui},
  labo = {dans},
  inria = {SEQUOIA}
}
@inbook{TouzetHUMANA07,
  author = {Touzet, H.},
  year = {2007},
  pages = {465-473},
  editor = {N. Bergman},
  title = {Comparative analysis of {RNA} genes: the {C}a{RNA}c software},
  publisher = {Humana Press},
  volume = {Methods in Molecular Biology,  Special issue on comparative genomics I},
  pdf = {http://hal.archives-ouvertes.fr/docs/00/17/85/57/PDF/comparativerna.pdf},
  doi = {10.1007/978-1-59745-514-5_29},
  aeres = {ACL},
  selectif = {oui},
  labo = {dans},
  inria = {SEQUOIA}
}
@inproceedings{FontaineTouzetBIBM07,
  author = {Fontaine, Arnaud and Touzet, H{\'e}l{\`e}ne},
  title = {Computational identification of protein-coding sequences by comparative analysis},
  booktitle = {Proceedings of the 1st {IEEE} international conference on
  {B}ioinformatics and {B}iomedecine ({BIBM}), Silicon Valley, California},
  year = {2007},
  pages = {95--102},
  publisher = {IEEE Computer Society},
  url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=4413018&arnumber=4413042&count=71&index=23},
  doi = {10.1109/BIBM.2007.11},
  pdf = {http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=4413042&isnumber=4413018},
  aeres = {ACT},
  selectif = {oui},
  labo = {dans},
  inria = {SEQUOIA}
}
@inproceedings{CabocheEtAlSFM07,
  author = {S{\'e}gol{\`e}ne Caboche and Val{\'e}rie Lecl{\`e}re and Maude Pupin and Gregory Kucherov and Philippe Jacques},
  booktitle = {septi{\`e}me congr{\'e}s de la Soci{\'e}t{\'e} Francaise de Microbiologie ({SFM})},
  title = {Norine: une nouvelle base de donn{\'e}es qui met en exergue la biodiversit{\'e} des structures et des activit{\'e}s des peptides synth{\'e}tis{\'e}s  par la voie non-ribosomale ({NRPS})},
  year = {2007},
  note = {(poster)},
  aeres = {AFF},
  selectif = {non},
  labo = {dans},
  inria = {SEQUOIA}
}
@article{CabocheEtAlNAR07,
  title = {{NORINE}: a database of nonribosomal peptides},
  author = {S{\'e}gol{\`e}ne Caboche and Maude Pupin and Val{\'e}rie Lecl{\`e}re and Arnaud Fontaine and Philippe Jacques and Gregory Kucherov},
  journal = {Nucleic Acids Research},
  year = {2007},
  doi = {10.1093/nar/gkm792},
  url = {http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D326},
  pdf = {http://nar.oxfordjournals.org/cgi/reprint/36/suppl_1/D326},
  aeres = {ACL},
  selectif = {oui},
  labo = {dans},
  inria = {SEQUOIA}
}
@inproceedings{KucherovNoeRoytbergCIAA07,
  author = {Kucherov, G. and No{\'e}, L. and Roytberg, M.},
  title = {Subset Seed Automaton},
  booktitle = {Proceedings of the  12th International Conference on
Implementation and Application of Automata ({CIAA}), Prague (Czech Republic), July 16-18, 2007},
  pages = {180--191},
  year = {2007},
  editor = {Holub, J. and Zdarek, J.},
  volume = {4783},
  url = {http://www.springerlink.com/content/y824l20554002756/},
  pdf = {http://www.lifl.fr/~noe/files/pp_CIAA07.pdf},
  postscript = {http://www.lifl.fr/~noe/files/pp_CIAA07.ps.gz},
  doi = {10.1007/978-3-540-76336-9_18},
  series = {Lecture Notes in Computer Science},
  publisher = {Springer Verlag},
  aeres = {ACT},
  selectif = {oui},
  labo = {dans},
  inria = {SEQUOIA}
}
@article{GiraudVeberLavenierIJFCS07,
  author = {Mathieu Giraud and Philippe Veber and Dominique Lavenier},
  title = {Path-Equivalent Developments in Acyclic Weighted Automata},
  journal = {International Journal of Foundations of Computer Science},
  number = {4},
  pages = {799-812},
  volume = {18},
  year = {2007},
  doi = {10.1142/S012905410700498X},
  pdf = {http://www.lifl.fr/~giraud/publis/gvl-ijfcs-07-preprint.pdf},
  aeres = {ACL},
  inria = {Sequoia},
  labo = {dans}
}
@inproceedings{PeterlongoEtAlPBC07,
  author = {Pierre Peterlongo and Laurent No{\'e} and Dominique Lavenier and Gil
les Georges and Julien Jacques and Gregory Kucherov and Mathieu Giraud},
  booktitle = {Parallel Processing and Applied Mathematics / Parallel Biocomputi
ng Conference (PPAM / PBC 07)},
  editor = {Wyrzykowski, R. and Dongarra, J. and Karczewski, K. and Wasniewski, 
J.},
  selectif = {non},
  aeres = {ACT},
  inria = {Sequoia},
  labo = {dans},
  pages = {1240-1248},
  series = {Lecture Notes in Computer Science (LNCS)},
  title = {Protein similarity search with subset seeds on a dedicated reconfigur
able hardware},
  doi = {10.1007/978-3-540-68111-3},
  pdf = {http://www.lifl.fr/~giraud/publis/peterlongo-pbc-07.pdf},
  url = {http://www.springerlink.com/content/2280v0131631528r/},
  volume = {4967},
  year = {2008}
}
@inproceedings{DuchesneGiraudMabroukCOCOON07,
  author = {Jean-Eudes Duchesne and Mathieu Giraud and Nadia El Mabrouk},
  booktitle = {International Computing and Combinatorics Conference ({COCOON})},
  doi = {10.1007/978-3-540-73545-8_6},
  pages = {27-39},
  publisher = {Springer},
  series = {Lecture Notes in Computer Science},
  title = {Seed-based exclusion method for non-coding RNA gene search},
  pdf = {http://www.lifl.fr/~giraud/publis/dgem-cocoon-07-lncs.pdf},
  doi = {10.1007/978-3-540-73545-8_6},
  url = {http://www.springerlink.com/content/r2n71753j7q5mm07/},
  volume = {4598},
  year = {2007},
  aeres = {ACT},
  inria = {Sequoia},
  labo = {dans},
  selectif = {oui}
}
@inproceedings{FontaineEtAlJOBIM07,
  author = {Arnaud Fontaine and Mathieu Giraud and Laurent No{\'e} and H{\'e}l{\`e}ne Touzet},
  booktitle = {Journ{\'e}es Ouvertes Biologie Informatique Math{\'e}matiques ({JOBIM})},
  title = {Graines espac{\'e}es et recherche d'{ARN} non-codants},
  year = {2007},
  note = {(poster)},
  pdf = {http://www.lifl.fr/~fontaina/fontaine-yass-rna-jobim07.pdf},
  aeres = {AFF},
  inria = {Sequoia},
  labo = {dans}
}
@article{GrzebelusEtAlBMCGenomics07,
  author = {Grzebelus, D. and Lasota, L. and Gambin, T. and Kucherov, G. and Gambin, A.},
  title = {Diversity and structure of {PIF}/{H}arbinger-like elements in the genome of {\em Medicago truncatula}},
  journal = {BMC Genomics},
  year = {2007},
  volume = {8},
  number = {409},
  doi = {10.1186/1471-2164-8-409},
  url = {http://www.biomedcentral.com/1471-2164/8/409/},
  pdf = {http://www.biomedcentral.com/content/pdf/1471-2164-8-409.pdf},
  aeres = {ACL},
  selectif = {oui},
  labo = {dans},
  inria = {SEQUOIA}
}
@article{CsurosNoeKucherovTiG07,
  author = {Cs\"{u}r\"{o}s, M. and No\'{e}, L. and Kucherov, G.},
  title = {Reconsidering the significance of genomic word frequencies},
  journal = {Trends in Genetics},
  year = {2007},
  volume = {23},
  number = {11},
  pages = {543--546},
  month = {November},
  doi = {doi:10.1016/j.tig.2007.07.008},
  pdf = {http://www.iro.umontreal.ca/~csuros/papers/spectrum-DPL-full.pdf},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S0168952507002983},
  aeres = {ACL},
  selectif = {oui},
  labo = {dans},
  inria = {SEQUOIA}
}
@inproceedings{FontaineTouzetBBC07,
  author = {Fontaine, A. and Touzet, H.},
  title = {Identification of protein-coding genes and {RNA} genes by comparative analysis},
  booktitle = {Benelux Bioinformatics Conference ({BBC})},
  year = {2007},
  pdf = {http://www.lifl.fr/~fontaina/bbc07.pdf},
  note = {(poster)}
}
@misc{MANCHERON2007a,
  author = {Alban Mancheron and Jean-\'Emile Symphor},
  title = {{Finding Frequent Subsequences in a Set of Texts}},
  url = {http://hal.inria.fr/inria-00257561/fr/},
  pdf = {http://hal.archives-ouvertes.fr/docs/00/25/75/61/PDF/CSAq.pdf},
  year = {2007},
  howpublished = {HAL}
}
@misc{MANCHERON2007b,
  author = {Alban Mancheron and Jean-\'Emile Symphor},
  title = {{On-line \& Incremental Update Properties of the
                  Subsequence Automaton}},
  url = {http://hal.inria.fr/inria-00257567/fr/},
  pdf = {http://hal.archives-ouvertes.fr/docs/00/25/75/67/PDF/iSA.pdf},
  year = {2007},
  howpublished = {HAL}
}

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