2005.bib

@comment{{This file has been generated by bib2bib 1.97}}
@comment{{Command line: bib2bib -oc cite2005 -ob 2005.bib 2005.bib}}
@inproceedings{BouvelGrebinskiKucherovWG05,
  author = {Bouvel, M. and Grebinski, V. and Kucherov, G.},
  title = {Combinatorial search on graphs motivated by bioinformatics applicaitons: a brief survey},
  booktitle = {Proceedings of the  31st International Workshop on
  Graph-Theoretic Concepts in Computer Science (WG), Metz (France), June 23-25, 2005},
  pages = {16--27},
  year = {2005},
  editor = {Kratsch, D.},
  volume = {3787},
  series = {Lecture Notes in Computer Science},
  publisher = {Springer Verlag},
  doi = {doi:10.1007/11604686},
  url = {http://www.springerlink.com/content/7715g48783482846/},
  pdf = {http://www.springerlink.com/content/7715g48783482846/fulltext.pdf}
}
@inproceedings{Giraud05:cible,
  author = {Mathieu Giraud and Pascale Quignon and {\'E}lodie Retout
                  and Emmanuelle Morin and Anne-Sophie Valin and
                  Dominique Lavenier and Maud Rimbault and Francis
                  Galibert and Jacques Nicolas},
  title = {Assemblage cibl{\'e} : recherche d'une famille de g{\`e}nes
                  sur un g{\'e}nome non assembl{\'e}},
  booktitle = {Journ{\'e}es Ouvertes Biologie Informatique
                  Math{\'e}matiques (JOBIM 2005)},
  year = 2005
}
@inproceedings{Giraud05:majecstic,
  author = {Mathieu Giraud and Laurent No{\'e} and Gregory Kucherov
                  and Dominique Lavenier},
  title = {Recherches de motifs et de similarit{\'e}s en
                  bioinformatique : mod{\'e}lisations, solutions
                  logicielles et mat{\'e}rielles},
  booktitle = {MajecSTIC},
  year = 2005
}
@inproceedings{Tempel05:jobim,
  author = {S{\'e}bastien Tempel and Mathieu Giraud and Isra\"el-C{\'e}sar
                  Lerman and Ivab Cou{\'e}e and Abdelhak El Amrani and
                  Jacques Nicolas},
  title = {Domain Organization within repeated {DNA} sequences
                  : Application to the study of a new family of
                  transposable elements in Arabidopsis thaliana},
  booktitle = {poster pour JOBIM 2005},
  year = 2005
}
@inbook{Lavenier05:springer,
  author = {Dominique Lavenier and Mathieu Giraud},
  editor = {Maya B. Gokhale and Paul S. Graham},
  title = {Reconfigurable Computing},
  titlecite = {Reconfigurable Computing \cite{Gokhale05:springer}},
  chapter = {Bioinformatics Applications},
  publisher = {Springer},
  year = 2005,
  doi = {10.1007/0-387-26106-0_8},
  url = {http://www.springerlink.com/content/u67454g462252nu2/},
  pdf = {http://dx.doi.org/10.1007/0-387-26106-0_8}
}
@article{Guyetant05:pc,
  author = {St{\'e}phane Guyetant and Mathieu Giraud and Ludovic
                  L'Hours and Steven Derrien and St{\'e}phane Rubini and
                  Dominique Lavenier and Fr{\'e}d{\'e}ric Raimbault},
  title = {Cluster of Re-configurable Nodes for Scanning Large
                  Genomic Banks},
  journal = {Parallel Computing},
  year = 2005,
  volume = 31,
  number = 1,
  pages = {73--96},
  doi = {10.1016/j.parco.2004.12.005},
  url = {http://dx.doi.org/10.1016/j.parco.2004.12.005}
}
@article{Quignon05:or,
  author = {Pascale Quignon and Mathieu Giraud and Maud Rimbault
                  and Patricia Lavigne and Sandrine Tacher and
                  Emmanuelle Morin and {\'E}lodie Retout and Anne-Sophie
                  Valin and Kerstin Lindblad-Toh and Jacques Nicolas
                  and Francis Galibert},
  title = {The dog and rat olfactory receptor repertoires},
  journal = {Genome Biology},
  volume = 6,
  year = 2005,
  number = 10,
  pages = {R83},
  doi = {10.1186/gb-2005-6-10-r83},
  url = {http://genomebiology.com/2005/6/10/R83},
  pdf = {http://dx.doi.org/10.1186/gb-2005-6-10-r83}
}
@article{Giraud05:jalc,
  author = {Mathieu Giraud and Dominique Lavenier},
  title = {Dealing with hardware space limits when removing
                  epsilon-transitions in a genomic weighted finite
                  automaton},
  journal = {Journal of Automata, Languages and Combinatorics},
  volume = {10},
  number = {2/3},
  year = {2005},
  postscript = {http://www.lifl.fr/~giraud/publis/jalc-preprint.ps.gz}
}
@inproceedings{CPM05,
  title = {A linear tree edit distance algorithm for similar ordered trees},
  author = {Touzet, H.},
  booktitle = {(CPM)},
  series = {Lecture Notes in Computer Science},
  publisher = {Springer Verlag},
  volume = {3537},
  pages = {334-345},
  year = {2005},
  doi = {10.1186/gb-2005-6-10-r83},
  url = {http://www.springerlink.com/content/jmh4t77ge4ach0y0/},
  pdf = {http://www.lifl.fr/~touzet/Publications/cpm05touzet.pdf}
}
@inproceedings{FT05,
  title = {How to detect non-coding {RNA}s ?},
  author = {Fontaine, A. and Touzet, H.},
  booktitle = {{JOBIM}},
  pdf = {http://www.lifl.fr/~touzet/Publications/detection.pdf},
  year = {2005}
}
@article{DT05,
  title = {Decomposition algorithms for the tree edit distance problem},
  author = {Dulucq S. and Touzet H.},
  journal = {Journal of Discrete Algorithms},
  volulme = {3(2-4)},
  year = {2005},
  pages = {448-471},
  doi = {10.1016/j.jda.2004.08.018},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S1570866704000656},
  pdf = {http://www.lifl.fr/~touzet/Publications/touzetdulucq.pdf}
}
@phdthesis{touzet:hdr,
  title = {Structures combinatoires pour l'analyse de g{\'e}nomes},
  author = {Touzet, H.},
  school = {Universit\'e des Sciences et Technologies de Lille},
  year = {2005},
  pdf = {http://www.lifl.fr/~touzet/Publications/hdrtouzet.pdf}
}
@inproceedings{KucherovNoeRoytbergWABI05,
  author = {Kucherov, G. and No{\'e}, L. and Roytberg, M.},
  title = {A unifying framework for seed sensitivity and its application to subset seeds},
  booktitle = {Proceedings of the 5th International Workshop in Algorithms in Bioinformatics (WABI),  Mallorca (Spain)},
  pages = {251--263},
  year = {2005},
  editor = {Casadio, R and Myers, G},
  volume = {3692},
  series = {Lecture Notes in Computer Science},
  publisher = {Springer Verlag},
  url = {http://www.springerlink.com/content/72384x40t0v2j254/},
  pdf = {http://www.lifl.fr/~noe/files/pp_WABI05.pdf},
  postscript = {http://www.lifl.fr/~noe/files/pp_WABI05.ps.gz},
  doi = {10.1007/11557067_21}
}
@article{NoeKucherovNAR05,
  author = {No{\'e}, L. and Kucherov, G.},
  title = {{YASS}: enhancing the sensitivity of {DNA} similarity search},
  journal = {Nucleic Acids Research},
  year = {2005},
  volume = {33 (web-server issue)},
  pages = {W540--W543},
  doi = {10.1093/nar/gki478},
  pdf = {http://nar.oxfordjournals.org/cgi/reprint/33/suppl_2/W540.pdf},
  url = {http://nar.oxfordjournals.org/cgi/content/short/33/suppl_2/W540}
}
@article{KucherovNoeRoytbergTCBB05,
  author = {Kucherov, G. and No{\'e}, L. and Roytberg, M.},
  title = {Multiseed lossless filtration},
  journal = {IEEE Transactions on Computational Biology and Bioinformatics (TCBB)},
  pages = {51 -- 61},
  year = {2005},
  volume = {2},
  number = {1},
  doi = {10.1109/TCBB.2005.12},
  url = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2005.12},
  pdf = {http://www.lifl.fr/~noe/files/pp_TCBB05_preprint.pdf},
  postscript = {http://www.lifl.fr/~noe/files/pp_TCBB05_preprint.ps.gz}
}
@phdthesis{NoePHD05,
  author = {No{\'e},L},
  title = {Recherche de similarit{\'e}s dans les s{\'e}quences d'ADN:
                  mod{\`e}les et algorithmes pour la conception de graines efficaces},
  school = {Universit{\'e} Henri Poincar{\'e} - Nancy},
  year = {2005},
  pdf = {http://www.lifl.fr/~noe/files/phd.pdf},
  postscript = {http://www.lifl.fr/~noe/files/phd.ps.gz}
}
@article{cvl+05,
  title = {Evolution of plant-like crystalline storage polysaccharide in the protozoan parasite Toxoplasma gondii argues for a red alga ancestry},
  author = {Coppin, A. and Varr{\'e}, J.-S.  and Lienard, L. and Dauvill{\'e}e, D. and Gu{\'e}rardel, Y. and Soyer-Gobillard, M.-O.and Bul{\'e}on, A. and  Ball, S. and  Tomavo, S.},
  journal = {Journal of Molecular Evolution},
  volume = {60},
  number = {2},
  pages = {257-267},
  year = {2005},
  doi = {10.1007/s00239-004-0185-6},
  url = {http://www.springerlink.com/content/g25w0m32tl617376/},
  pdf = {http://www.springerlink.com/content/g25w0m32tl617376/fulltext.pdf}
}

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