@INPROCEEDINGS{BlinTouzetSPIRE06,
  author = {Blin, G. and Touzet, H.},
  title = {How to Compare Arc-Annotated Sequences: The Alignment Hierarchy},
  booktitle = {13th International Symposium on String Processing and Information Retrieval (SPIRE)},
  pages = {291--303},
  year = {2006},
  volume = {4209},
  series = {Lecture Notes in Computer Science},
  publisher = {Springer Verlag},
  doi = {10.1007/11880561_24},
  url = {http://www.springerlink.com/content/4k37q116j2720832/}
}

@ARTICLE{TouzetJDA06,
  author = {Touzet, H.},
  title = {Comparing similar ordered trees in linear-time},
  journal = {Journal of Discrete Algorithms},
  year = {2006},
  doi = {10.1016/j.jda.2006.07.002},
  url = {http://dx.doi.org/10.1016/j.jda.2006.07.002}
}

@INBOOK{TouzetHUMANA06,
  author = {H. Touzet},
  year = {2006},
  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},
  note = {in press}
}

@INPROCEEDINGS{LiefoogheTouzetVarreCPM06, 
  author = {Liefooghe, A. and Touzet, H. and Varr{\'e}, J.-S.},
  title = {Large Scale Matching for Position Weight Matrices.},
  booktitle = {Proceedings 17th Annual Symposium on Combinatorial Pattern Matching (CPM)},
  pages = {401--412},
  year = {2006},
  volume = {4009},
  series = {Lecture Notes in Computer Science},
  publisher = {Springer Verlag},
  doi = {doi:10.1007/11780441_36},
  url = {http://www.springerlink.com/content/7113757vj6205067/},
  pdf = {http://www.springerlink.com/content/7113757vj6205067/fulltext.pdf}
}

@ARTICLE{DefranceTouzetBMC06,
  title = {Predicting transcription factor binding sites using local over-representation and comparative genomics},
  author = {Defrance, M. and Touzet, H.},
  journal = {{BMC} Bioinformatics},
  year = {2006},
  doi = {doi:10.1186/1471-2105-7-396},
  url = {http://www.biomedcentral.com/1471-2105/7/396/abstract}
}

@INPROCEEDINGS{TouzetCPM05,
  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},
  url = {http://dx.doi.org/10.1007/11496656_29},
}

@INPROCEEDINGS{FTJOBIM05,
  title = {How to detect non-coding {RNA}s ?},
  author = {Fontaine, A. and Touzet, H.},
  booktitle = {{JOBIM}},
  year = {2005}
}

@ARTICLE{DulucqTouzetJDA05,
  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},
  url = {http://dx.doi.org/10.1016/j.jda.2004.08.018},
}

@PHDTHESIS{touzet:hdr,
  title = {Structures combinatoires pour l'analyse de génomes},
  author = {Touzet, H.},
  school = {Universit\'e des Sciences et Technologies de Lille},
  year = {2005},
  pdf = {http://www.lifl.fr/~touzet/Publications/hdrtouzet.pdf}
}

@ARTICLE{TouzetPerriquetNAR04, 
  author = {Hélène Touzet and Olivier Perriquet},
  journal = {Nucleic Acids yResearch},
  title = {{CARNAC}: folding families of related {RNA}s},
  volume = {32 (Supplement 2)},
  pages = {142-145},
  url = {http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_2/W142},
  year = {2004}
}

@ARTICLE{DefranceJOBIM04,
  author = {Defrance, Matthieu and Touzet, Hélène and Gosselin, Karo and  Abbadie, Corinne},
  title = {Recherche d'éléments régulateurs communs, application aux gènes cibles des facteurs de transcription Rel/NF-kB},
  year = {2004},
  pdf = {.http://www.lifl.fr/~touzet/Publications/jobim04.pdf}
}

@ARTICLE{PerriquetTouzetDauchetBioinformatics03,
  AUTHOR = {O. Perriquet and H. Touzet and M. Dauchet},
  TITLE = {Finding the common structure shared by two homologous {RNA}s},
  JOURNAL = {Bioinformatics},
  VOLUME = {19},
  YEAR = {2003},
  PAGES = {108-116},
  URL = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12499300&dopt=Abstract}
}

@ARTICLE{TouzetIPL03, 
  TITLE = {Tree edit distance with gaps},
  AUTHOR = {H. Touzet},
  JOURNAL = {Information Processing Letters},
  VOLUME = {85},
  NUMBER = {3},
  YEAR = {2003},
  PAGES = {123-129},
  PDF = {http://www.lifl.fr/~touzet/Publications/ipltouzet.pdf}
}

@ARTICLE{DulucqTouzetCPM03,
  TITLE = {Analysis of tree edit distance algorithms},
  AUTHOR = {S.Dulucq and H. Touzet},
  JOURNAL = {Proceedings of CPM'03},
  EDITOR = {Lecture Notes in Computer Science},
  VOLUME = {2676},
  PAGES = {83-95},
  YEAR = {2003},
  PDF = {http://www.lifl.fr/~touzet/Publications/cpmtouzet.pdf}
}

@ARTICLE{eccb03,
  TITLE = {A Fast Algorithm for Analysing Regulatory Regions of Related Genes},
  AUTHOR = {M. Defrance and H. Touzet and S. Janot},
  JOURNAL = {Session poster ECCB 2003},
  YEAR = {2003},
  PDF = {http://www.lifl.fr/~touzet/Publications/postereccb.pdf}
}

@ARTICLE{TouzetIC02,
  AUTHOR = {H. Touzet},
  TITLE = {A Characterisation of Multiply Recursive Functions with Higman's Lemma},
  JOURNAL = {Information and Computation},
  VOLUME = 178,
  PAGES = {534-544},
  YEAR = 2002
}