publications.bib

@inproceedings{GirdeaNoeKucherovWABI09Poster,
  author = {G{\^i}rdea, Marta and No{\'e}, Laurent and Kucherov, Gregory},
  title = {Read Mapping Tool for {AB} {SOLiD} Data},
  booktitle = {9th Workshop on Algorithms in Bioinformatics (WABI), September 12-13, 2009, Philadelphia (USA)},
  year = {2009},
  month = {September},
  note = {(poster)},
  abstract = {AB SOLiD sequencers [A Theoretical Understanding of 2 Base
Color Codes and Its Application to Annotation, Error Detection, and Error
Correction] produce reads encoded in a 4 color space, whose error-correcting
properties allow to better distinguish SNPs from reading errors. We developed a
tool for mapping AB SOLiD reads, that aims at obtaining better results by
making full use of the encoding properties and the read qualities.},
  pdf = {http://www.lifl.fr/~noe/files/poster_WABI09.abstract.pdf},
  postscript = {http://www.lifl.fr/~noe/files/poster_WABI09.abstract.ps.gz},
  inria = {Sequoia},
  labo = {dans},
  x-editorial-board = {yes},
  x-international-audience = {yes},
  x-proceedings = {no},
  aeres = {ACT},
  selectif = {non}
}

@inproceedings{GirdeaKucherovNoeJOBIM08Poster,
  author = {G{\^i}rdea, Marta and Kucherov, Gregory and No{\'e}, Laurent},
  title = {Protein sequence alignment via anti translation},
  booktitle = {Proceedings of the 9th Open Days in Biology, Computer Science and Mathematics (JOBIM), June 30-July 2, 2008, Lille (France)},
  year = {2008},
  month = {June},
  pages = {157--158},
  pdf = {http://www.lifl.fr/~girdea/at/files/jobim044.pdf},
  note = {(short talk with poster)},
  abstract = {We propose a new approach to protein sequence alignment, where
the basic idea is to find the best pairwise alignment between two DNA sequences,
each of which encodes one of the given proteins. A dynamic programming algorithm
was designed for the alignment of directed graphs which combine all these
putative DNA sequences. Our goal is to detect protein evolutionary relations
that are not captured by other methods.},
  inria = {Sequoia},
  labo = {dans},
  x-editorial-board = {yes},
  x-international-audience = {no},
  x-proceedings = {yes},
  aeres = {ACT},
  selectif = {oui}
}

@inproceedings{FurletovaKucherovNoeRoytbergTsitovichBGRS08,
  author = {Furletova, Eugenia and Kucherov, Gregory and No{\'e}, Laurent and Roytberg, Mikhail A. and Tsitovich, Ivan},
  title = {Transitive Subset Seeds for Protein Alignment},
  booktitle = {Proceedings of the 6th International Conference on {B}ioinformatics of {G}enome {R}egulation and {S}tructure ({BGRS}), July 22-28, 2008, Novosibirsk (Russia)},
  pages = {77},
  month = {July},
  year = {2008},
  pdf = {http://www.lifl.fr/~noe/files/resume_BGRS08_subset_seeds_protein.pdf}
}

@inproceedings{FontaineGiraudNoeTouzetJOBIM07Poster,
  author = {Fontaine, Arnaud and Giraud, Mathieu and No{\'e}, Laurent and Touzet, H{\'e}l{\`e}ne},
  title = {Graines espac{\'e}es et recherche d'{ARN} non-codants},
  booktitle = {Proceedings of the 8th Open Days in Biology, Computer Science and Mathematics (JOBIM), July 10-12, 2007, Marseille (France)},
  year = {2007},
  month = {July},
  pages = {389--390},
  pdf = {http://www2.lifl.fr/~fontaina/fontaine-yass-rna-jobim07.pdf},
  note = {(poster)},
  abstract = {Sequence comparison is widely used to help discovering novel
non-coding {RNA}s in newly sequenced genomes. In this context, Blast-like
homology search tools are of great interest. We show here that the usage of
software based on "spaced seeds" has a positive impact on non-coding {RNA}
identification.},
  inria = {Sequoia},
  labo = {dans},
  x-editorial-board = {yes},
  x-international-audience = {no},
  x-proceedings = {yes},
  aeres = {ACT},
  selectif = {non}
}

@inproceedings{FurletovaKucherovNoeRoytbergTsitovichMCCMB07,
  author = {Furletova, Eugenia and Kucherov, Gregory and No{\'e}, Laurent and Roytberg, Mikhail A. and Tsitovich, Ivan},
  title = {Statisical Approach to the Design of Subset Seeds for Protein Alignment},
  booktitle = {Proceedings of the International {M}oscow {C}onference on {C}omputational {M}olecular {B}iology ({MCCMB}), July 27-31, 2007, Moscow (Russia)},
  pages = {94--95},
  month = {July},
  year = {2007},
  pdf = {http://www.lifl.fr/~noe/files/resume_MCCMB07_subset_seeds_protein.pdf}
}

@inproceedings{GiraudNoeKucherovLavenierMAJECSTIC05,
  author = {Giraud, Mathieu and No{\'e}, Laurent and Kucherov, Gregory and Lavenier, Dominique},
  title = {Recherches de motifs et de similarit{\'e}s en bioinformatique : mod{\'e}lisations, solutions logicielles et mat{\'e}rielles (tutoriel)},
  booktitle = {in {M}ajec{STIC} : Manifestation des Jeunes Chercheurs francophones dans les domaines des {STIC} , Rennes},
  pages = {18--37},
  hal-url = {http://hal.inria.fr/inria-00001036/en/},
  opteprint = {},
  year = {2005}
}

@inproceedings{KucherovNoeRoytbergMCCMB05,
  author = {Kucherov, Gregory and No{\'e}, Laurent and Roytberg, Mikhail A.},
  title = {A unifying framework for seed sensitivity and its application to subset seeds},
  booktitle = {Proceedings of the International {M}oscow {C}onference on {C}omputational {M}olecular {B}iology ({MCCMB}), July 18-21, 2005, Moscow (Russia)},
  pages = {195--196},
  month = {July},
  year = {2005}
}

@inproceedings{KucherovNoeRoytbergJOBIM05Poster,
  author = {Kucherov, Gregory and No{\'e}, Laurent and Roytberg, Mikhail A.},
  title = {A unifying framework for seed sensitivity and its application to subset seeds},
  booktitle = {Proceedings of the 6th Open Days in Biology, Computer Science and Mathematics (JOBIM), July 6-8, 2005, Lyon (France)},
  year = {2005},
  pdf = {http://pbil.univ-lyon1.fr/events/jobim2005/proceedings/P114Kucherov.pdf},
  note = {poster}
}

@inproceedings{VitreschakNoeKucherovBGRS04,
  author = {Vitreschak, Alexei G. and No{\'e}, Laurent and Kucherov, Gregory},
  title = {Computer Analysis of Multiple Repeats in Bacteria},
  booktitle = {Proceedings of the 4th International Conference on {B}ioinformatics of {G}enome {R}egulation and {S}tructure ({BGRS}), July 25-30, 2004, Novosibirsk (Russia)},
  pages = {297--299},
  year = {2004},
  volume = {2},
  month = {July},
  organization = {{I}nstitute of {C}ytology and {G}enetics},
  pdf = {http://www.lifl.fr/~noe/files/resume_BGRS04_multiple_repeats.pdf},
  html = {http://www.bionet.nsc.ru/meeting/bgrs_proceedings/papers/2004/BGRS_2004_V2_073.pdf}
}

@inproceedings{NoeKucherovBGRS04,
  author = {No{\'e}, Laurent and Kucherov, Gregory},
  title = {{YASS} : Enhancing the sensitivity of {DNA} similarity search},
  booktitle = {Proceedings of the 4th International Conference on {B}ioinformatics of {G}enome {R}egulation and {S}tructure ({BGRS}), July 25-30, 2004, Novosibirsk (Russia)},
  pages = {289--292},
  year = {2004},
  volume = {2},
  month = {July},
  organization = {{I}nstitute of {C}ytology and {G}enetics},
  pdf = {http://www.lifl.fr/~noe/files/resume_BGRS04_yass.pdf},
  hal-url = {http://hal.inria.fr/inria-00100004/en/},
  html = {http://www.bionet.nsc.ru/meeting/bgrs_proceedings/papers/2004/BGRS_2004_V2_071.pdf}
}

@inproceedings{NoeKucherovECCB02Poster,
  author = {No{\'e}, Laurent and Kucherov, Gregory},
  title = {{A new method of finding similarity regions in {DNA} sequences}},
  booktitle = {{European Conference on Computational Biology (ECCB), Saarbr{\"u}cken, Germany}},
  year = {2002},
  series = {European Conference on Computational biology - ECCB'2002. Poster Abstracts},
  pages = {173--174},
  month = {October},
  note = {poster},
  url = {http://domino.mpi-inf.mpg.de/internet/eccb2002.nsf/0/3adfa323ce6a6c3ac1256c1400464a9f?OpenDocument},
  pdf = {http://www.lifl.fr/~noe/files/poster_ECCB02.abstract.pdf},
  postscript = {http://www.lifl.fr/~noe/files/poster_ECCB02.abstract.ps.gz}
}

@inproceedings{KucherovNoeRECOMB03Poster,
  author = {Kucherov, Gregory and No{\'e}, Laurent},
  title = {YASS : similarity search in {DNA} sequences},
  booktitle = {The Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB), Berlin (Germany)},
  year = {2003},
  pages = {81--82},
  month = {April},
  note = {poster},
  pdf = {http://www.lifl.fr/~noe/files/poster_RECOMB03.abstract.pdf},
  postscript = {http://www.lifl.fr/~noe/files/poster_RECOMB03.abstract.ps.gz}
}

@techreport{KucherovNoeRoytbergRRINRIA04,
  author = {Kucherov, Gregory and No{\'e}, Laurent and Roytberg, Mikhail A.},
  title = {A unifying framework for seed sensitivity and its application to subset seeds},
  institution = {INRIA},
  year = {2004},
  number = {RR-5374},
  month = {November},
  type = {{R}esearch {R}eport},
  pdf = {http://www.lifl.fr/~noe/files/rr_subset04.pdf},
  postscript = {http://www.lifl.fr/~noe/files/rr_subset04.ps.gz},
  hal-url = {http://hal.inria.fr/inria-00070629/en/}
}

@techreport{KucherovNoePontyRRINRIA03,
  author = {Kucherov, Gregory and No{\'e}, Laurent and Ponty, Yann},
  title = {Estimating seed sensitivity on homogeneous alignments},
  institution = {INRIA},
  year = {2003},
  number = {RR-5047},
  month = {Novemnber},
  type = {{R}esearch {R}eport},
  pdf = {http://www.lifl.fr/~noe/files/rr_ha03.pdf},
  postscript = {http://www.lifl.fr/~noe/files/rr_ha03.ps.gz},
  hal-url = {http://hal.inria.fr/inria-00071536/en/}
}

@techreport{NoeKucherovRRINRIA03,
  author = {No{\'e}, Laurent and Kucherov, Gregory},
  title = {{YASS}: Similarity Search in {DNA} Sequences},
  institution = {INRIA},
  year = {2003},
  number = {RR-4852},
  month = {June},
  type = {{R}esearch {R}eport},
  pdf = {http://www.lifl.fr/~noe/files/rr_yass03.pdf},
  postscript = {http://www.lifl.fr/~noe/files/rr_yass03.ps.gz},
  hal-url = {http://hal.inria.fr/inria-00071731/en/}
}

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