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Pierre PETERLONGO Print

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peterlongo Title Research Associate
Mail This e-mail address is being protected from spam bots, you need JavaScript enabled to view it
Address Symbiose
  INRIA/Irisa - Campus de Beaulieu
  35042 RENNES Cedex - France
Tel +33 2 99 84 74 59
Fax +33 2 99 84 71 71
   
   
Current Position

Research Associate at Symbiose project team

 

 

 

 

My citation


"Crains surtout pas le ridicule quand on ose pas des fois on recule"

La rue Kétanou

 

Research


Main Research Topics

  • Next Generation Sequencers.
    • Technological watch
    • De novo assembly
    • Exploitation of non assembled reads
  • Information extraction
    • Filters and seeds
    • Universal primer design
  • Stringology and combinatorial problems

 

Available Tool

 
  • Tuiuiu, a filter for finding multiple repeats in sequences is available here.

 

Publications

  • International Journal Papers

M. Gallé, P. Peterlongo, F. Coste
In place update of suffix array while recoding words,
International Journal of Foundation of Computer Science, in press.

Peterlongo, G. Sacomoto, A. Pereira do Lago, N. Pisanti, M.-F. Sagot

Lossless filter for multiple repeats with bounded edit distances
BMC Algorithms for Molecular Biology 2009, 4:3 doi:10.1186/1748-7188-4-3

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P. Peterlongo, L. Noé, D. Lavenier, J. Jacques, G. Kucherov, M. Giraud

Optimal neighborhood indexing for protein similarity search
BMC Bioinformatics, 2008 Dec 16;9:534.

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P. Antoniou, M. Crochemore, C. S. Iliopoulos, P. Peterlongo

Acquisition of common motifs with gaps in a set of sequences using suffix trees
In submission to Journal of Computational Biology

  

P. Peterlongo, N. Pisanti, F. Boyer, A. Pereira do Lago, M.-F. Sagot,

Lossless filter for multiple repetitions with Hamming distance,
Journal of Discrete Algorithms, DOI : 10.1016/j.jda.2007.03.003

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P.Peterlongo, J. Allali, M-F.Sagot: Indexing gapped-factors using a tree,
International Journal of Foundation of Computer Science,		 pdf.gif

C.S.Iliopoulos, J.McHugh, P.Peterlongo, N.Pisanti, W.Rytter, M.Sagot:

A first approach to finding common motifs with gaps,
International Journal of Foundation of Computer Science, 16(6), 1145--1155, 2005

 

 

  • Conferences

M. Federico, P. Peterlongo, N. Pisanti

An optimized filter for finding multiple repeats in DNA sequences

AICCSA 2010

P. Peterlongo, J. Nicolas, D. Lavenier, R. Vorc'h, J. Querellou

c-GAMMA: Comparative Genome Analysis of Molecular Markers
PRIB 2009
M. Gallé, P. Peterlongo, F. Coste
In place update of suffix array while recoding words,
PSC 2008
P. Peterlongo, L. Noé, D. Lavenier, G. Georges, J. Jacques, G. Kucherov, M. Giraud
Protein similarity search with subset seeds on a dedicated reconfigurable hardware,
Proceedings of Parallel Bio-Computing (PBC 2007) - To appear in Springer LNCS
P. Antoniou, M. Crochemore, C.S. Iliopoulos, P. Peterlongo,
Application of suffix trees for the acquisition of common motifs with gaps in a set of strings,
Proceedings of International Conference on Language and Automata Theory and Applications (LATA 2007)
P. Peterlongo, J. Allali, M.-F. Sagot,
The Gapped-Factor Tree,
Prague Stringology Conference (PSC 2006)
P. Antoniou, J. Holub, C.S. Iliopoulos, B. Melichar, P. Peterlongo,
Finding Common Motifs with Gaps using Finite Automata,
Proceedings of the 11th International Conference on Implementation and Application of Automata (CIAA 2006)
P. Peterlongo, N. Pisanti, F. Boyer, M.-F. Sagot:
Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure, the Bi-Factor Array,
Proceedings of String Processing and Information Retrieval (SPIRE 2005), Springer LNCS 3772, pages 179-190, 2005.
C. Iliopoulos, J. McHugh, P. Peterlongo, N. Pisanti, W. Rytter, M.-F. Sagot:
A First Approach to Finding Common Motifs with Gaps,
Proceedings of Prague Stringology Conference (PSC), pages 88-97, 2004

 

  • Poster

    P. Peterlongo, N. Pisanti, A. Pereira do Lago, M.-F. Sagot,
    Ed'Nimbus: A Lossless Filter for Long Multiple Repetitions with Edit Distance ,
    Jobim 2006 - png (900 K, french)

  • Technical report

    P. Peterlongo, N. Pisanti, A. Pereira do Lago, M.-F. Sagot
    Lossless Filter for Long Multiple Repetitions with Edit Distance - ps.gz

 

 

 

Boabab

  • Member of the Baobab team (Lyon)

Cooperations

 

 

PhD

 

 

 
  • Title: "DNA sequence filtration for finding long multiple approximate repetitions"
  • Obtained the September 21, 2006. The jury was:
  • Manuscript (4 MB - french)
  • Slides (4.2 MB - french)

 

 
 
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