research | projects, teaching, popular science | publications | vitae

Mathieu Giraud

mathieu.giraud [at] lifl.fr
PhD, Chargé de recherche CNRS (associate researcher)
Bonsai/Sequoia bioinformatics group at LIFL / INRIA Lille

Address: INRIA Lille — Sequoia
Parc Scientifique de la Haute Borne
40, avenue Halley
59650 Villeneuve d'Ascq — France
Phone: +33 3 59 57 79 13, Fax: +33 3 59 57 78 50,

Alternate address: LIFL (Laboratoire d'Informatique Fondamentale de Lille)
Université de Lille 1
59 655 Villeneuve d'Ascq cedex — France
Phone: +33 3 28 77 85 55, Fax: +33 3 28 77 85 37,

2012 News

• Stringmasters 2012 in Rouen
• Colloque Debussy in Paris
• Visit of ENS Cachan Bretagne (I co-organize)
• Current submissions :
  • a paper in revision to Journal of Computational Biology, with A. Saffarian and H. Touzet, on RNA suboptimal structures.
  • a paper for CMMR 2012, with R. Groult and F. Levé, on musical structure analysis

2011 News

• We organize SeqBio 2011
• PhD defense of Azadeh Saffarian
• Paper accepted to PBC 2011, with Tuan Tu Tran and Jean-Stéphane Varré, Bit-Parallel Multiple Pattern Matching
• Paper accepted to ISMIR 2011, with Florence Levé and Richard Groult (Amiens), Rhythm Extraction from Polyphonic Symbolic Music
• Biomanycores presented at JOBIM 2011 (June) as well as at BOSC 2011 (July)
• ANR MAPPI project started
• Chapter Manycore high-performance computing in bioinformatics published in this book, with B. Schmidt, S. Janot and J.-S. Varré.
  Get the preprint at HAL !

Research interests : bioinformatics, high-performance computing, text algorithmics, musicology

• RNA patterns, indexation, RNA suboptimal structures, ncRNA discovery
• high-performance computing in bioinformatics
• word combinatorics
• musicology, symbolic musical sequences, structure analysis
• misc keywords: FPGA, reconfigurable computing, multi-core, GPGPU, suffix trees, repetitions detection, runs, Bloom filters, sequence similarity, sequence indexing, sequence assembly...

• weigthed finite automata, epsilon-transitions (2004-2006)
• identification of the canine olfactive repertory (2004-2005)

Software and tools

• At bioinfo.lifl.fr: Regliss (RNA locally optimal structures), ReBLOSUM (Rectangular BLOSUM matrices), TFM-CUDA (GPU PWM tools)
• At U. Bielefeld: ADP CUDA
• Biomanycores

PhD Students

• Azadeh Saffarian (RNA, indexation), with Hélène Touzet, defended in november 2011
• Tuan Tu Tran (GPU, manycores), with Jean-Stéphane Varré

Reviewing activities

• Reviewer for BMC Bioinformatics, Journal of Theoretical Biology (JTB), International Journal of Foundations of Computer Science (IJFCS), STACS 2011, PPAM/PBC 2011 (PC member), ICCS/WEPA 2010 (PC member), JOBIM/Calcul 2009 (PC member), PSC 2009, IWOCA 2009, STACS 2009, MFCS 2008, CPM 2008, JOBIM 2008, ReConFig 2008
• Before 2008: Reviewer for BMC Bioinformatics, JOBIM 2007, MajecSTIC 2007, WABI 2006, FPL 2005, MajecSTIC 2005

• Elected member of INRIA national Evaluation Comittee (2008-2011, and 2011-2014).
• Member (since 2008) and scientific secretary (since 2009) of Gilles Kahn PhD Award comittee.

Master/PhD proposals

Excellent students interested in some of my research themes can always contact me. Please send a curriculum vitae and explain what research could keep you awake at night :)

Teaching and popular science (French)

• Bioinformatics, Algorithmics, Computer Architecture.
• Animations grand public (puzzles bioinformatiques):
  • 2005: Symbiologik, jouez avec les gènes.
  • 2007: SciencesOparK
  • 2010: Palais de la découverte (science museum in Paris)

Publications

• Lists of publications from Google, HAL, DBLP.

Positions and education

• 2006 — present : CNRS researcher, Sequoia bioinformatics group at LIFL, INRIA, Lille.
  • 2010 (1 month) : visit at Universitat Bielefeld
• 2006 (4 months) : Laboratoire de biologie informatique et théorique (LBIT), Université de Montréal, with N. El-Mabrouk and J-E Duchesne
• 2002 — 2006 : PhD with D. Lavenier and J. Nicolas at Symbiose / IRISA (Rennes)
• 1998 — 2002 : MSc at ENS Lyon
• 2000 (2 months) : on-line arithmetics, at EPFL, Lausanne, with J.-L. Beuchat.
• 1999 (6 weeks) : Bioinformatics, at LORIA, Nancy, with G. Kucherov.

Last update : January 2012

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