research | teaching, popular science | publications, vitae

Mathieu Giraud

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

Contact information

2012 News

• 17 january : ANR JCJC submitted
• Deadline for HiCOMB 2013 is on December 23
• 7 December : I give a talk on fugue analysis at the Séminaire MaMuX (IRCAM, Paris)
• 1 December: results of Gilles Kahn PhD award
• October : presenting our second paper on fugue analysis, with Richard Groult and Florence Levé, at ISMIR 2012
• October: RNA Locally Optimal Secondary Structures published in Journal of Computational Biology, with A. Saffarian, A. de Monte and H. Touzet, on RNA suboptimal structures. Preprint here.
• 27 September : Talk on computational music analysis at LIFL
• 15 September: deadline for Gilles Kahn PhD Award

• June : Project on Next-Gen Sequencing and Leukemia funded by Région Nord-Pas-de-Calais. Thank you Région !
• June : Manycore and bioinformatics in Lille (we organize)
• April-May : visit to Emilios Cambouropoulos, comparison of musical sequences
• March : paper accepted to CMMR 2012, with R. Groult and F. Levé, on fugue analysis.
• January : Stringmasters 2012 in Rouen
• January : Colloque Debussy in Paris
• January : Visit of ENS Cachan Bretagne (I co-organize)

2011 News (show)

Research interests : text algorithms for bioinformatics and musicology

• Bioinformatics
  • NGS algorithms, indexation, hematology and leukemia analysis
  • RNA patterns, RNA suboptimal structures, ncRNA discovery
  • GPU and manycore high-performance computing in bioinformatics

• Computer musicology
  • comparison of symbolic musical sequences
  • structure analysis

• Some keywords/buzzwords: multi-core, GPGPU, suffix trees, word combinatorics, repetitions detection, runs, Bloom filters, sequence similarity, sequence indexing, sequence assembly...

• Past research themes
  • FPGA and reconfigurable computing (2004-2007)
  • weigthed finite automata, epsilon-transitions (2004-2006)
  • identification of the canine olfactive repertory (2004-2005)

Software and tools

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

PhD Students

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

Administrative activities

• 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.

• Reviewer for Plos One, BMC Bioinformatics, Journal of Theoretical Biology (JTB), International Journal of Foundations of Computer Science (IJFCS), Parallel Computing, JOBIM 2012 (PC member), 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...

Master/PhD proposals

Excellent students in algorithms for bioinformatics or for musicology 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 and High Performance Computing
• Animations grand public et scolaires: les puzzles du génomes

Publications

• Lists of publications from Google, HAL, DBLP.

Short Bio

Mathieu Giraud is a CNRS Associate Researcher in the Laboratoire d'Informatique Fondamentale de Lille (LIFL), the departement of Computer Science of the Université Lille 1, in France. He is also a member of the joint Bonsai project with the Institut National de Recherche en Informatique et Automatique (INRIA). He serves as member of the INRIA national evaluation board.

He obtained a MS in École Normale Supérieure de Lyon in 2002, and a PhD from the University Rennes 1 in 2005. He worked on weighted automata and specialized architectures using FPGAs. His current research interests target text algorithms, bioinformatics, RNA bioinformatics, high-performance computing using GPUs and many-cores architectures, and computer musicology.

Positions and education

• 2006 — present : CNRS researcher, Bonsai bioinformatics group at LIFL, INRIA, Lille.
  • 2012 (1 month) : visit at Aristotle University of Thessaloniki, to Emilios Cambouropoulos
  • 2010 (1 month) : visit at Universitat Bielefeld, to Peter Steffen and Robert Giegerich
• 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 : summer 2012

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