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

Mathieu Giraud

PhD, Chargé de recherche CNRS (associate researcher, with tenure)
Sequoia bioinformatics group at LIFL / INRIA Lille

Address: INRIA Lille - Nord Europe
Parc Scientifique de la Haute Borne - Park Plaza A
40, avenue Halley
59650 Villeneuve d'Ascq - France
Phone: +33 3 59 57 79 13, Fax: +33 3 59 57 78 50, Mail: giraud [at] lifl.fr

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,

News

• January : I have been accepted for the NVIDIA Professor Partnership Program. I received some funding through this program. Students can apply to open projects.
• February: Workshop on Massively Multiprocessor and Multicore Computers, Paris
• March: Visit of Peter Steffen on ADP and GPU
• April: first release of Biomanycores
• June: CPM 2009 [we organize]
• June: ISPDC 2009 [accepted paper]
• September: PBC/PPAM 2009 [accepted paper]

• September-October: working on two book chapters, to be published in 2010
  • with P. Peterlongo and N. Pisanti, Filters and Seeds Approaches for Fast Homology Searches in Large Datasets, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, ed. by M. Elloumi and A. Y. Zomaya
  • with B. Schmidt, S. Janot and J.-S. Varré, Manycore high-performance computing in bioinformatics, in Genome-scale Pattern Analysis in the Post-ENCODE Era, ed. by L. Elnitski, H. Piontkivska, and L. Welch
• December: local workshop CIGIL on High-Performance Computing, including one half-day on GPU [we organize]

Research interests : bioinformatics, high-performance computing

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

Current PhD Students

• Azadeh Saffarian (RNA, indexation), with Hélène Touzet
• Tuan Tu Tran (manycores), with Jean-Stéphane Varré

Reviewing activities

• Reviewer for Journal of Theoretical Biology (JTB), International Journal of Foundations of Computer Science (IJFCS), 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).
• Member of Gilles Kahn PhD Award comittee

PhD proposals

• (2009, closed) Massively parallel algorithms and data-structures for bioinformatics, with Jean-Stéphane Varré with INRIA funding and support from NVIDIA.

I have currently no further PhD funding opportunities.

Projects proposals

• (2009, closed) Bit-parallelism and computation on graphical processor units, (closed for submission) with Jean-Stéphane Varré. Supported by NVIDIA.
• (2007, closed) "Genome on Chip" (french), co-encadré avec Philippe Marquet (attribué)
• (2007, closed) "Indexation pour l'ARN", co-encadré avec Hélène Touzet (attribué)

Subjects and project lengths (2 - 6 months) can be adapted with the preferences and the background of the student.

Ces sujets sont pour des stages M1/M2 ou un stage ingénieur. Les sujets et les durées (2 - 6 mois) peuvent s'adapter aux préférences et au parcours du stagiaire. D'autres sujets sont possibles, contactez-moi.

Teaching and popular science (French)

• Bioinformatics and architecture du M2 Recherche en informatique de Lille 1
• Animation grand public: Symbiologik, jouez avec les gènes. Nouveaux puzzles présentés à SciencesOparK

Publications

• List of publications
• other lists from Google, HAL, DBLP.

Positions and education

• 2006 - present : CNRS researcher, Sequoia bioinformatics group at LIFL, INRIA, Lille.
• 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 : December 2009

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