- Septembre: Un poste de post-doc ou CDD ingénieur est disponible à l'institut Necker, à Paris, en collaboration avec notre équipe
- May: our paper on multiclonal clusterization of V(D)J repertoires has has just been published in BMC Genomics, with M. Salson, M. Duez and colleagues from the Lille hospital
- Nous proposons une thèse co-financée par Lille 1 et la région sur l'indexation de réarrangements V(D)J
- 15 April (in French): Journée du GDR ESARS à Lille sur la structure musicale
- 27-28 March: Attending Congrès de la SFH (Société Française d'Hématologie)
- March: Mikaël Salson is in EuroClonality-NGS workgroup for our collaboration on Vidjil
- February: Visiting Olivier Lartillot in Jyväskylä University (Finland), working on melodic patterns
- February: Vidjil source is now on GitHub
2013 News (show)
- December (in French): Je propose plusieurs stages de recherche pour M2 ou école d'ingénieur, tous financés, pour 2014
- December: Submitted our work on fugue analysis to Computer Music Journal, with R. Groult, E. Leguy and F. Levé
- October: Submitted our work on leukemia to BMC Genomics, with M. Salson, M. Duez and colleagues from the Lille hospital
- October: ANR on Sonata Forms submitted
- October: Attending ESLHO Symposium in Rotterdam with the Vidjil team (Mikaël Salson, Marc Duez) and colleagues from the Lille hospital.
- October: I go to CMMR 2013 in Marseille, presenting a work on variations with Emilios Cambouroupoulos
- July: Going to the JOBIM 2013 bioinformatics conference, presenting our work on leukemia
- June: I participate to FMA 2013, presenting a work on melody contours, with Christina Anagnostopoulou
- February : talk by Mikaël Salson in Montpellier on our work on leukemia
2012 News (show)
- Deadline for HiCOMB 2013 is on December 23
- 21 december : PhD defense of Tuan Tu Tran (indexing structures on GPU, co-directed with Jean-Stéphane Varré)
- 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)
- December : We organize SeqBio 2011
- November : 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 : text algorithms for bioinformatics and musicology
BioinformaticsI am a member of the Bonsai bioinformatics group (Pr. Hélène Touzet) at LIFL / INRIA Lille, mainly working on NGS algorithms.
- NGS algorithms and indexation, especialy for hematology and leukemia analysis, together with Mikaël Salson
- RNA patterns, RNA suboptimal structures, ncRNA discovery
- GPU/manycore high-performance computing in bioinformatics
Past research themes
- FPGA and reconfigurable computing (2004-2007)
- weigthed finite automata, epsilon-transitions (2004-2006)
- identification of the canine olfactive repertory (2004-2005)
Computer musicologyI am the head of the "Algorithmic musicology" exploratory action at LIFL/MIS. We focus on computational analysis of symbolic scores : given a music score (for example MIDI or .krn file), we aim to compute several analyses, ultimately studying the high-level structure of music. We try to propose models and methods that are both algorithmically efficient and musically pertinent.
- modeling and comparison of symbolic musical sequences: patterns, harmony, rhythms
- structure analysis : fugues, sonata forms...
Softwares and tools
- Vidjil, high-throughput V(D)J repertoire analysis
- 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
- Azadeh Saffarian (RNA bioinformatics, indexation), with Hélène Touzet, defended in november 2011
- Tuan Tu Tran (bioinformatics with GPU/manycores), with Jean-Stéphane Varré, defended in december 2012
- Nicolas Guiomard-Kagan (MIR, polyphony), with Vincent Villain, Florence Levé and Richard Groult (MIS), started in 2013
- Elected member of INRIA national Evaluation Comittee (2008-2011 and 2011-2014).
- Member (2008-2012) and scientific secretary (2009-2012) 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 2013 (PC member), HiComb 2013 (PC member), ICCS/WEPA 2012 (PC member), 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 proposalsJe propose en 2014 une thèse et deux stages de recherche pour M2 ou école d'ingénieur:
- (PhD, 2014, closed) Indexation de rearrangements lymphoïdes VDJ pour le suivi de la leucemie (bioinformatique, algorithmique du texte)
- (Master, 2014, open for applicants) Modèles probabilistes pour les structures musicales (informatique musicale, apprentissage)
- (Master, 2014, closed) Variations musicales et motifs de transfomations (informatique musicale, algorithmique du texte, langages formels)
Teaching and popular science (French)
- Bioinformatics, Algorithmics, Computer Architecture and High Performance Computing
- Animations grand public et scolaires: les puzzles du génomes
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 (LIFL, Inria) and Algomus exploratory action (LIFL, MIS), 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
Last update : summer 2014Personal page