- 2 postes MCF (4181, 4182) sont ouverts au recrutement à l'Université Lille 3 sur des thématiques liées à Algomus. Les candidats sont invités à me contacter le plus rapidement possible.
- February: EuroClonality-NGS working group in Prague
- January: participing to the Music Similarity workshop in Leiden
- November 2014: Tatiana Rocher has joined the Bonsai team for a PhD on new indexation methods for developing Vidjil. Welcome Tatiana !
2014 News (show)
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 CRIStAL / INRIA Lille, mainly working on NGS algorithms.
- NGS algorithms and indexation,
especialy for hematology and leukemia analysis,
together with Mikaël Salson
See the Vidjil website
- 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 CRIStAL/MIS/SCV. 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, rhythm, texture
- structure analysis : fugues, variations, sonata forms...
- 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
- Tatiana Roched (V(D)J bioinformatics, indexation), with Mikaël Salson, started in 2014
- 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, ISMIR 2014, 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, closed) 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)
- I teach lectures on Bioinformatics, Algorithmics, Computer Architecture and High Performance Computing
- Animations grand public et scolaires: les tapis musicaux, les puzzles du génomes
Mathieu Giraud is a CNRS Associate Researcher in the Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL), the departement of Computer Science of the Université Lille, in France. He is also a member of the joint Bonsai project with the Institut National de Recherche en Informatique et Automatique (Inria). He is a former 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, on high-performance computing using GPUs and many-cores architectures, and on RNA bioinformatics. His current research interests target text algorithms for bioinformatics and computer musicology
Positions and education
- 2006 — present : CNRS researcher, Bonsai bioinformatics group (CRIStAL, Inria) and Algomus exploratory action (CRIStAL, MIS, SCV), 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
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