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Annuaire


LAURENT MOUCHARD


MAITRE DE CONFERENCES

ST/ID/Mouchard
Tél : +33 2 35 14 00 40
Fax : +33 2 35 14 71 40
laurent.mouchard@univ-rouen.fr



Bureau : BER 101 D: 1st Floor, Bât. Monod - Fac. of Sci., Mont-St-Aignan
Bureau 2 : QuantIF: 1st Floor, Bât Research, Fac. of Medicine, Martainville

DEPARTEMENT D'INFORMATIQUE
LABORATOIRE D'INFORMATIQUE, DE TRAITEMENT DE L'INFORMATION ET DES SYSTEMES
Assistant Professor in Computer Science and Computational Biology

Disciplines enseignées

University of Rouen

- MSc2 Computational Biology: 1. Linux (bash programming); 2. RDBMS (MySQL, PHP, GD); 3. Adv. Web Techno. (XML, XSLT, XSL-FO, RSS, Web services) - BSc3 Biomedical Engineering: 1. Adv. Informatics II - BSc2 Biomedical Engineering: 1. Adv. Informatics I - BSc1 Environmental and Life Sciences: 1. Intro to HTML+CSS, MySQL and PHP

King's College London

- MSc Computer Science: 1. Cryptography and Information Security 2. Adv. Security Topics

Thèmes de recherche

Dynamic (compact) data structures to index texts: reads mapping and de novo assembly for NGS technologies. Efficient representation of a large set of highly similar texts with a specific focus on biological sequences: 1000 genomes project and Personal Genome Project . Fusion of multimodal medical images based on Belief Functions Theory: TDM and PET images using three different radiotracers. Applications to the segmentation of tumor lesion.

CV

Affiliation (Have a look at the rightmost column)
2001-... Part-time Visiting Lecturer (Teaching Mobility, ERASMUS) at King's College London
2000 Participation to the Assembly of the Human Genome, invited external collaborator (7 months) Celera Genomics, MD, USA.
1999-... Assistant Professor at Université de Rouen
1995-1997 System and Network Administrator (École d'Architecture de Normandie).
1992-1994 System Administrator of Massively Parallel Systems at Centre de Ressources Informatiques de Haute-Normandie.
In charge of deploying the regional infrastructure for Internet.
1988-1991 Professor of Mathematics for A-level students.

Education
1998 PhD in Computational Biology, Univ. Rouen
1994 MPhil in Computational Science, Univ. Rouen
1989 MSc in Mathematical Foundation of Computer Science, Univ. Rouen
1988 CAPES Mathematics
1987 BSc in Mathematics, Univ. Rouen

Informations Complémentaires

Former PhD students include:

Richard Groult (Assistant Professor at the University of Amiens)
Mikaël Salson (Assistant Professor at the University of Lille 1)

I'm currently co-supervising Benoît Lelandais (PhD on Fusion of multimodal medical images using belief functions)

Recent Program committee
CUBE 2012, IWOCA 2012, SPIRE 2011, IWOCA 2011, SPIRE 2010, IWOCA 2010, ...

Recent organizing committee
LSD/LAW 2012, Stringmasters 2012, LSD/LAW 2011, Stringmasters 2011, IWOCA 2010, ...

Recent Invited Conferences
CUBE 2012, Pune India
IWOCA 2012, Kalasalingam University, India
Stringology 2011, Haifa university, Israel
London Stringology Days 2011, London, UK
Stringology 2009, Bar Ilan university, Tel Aviv, Israël.
South African Stringmasters 2009, StellenBosch, Afrique du Sud.
Australian Stringmasters 2009, Perth, Australie.

References
[11] C. S. Iliopoulos and L. Mouchard. Quasiperiodicity and string covering. Theor. Comput. Sci., 218(1):205-216, 1999.

[12] C.S. Iliopoulos, M. Kumar, L. Mouchard, and S. Venkatesh. Motif evolution in polyphonic musical sequences. In Proceedings of the 11th Australasian Workshop On Combinatorial Algorithms, pages 53-66, 2000.

[13] C.S. Iliopoulos, T. Lecroq, L. Mouchard, and Y. J. Pinzon. Computing repetitions in musical sequences. In Proceedings of Prague Stringology Club Workshop 2000, pages 49-59, 2000.

[14] L. Mouchard. Normal forms of quasiperiodic strings. Theor. Comput. Sci., 249(2):313-324, 2000.

[15] M. Régnier and L. Mouchard. Periods and quasiperiods characterization. In Springer-Verlag, editor, Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching, Lecture Notes in Computer Science, pages 388-396, Berlin, 2000.

[16] C. S. Iliopoulos, J. Holub, B. Melichar, and L. Mouchard. Distributed pattern matching using nite automata. J. Aut. Lang. Comb., 6(2):191-204, 2001.

[17] C. S. Iliopoulos, T. Lecroq, L. Mouchard, and Y. J. Pinzon. Computing approximate repetitions in musical sequences. Int. J. Comput. Math., 83(1), 2001.

[18] C.S. Iliopoulos, L. Mouchard, and Y. J. Pinzon. The max-shift algorithm for approximate string matching. In Proceedings of Workshop on Algorithms and Experiments 2001, number 2141 in Lecture Notes in Computer Science, pages 13-25, 2001.

[19] J.C. Venter, M.D. Adams, E.W. Myers, and Celera Corporation. The sequence of the human genome. Science, 291(5507):1304-51, 2001.

[20] E. Cambouropoulos, M. Crochemore, C. S. Iliopoulos, L. Mouchard, and Y. J. Pinzon. Computing approximate repetitions in musical sequences. International Journal of Computer Mathematics, 79(11):1135-1148, 2002.

[21] C.S. Iliopoulos, M. Mohamed, L. Mouchard, K. Perdikuri, W. Smyth, and A. Tsakalidis. String regularities with don't cares. In Proceedings of Prague Stringology Club Workshop 2002, pages 49-59, 2002.

[22] D. Lavenier, H. Leroy, M. Hurn, R. Andonov, L. Mouchard, and F. Guinand. Le projet Génogrid : une expérimentale pour la génomique. In Proceedings of Journées Ouvertes Biologie Informatique et Mathématique 2002, pages 27-32, 2002.

[23] R. Groult, M. Léonard, and L. Mouchard. Evolutive tandem repeats using hamming distance. In Proceedings of the 27th International Symposium on Mathematical Foundations of Computer Science, pages 292-304, Warszawa - Otwock, Poland, 2002. Lecture Notes in Computer Science 2420, K. Diks, W. Rytter (Eds.),
Springer.

[24] R. Groult, M. Léonard, and L. Mouchard. A linear algorithm for the detection of evolutive tandem repeats. In Proceedings of the Prague Stringology Conference '03, pages 77-90, Prague, Czech Republic, 2003. Milan Simanek.

[25] C. S. Iliopoulos, M. Mohamed, L. Mouchard, K. Perdikuri, W. F. Smyth, and A. Tsakalidis. String regularities with don't cares (extended version). Nordic Journal of Computing, 10(1):40-51, 2003.

[26] C. S. Iliopoulos, L. Mouchard, K. Perdikuri, and A. Tsakalidis. Computing the repetitions in a weighted sequence. In Proceedings of the Prague Stringology Conference '03, pages 91-98, Prague, Czech Republic, 2003. Milan Simanek.

[27] R. Groult, M. Léonard, and L. Mouchard. Speeding up the detection of evolutive tandem repeats. Theor. Comput. Sci., 310:309-328, 2004.

[28] R. Groult, M. Léonard, and L. Mouchard. chapter Evolutive tandem repeats : a survey, pages 75-108. Nato book series. KCL press, 2004.

[29] S. Istrail, G. G. Sutton, L. Florea, A. L. Halpern, C. M. Mobarry, R. Lippert, B. Walenz, H. Shatkay, I. Dew, J. R. Miller, M. J. Flanigan, N. J. Edwards, R. Bolanos, D. Fasulo, B. V. Halldorsson, S. Hannenhalli, R. Turner, S. Yooseph, F. Lu, D. R. Nusskern, B. Chris Shue, X. Holly Zheng, F. Zhong, A. L. Delcher, D. H. Huson, S. A. Kravitz, L. Mouchard, K. Reinert, K. A. Remington, A. G. Clark, M. S. Waterman, E. E. Eichler, M. D. Adams, M. W. Hunkapillar, E. W. Myers, and J. C. Venter. Whole-genome shotgun assembly and comparison of human genome assemblies. Proceedings of the national academy of science (PNAS), 101(7):1916-1921, 2004.

[30] M. Christodoulakis, C. S. Iliopoulos, L. Mouchard, and K. Tsichlas. Pattern matching in weighted sequences. In Proceedings of the Algorithms and Computational Methods for Biochemical and Evolutionary Networks '04, Recife, Brazil, December 2004.

[31] C. S. Iliopoulos, L. Mouchard, K. Perdikuri, and A. K. Tsakalidis. Computing the repetitions in a biological weighted sequence. Journal of Automata, Languages and Combinatorics, 10(5/6):687-696, 2005.

[32] N. Machour, J. Place, F. Tron, R. Charlionet, L. Mouchard, C. Morin, A. Desbène, and P-L. Desbène. Analysis of virtual two-dimensional gels based upon anity capillary electrophoresis hyphenated to ion trap mass spectrometry. Electrophoresis, 26(7-8):1466-75, 2005.

[33] F. Arikat, A. Bakalis, M. Christodoulakis, C. S. Iliopoulos, and L. Mouchard. Experimental results in pattern matching on weighted sequences. In Proceedings of the International Conference on Numerical Analysis and Applied Mathematics (ICNAAM'05), Rhodes, Greece, September 2005.

[34] R. Groult, M. Léonard, and L. Mouchard. A linear algorithm for the detection of evolutive tandem repeats. Journal of Automata, Languages and Combinatorics, 10(5/6):671-685, 2005.

[35] M. S. Rahman, C. S. Iliopoulos, and L. Mouchard. Pattern matching in degenerate DNA/RNA sequences. In Proceedings of the Workshop on Algorithms and Computation 2007, pages 109-120, Dhaka, Bangladesh, 2007.

[36] C. Iliopoulos, I. Jayasekera, and L. Mouchard. Fast practical exact and approximate pattern matching in protein sequences. In Proceedings of the 17th Australasian Workshop On Combinatorial Algorithms, Australia, 2007.

[37] K. Park and L. Mouchard. Combinatorial pattern matching. J. Discrete Algorithms, 5(4):635, 2007.

[38] C. S. Iliopoulos, L. Mouchard, and M. S. Rahman. A new approach to pattern matching in degenerate DNA/RNA sequences and distributed pattern matching. Mathematics in Computer Science, 1(4):557-569, 2008.

[39] M. Salson, T. Lecroq, M. Léonard, and L. Mouchard. Dynamic Burrows-Wheeler transform. In Jan Holub and Jan Zdarek, editors, Proceedings of the Prague Stringology Conference 2008, pages 13-25, Czech Technical University in Prague, Czech Republic, 2008.

[40] M. Salson, T. Lecroq, M. Léonard, and L. Mouchard. A four-stage algorithm for updating a Burrows-Wheeler Tranform. Theor. Comput. Sci., 2009. Accepted, to appear.

[41] M. Salson, T. Lecroq, M. Léonard, and L. Mouchard. Dynamic extended suffix array. J. Discrete Algorithms, 2009. Accepted, to appear.







International Federation for Information Processing
- Chair of the WG 12.8 - Intelligent Bioinformatics and Biomedical Systems - TC 12 on Artifical Intelligence - IFIP - International Federation for Information Processing.

Assembly of the Human Genome
- Participation to the Assembly of the Human Genome, invited external collaborator (7 months) Celera Genomics, MD, USA.

Société Française de BioInformatique
- Elected board member of the Société Française de BioInformatique (2011)
- Cofounder of the Société Française de BioInformatique (2004)

European Commission
- Independent Expert for the European commission (since 2006)

Agence Nationale de la Recherche
- Independent Expert for the French Agence Nationale de la Recherche (since 2006)

King's College London
- Part-time Visiting Lecturer (Teaching Mobility, ERASMUS) at King's College London (since 2001)

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