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1 L. Mouchard. Improving the significance of biological sequences comparison score. In C. Venter, editor, Proceedings of the first annual Conference on Computational Biology, page 21. The Institute for Genomic Research, 1997. Best poster by a PhD student.

2 V. Norris, J. Alexandre, S. Barray, L. Mouchard, and L. Quillet. A mechanical approach to the distribution and orientation of genes on genetic maps. Molecular Microbiology, 27(1):235-237, 1998.

3 C. S. Iliopoulos, M. Kumar, L. Mouchard, and S. Venkatesh. Computing all motif occurrences in polyphonic musical sequences. Technical Report 9-98, School of Computing, Curtin University, Australia, 1998.

4 C. S. Iliopoulos, L. Mouchard, and S. Venkatesh. Optimal computation of all the repetitions in a string. Technical Report 8-98, School of Computing, Curtin University, Australia, 1998.

5 L. Mouchard. Canonical decompositions of quasiperiodic words. In C. S. Iliopoulos, editor, Proceedings of the 9th Australasian Workshop On Combinatorial Algorithms, pages 74-84, Perth, WA, Australia, 1998.

6 L. Mouchard. Superpositions dans les séquences. Thèse de doctorat, Université de Rouen, 1998.

7 J.-P. Duval and L. Mouchard. Sequences obtained from a series of permutations of borders and ultimately periodic words. J. Aut. Lang. Comb., 4(3):205-211, 1999.

8 E. Cambouropoulos, M. Crochemore, C. S. Iliopoulos, L. Mouchard, and Y. J. Pinzon. Algorithms for computing approximate repetitions in musical sequences. In Proceedings of the 10th Australasian Workshop On Combinatorial Algorithms, pages 129-144, 1999.

9 J. Holub, C. S. Iliopoulos, B. Melichar, and L. Mouchard. Distributed string matching using finite automata. In Proceedings of the 10th Australasian Workshop On Combinatorial Algorithms, pages 114-128, 1999.

10 C. S. Iliopoulos and L. Mouchard. An O(n log n) algorithm for computing all maximal quasiperiodicities in strings. In C. S. Calude and M. J. Dinneen, editors, Combinatorics, Computation and Logic. Proceedings of DMTCS’99 and CATS’99, Lecture Notes in Computer Science, pages 262-272, Auckland, New-Zealand, 1999. Springer-Verlag, Singapore.

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 finite 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. Hurfin, R. Andonov, L. Mouchard, and F. Guinand. Le projet génogrid : une grille 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 Costas S. Iliopoulos, Laurent Mouchard, Katerina Perdikuri, and Athanasios 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 affinity 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 Richard Groult, Martine Léonard, and Laurent 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. Sohel Rahman, Costas S. Iliopoulos, and Laurent 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 Kunsoo Park and Laurent 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 Mikaël Salson, Thierry Lecroq, Martine Léonard, and Laurent Mouchard. Dynamic Burrows-Wheeler transform. In Jan Holub and Jan Zdárek, 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.

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