Last update: February 6, 2012.
International journals:
Jean-Philippe Doyon ,
Cedric Chauve et Sylvie Hamel, An efficient method for exploring the space of
gene tree/species tree reconciliations in a probabilistic framework, IEEE/ACM
Transactions on Computational Biology and Bioinformatics, Vol.9, No. 1, pp. 26--39, 2012.
Aida Ouangraoua , Valentin Guignon,
Cedric Chauve and Sylvie Hamel , A new algorithm for aligning
nested arc-annotated sequences under arbitrary weight schemes, Theoretical Computer Science, Volume 412, Issues 8-10, pp. 753-764, 2011.
Guillaume Blin ,
Maxime Crochemore , Sylvie Hamel
and Stéphane Vialette , Medians of an odd number of
permutations, Pure Mathematics and Applications, Volume 21, Issue 2, pp. 161-175, 2010.
Olivier Kaczor, Yann-Gaël Guéhéneuc and Sylvie Hamel,
Identification of design motifs with pattern matching algorithms, Information Software Technology, 52(2), pp.152-168, 2009.
Jean-Philippe Doyon ,
Cedric Chauve and Sylvie Hamel, Space of Gene/Species Trees Reconciliations
and Parsimonious Models , Journal of Computational Biology, 16 (10), pp. 1399-1418, 2009.
K.St-Onge, P.Thibault, S. Hamel,
F. Major, Modeling and Aligning
the Sarcin-Ricin Motif by Graph-Grammars, Nucleic Acid Research, Vol. 35, No. 5, pp.1726-1736, 2007.
S.Brlek,
S.Hamel, M.Nivat,
C.Reutenauer, On the Palindromic Complexity of Infinite Words,
International Journal of Foundations of Computer Science, 15-2, pp.293-306, 2004.
A.Bergeron and
S.Hamel, From Cascade Decompositions to Bit-Vector
Algorithms, Theoretical Computer Science, 313, pp. 3-16, 2004.
(Extended version of "Cascade Decomposition are Bit-Vector Algorithms",
presented at CIAA01.)
A.Bergeron and
S.Hamel, Vector Algorithms for Approximate String
Matching, International Journal of Foundations of Computer Science, 13-1,
pp. 53-66, 2002.
F. Bergeron and
S. Hamel, Intersections of modules related to Macdonald's
polynomials, Discrete Mathematics, 217, pp.51-64, 2000.
International Conferences:
Jérôme Azé, Thomas Bourquard, Sylvie Hamel,
Anne Poupon et Dave W. Ritchie, Using Kendall-tau meta-
bagging to improve Protein-Protein Docking predictions, Lecture Notes in Bioinformatics 7036, PRIB 2011 (6th IAPR International Conference on Pattern Recognition in Bioinformatics),
pp. 284-295, 2011.
Fehmi Jaafar,
Yann-Gaël Guéhéneuc, Sylvie Hamel et Giuliano Antoniol,
An Exploratory Study of Macro Co-changes, Proceedings of the 18th Working Conference on Reverse Engineering (WCRE), IEEE Computer Society Press, pp. 325-334, 2011.
Salima Hassaine, Ferdaous Boughanmi,
Yann-Gaël Guéhéneuc, Sylvie Hamel et
Giuliano Antoniol, A seismology-inspired approach to study change propagation , Proceedings of the 27th IEEE International
Conference on Software Maintenance (ICSM), IEEE Computer Society Press, pp. 53-62, 2011.
Salima Hassaine, Ferdaous Boughanmi,
Yann-Gaël Guéhéneuc, Sylvie Hamel et
Giuliano Antoniol, Change Impact Analysis: an Earthquake Metaphor, Proceedings of the 19th IEEE Internationale Conference on Program
Comprehension, IEEE Computer Society Press, pp. 209-210, 2011. (Poster)
Sarah Cohen-Boulakia, Alain Denise et Sylvie Hamel, Using Medians to generate consensus
rankings for biological data, Lecture Notes in Computer Science 4580, SSDBM 2011 (23rd Scientific and Statistical Database Management Conference), pp. 73-90, 2011.
Salima Hassaine,
Foutse Khomh , Yann-Gaël Guéhéneuc and Sylvie Hamel,
IDS: An Immunology-inspired Approach for the Detection of Software Design Smells, QUATIC 2010 (Seventh International Conference on Quality of Information and
Communications Technology), pp.343-348, 2010.
Guillaume Blin , Sylvie Hamel
and Stéphane Vialette , Comparing RNA structures with biologically rel-
evant operations cannot be done without strong combinatorial restrictions, Lecture Notes in Computer Science 5942, WALCOM2010 (Workshop on Algorithms and
Computations), pp.149-160, 2010.
G. Blin ,
M. Crochemore , S. Hamel
and
S. Vialette , Finding the median of three permutations under the Kendall-tau distance ,
accepté à Permutation Pattern 2009, avril 2009.
Jean-Philippe Doyon ,
Cedric Chauve and Sylvie Hamel, Algorithms for exploring the space of gene
tree/species tree reconciliations , Lecture Notes in Bioinformatics 5267, RECOMBCG
2008 Recomb Comparative Genomics 2008), pp.1-13, 2008.
M. Benoît-Gagné et S.Hamel, A new and fast way to sort a permutation
by transpositions , Lecture Notes in Computer Science 4580 (Combinatorial Pattern Matching), pp. 131-141, 2007.
O.Kaczor,
Y.-G. Guéhéneuc et S.Hamel, Efficient Identification of
Design Patterns with Bit-Vector Algorithms, proceedings of the 10th European Conference on Software Maintenance and
Reengineering, IEEE Computer Society Press, pp.173--182, 2006.
S.Hamel, A study of some easily parallellizable automata , Proceedings de JCIS 2006
pp. 779-783, 2006.
V.Guignon,
C.Chauve and S.Hamel, An
edit distance between RNA stem-loops , Lecture Notes in Computer Science 3772 (String Processing
and Information REtrival), pp. 335-347, 2005.
C.Chauve ,
V.Guignon and S.Hamel,
Distance d'édition entre "tige-boucles", Proceedings de JOBIM 2005 (Journées
Ouvertes en Biologie Informatique et Mathématiques), 3 pages, 2005.
S.Hamel, Finding global similarities between proteins
using vector algorithms , Proceedings de JCIS 2005 (Joint Conference on Information Science),
pp. 1221--1225, 2005.
A.Bergeron and
S.Hamel, Cascade Decompositions are Bit-Vector Algorithms
, Lecture Notes in Computer Science 2494 (International Conference on Implementation
and Application of Automata), pp.13-26, 2002.
A.Bergeron and
S.Hamel, Fast Implementations of Automata Computations,
Lecture Note in Computer Science 2088 (International Conference on Implementation
and Application of Automata), pp.47-56, 2001.
Research reports:
Salima Hassaine,
Yann-Gaël Guéhéneuc and Sylvie Hamel, Évolution Biologique et
Applications en Génie Logiciel, rapport interne EPMRT2010-03, Département de génie informatique et génie logiciel, École polytechnique
de Montréal, 2010.
Jean-Philippe Doyon , Sylvie Hamel and
Cedric Chauve , An efficient method for exploring the space of gene tree/species tree reconciliations in a probabilistic framework, rapport interne
RR-10002 (2010) 19, LIRMM, 2010.
Jean-Philippe Doyon ,
Cedric Chauve and Sylvie Hamel, Algorithms for exploring the space of gene
tree/species tree reconciliations , rapport interne 1323, DIRO, 2008.
G. Blin ,
S. Hamel and S. Vialette , Comparing RNA structures using a full set of
biologically relevant edit operations is intractable , CoRR abs/0812.3946, 2008.
A. Ouangraoua , V.Guignon,
Cedric Chauve and S. Hamel ,
New algorithms for align-ing nested arc-annotated sequences , rapport interne RR-1443-08, Labri (Laboratoire
Bordelais de Recherche en Informatique), avril 2008.