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Selected publications
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2005
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C. Chauve, V. Guignon, and S. Hamel, An edit distance between RNA
stem-loops, SPIRE 2005.
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C. Chauve, V. Guignon, and S. Hamel, Distance d'édition entre
"tige-boucles", JOBIM 2005.
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N. El-Mabrouk, Genome rearrangements with gene families, Mathematics of
Evolution and Phylogeny, ed. Olivier Gascuel, Oxford University Press,
2005, in press.
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H. Germain, S. Rudd, C Zotti, S. Caron, M. O'Brien, S.C. Chantha, M. Lagacé,
F. Major, and D.P. Matton, A 6374 unigene set corresponding to weakly
expressed transcripts following fertilization in Solanum chacoense
Bitt., and expression profile of 30 receptor-like kinases expressed
during early embryo development, Plant Molecular Biology, in
press.
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Y-G. Guéhéneuc, S. Hamel, and O. Kaczor, Efficient Identification of
Design Patterns with Vector Algorithms, submitted.
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S. Hamel, Finding global similarities between proteins using vector
algorithms, Proceedings of the Join Conference on Information Science,
1221-1225, 2005.
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F. Major and P. Thibault, Computer Modelling of RNA Three-Dimensional
Structures. Encyclopedia of Molecular Biology and Molecular
Medicine, Robert A. Meyers ed., VCH Publishers Inc. New-York,
NY, in press.
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C. Olivier, G. Poirier, P. Gendron, A. Boisgontier, F. Major, and P.
Chartrand, Identification of a Conserved RNA Motif Essential for She2p
Recognition and mRNA Localization to the Yeast Bud. Molecular and
Cellular Biology, 25:4752-4766, 2005.
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M. Parisien and F. Major, A New Catalog of Protein Β-Sheets.
Proteins: Structure, Function and Bioinformatics, in press.
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D. Sankoff, J.F. Lefebvre, E. Tillier, A. Maler, and N. El-Mabrouk, The
distribution of inversion lengths in prokaryotes, Comparative Genomics,
RECOMB 2004 International Workshop, Lecture Notes in Computer
Science, Vol. 3388, 2005.
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2004
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A. Bergeron and S. Hamel, From cascade decomposition to bit-vector
algorithms, Theoretical Computer Science, 313:3-16, 2004.
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S. Brlek, S. Hamel, M. Nivat, and C. Reutenauer, On the Palindromic
Complexity of Infinite Words, in J. Berstel, J. Karhumaki, D. Perrin,
Eds, Combinatorics on Words with Applications, International Journal
of Foundation of Computer Science, 15(2):293-306, 2004.
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B. Drisaldi, J. Coomaraswamy, P. Mastrangelo, B. Strome, J. Yang, J.C.
Watts, M.A. Chishti, M. Marvi, O. Windl, R. Ahrens, F. Major, M.S. Sy,
H. Kretzschmar, P.E. Fraser, H.T. Mount, and D. Westaway, Genetic
mapping of activity determinants within cellular prion proteins:
N-terminal modules in PrPC offset pro-apoptotic activity of the Doppel
helix B/B' region, J Biol Chem., 279(53):55443-55454,
PMID: 15459186, 2004.
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N. El-Mabrouk, M. Raffinot, J.E. Duchesne, M. Lajoie, and N. Luc,
Approximate matching of secondary structures'', Journal of
Bioinformatics and computational Biology, 3(2), 2005.
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N. El-Mabrouk, Deriving haplotypes through recombination and gene
conversion, Journal of Bioinformatics and Computational
Biology, 2(2):241-56, 2004.
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N. El-Mabrouk and D. Labuda, Haplotypes histories as pathways of
recombinations, Bioinformatics, 20:1836-1841, 2004.
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V. Guignon, C. Chauve, and S. Hamel, Faster RNA secondary structure
alignment, colloque Robert-Cedergren, 2004.
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S. Hamel, Algorithmes vectoriels et bioinformatique, Publications du
Laboratoire de Combinatoire et d'Informatique Mathématiques, 31,
2004.
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S. Hamel, Computing the Global Similarity of two Strings with a Vector
Algorithm, Currents in Computational Molecular Biology 2004,
A. Gramada and P.E. Bourne Eds, 317-318, 2004.
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A. Lambert, J.F. Fontaine, M. Legendre, F. Leclerc, E. Permal, F. Major,
H. Putzer, O. Delfour, B. Michot, and D. Gautheret. The ERPIN server: an
interface to profile-based RNA motif identification, Nucleic Acids
Res., 32:W160-W165, PMID: 15215371, 2004.
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R. Pinard, D. Lambert, G. Pothiawala, F. Major, and J.M. Burke,
Modifications and deletions of helices within the hairpin
ribozyme-substrate complex: An active ribozyme lacking helix 1,
RNA, 10(3):395-402, PMID: 14970385, 2004. - MC-Sym script
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M. Tikah M., S. Hamel, and A.-R. Schmitzer, Modélisation in-silico de
l'enzyme para-hydroxybenzoate hydroxylase (PHBH) et application au
développement de catalyseurs artificiels, colloque Robert-Cedergren,
2004.
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2003
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N. El-Mabrouk and D. Sankoff, The Reconstruction of Doubled
Genomes, SIAM journal on computing, 32(3):754-792, 2003.
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S. Hamel, How to construct vector algorithms to accelerate some automata
computations, Workshop on Semigroup and Automata, Université
McGill, 2003.
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B. Hoffmann, G.T. Mitchell, P. Gendron, F. Major,
A.A. Andersen, R.A. Collins, and P. Legault, NMR structure of the active
conformation of the Varkud satellite ribozyme cleavage
site, PNAS, 100(12):7003-7008, PMID: 12782785, 2003.
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J.F. Lefebvre, N. El-Mabrouk, E. Tillier, and D. Sankoff, Detection and
validation of single gene inversions, Bioinformatics, Vol. 19,
Suppl. 1, special issue, 11th International Conference on Intelligent
Systems for Molecular Biology (ISMB), 190-196, 2003.
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F. Major and P. Gendron, RNA tertiary structure prediction, Nature
Encyclopedia of the Human Genome (Nature EHG), DN Cooper (Ed),
Nature Publishing Group, 2003.
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F. Major, Building three-dimensional ribonucleic acid structures,
IEEE Computing in Science and Engineering, 5(5):44-53,
2003.
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2002
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Y. Ajana, J.F. Lefebvre, E. Tillier, and N. El-Mabrouk, Exploring
the set of all minimal sequences of reversals - An application to
test the replication-directed reversal hypothesis, Second
Workshop on Algorithms in Bioinformatics (WABI'02), Lecture
Notes in Computer Science, 2452:300-315, 2002.
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A. Bergeron and S. Hamel, Cascade Decompositions are Bit-Vector
Algorithms, Lecture Notes in Computer Science 2494, CIAA01
(International Conference on Automata Computation, 13-26, 2002.
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A. Bergeron and S. Hamel, Vector Algorithms for Approximate String
Matching, International Journal of Foundations of Computer Science
(IJFCS), 13(1):53-66, 2002.
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N. Bourassa and F. Major, Implication of the prohead RNA in phage phi29 DNA
packaging, Biochimie, 84(9):945-51, PMID: 12458086, 2002.
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L. David, P. Amara, M.J. Field, and F. Major, Parametrization of a force
field for metals complexed to biomacromolecules: applications to Fe(II),
Cu(II) and Pb(II), J Computer-Aided Mol. Des.,
16(8-9):635-651, 2002.
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N. El-Mabrouk and M. Raffinot, Approximate Matching of Secondary
Structures, Proceedings of the sixth annual international conference on
computational molecular biology (RECOMB02), 156-164, 2002.
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S. Lemieux and F. Major, RNA canonical and non-canonical base pairing
types: a recognition method and complete repertoire, NAR,
30(19):4250-4263, PMID: 12364604, 2002.
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A. Waugh, P. Gendron, R. Altman, J.W. Brown, D. Case, D. Gautheret,
S.C. Harvey, N. Leontis, J. Westbrook, E. Westhof, M. Zuker, and
F. Major, RNAML: A Standard Syntax for Exchanging RNA Information,
RNA, 8(6):707-717, PMID: 12088144, 2002.
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2001
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I. Barrette, G. Poisson, P. Gendron, and F. Major, Pseudoknots in prion
protein mRNAs confirmed by comparative sequence analysis and pattern
searching, NAR, 29(3):753-758, PMID: 11160898, 2001.
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A. Bergeron and S. Hamel, Fast Implementation of Automata Computations,
Lecture Notes in Computer Science 2088, CIAA00 (International
Conference on Automata Computation), 2001.
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L. David, D. Lambert, P. Gendron, and F. Major, Leadzyme, Methods in
Enzymology, Allen W. Nicholson (Ed); Academic Press Inc.,
NY, 341:518-540, PMID: 11582802, 2001.
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MC-Sym model of the lead-activated ribozyme showing the computing position of the lead atom.
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N. El-Mabrouk, Recovery of ancestral tetraploids, Comparative
Genomics: Empirical and Analytical Approaches to Gene Order Dynamics,
Map alignment and the Evolution of Gene Families, 465-477,
Dordrecht: Kluwer Academic, 2001.
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P. Gendron, S. Lemieux, and F. Major, Quantitative analysis of nucleic
acid three-dimensional
structures, J. Mol. Biol., 308(5):919-936, PMID:
11352582, 2001.
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Protein L11 in contact with a section of the annotated ribosome (yellow indicates residues involved in peculiar relations)
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S. Hamel and A. Bergeron, A Vector Algorithm for Approximate String
Matching with Arbitrary Weighted Distances, Currents in Computational
Molecular Biology 2001, 1-2, 2001.
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F. Major and R. Griffey, Computational Methods for Nucleic Acids
Structure Determination, Current Opinion in Structural
Biology, 11(3):282-286, PMID: 11406375, 2001.
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R. Pinard, K.J. Hampel, J.E. Heckman, D. Lambert, F. Major, and
J.M. Burke, Functional involvement of G8 in the hairpin ribozyme
cleavage mechanism, EMBO J. 20(22):6434-6442, PMID:
11707414, 2001.
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R. Pinard, D. Lambert, J.E. Heckman, J.A. Esteban, C.W. Gundlach 4th,
K.J. Hampel, G.D. Glick, N.G. Walter, F. Major, and J.M. Burke, The
hairpin ribozyme substrate binding domain: A highly constrained
D-shaped conformation. J. Mol. Biol. 307(1):51-65, PMID:
11243803, 2001.
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D. Sankoff, N. El-Mabrouk, Computational Methods for Genome Comparison
and Applications, Current Topics in Computational Biology, Chapter
10, Computational Molecular Biology Series, MIT Press, 2001.
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D. Sankoff, N. El-Mabrouk, Duplication, rearrangement and
reconciliation, Comparative Genomics: Empirical and Analytical
Approaches to Gene Order Dynamics, Map alignment and the Evolution of
Gene Families, 537-550, Dordrecht: Kluwer Academic, 2001.
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2000
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F. Bergeron and S. Hamel, Intersections of modules related to
Macdonald's polynomials, Discrete Mathematics, 217:51-64,
2000.
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N. El-Mabrouk, Genome rearrangement by reversals and
insertions/deletions of contiguous segments, 11th Annual Symposium,
Combinatorial Pattern Matching, Lecture Notes in Computer Science,
Vol. 1848:222-234, Montreal, Canada, 2000.
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N. El-Mabrouk, Reconstruction d'un génome dupliqué
ancestral, Journées Ouvertes Biologie Informatique
Mathématiques (JOBIM2000), 129-140, Montpellier, France, 2000.
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N. El-Mabrouk, Sorting Signed Permutations by Reversals and
Insertions/Deletions of Contiguous Segments, Journal of Discrete
Algorithms, 1(1):105-122, 2000.
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D. Sankoff and N. El-Mabrouk, Reconstitution de l'ordre des gènes
dans les génomes ancestraux à partir de données sur
les familles multigéniques, Journées Ouvertes Biologie
Informatique Mathématiques (JOBIM2000), 303-313, Montpellier,
France, 2000.
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1999
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N. El-Mabrouk, Bryant, and D. Sankoff, Reconstructing the Pre-Doubling
Genome, Proceedings of the third annual international conference on
computational molecular biology (RECOMB'99), 154-163, ACM press,
1999.
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N. El-Mabrouk, D. Sankoff, Hybridization and Genome Rearrangement, 10th
Annual Symposium, Combinatorial Pattern Matching, Lecture Notes in
Computer Science, Vol. 1645:78-87, Warwick University, UK,
1999.
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N. El-Mabrouk and D. Sankoff, On the reconstruction of ancient doubled
circular genomes using minimum reversal, Genome Informatics,
Series No. 10:83-93, Universal Academy Press, Tokyo, 1999.
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R. Pinard, D. Lambert, N.G. Walter, J.E. Heckman, F. Major, and
J.M. Burke, Structural Basis for the Guanosine Requirement of the
Hairpin Ribozyme, Biochemistry, 38(49): 16035-16039, PMID:
10587425, 1999. - MC-Sym script - MC-Sym executable and database used.
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1998
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R. Cedergren and F. Major, Modeling the Tertiary Structure of RNA,
RNA Structure and Function, R.W. Simons and M. Grunberg-Manago
eds., Cold Spring Harbor Press, Cold Spring Harbor, NY., 37-75, 1998.
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N. El-Mabrouk, J. Nadeau, and D. Sankoff, Genome Halving, 9th Annual
Symposium, Combinatorial Pattern Matching, Lecture Notes in Computer
Science, Vol. 1448, M. Farach editor, 235-250, Piscataway,
USA, 1998.
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P. Gendron, D. Gautheret, and F. Major, Structural ribonucleic acid
motifs identification and classification, High Performance
Computing Systems and Applications, Kluwer Academic Press,
323-331, 1998.
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J. Glascow, T. LittleJohn, F. Major, R. Lathrop, D. Sankoff, and
C. Sensen (Eds), Proceedings of the sixth international conference
on intelligent systems for molecular biology, AAAI Press, Menlo
Park, CA. 1998.
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S. Lemieux, P. Chartrand, R. Cedergren and F. Major, Modeling active RNA
structures using the intersection of conformational space: application
to the lead-activated ribozyme. RNA, 4(7):739-49, PMID:
9671048, 1998.
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S. Lemieux, S. Oldziej, and F. Major, Nucleic Acids: Qualitative
Modeling, Encyclopedia of Computational Chemistry,
N.L. Allinger et al. eds., John Wiley & Sons, 1930-1941, 1998.
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F. Major, S. Lemieux, and M. Ftouhi, Computer RNA Three-Dimensional
Modeling from Low-Resolution Data and Multiple-Sequence Information,
Molecular Modeling and Structural Determination of Nucleic
Acids, N.B. Leontis and J. Santa Lucia eds., American Chemical
Society Books, Washington, D.C. 394-404, 1998.
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M. Parisien, M.C. Peitsch, and F. Major, A protein conformational search
space defined by secondary structure contacts, Proceedings of the
Pacific Symposium on Biocomputing, R. Altman et al. eds., World
Scientific Publishers, Singapore, 425-436, 1998.
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F. Zhang, S. Lemieux, X. Wu, D. St-Arnaud, C.T. McMurray, F. Major, and
D. Anderson, A Hexameric Oligomer of RNA Functions in Packaging of
Bacteriophage Phi-29 DNA in Vitro, Molecular Cell,
2(1):141-147, PMID: 9702201, 1998.
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Prohead RNA of bacteriophage phi29
(Pdb file)
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1996
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J.W. Brown, J.M. Nolan, E.S. Haas, M.A. Rubio, F. Major, and N.R. Pace,
Comparative analysis of ribonuclease P RNA using gene sequences from
natural microbial populations reveals tertiary structural
elements, Proc Natl Acad Sci, 93(7):3001-3006, PMID:
8610158, 1996.
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N. El-Mabrouk and M. Crochemore, Boyer-Moore strategy to
efficient approximate string matching, 7th Annual
Symposium, Combinatorial Pattern Matching, Lecture Notes in
Computer Science, 1075, D. Hirschberg and G.Myers
editors, 24-38, California 1996.
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N. El-Mabrouk and F. Lisacek, Very fast identification of RNA motifs in
genomic DNA. Application to tRNA search in the yeast genome, Journal of
Molecular Biology, 264:46-55, 1996.
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F. Major and D. Gautheret, Computer Modeling of RNA 3-D
Structures, Encyclopedia of Molecular Biology and Molecular
Medicine, Robert A. Meyers ed., VCH Publishers Inc., New-York, NY,
371-388, 1996.
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W.J. Wilbur, F. Major, J. Spouge, and S. Bryant, The statistics of
unique native states for random peptides, Biopolymers,
38(4):447-59, PMID: 8867208, 1996.
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1995
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M. Foucrault and F. Major, Symbolic generation and clustering of RNA 3-D
motifs. Proc Int Conf Intell Syst Mol Biol., 3:121-6,
PMID: 7584428, 1995.
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F. Major, Computer Modeling of RNA Three-Dimensional
Structures, Molecular Biology and Biotechnology: A Comprehensive Desk
Reference, Robert A. Meyers ed., VCH Publishers Inc., New-York, NY,
847-850, 1995.
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M. Turcotte, G. Lapalme, and F. Major, Exploring the conformations of
nucleic acids, J Functional Programming, 5:443-460, 1995.
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1994
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T.R. Easterwood, F Major, A. Malhotra, and S.C. Harvey, Orientations of
transfer RNA in the ribosomal A and P sites, NAR,
22(18):3779-86, PMID: 7937092, 1994.
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