Selected publications


C. Chauve, V. Guignon, and S. Hamel, An edit distance between RNA stem-loops, SPIRE 2005.

C. Chauve, V. Guignon, and S. Hamel, Distance d'édition entre "tige-boucles", JOBIM 2005.

N. El-Mabrouk, Genome rearrangements with gene families, Mathematics of Evolution and Phylogeny, ed. Olivier Gascuel, Oxford University Press, 2005, in press.

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.

Y-G. Guéhéneuc, S. Hamel, and O. Kaczor, Efficient Identification of Design Patterns with Vector Algorithms, submitted.

S. Hamel, Finding global similarities between proteins using vector algorithms, Proceedings of the Join Conference on Information Science, 1221-1225, 2005.

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.

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.

M. Parisien and F. Major, A New Catalog of Protein Β-Sheets. Proteins: Structure, Function and Bioinformatics, in press.

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.


A. Bergeron and S. Hamel, From cascade decomposition to bit-vector algorithms, Theoretical Computer Science, 313:3-16, 2004.

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.

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.

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.

N. El-Mabrouk, Deriving haplotypes through recombination and gene conversion, Journal of Bioinformatics and Computational Biology, 2(2):241-56, 2004.

N. El-Mabrouk and D. Labuda, Haplotypes histories as pathways of recombinations, Bioinformatics, 20:1836-1841, 2004.

V. Guignon, C. Chauve, and S. Hamel, Faster RNA secondary structure alignment, colloque Robert-Cedergren, 2004.

S. Hamel, Algorithmes vectoriels et bioinformatique, Publications du Laboratoire de Combinatoire et d'Informatique Mathématiques, 31, 2004.

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.

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.

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

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.


N. El-Mabrouk and D. Sankoff, The Reconstruction of Doubled Genomes, SIAM journal on computing, 32(3):754-792, 2003.

S. Hamel, How to construct vector algorithms to accelerate some automata computations, Workshop on Semigroup and Automata, Université McGill, 2003.

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.

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.

F. Major and P. Gendron, RNA tertiary structure prediction, Nature Encyclopedia of the Human Genome (Nature EHG), DN Cooper (Ed), Nature Publishing Group, 2003.

F. Major, Building three-dimensional ribonucleic acid structures, IEEE Computing in Science and Engineering, 5(5):44-53, 2003.


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.

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.

A. Bergeron and S. Hamel, Vector Algorithms for Approximate String Matching, International Journal of Foundations of Computer Science (IJFCS), 13(1):53-66, 2002.

N. Bourassa and F. Major, Implication of the prohead RNA in phage phi29 DNA packaging, Biochimie, 84(9):945-51, PMID: 12458086, 2002.

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.

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.

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.

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.


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.

A. Bergeron and S. Hamel, Fast Implementation of Automata Computations, Lecture Notes in Computer Science 2088, CIAA00 (International Conference on Automata Computation), 2001.

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.

MC-Sym model of the lead-activated ribozyme showing the computing position of the lead atom.

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.

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.

Protein L11 in contact with a section of the annotated ribosome (yellow indicates residues involved in peculiar relations)

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.

F. Major and R. Griffey, Computational Methods for Nucleic Acids Structure Determination, Current Opinion in Structural Biology, 11(3):282-286, PMID: 11406375, 2001.

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.

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.

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.

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.


F. Bergeron and S. Hamel, Intersections of modules related to Macdonald's polynomials, Discrete Mathematics, 217:51-64, 2000.

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.

N. El-Mabrouk, Reconstruction d'un génome dupliqué ancestral, Journées Ouvertes Biologie Informatique Mathématiques (JOBIM2000), 129-140, Montpellier, France, 2000.

N. El-Mabrouk, Sorting Signed Permutations by Reversals and Insertions/Deletions of Contiguous Segments, Journal of Discrete Algorithms, 1(1):105-122, 2000.

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.


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.

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.

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.

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.


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.

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.

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.

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.

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.

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.

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.

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.

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.

Prohead RNA of bacteriophage phi29
(Pdb file)


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.

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.

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.

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.

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.


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.

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.

M. Turcotte, G. Lapalme, and F. Major, Exploring the conformations of nucleic acids, J Functional Programming, 5:443-460, 1995.


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.