Dallaire P, Major F. Exploring alternative RNA structure sets using MC-Flashfold and db2cm, Methods Mol Biol. 2016 1490:237-51.

Dallaire P, Tan H, Szulwach K, Ma C, Jin P, Major F. Structural dynamics control the microRNA maturation pathway, Nucleic Acids Res. 2016 gkw793 [Epub ahead of print]


Weill N, Lisi V, Scott N, Dallaire P, Pelloux J, Major F. MirBooking simulates the stoichiometric mode of action of microRNAs, Nucleic Acids Res. 2015 43(14):6730-8.

Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D’Amaré AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E. RNA-puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures, RNA 2015 21(6):1066-84.

Wheeler EC, Washburn MC, Major F, Rusch DB, Hundley HA. Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript, RNA Biol. 2015 12(2):162-74.


Blanchet MF, St-Onge K, Lisi V, Robitaille J, Hamel S, Major F. Computational identification of RNA functional determinants by three-dimensional quantitative structure-activity relationships, Nucleic Acids Res. 42(17):11261-71.

Leong S, Roy J, Parisien M, Major F. Predict RNA 2D and 3D structure over the internet using MC-Tools, Handbook of RNA Biochemistry, Hartmann, Bindereif, Schön and Westhof Eds. Wiley-VCH, Weinheim, Germany, 1384 p.


Gkogkas CG, Khoutorsky A, Ran I, Rampakakis E, Nevarko T, Weatherill DB, Vasuta C, Yee S, Truitt M, Dallaire P, Major F, Lasko P, Ruggero D, Nader K, Lacaille JC, Sonenberg N. Autism-related deficits via dysregulated eIF4E-dependent translational control, Nature 493(7432):371-7.


Parisien M, Major F. Determining RNA Three-Dimensional Structures Using Low-Resolution Data, J Struct Biol 179(3):252-60.

Reinharz V, Major F, Waldispühl J. Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure, Bioinformatics 28(12):i207-i214.

Cruz J, Blanchet MF, et al. RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction, RNA (disponible en-ligne)

Parisien M, Major F. Determining RNA Three-Dimensional Structures Using Low-Resolution Data, J Struct Biol. (disponible en-ligne)


Kloc M, Dallaire P, Reunov A, Major F. Structural messenger RNA contains cytokeratin polymerization and depolymerization signals, Cell Tissue Res. 346(2):209-22.

Lerman Y, Kennedy S, Shankar N, Parisien M, Major F, Turner D. NMR Structure of a 4X4 Nucleotide RNA Internal Loop from an R2 Retrotransposon: Identification of a Three Purine-Purine Sheared Pair Motif and Comparison to MC-SYM Predictions, RNA 17(9):1664-77.


Mullen M, Olson K, Dallaire P, Major F, Assmann S, Bevilacqua, P. RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: Prevalence and possible functional roles, Nucleic Acids Res. 38(22):8149-8163.

Yang S, Parisien M, Major F, Roux B. RNA Structure Determination Using SAXS Data, J Phys Chem B 2010 114(31):10039-48.

Cruz-Toledo J, Dumontier M, Parisien M, Major F. RKB: A Semantic Web Knowledge Base for RNA, J Biomed Semantics 2010 Jun 22;1 Suppl 1:S2.

De Guire V, Caron M, Scott N, Ménard C, Gaumont-Leclerc MF, Chartrand P, Major F, Ferbeyre G. Designing small multiple-target artificial RNAs, Nucleic Acids Res. 2010 38(13):e140 Epub.


Dumontier M, Cruz-Toledo J, Parisien M, Major F. RKB: A Semantic Web Knowledge Base for RNA, Bio-Ontologies 2009: Stockholm, Sweden. 35.

Ensterö M, Daniel C, Wahlstedt H, Major F, Ohman M. Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA, Nucleic Acids Res. 2009 37(20):6916-26.

Parisien M, Almeida Cruz J, Westhof E, Major F. New metrics for comparing and assessing discrepancies between RNA 3D structures and models, RNA 15(10):1875-85.

McGraw AP, Mokdad A, Major F, Bevilacqua PC, Babitzke P. Molecular basis of TRAP-5’SL RNA interaction in the Bacillus subtilis trp operon transcription attenuation mechanism, RNA 2009 Jan;15(1):55-66.


Parisien M, Major F. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 2008, 452(7183):51-55.

Bouchard P, Lacroix-Labonté J, Desjardins G, Lampron P, Lisi V, Lemieux S, Major F, Legault P. Role of SLV in SLI Substrate Recognition by the Neurospora VS Ribozyme, RNA 2008, 14(4):736-48.


Lisi V, Major F. A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence-structure relationships, RNA 2007 13(9):1537-1545. LisiMajor-SuppMat-RNA2007-005975.pdf.

Parisien M, Major F. Ranking the Factors That Contribute to Protein ß-Sheet Folding, Proteins: Structure, Function and Bioinformatics 2007 68(4):824-829.

Kim YK, Furic L, Parisien M, Major F, DesGroseillers L, Maquat LE. Staufen1 Regulates Diverse Classes of Mammalian Transcripts, EMBO J 2007 26(11):2670-2681.

St-Onge K., Thibault P, Hamel S., Major F. Modeling and aligning RNA motifs by graph-grammars, Nucleic Acids Res. 2007 35(5):1726-1736.

Sylvestre Y, De Guire V, Querido E., Mukhopadhyay UK, Major F., Ferbeyre G, Chartrand P. An E2F/mirR-20a auto-regulatory feed-back loop, J Biol Chem 2007 282(4):2135-2143.


Lemieux S, Major F. Automated extraction and classification of RNA tertiary structure cyclic motifs. Nucleic Acids Res 2006, 34(8):3240-3246.

Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, Major F, Mathews DH, Richardson JS, Williamson JR, Westhof E. The RNA Ontology Consortium: An open invitation to the RNA community. RNA 2006, 12(4):533-541.

Caron E, Cote C, Parisien M, Major F, Perreault C. Identification of two distinct intracellular localization signals in STT3-B. Arch Biochem Biophys 2006, 445(1):108-114.


Germain H, Rudd S, Zotti C, Caron S, O’Brien M, Chantha SC, Lagacé M, Major F, Matton DP. 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 Mol Biol 2005 59(3):513-529.

Parisien M, Major F. A New Catalog of Protein -Sheets. Proteins 2005, 61(3):545-558.

Olivier C, Poirier G, Gendron P, Boisgontier A, Major F, Chartrand P. Identification of a Conserved RNA Motif Essential for She2p Recognition and mRNA Localization to the Yeast Bud. Mol Cell Biol 2005, 25:4752-4766.


Drisaldi B, … Major F (11th/16) … Westaway D. Genetic mapping of activity determinants within cellular prion proteins&color; N-terminal modules in PrPC offset pro-apoptotic activity of the Doppel helix B/B’ region. J Biol Chem 2004, 279(53):55443-55454.

Lambert A, Fontaine JF, Legendre M, Leclerc F, Permal E, Major F, Putzer H, Delfour O, Michot B, Gautheret D. The ERPIN server: an interface to profile-based RNA motif identification. Nucleic Acids Res 2004, 32(Web Server Issue):W160-W165.

Pinard R, Lambert D, Pothiawala G, Major F, Burke JM. Modifications and deletions of helices within the hairpin ribozyme-substrate complex: An active ribozyme lacking helix 1. RNA 2004, 10(3):395-402.


Major F. Building Three-Dimensional Ribonucleic Acid Structures. IEEE Comp Sc Eng 2003, 5(5):44-53.

Hoffmann B, Mitchell GT, Gendron P, Major F, Andersen AA, Collins RA, Legault P. NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site. Proc Natl Acad Sci USA 2003, 100(12):7003-7008.


David L, Amara P, Field MJ, Major F. Parametrization of a force field for metals complexed to biomacromolecules: applications to Fe(II), Cu(II) and Pb(II). J Comput Aided Mol Des 2002, 16(8-9):635-651.

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

Lemieux S, Major F. RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire. Nucleic Acids Res 2002, 30(19):4250-63.

Waugh A, Gendron P, Altman R, Brown JW, Case D, Gautheret D, Harvey SC, Leontis N, Westbrook J, Westhof E, Zuker M, Major F. RNAML: a standard syntax for exchanging RNA information. RNA 2002, 8(6):707-717.


Pinard R, Hampel KJ, Heckman JE, Lambert D, Chan PA, Major F, Burke JM. Functional involvement of G8 in the hairpin ribozyme cleavage mechanism. EMBO J. 2001 Nov 15;20(22):6434-42.

David L, Lambert D, Gendron P, Major F. Leadzyme. Methods Enzymol. 2001;341:518-40.

Major F, Griffey R. Computational methods for RNA structure determination. Curr Opin Struct Biol. 2001 Jun;11(3):282-6.

Gendron P, Lemieux S, Major F. Quantitative analysis of nucleic acid three-dimensional structures. J Mol Biol. 2001 May 18;308(5):919-36.

Pinard R, Lambert D, Heckman JE, Esteban JA, Gundlach CW 4th, Hampel KJ, Glick GD, Walter NG, Major F, Burke JM. The hairpin ribozyme substrate binding-domain: a highly constrained D-shaped conformation. J Mol Biol. 2001 Mar 16;307(1):51-65.

Barrette I, Poisson G, Gendron P, Major F. Pseudoknots in prion protein mRNAs confirmed by comparative sequence analysis and pattern searching. Nucleic Acids Res. 2001 Feb 1;29(3):753-8.