2019

Hardy, M, Audemard, É., Migneault, F., Feghaly, A., Brochu, S., Gendron, P., Boilard, É., Major, F., Dieudé, M., Hébert, M., Perreault, C. Apoptotic endothelial cells release small extracellular vesicles loaded with immunostimulatory viral-like RNAs. Scientific Reports 9, no. 1, 2045-2322; 10.1038/s41598-019-43591-y (2019).

2018

Yan, Y, Acevedo, M., Mignacca, L., Desjardins, P., Scott, N., Imane, R., Quenneville, J., Robitaille, J., Feghaly, A., Gagnon, E., Ferbeyre, G., Major, F. The sequence features that define efficient and specific hAGO2-dependent miRNA silencing guides. Nucleic Acids Research ; 10.1093/nar/gky546 (2018).

2017

Yao, J, Reinharz, V., Major, F., Waldispühl, J. RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data. Nucleic Acids Research 45, no. W1, 1362-4962; 10.1093/nar/gkx429 (2017).

Miao, Z, Adamiak, R., Antczak, M., Batey, R., Becka, A., Biesiada, M., Boniecki, M., Bujnicki, J., Chen, S., Cheng, C., Chou, F., Ferré-D’Amaré, A., Das, R., Dawson, W., Ding, F., Dokholyan, N., Dunin-Horkawicz, S., Geniesse, C., Kappel, K., Kladwang, W., Krokhotin, A., Łach, G., Major, F., Mann, T., Magnus, M., Pachulska-Wieczorek, K., Patel, D., Piccirilli, J., Popenda, M., Purzycka, K., Ren, A., Rice, G., Santalucia, J., Sarzynska, J., Szachniuk, M., Tandon, A., Trausch, J., Tian, S., Wang, J., Weeks, K., Williams, B., Xiao, Y., Xu, X., Zhang, D., Zok, T., Westhof, E. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA (New York, N.Y.) 23, no. 5, 1469-9001; 10.1261/rna.060368.116 (2017).

2016

Dallaire, P, Major, F. Exploring Alternative RNA Structure Sets Using MC-Flashfold and db2cm. RNA Structure Determination 1490 (2016).

Dallaire, P, Tan, H., Szulwach, K., Ma, C., Jin, P., Major, F. Structural dynamics control the MicroRNA maturation pathway. Nucleic Acids Research 44, no. 20, 1362-4962; 10.1093/nar/gkw793 (2016).

2015

Weill, N, Lisi, V., Scott, N., Dallaire, P., Pelloux, J., Major, F. MiRBooking simulates the stoichiometric mode of action of microRNAs. Nucleic Acids Research 43, no. 14, 0305-1048, 1362-4962; 10.1093/nar/gkv619 (2015).

Miao, Z, Adamiak, R., Blanchet, M., Boniecki, M., Bujnicki, J., Chen, S., Cheng, C., Chojnowski, G., Chou, F., Cordero, P., Cruz, J., Ferré-D’Amaré, A., Das, R., Ding, F., Dokholyan, N., Dunin-Horkawicz, S., Kladwang, W., Krokhotin, A., Lach, G., Magnus, M., Major, F., Mann, T., Masquida, B., Matelska, D., Meyer, M., Peselis, A., Popenda, M., Purzycka, K., 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 21, no. 6, 1355-8382, 1469-9001; 10.1261/rna.049502.114 (2015).

Wheeler, E, Washburn, M., Major, F., Rusch, D., Hundley, H. Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript. RNA Biology 12, no. 2, 1547-6286; 10.1080/15476286.2015.1017220 (2015).

2014

Blanchet, M, 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 Research 42, no. 17, 0305-1048; 10.1093/nar/gku816 (2014).

Koan, S, Roy, J., Parisien, M., Major, F. Predict RNA 2D and 3D Structure over the Internet Using MC-Tools. Handbook of RNA Biochemistry (2014).

2013

Gkogkas, C, Khoutorsky, A., Ran, I., Rampakakis, E., Nevarko, T., Weatherill, D., Vasuta, C., Yee, S., Truitt, M., Dallaire, P., Major, F., Lasko, P., Ruggero, D., Nader, K., Lacaille, J., Sonenberg, N. Autism-related deficits via dysregulated eIF4E-dependent translational control. Nature 493, no. 7432, 1476-4687; 10.1038/nature11628 (2013).

2012

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, no. 12, 1367-4803; 10.1093/bioinformatics/bts226 (2012).

Cruz, J, Blanchet, M., Boniecki, M., Bujnicki, J., Chen, S., Cao, S., Das, R., Ding, F., Dokholyan, N., Flores, S., Huang, L., Lavender, C., Lisi, V., Major, F., Mikolajczak, K., Patel, D., Philips, A., Puton, T., Santalucia, J., Sijenyi, F., Hermann, T., Rother, K., Rother, M., Serganov, A., Skorupski, M., Soltysinski, T., Sripakdeevong, P., Tuszynska, I., Weeks, K., Waldsich, C., Wildauer, M., Leontis, N., Westhof, E. RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction. RNA 18, no. 4, 1355-8382, 1469-9001; 10.1261/rna.031054.111 (2012).

Parisien, M, Major, F. Determining RNA three-dimensional structures using low-resolution data. Journal of Structural Biology 179, no. 3, 1047-8477; 10.1016/j.jsb.2011.12.024 (2012).

2011

Kloc, M, Dallaire, P., Reunov, A., Major, F. Structural messenger RNA contains cytokeratin polymerization and depolymerization signals. Cell and Tissue Research 346, no. 2, 0302-766X, 1432-0878; 10.1007/s00441-011-1255-x (2011).

Lerman, Y, Kennedy, S., Shankar, N., Parisien, M., Major, F., Turner, D. NMR structure of a 4 × 4 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, no. 9, 1355-8382, 1469-9001; 10.1261/rna.2641911 (2011).

2010

Yang, S, Parisien, M., Major, F., Roux, B. RNA Structure Determination Using SAXS Data. The Journal of Physical Chemistry B 114, no. 31, 1520-6106; 10.1021/jp1057308 (2010).

Cruz-Toledo, J, Dumontier, M., Parisien, M., Major, F. RKB: a Semantic Web knowledge base for RNA. Journal of Biomedical Semantics 1, no. 1, 2041-1480; 10.1186/2041-1480-1-S1-S2 (2010).

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 Research 38, no. 22, 1362-4962; 10.1093/nar/gkq804 (2010).

De Guire, V, Caron, M., Scott, N., Ménard, C., Gaumont-Leclerc, M., Chartrand, P., Major, F., Ferbeyre, G. Designing small multiple-target artificial RNAs. Nucleic Acids Research 38, no. 13, 1362-4962; 10.1093/nar/gkq354 (2010).

2009

McGraw, A, Mokdad, A., Major, F., Bevilacqua, P., Babitzke, P. Molecular basis of TRAP-5’SL RNA interaction in the Bacillus subtilis trp operon transcription attenuation mechanism. RNA (New York, N.Y.) 15, no. 1, 1469-9001; 10.1261/rna.1314409 (2009).

Parisien, M, Cruz, J., Westhof, E., Major, F. New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA (New York, N.Y.) 15, no. 10, 1469-9001; 10.1261/rna.1700409 (2009).

Ensterö, M, Daniel, C., Wahlstedt, H., Major, F., Öhman, M. Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA. Nucleic Acids Research 37, no. 20, 0305-1048; 10.1093/nar/gkp731 (2009).

2008

Parisien, M, Major, F. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452, no. 7183, 1476-4687; 10.1038/nature06684 (2008).

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 (New York, N.Y.) 14, no. 4, 1469-9001; 10.1261/rna.824308 (2008).

2007

St-Onge, K, Thibault, P., Hamel, S., Major, F. Modeling RNA tertiary structure motifs by graph-grammars. Nucleic Acids Research 35, no. 5, 1362-4962; 10.1093/nar/gkm069 (2007).

Kim, Y, Furic, L., Parisien, M., Major, F., DesGroseillers, L., Maquat, L. Staufen1 regulates diverse classes of mammalian transcripts. The EMBO journal 26, no. 11, 0261-4189; 10.1038/sj.emboj.7601712 (2007).

Parisien, M, Major, F. Ranking the factors that contribute to protein β-sheet folding. Proteins: Structure, Function, and Bioinformatics 68, no. 4, 1097-0134; 10.1002/prot.21475 (2007).

Lisi, V, Major, F. A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence structure relationships. RNA (New York, N.Y.) 13, no. 9, 1355-8382; 10.1261/rna.597507 (2007).

Sylvestre, Y, De Guire, V., Querido, E., Mukhopadhyay, U., Bourdeau, V., Major, F., Ferbeyre, G., Chartrand, P. An E2F/miR-20a autoregulatory feedback loop. The Journal of Biological Chemistry 282, no. 4, 0021-9258; 10.1074/jbc.M608939200 (2007).

2006

Caron, É, Côté, C., Parisien, M., Major, F., Perreault, C. Identification of two distinct intracellular localization signals in STT3-B. Archives of Biochemistry and Biophysics 445, no. 1, 0003-9861; 10.1016/j.abb.2005.10.007 (2006).

Lemieux, S, Major, F. Automated extraction and classification of RNA tertiary structure cyclic motifs. Nucleic Acids Research 34, no. 8, 0305-1048; 10.1093/nar/gkl120 (2006).

Leontis, N, Altman, R., Berman, H., Brenner, S., Brown, J., Engelke, D., Harvey, S., Holbrook, S., Jossinet, F., Lewis, S., Major, F., Mathews, D., Richardson, J., Williamson, J., Westhof, E. The RNA Ontology Consortium: an open invitation to the RNA community. RNA (New York, N.Y.) 12, no. 4, 1355-8382; 10.1261/rna.2343206 (2006).

2005

Parisien, M, Major, F. A new catalog of protein beta-sheets. Proteins 61, no. 3, 1097-0134; 10.1002/prot.20677 (2005).

Germain, H, Rudd, S., Zotti, C., Caron, S., O’Brien, M., Chantha, S., Lagacé, M., Major, F., Matton, D. A 6374 unigene set corresponding to low abundance transcripts expressed following fertilization in Solanum chacoense Bitt, and characterization of 30 receptor-like kinases. Plant Molecular Biology 59, no. 3, 0167-4412; 10.1007/s11103-005-0536-8 (2005).

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. Molecular and Cellular Biology 25, no. 11, 0270-7306; 10.1128/MCB.25.11.4752-4766.2005 (2005).

2004

Lambert, A, Fontaine, J., 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 Research 32, no. Web Server issue, 1362-4962; 10.1093/nar/gkh418 (2004).

Drisaldi, B, Coomaraswamy, J., Mastrangelo, P., Strome, B., Yang, J., Watts, J., Chishti, M., Marvi, M., Windl, O., Ahrens, R., Major, F., Sy, M., Kretzschmar, H., Fraser, P., Mount, H., Westaway, D. 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. Journal of Biological Chemistry 279, no. 53, 0021-9258, 1083-351X; 10.1074/jbc.M404794200 (2004).

Pinard, R, Lambert, D., Pothiawala, G., Major, F., Burke, J. Modifications and deletions of helices within the hairpin ribozyme-substrate complex: an active ribozyme lacking helix 1. RNA (New York, N.Y.) 10, no. 3, 1355-8382 (2004).

2003

Major, F Building three-dimensional ribonucleic acid structures. Computing in Science Engineering 5, no. 5, 1521-9615; 10.1109/MCISE.2003.1225860 (2003).

Hoffmann, B, Mitchell, G., Gendron, P., Major, F., Andersen, A., Collins, R., Legault, P. NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site. Proceedings of the National Academy of Sciences of the United States of America 100, no. 12, 0027-8424; 10.1073/pnas.0832440100 (2003).

2002

Waugh, A, Gendron, P., Altman, R., Brown, J., Case, D., Gautheret, D., Harvey, S., Leontis, N., Westbrook, J., Westhof, E., Zuker, M., Major, F. RNAML: a standard syntax for exchanging RNA information.. RNA 8, no. 6, 1355-8382, 1469-9001 (2002).

Lemieux, S, Major, F. RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire. Nucleic Acids Research 30, no. 19, 1362-4962 (2002).

David, L, Amara, P., Field, M., Major, F. Parametrization of a force field for metals complexed to biomacromolecules: applications to Fe(II), Cu(II) and Pb(II). Journal of Computer-Aided Molecular Design 16, no. 8-9, 0920-654X (2002).

Bourassa, N, Major, F. Implication of the prohead RNA in phage phi29 DNA packaging. Biochimie 84, no. 9, 0300-9084 (2002).

2001

Pinard, R, Lambert, D., Heckman, J., Esteban, J., Gundlach, C., Hampel, K., D.Glick, G., Walter, N., Major, F., Burke, J. The hairpin ribozyme substrate binding-domain: A highly constrained D-shaped conformation11Edited by J. A. Doudna. Journal of Molecular Biology 307, no. 1, 0022-2836; 10.1006/jmbi.2000.4472 (2001).

Barrette, I, Poisson, G., Gendron, P., Major, F. Pseudoknots in prion protein mRNAs confirmed by comparative sequence analysis and pattern searching. Nucleic Acids Research 29, no. 3, 0305-1048 (2001).

Gendron, P, Lemieux, S., Major, F. Quantitative analysis of nucleic acid three-dimensional structures11Edited by I. Tinoco. Journal of Molecular Biology 308, no. 5, 0022-2836; 10.1006/jmbi.2001.4626 (2001).

Major, F, Griffey, R. Computational methods for RNA structure determination. Current Opinion in Structural Biology 11, no. 3, 0959-440X; 10.1016/S0959-440X(00)00203-7 (2001).

Pinard, R, Hampel, K., Heckman, J., Lambert, D., Chan, P., Major, F., Burke, J. Functional involvement of G8 in the hairpin ribozyme cleavage mechanism. The EMBO Journal 20, no. 22, 0261-4189, 1460-2075; 10.1093/emboj/20.22.6434 (2001).

Supplementary Material