2018

Yan, Yifei, Acevedo Mariana, Mignacca Lian, Desjardins Philippe, Scott Nicolas, Imane Roqaya, Quenneville Jordan, Robitaille Julie, Feghaly Albert, Gagnon Etienne, Ferbeyre Gerardo, Major François. “The sequence features that define efficient and specific hAGO2-dependent miRNA silencing guides”, Nucleic Acids Research (2018). 10.1093/nar/gky546.

2017

Yao, Jason, Reinharz Vladimir, Major François, Waldispühl Jérôme. “RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data”, Nucleic Acids Research 45, no. W1 (2017): 1362-4962. 10.1093/nar/gkx429.

Miao, Zhichao, Adamiak Ryszard W., Antczak Maciej, Batey Robert T., Becka Alexander J., Biesiada Marcin, Boniecki Michał J., Bujnicki Janusz M., Chen Shi-Jie, Cheng Clarence Yu, Chou Fang-Chieh, Ferré-D’Amaré Adrian R., Das Rhiju, Dawson Wayne K., Ding Feng, Dokholyan Nikolay V., Dunin-Horkawicz Stanisław, Geniesse Caleb, Kappel Kalli, Kladwang Wipapat, Krokhotin Andrey, Łach Grzegorz E., Major François, Mann Thomas H., Magnus Marcin, Pachulska-Wieczorek Katarzyna, Patel Dinshaw J., Piccirilli Joseph A., Popenda Mariusz, Purzycka Katarzyna J., Ren Aiming, Rice Greggory M., Santalucia John, Sarzynska Joanna, Szachniuk Marta, Tandon Arpit, Trausch Jeremiah J., Tian Siqi, Wang Jian, Weeks Kevin M., Williams Benfeard, Xiao Yi, Xu Xiaojun, Zhang Dong, Zok Tomasz, Westhof Eric. “RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme”, RNA (New York, N.Y.) 23, no. 5 (2017): 1469-9001. 10.1261/rna.060368.116.

2016

Dallaire, Paul, Major François. “Exploring Alternative RNA Structure Sets Using MC-Flashfold and db2cm”, RNA Structure Determination 1490 (2016).

Dallaire, Paul, Tan Huiping, Szulwach Keith, Ma Christopher, Jin Peng, Major François. “Structural dynamics control the MicroRNA maturation pathway”, Nucleic Acids Research 44, no. 20 (2016): 1362-4962. 10.1093/nar/gkw793.

2015

Weill, Nathanaël, Lisi Véronique, Scott Nicolas, Dallaire Paul, Pelloux Julie, Major François. “MiRBooking simulates the stoichiometric mode of action of microRNAs”, Nucleic Acids Research 43, no. 14 (2015): 0305-1048, 1362-4962. 10.1093/nar/gkv619.

Miao, Zhichao, Adamiak Ryszard W., Blanchet Marc-Frédérick, Boniecki Michal, Bujnicki Janusz M., Chen Shi-Jie, Cheng Clarence, Chojnowski Grzegorz, Chou Fang-Chieh, Cordero Pablo, Cruz José Almeida, Ferré-D’Amaré Adrian R., Das Rhiju, Ding Feng, Dokholyan Nikolay V., Dunin-Horkawicz Stanislaw, Kladwang Wipapat, Krokhotin Andrey, Lach Grzegorz, Magnus Marcin, Major François, Mann Thomas H., Masquida Benoît, Matelska Dorota, Meyer Mélanie, Peselis Alla, Popenda Mariusz, Purzycka Katarzyna J., Serganov Alexander, Stasiewicz Juliusz, Szachniuk Marta, Tandon Arpit, Tian Siqi, Wang Jian, Xiao Yi, Xu Xiaojun, Zhang Jinwei, Zhao Peinan, Zok Tomasz, Westhof Eric. “RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures”, RNA 21, no. 6 (2015): 1355-8382, 1469-9001. 10.1261/rna.049502.114.

Wheeler, Emily C., Washburn Michael C., Major Francois, Rusch Douglas B., Hundley Heather A.. “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 (2015): 1547-6286. 10.1080/15476286.2015.1017220.

2014

Blanchet, Marc-Frédérick, St-Onge Karine, Lisi Véronique, Robitaille Julie, Hamel Sylvie, Major François. “Computational identification of RNA functional determinants by three-dimensional quantitative structure–activity relationships”, Nucleic Acids Research 42, no. 17 (2014): 0305-1048. 10.1093/nar/gku816.

Koan, Stephen Leong, Roy Jonathan, Parisien Marc, Major François. “Predict RNA 2D and 3D Structure over the Internet Using MC-Tools”, Handbook of RNA Biochemistry (2014).

2013

Gkogkas, Christos G., Khoutorsky Arkady, Ran Israeli, Rampakakis Emmanouil, Nevarko Tatiana, Weatherill Daniel B., Vasuta Cristina, Yee Stephanie, Truitt Morgan, Dallaire Paul, Major François, Lasko Paul, Ruggero Davide, Nader Karim, Lacaille Jean-Claude, Sonenberg Nahum. “Autism-related deficits via dysregulated eIF4E-dependent translational control”, Nature 493, no. 7432 (2013): 1476-4687. 10.1038/nature11628.

2012

Reinharz, Vladimir, Major François, Waldispühl Jérôme. “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 (2012): 1367-4803. 10.1093/bioinformatics/bts226.

Cruz, José Almeida, Blanchet Marc-Frédérick, Boniecki Michal, Bujnicki Janusz M., Chen Shi-Jie, Cao Song, Das Rhiju, Ding Feng, Dokholyan Nikolay V., Flores Samuel Coulbourn, Huang Lili, Lavender Christopher A., Lisi Véronique, Major François, Mikolajczak Katarzyna, Patel Dinshaw J., Philips Anna, Puton Tomasz, Santalucia John, Sijenyi Fredrick, Hermann Thomas, Rother Kristian, Rother Magdalena, Serganov Alexander, Skorupski Marcin, Soltysinski Tomasz, Sripakdeevong Parin, Tuszynska Irina, Weeks Kevin M., Waldsich Christina, Wildauer Michael, Leontis Neocles B., Westhof Eric. “RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction”, RNA 18, no. 4 (2012): 1355-8382, 1469-9001. 10.1261/rna.031054.111.

Parisien, Marc, Major François. “Determining RNA three-dimensional structures using low-resolution data”, Journal of Structural Biology 179, no. 3 (2012): 1047-8477. 10.1016/j.jsb.2011.12.024.

2011

Kloc, Malgorzata, Dallaire Paul, Reunov Arkadiy, Major Francois. “Structural messenger RNA contains cytokeratin polymerization and depolymerization signals”, Cell and Tissue Research 346, no. 2 (2011): 0302-766X, 1432-0878. 10.1007/s00441-011-1255-x.

Lerman, Yelena V., Kennedy Scott D., Shankar Neelaabh, Parisien Marc, Major Francois, Turner Douglas H.. “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 (2011): 1355-8382, 1469-9001. 10.1261/rna.2641911.

2010

Yang, Sichun, Parisien Marc, Major François, Roux Benoît. “RNA Structure Determination Using SAXS Data”, The Journal of Physical Chemistry B 114, no. 31 (2010): 1520-6106. 10.1021/jp1057308.

Cruz-Toledo, Jose, Dumontier Michel, Parisien Marc, Major François. “RKB: a Semantic Web knowledge base for RNA”, Journal of Biomedical Semantics 1, no. 1 (2010): 2041-1480. 10.1186/2041-1480-1-S1-S2.

Mullen, Melissa A., Olson Kalee J., Dallaire Paul, Major François, Assmann Sarah M., Bevilacqua Philip C.. “RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles”, Nucleic Acids Research 38, no. 22 (2010): 1362-4962. 10.1093/nar/gkq804.

De Guire, Vincent, Caron Maxime, Scott Nicolas, Ménard Catherine, Gaumont-Leclerc Marie-France, Chartrand Pascal, Major François, Ferbeyre Gerardo. “Designing small multiple-target artificial RNAs”, Nucleic Acids Research 38, no. 13 (2010): 1362-4962. 10.1093/nar/gkq354.

2009

McGraw, Adam P., Mokdad Ali, Major François, Bevilacqua Philip C., Babitzke Paul. “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 (2009): 1469-9001. 10.1261/rna.1314409.

Parisien, Marc, Cruz José Almeida, Westhof Eric, Major François. “New metrics for comparing and assessing discrepancies between RNA 3D structures and models”, RNA (New York, N.Y.) 15, no. 10 (2009): 1469-9001. 10.1261/rna.1700409.

Ensterö, Mats, Daniel Chammiran, Wahlstedt Helene, Major François, Öhman Marie. “Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA”, Nucleic Acids Research 37, no. 20 (2009): 0305-1048. 10.1093/nar/gkp731.

2008

Parisien, Marc, Major François. “The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data”, Nature 452, no. 7183 (2008): 1476-4687. 10.1038/nature06684.

Bouchard, Patricia, Lacroix-Labonté Julie, Desjardins Geneviève, Lampron Philipe, Lisi Véronique, Lemieux Sébastien, Major François, Legault Pascale. “Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme”, RNA (New York, N.Y.) 14, no. 4 (2008): 1469-9001. 10.1261/rna.824308.

2007

St-Onge, Karine, Thibault Philippe, Hamel Sylvie, Major François. “Modeling RNA tertiary structure motifs by graph-grammars”, Nucleic Acids Research 35, no. 5 (2007): 1362-4962. 10.1093/nar/gkm069.

Kim, Yoon Ki, Furic Luc, Parisien Marc, Major François, DesGroseillers Luc, Maquat Lynne E.. “Staufen1 regulates diverse classes of mammalian transcripts”, The EMBO journal 26, no. 11 (2007): 0261-4189. 10.1038/sj.emboj.7601712.

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

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

Sylvestre, Yannick, De Guire Vincent, Querido Emmanuelle, Mukhopadhyay Utpal K., Bourdeau Véronique, Major François, Ferbeyre Gerardo, Chartrand Pascal. “An E2F/miR-20a autoregulatory feedback loop”, The Journal of Biological Chemistry 282, no. 4 (2007): 0021-9258. 10.1074/jbc.M608939200.

2006

Caron, Étienne, Côté Caroline, Parisien Marc, Major François, Perreault Claude. “Identification of two distinct intracellular localization signals in STT3-B”, Archives of Biochemistry and Biophysics 445, no. 1 (2006): 0003-9861. 10.1016/j.abb.2005.10.007.

Lemieux, Sébastien, Major François. “Automated extraction and classification of RNA tertiary structure cyclic motifs”, Nucleic Acids Research 34, no. 8 (2006): 0305-1048. 10.1093/nar/gkl120.

Leontis, Neocles B., Altman Russ B., Berman Helen M., Brenner Steven E., Brown James W., Engelke David R., Harvey Stephen C., Holbrook Stephen R., Jossinet Fabrice, Lewis Suzanna E., Major François, Mathews David H., Richardson Jane S., Williamson James R., Westhof Eric. “The RNA Ontology Consortium: an open invitation to the RNA community”, RNA (New York, N.Y.) 12, no. 4 (2006): 1355-8382. 10.1261/rna.2343206.

2005

Parisien, Marc, Major François. “A new catalog of protein beta-sheets”, Proteins 61, no. 3 (2005): 1097-0134. 10.1002/prot.20677.

Germain, Hugo, Rudd Stephen, Zotti Corine, Caron Sébastien, O’Brien Martin, Chantha Sier-Ching, Lagacé Marie, Major François, Matton Daniel P.. “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 (2005): 0167-4412. 10.1007/s11103-005-0536-8.

Olivier, Catherine, Poirier Guillaume, Gendron Patrick, Boisgontier Anita, Major François, Chartrand Pascal. “Identification of a conserved RNA motif essential for She2p recognition and mRNA localization to the yeast bud”, Molecular and Cellular Biology 25, no. 11 (2005): 0270-7306. 10.1128/MCB.25.11.4752-4766.2005.

2004

Lambert, André, Fontaine Jean-Fred, Legendre Matthieu, Leclerc Fabrice, Permal Emmanuelle, Major François, Putzer Harald, Delfour Olivier, Michot Bernard, Gautheret Daniel. “The ERPIN server: an interface to profile-based RNA motif identification”, Nucleic Acids Research 32, no. Web Server issue (2004): 1362-4962. 10.1093/nar/gkh418.

Drisaldi, Bettina, Coomaraswamy Janaky, Mastrangelo Peter, Strome Bob, Yang Jing, Watts Joel C., Chishti M. Azhar, Marvi Melissa, Windl Otto, Ahrens Rosemary, Major François, Sy Man-Sun, Kretzschmar Hans, Fraser Paul E., Mount Howard T. J., Westaway David. “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 (2004): 0021-9258, 1083-351X. 10.1074/jbc.M404794200.

Pinard, Robert, Lambert Dominic, Pothiawala Gulnar, Major François, Burke John M.. “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 (2004): 1355-8382.

2003

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

Hoffmann, Bernd, Mitchell G. Thomas, Gendron Patrick, Major Francois, Andersen Angela A., Collins Richard A., Legault Pascale. “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 (2003): 0027-8424. 10.1073/pnas.0832440100.

2002

Waugh, Allison, Gendron Patrick, Altman Russ, Brown James W., Case David, Gautheret Daniel, Harvey Stephen C., Leontis Neocles, Westbrook John, Westhof Eric, Zuker Michael, Major François. “RNAML: a standard syntax for exchanging RNA information.”, RNA 8, no. 6 (2002): 1355-8382, 1469-9001.

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

David, Laurent, Amara Patricia, Field Martin J., Major François. “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 (2002): 0920-654X.

Bourassa, Nancy, Major François. “Implication of the prohead RNA in phage phi29 DNA packaging”, Biochimie 84, no. 9 (2002): 0300-9084.

2001

Pinard, Robert, Lambert Dominic, Heckman Joyce E, Esteban José A, Gundlach C. William, Hampel Ken J, D.Glick Gary, Walter Nils G, Major François, Burke John M. “The hairpin ribozyme substrate binding-domain: A highly constrained D-shaped conformation11Edited by J. A. Doudna”, Journal of Molecular Biology 307, no. 1 (2001): 0022-2836. 10.1006/jmbi.2000.4472.

Barrette, Isabelle, Poisson Guylaine, Gendron Patrick, Major François. “Pseudoknots in prion protein mRNAs confirmed by comparative sequence analysis and pattern searching”, Nucleic Acids Research 29, no. 3 (2001): 0305-1048.

Gendron, Patrick, Lemieux Sébastien, Major François. “Quantitative analysis of nucleic acid three-dimensional structures11Edited by I. Tinoco”, Journal of Molecular Biology 308, no. 5 (2001): 0022-2836. 10.1006/jmbi.2001.4626.

Major, François, Griffey Richard. “Computational methods for RNA structure determination”, Current Opinion in Structural Biology 11, no. 3 (2001): 0959-440X. 10.1016/S0959-440X(00)00203-7.

Pinard, Robert, Hampel Ken J., Heckman Joyce E., Lambert Dominic, Chan Philip A., Major Francois, Burke John M.. “Functional involvement of G8 in the hairpin ribozyme cleavage mechanism”, The EMBO Journal 20, no. 22 (2001): 0261-4189, 1460-2075. 10.1093/emboj/20.22.6434.

Supplementary Material