74 results
Long-term severe hypoxia adaptation induces non-canonical EMT and a novel Wilms Tumor 1 (WT1) isoform.
Quenneville J, Feghaly A, Tual M, Thomas K, Major F, Gagnon E
Cancer Gene Ther
2024-07-08
;.
Automatic recognition of complementary strands: lessons regarding machine learning abilities in RNA folding.
Chasles S, Major F
Front Genet
2023-09-04
;14:1254226.
D-ORB: A Web Server to Extract Structural Features of Related But Unaligned RNA Sequences.
Dupont MJ, Major F
J Mol Biol
2023-08-01
;435(
15
):168181.
The DynaSig-ML Python package: automated learning of biomolecular dynamics-function relationships.
Mailhot O, Major F, Najmanovich R
Bioinformatics
2023-04-20
;.
Sequence-sensitive elastic network captures dynamical features necessary for miR-125a maturation.
Mailhot O, Frappier V, Major F, Najmanovich RJ
PLoS Comput Biol
2022-12-14
;18(
12
):e1010777.
CAMAP: Artificial neural networks unveil the role of codon arrangement in modulating MHC-I peptides presentation.
Daouda T, Dumont-Lagacé M, Feghaly A, Benslimane Y, Panes R, Courcelles M, Benhammadi M, Harrington L, Thibault P, Major F, Bengio Y, Gagnon E, Lemieux S, Perreault C
PLoS Comput Biol
2021-10-22
;17(
10
):e1009482.
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.
Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki J, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, Ding F, Geniesse C, Jiang Y, Joshi A, Krokhotin A, Magnus M, Mailhot O, Major F, Mann TH, Piątkowski P, Pluta R, Popenda M, Sarzynska J, Sun L, Szachniuk M, Tian S, Wang J, Wang J, Watkins AM, Wiedemann J, Xiao Y, Xu X, Yesselman JD, Zhang D, Zhang Y, Zhang Z, Zhao C, Zhao P, Zhou Y, Zok T, Żyła A, Ren A, Batey RT, Golden BL, Huang L, Lilley DM, Liu Y, Patel DJ, Westhof E
RNA
2020-08-01
;26(
8
):982-995.
From transient recognition to efficient silencing: a RISCky business.
Major F
Nat. Struct. Mol. Biol.
2020-06-01
;27(
6
):519-520.
A transcriptome-based approach to identify functional modules within and across primary human immune cells.
Mola S, Foisy S, Boucher G, Major F, Beauchamp C, Karaky M, Goyette P, Lesage S, Rioux JD
PLoS ONE
2020-01-01
;15(
5
):e0233543.
Apoptotic endothelial cells release small extracellular vesicles loaded with immunostimulatory viral-like RNAs.
Hardy MP, Audemard É, Migneault F, Feghaly A, Brochu S, Gendron P, Boilard É, Major F, Dieudé M, Hébert MJ, Perreault C
Sci Rep
2019-05-10
;9(
1
):7203.
The sequence features that define efficient and specific hAGO2-dependent miRNA silencing guides.
Yan Y, Acevedo M, Mignacca L, Desjardins P, Scott N, Imane R, Quenneville J, Robitaille J, Feghaly A, Gagnon E, Ferbeyre G, Major F
Nucleic Acids Res.
2018-09-19
;46(
16
):8181-8196.
RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data.
Yao J, Reinharz V, Major F, Waldispühl J
Nucleic Acids Res.
2017-07-03
;45(
W1
):W440-W444.
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.
Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B, Xiao Y, Xu X, Zhang D, Zok T, Westhof E
RNA
2017-05-01
;23(
5
):655-672.
Structural dynamics control the MicroRNA maturation pathway.
Dallaire P, Tan H, Szulwach K, Ma C, Jin P, Major F
Nucleic Acids Res.
2016-11-16
;44(
20
):9956-9964.
Exploring Alternative RNA Structure Sets Using MC-Flashfold and db2cm.
Dallaire P, Major F
Methods Mol. Biol.
2016-09-25
;1490:237-51.
MiRBooking simulates the stoichiometric mode of action of microRNAs.
Weill N, Lisi V, Scott N, Dallaire P, Pelloux J, Major F
Nucleic Acids Res.
2015-08-18
;43(
14
):6730-8.
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.
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
2015-06-01
;21(
6
):1066-84.
Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript.
Wheeler EC, Washburn MC, Major F, Rusch DB, Hundley HA
RNA Biol
2015-02-01
;12(
2
):162-74.
Computational identification of RNA functional determinants by three-dimensional quantitative structure-activity relationships.
Blanchet MF, St-Onge K, Lisi V, Robitaille J, Hamel S, Major F
Nucleic Acids Res.
2014-09-08
;42(
17
):11261-71.
Autism-related deficits via dysregulated eIF4E-dependent translational control.
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
Nature
2013-01-17
;493(
7432
):371-7.
Determining RNA three-dimensional structures using low-resolution data.
Parisien M, Major F
J. Struct. Biol.
2012-09-01
;179(
3
):252-60.
Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure.
Reinharz V, Major F, Waldispühl J
Bioinformatics
2012-06-15
;28(
12
):i207-i214.
RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction.
Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, Patel DJ, 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 KM, Waldsich C, Wildauer M, Leontis NB, Westhof E
RNA
2012-04-01
;18(
4
):610-25.
Structural messenger RNA contains cytokeratin polymerization and depolymerization signals.
Kloc M, Dallaire P, Reunov A, Major F
Cell Tissue Res.
2011-11-01
;346(
2
):209-22.
NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions.
Lerman YV, Kennedy SD, Shankar N, Parisien M, Major F, Turner DH
RNA
2011-09-01
;17(
9
):1664-77.
RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles.
Mullen MA, Olson KJ, Dallaire P, Major F, Assmann SM, Bevilacqua PC
Nucleic Acids Res.
2010-12-01
;38(
22
):8149-63.
RNA structure determination using SAXS data.
Yang S, Parisien M, Major F, Roux B
J Phys Chem B
2010-08-12
;114(
31
):10039-48.
Designing small multiple-target artificial RNAs.
De Guire V, Caron M, Scott N, Ménard C, Gaumont-Leclerc MF, Chartrand P, Major F, Ferbeyre G
Nucleic Acids Res.
2010-07-01
;38(
13
):e140.
RKB: a Semantic Web knowledge base for RNA.
Cruz-Toledo J, Dumontier M, Parisien M, Major F
J Biomed Semantics
2010-01-01
;1 Suppl 1:S2.
Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA.
Ensterö M, Daniel C, Wahlstedt H, Major F, Ohman M
Nucleic Acids Res.
2009-11-01
;37(
20
):6916-26.
New metrics for comparing and assessing discrepancies between RNA 3D structures and models.
Parisien M, Cruz JA, Westhof E, Major F
RNA
2009-10-01
;15(
10
):1875-85.
Molecular basis of TRAP-5’SL RNA interaction in the Bacillus subtilis trp operon transcription attenuation mechanism.
McGraw AP, Mokdad A, Major F, Bevilacqua PC, Babitzke P
RNA
2009-01-01
;15(
1
):55-66.
Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme.
Bouchard P, Lacroix-Labonté J, Desjardins G, Lampron P, Lisi V, Lemieux S, Major F, Legault P
RNA
2008-04-01
;14(
4
):736-48.
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data.
Parisien M, Major F
Nature
2008-03-06
;452(
7183
):51-5.
Ranking the factors that contribute to protein beta-sheet folding.
Parisien M, Major F
Proteins
2007-09-01
;68(
4
):824-9.
A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence structure relationships.
Lisi V, Major F
RNA
2007-09-01
;13(
9
):1537-45.
Staufen1 regulates diverse classes of mammalian transcripts.
Kim YK, Furic L, Parisien M, Major F, DesGroseillers L, Maquat LE
EMBO J.
2007-06-06
;26(
11
):2670-81.
An E2F/miR-20a autoregulatory feedback loop.
Sylvestre Y, De Guire V, Querido E, Mukhopadhyay UK, Bourdeau V, Major F, Ferbeyre G, Chartrand P
J. Biol. Chem.
2007-01-26
;282(
4
):2135-43.
Modeling RNA tertiary structure motifs by graph-grammars.
St-Onge K, Thibault P, Hamel S, Major F
Nucleic Acids Res.
2007-01-01
;35(
5
):1726-36.
The RNA Ontology Consortium: an open invitation to the RNA community.
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
RNA
2006-04-01
;12(
4
):533-41.
Identification of two distinct intracellular localization signals in STT3-B.
Caron E, Côté C, Parisien M, Major F, Perreault C
Arch. Biochem. Biophys.
2006-01-01
;445(
1
):108-14.
Automated extraction and classification of RNA tertiary structure cyclic motifs.
Lemieux S, Major F
Nucleic Acids Res.
2006-01-01
;34(
8
):2340-6.
A new catalog of protein beta-sheets.
Parisien M, Major F
Proteins
2005-11-15
;61(
3
):545-58.
A 6374 unigene set corresponding to low abundance transcripts expressed following fertilization in Solanum chacoense Bitt, and characterization of 30 receptor-like kinases.
Germain H, Rudd S, Zotti C, Caron S, O'Brien M, Chantha SC, Lagacé M, Major F, Matton DP
Plant Mol. Biol.
2005-10-01
;59(
3
):515-32.
Identification of a conserved RNA motif essential for She2p recognition and mRNA localization to the yeast bud.
Olivier C, Poirier G, Gendron P, Boisgontier A, Major F, Chartrand P
Mol. Cell. Biol.
2005-06-01
;25(
11
):4752-66.
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.
Drisaldi B, Coomaraswamy J, Mastrangelo P, Strome B, Yang J, Watts JC, Chishti MA, Marvi M, Windl O, Ahrens R, Major F, Sy MS, Kretzschmar H, Fraser PE, Mount HT, Westaway D
J. Biol. Chem.
2004-12-31
;279(
53
):55443-54.
The ERPIN server: an interface to profile-based RNA motif identification.
Lambert A, Fontaine JF, Legendre M, Leclerc F, Permal E, Major F, Putzer H, Delfour O, Michot B, Gautheret D
Nucleic Acids Res.
2004-07-01
;32(
Web Server issue
):W160-5.
Modifications and deletions of helices within the hairpin ribozyme-substrate complex: an active ribozyme lacking helix 1.
Pinard R, Lambert D, Pothiawala G, Major F, Burke JM
RNA
2004-03-01
;10(
3
):395-402.
NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site.
Hoffmann B, Mitchell GT, Gendron P, Major F, Andersen AA, Collins RA, Legault P
Proc. Natl. Acad. Sci. U.S.A.
2003-06-10
;100(
12
):7003-8.
RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire.
Lemieux S, Major F
Nucleic Acids Res.
2002-10-01
;30(
19
):4250-63.