Nguyen HD, Allaire A, Diamandis P, Bisaillon M, Scott MS, Richer M. (2020) A machine learning analysis of a "normal-like" IDH-WT diffuse glioma transcriptomic subgroup associated with prolonged survival reveals novel immune and neurotransmitter-related actionable targets. BMC Med Oct 16.

Stephens E, Roy M, Bisson M, Nguyen HD, Scott MS, Boire G, Bouchard L, Roux S. (2020) Osteoclast signaling-targeting miR-146a-3p and miR-155-5p are downregulated in Paget's disease of bone. Biochim Biophys Acta Mol Basis Dis. May 30.

Lambert É, Babeu JP, Simoneau J, Raisch J, Lavergne L, Lévesque D, Jolibois É, Avino M, Scott MS, Boudreau F, Boisvert FM. (2020) Human Hepatocyte Nuclear Factor 4-α Encodes Isoforms with Distinct Transcriptional Functions. Mol. Cell Proteomics. May.

Boivin V, Reulet G, Boisvert O, Couture S, Elela SA, Scott MS. (2020) Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA. Nucleic Acids Res. March 18.

Dubois ML, Meller A, Samandi S, Brunelle M, Frion J, Brunet MA, Toupin A, Beaudoin MC, Jacques JF, Lévesque D, Scott MS, Lavigne P, Roucou X, Boisvert FM. (2020) UBB pseudogene 4 encodes functional ubiquitin variants. Nat Commun. Mar 11.

Bergeron D, Fafard-Couture É, Scott MS. (2020) Small nucleolar RNAs: continuing identification of novel members and increasing diversity of their molecular mechanisms of action. Biochem. Soc. Trans. Apr 29.

Deschamps-Francoeur G, Simoneau J, Scott MS, Deschamps-Francoeur G, Simoneau J, Scott MS, Deschamps-Francoeur G, Simoneau J, Scott MS. (2020) Handling multi-mapped reads in RNA-seq. Comput Struct Biotechnol J .

Bouchard-Bourelle P, Desjardins-Henri C, Mathurin-St-Pierre D, Deschamps-Francoeur G, Fafard-Couture É, Garant JM, Elela SA, Scott MS. (2019) snoDB: an interactive database of human snoRNA sequences, abundance and interactions. Nucleic Acids Res. Oct 10.

Steimers E, Sawall M, Behrens R, Meinhardt D, Simoneau J, Münnemann K, Neymeyr K, von Harbou E. (2019) Application of a new method for simultaneous phase and baseline correction of NMR signals (SINC). Magn Reson Chem. Nov 11.

Boivin V, Faucher-Giguère L, Scott M, Abou-Elela S. (2019) The cellular landscape of mid-size noncoding RNA. Wiley Interdiscip Rev RNA. Mar 06.

Brunet MA, Brunelle M, Lucier JF, Delcourt V, Levesque M, Grenier F, Samandi S, Leblanc S, Aguilar JD, Dufour P, Jacques JF, Fournier I, Ouangraoua A, Scott MS, Boisvert FM, Roucou X. (2019) OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. Nucleic Acids Res. Jan 08.

Simoneau J, Dumontier S, Gosselin R, Scott MS. (2019) Current RNA-seq methodology reporting limits reproducibility. Brief. Bioinformatics. Dec 08.

Deschamps-Francoeur G, Boivin V, Abou Elela S, Scott MS. (2019) CoCo: RNA-seq read assignment correction for nested genes and multimapped reads. Bioinformatics. Dec 01.

Lauzier A, Normandeau-Guimond J, Vaillancourt-Lavigueur V, Boivin V, Charbonneau M, Rivard N, Scott MS, Dubois CM, Jean S. (2019) Colorectal cancer cells respond differentially to autophagy inhibition in vivo. Sci Rep. Aug 05.

Simoneau J, Scott MS. (2019) In silico analysis of RNA-seq requires a more complete description of methodology. Nat. Rev. Mol. Cell Biol. Aug.

Magomedova L, Tiefenbach J, Zilberman E, Le Billan F, Voisin V, Saikali M, Boivin V, Robitaille M, Gueroussov S, Irimia M, Ray D, Patel R, Xu C, Jeyasuria P, Bader GD, Hughes TR, Morris QD, Scott MS, Krause H, Angers S, Blencowe BJ, Cummins CL. (2019) ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development. Nucleic Acids Res. 04 08.

Sawall M, von Harbou E, Moog A, Behrens R, Schröder H, Simoneau J, Steimers E, Neymeyr K. (2018) Multi-objective optimization for an automated and simultaneous phase and baseline correction of NMR spectral data. J. Magn. Reson. Feb 21.

Boivin V, Deschamps-Francoeur G, Couture S, Nottingham RM, Bouchard-Bourelle P, Lambowitz AM, Scott MS, Abou-Elela S. (2018) Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes. RNA Apr 27.

Boivin V, Deschamps-Francoeur G, Scott MS. (2017) Protein coding genes as hosts for noncoding RNA expression. Semin. Cell Dev. Biol. Aug 12.

Garant JM, Perreault JP, Scott MS. (2017) Motif independent identification of potential RNA G-quadruplexes by G4RNA screener. Bioinformatics. Aug 03.

Jammali S, Kuitche E, Rachati A, Bélanger F, Scott M, Ouangraoua A. (2017) Aligning coding sequences with frameshift extension penalties. Algorithms Mol Biol. .

Armero VES, Tremblay MP, Allaire A, Boudreault S, Martenon-Brodeur C, Duval C, Durand M, Lapointe E, Thibault P, Tremblay-Létourneau M, Perreault JP, Scott MS, Bisaillon M. (2017) Transcriptome-wide analysis of alternative RNA splicing events in Epstein-Barr virus-associated gastric carcinomas. PLoS ONE. .

Balthazar P, Tucunduva DC, Luce MJ, Scott MS. (2017) Widespread pre-translational regulation of the inclusion of signal peptides in human proteins. Genomics. .

Ono M, Yamada K, Bensaddek D, Afzal V, Biddlestone J, Ortmann B, Mudie S, Boivin V, Scott MS, Rocha S, Lamond AI. (2016) Enhanced snoMEN Vectors Facilitate Establishment of GFP-HIF-1α Protein Replacement Human Cell Lines. PLoS ONE. .

Luce MJ, Akpawu AA, Tucunduva DC, Mason S, Scott MS. (2016) Extent of pre-translational regulation for the control of nucleocytoplasmic protein localization. BMC Genomics. .

Boudreault S, Martenon-Brodeur C, Caron M, Garant JM, Tremblay MP, Armero VE, Durand M, Lapointe E, Thibault P, Tremblay-Létourneau M, Perreault JP, Scott MS, Lemay G, Bisaillon M. (2016) Global Profiling of the Cellular Alternative RNA Splicing Landscape during Virus-Host Interactions. PLoS ONE. .

Tremblay MP, Armero VE, Allaire A, Boudreault S, Martenon-Brodeur C, Durand M, Lapointe E, Thibault P, Tremblay-Létourneau M, Perreault JP, Scott MS, Bisaillon M. (2016) Global profiling of alternative RNA splicing events provides insights into molecular differences between various types of hepatocellular carcinoma. BMC Genomics. .

Garant JM, Luce MJ, Scott MS, Perreault JP. (2015) G4RNA: an RNA G-quadruplex database. Database (Oxford). Jun 17.

Nguyen D, Grenier St-Sauveur V, Bergeron D, Dupuis-Sandoval F, Scott MS, Bachand F. (2015) A Polyadenylation-Dependent 3' End Maturation Pathway Is Required for the Synthesis of the Human Telomerase RNA. Cell Rep Dec 15.

Dupuis-Sandoval F, Poirier M, Scott MS. (2015) The emerging landscape of small nucleolar RNAs in cell biology. WIREs RNA. Apr 16.

Deschamps-Francoeur G, Garneau D, Dupuis-Sandoval F, Roy A, Frappier M, Catala M, Couture S, Barbe-Marcoux M, Abou-Elela S, Scott MS. (2014) Identification of discrete classes of small nucleolar RNA featuring different ends and RNA binding protein dependency. Nucleic Acids Res. Jul 29.

Scott MS, Ono M, Yamada K, Endo A, Barton GJ, Lamond AI. (2012) Human box C/D snoRNA processing conservation across multiple cell types. Nucleic Acids Res. Apr.

Scott MS, Ono M. (2011) From snoRNA to miRNA: Dual function regulatory non-coding RNAs. Biochimie. Nov.

Ono M, Scott MS, Yamada K, Avolio F, Barton GJ, Lamond AI. (2011) Identification of human miRNA precursors that resemble box C/D snoRNAs. Nucleic Acids Res. May.

Scott MS, Troshin PV, Barton GJ. (2011) NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. BMC Bioinformatics. .

Scott MS, Boisvert FM, Lamond AI, Barton GJ. (2011) PNAC: a protein nucleolar association classifier. BMC Genomics. .

Scott MS, Boisvert FM, McDowall MD, Lamond AI, Barton GJ. (2010) Characterization and prediction of protein nucleolar localization sequences. Nucleic Acids Res. Nov.

Ono M, Yamada K, Avolio F, Scott MS, van Koningsbruggen S, Barton GJ, Lamond AI. (2010) Analysis of human small nucleolar RNAs (snoRNA) and the development of snoRNA modulator of gene expression vectors. Mol. Biol. Cell May 1.

Scott MS, Avolio F, Ono M, Lamond AI, Barton GJ. (2009) Human miRNA precursors with box H/ACA snoRNA features. PLoS Comput. Biol. Sep.

McDowall MD, Scott MS, Barton GJ. (2009) PIPs: human protein-protein interaction prediction database. Nucleic Acids Res. Jan.

Jansen G, Lee AY, Epp E, Fredette A, Surprenant J, Harcus D, Scott M, Tan E, Nishimura T, Whiteway M, Hallett M, Thomas DY. (2009) Chemogenomic profiling predicts antifungal synergies. Mol. Syst. Biol. .

Han X, Feng X, Rattner JB, Smith H, Bose P, Suzuki K, Soliman MA, Scott MS, Burke BE, Riabowol K. (2008) Tethering by lamin A stabilizes and targets the ING1 tumour suppressor. Nat. Cell Biol. Nov.

Scott MS, Barton GJ. (2007) Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics. .

Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott MS, Gramolini AO, Morris Q, Hallett MT, Rossant J, Hughes TR, Frey B, Emili A. (2006) Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell. Apr 7.

Scott MS, Oomen R, Thomas DY, Hallett MT. (2006) Predicting the subcellular localization of viral proteins within a mammalian host cell. Virol. J. .

Scott MS, Calafell SJ, Thomas DY, Hallett MT. (2005) Refining protein subcellular localization. PLoS Comput. Biol. Nov.

Scott MS, Perkins T, Bunnell S, Pepin F, Thomas DY, Hallett M. (2005) Identifying regulatory subnetworks for a set of genes. Mol. Cell Proteomics. May.

Larocque D, Galarneau A, Liu HN, Scott M, Almazan G, Richard S. (2005) Protection of p27(Kip1) mRNA by quaking RNA binding proteins promotes oligodendrocyte differentiation. Nat. Neurosci. Jan.

Scott MS, Thomas DY, Hallett MT. (2004) Predicting subcellular localization via protein motif co-occurrence. Genome Res. Oct.

Scott M, Lu G, Hallett M, Thomas DY. (2004) The Hera database and its use in the characterization of endoplasmic reticulum proteins. Bioinformatics. Apr 12.

Vieyra D, Loewith R, Scott M, Bonnefin P, Boisvert FM, Cheema P, Pastyryeva S, Meijer M, Johnston RN, Bazett-Jones DP, McMahon S, Cole MD, Young D, Riabowol K. (2002) Human ING1 proteins differentially regulate histone acetylation. J. Biol. Chem. Aug 16.

Scott M, Bonnefin P, Vieyra D, Boisvert FM, Young D, Bazett-Jones DP, Riabowol K. (2001) UV-induced binding of ING1 to PCNA regulates the induction of apoptosis. J. Cell. Sci. Oct.

Scott M, Boisvert FM, Vieyra D, Johnston RN, Bazett-Jones DP, Riabowol K. (2001) UV induces nucleolar translocation of ING1 through two distinct nucleolar targeting sequences. Nucleic Acids Res. May 15.