Publications


2022

Nguyen HD, Diamandis P, Scott MS, Richer M. (2022) Deciphering of Adult Glioma Vulnerabilities through Expression Pattern Analysis of GABA, Glutamate and Calcium Neurotransmitter Genes. J Pers Med. 12(4). Apr 14.

Chauvin A, Bergeron D, Vencic J, Lévesque D, Paquette B, Scott MS, Boisvert FM. (2022) Downregulation of KRAB zinc finger proteins in 5-fluorouracil resistant colorectal cancer cells. BMC cancer. 22(1):363. Apr 4.

Faucher-Giguère L, Roy A, Deschamps-Francoeur G, Couture S, Nottingham RM, Lambowitz AM, Scott MS, Abou Elela S. (2022) High-grade ovarian cancer associated H/ACA snoRNAs promote cancer cell proliferation and survival. NAR Cancer. 4(1):zcab050. Mar.

Légaré C, Desgagné V, Poirier C, Thibeault K, White F, Clément AA, Scott MS, Jacques PÉ, Perron P, Guérin R, Hivert MF, Bouchard L. (2022) First trimester plasma microRNAs levels predict Matsuda Index-estimated insulin sensitivity between 24th and 29th week of pregnancy. BMJ Open Diabetes Res Care. 10(2). Mar.

Légaré C, Clément AA, Desgagné V, Thibeault K, White F, Guay SP, Arsenault BJ, Scott MS, Jacques PÉ, Perron P, Guérin R, Hivert MF, Bouchard L. (2022) Human plasma pregnancy-associated miRNAs and their temporal variation within the first trimester of pregnancy. Reprod Biol Endocrinol.. 20(1):14. Jan 14.

2021

Nguyen HD, Bisson M, Scott M, Boire G, Bouchard L, Roux S. (2021) miR profile in pagetic osteoclasts: from large-scale sequencing to gene expression study. J Mol Med (Berl). 99(12):1771-1781. Dec.

Zhou D, Couture S, Scott MS, Abou Elela S. (2021) RBFOX2 alters splicing outcome in distinct binding modes with multiple protein partners. Nucleic Acids Res.

Bergeron D, Laforest C, Carpentier S, Calvé A, Fafard-Couture É, Deschamps-Francoeur G, Scott MS. (2021) SnoRNA copy regulation affects family size, genomic location and family abundance levels. BMC Genomics. 22(1):414. Jun 5.

Fafard-Couture É, Bergeron D, Couture S, Abou-Elela S, Scott MS. (2021) Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships. Genome Biol. 22(1):172. Jun 4.

Dumont AA, Dumont L, Zhou D, Giguère H, Pileggi C, Harper ME, Blondin DP, Scott MS, Auger-Messier M. (2021) Cardiomyocyte-specific Srsf3 deletion reveals a mitochondrial regulatory role. FASEB J. 35(5):e21544. May.

Simoneau J, Dumontier S, Gosselin R, Scott MS. (2021) Current RNA-seq methodology reporting limits reproducibility. Brief Bioinform. 22(1):140-145. Jan 18.

Brunet MA, Lucier JF, Levesque M, Leblanc S, Jacques JF, Al-Saedi HRH, Guilloy N, Grenier F, Avino M, Fournier I, Salzet M, Ouangraoua A, Scott MS, Boisvert FM, Roucou X. (2021) OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. Nucleic Acids Res. 49(D1):D380-D388. Jan 8.

2020

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. 18(1):280. 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. 1866(10):165852. Oct 1.

Simoneau J, Gosselin R, Scott MS. (2020) Factorial study of the RNA-seq computational workflow identifies biases as technical gene signatures. NAR Genom Bioinform. 2(2):lqaa043. Jun 29.

Deschamps-Francoeur G, Simoneau J, Scott MS. (2020) Handling multi-mapped reads in RNA-seq. Comput Struct Biotechnol J. 18:1569-1576 Jun 12.

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. 19(5):808-827. May 19.

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. 48(2):645-656. Apr 29.

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. 48(5):2271-2286. Mar 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. 11(1):1306. Mar 11.

Steimers E, Sawall M, Behrens R, Meinhardt D, Simoneau J, Münnemann K, Neymeyr K, von Harbou E. (2020) Application of a new method for simultaneous phase and baseline correction of NMR signals (SINC). Magn Reson Chem. 58(3):260-270. Mar.

Bouchard-Bourelle P, Desjardins-Henri C, Mathurin-St-Pierre D, Deschamps-Francoeur G, Fafard-Couture É, Garant JM, Elela SA, Scott MS. (2020) snoDB: an interactive database of human snoRNA sequences, abundance and interactions. Nucleic Acids Res. 48(D1):D220-D225. Jan 8.

2019

Deschamps-Francoeur G, Boivin V, Abou Elela S, Scott MS. (2019) CoCo: RNA-seq read assignment correction for nested genes and multimapped reads. Bioinformatics. 35(23):5039-5047. Dec 1.

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. 9(1):11316. Aug 5.

Simoneau J, Scott MS. (2019) In silico analysis of RNA-seq requires a more complete description of methodology. Nat Rev Mol Cell Biol. 20(8):451-452. Aug.

Boivin V, Faucher-Giguère L, Scott M, Abou-Elela S. (2019) The cellular landscape of mid-size noncoding RNA. Wiley Interdiscip Rev RNA. 10(4):e1530. Jul.

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. 47(6):2856-2870. Apr 8.

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. 47(D1):D403-D410. Jan 8.

2018

Garant JM, Perreault JP, Scott MS. (2018) G4RNA screener web server: User focused interface for RNA G-quadruplex prediction. Biochimie. 151:115-118 Aug.

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. 24(7):950-965. Jul.

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. 289:132-141 Apr.

Boivin V, Deschamps-Francoeur G, Scott MS. (2018) Protein coding genes as hosts for noncoding RNA expression. Semin Cell Dev Biol. 75:3-12 Mar.

2017

Garant JM, Perreault JP, Scott MS. (2017) Motif independent identification of potential RNA G-quadruplexes by G4RNA screener. Bioinformatics. 33(22):3532-3537. Nov 15.

Balthazar P, Tucunduva DC, Luce MJ, Scott MS. (2017) Widespread pre-translational regulation of the inclusion of signal peptides in human proteins. Genomics. 109(2):113-122. Mar.

Jammali S, Kuitche E, Rachati A, Bélanger F, Scott M, Ouangraoua A. (2017) Aligning coding sequences with frameshift extension penalties. Algorithms Mol Biol. 12:10

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. 12(5):e0176880.

2016

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. 17:683 Aug 26.

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. 17:472 Jun 24.

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. 11(4):e0154759.

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. 11(9):e0161914.

2015

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. 13(10):2244-57. Dec 15.

Garant JM, Luce MJ, Scott MS, Perreault JP. (2015) G4RNA: an RNA G-quadruplex database. Database (Oxford). 2015:bav059 Jun 17.

Dupuis-Sandoval F, Poirier M, Scott MS. (2015) The emerging landscape of small nucleolar RNAs in cell biology. Wiley Interdiscip Rev RNA. 6(4):381-97. Apr 16.

2014

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. 42(15):10073-85. Sep.

2012

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. 40(8):3676-88. Apr.

2011

Scott MS, Ono M. (2011) From snoRNA to miRNA: Dual function regulatory non-coding RNAs. Biochimie. 93(11):1987-92. Nov.

Scott MS, Troshin PV, Barton GJ. (2011) NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. BMC Bioinformatics. 12:317 Aug 3.

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. 39(9):3879-91. May.

Scott MS, Boisvert FM, Lamond AI, Barton GJ. (2011) PNAC: a protein nucleolar association classifier. BMC Genomics. 12:74 Jan 27.

2010

Scott MS, Boisvert FM, McDowall MD, Lamond AI, Barton GJ. (2010) Characterization and prediction of protein nucleolar localization sequences. Nucleic Acids Res. 38(21):7388-99. 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. 21(9):1569-84. May 1.

2009

Scott MS, Avolio F, Ono M, Lamond AI, Barton GJ. (2009) Human miRNA precursors with box H/ACA snoRNA features. PLoS Comput Biol. 5(9):e1000507. Sep.

McDowall MD, Scott MS, Barton GJ. (2009) PIPs: human protein-protein interaction prediction database. Nucleic Acids Res. 37(Database issue):D651-6. 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. 5:338

2008

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. 10(11):1333-40. Nov.

2007

Scott MS, Barton GJ. (2007) Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics. 8:239 Jul 5.

2006

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. 125(1):173-86. 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. 3:24 Apr 4.

2005

Scott MS, Calafell SJ, Thomas DY, Hallett MT. (2005) Refining protein subcellular localization. PLoS Comput Biol. 1(6):e66. 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. 4(5):683-92. 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. 8(1):27-33. Jan.

2004

Scott MS, Thomas DY, Hallett MT. (2004) Predicting subcellular localization via protein motif co-occurrence. Genome Res. 14(10A):1957-66. Oct.

Scott M, Lu G, Hallett M, Thomas DY. (2004) The Hera database and its use in the characterization of endoplasmic reticulum proteins. Bioinformatics. 20(6):937-44. Apr 12.

2002

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. 277(33):29832-9. Aug 16.

2001

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. 114(Pt 19):3455-62. 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. 29(10):2052-8. May 15.