Leblanc S, Yala F, Provencher N, Lucier JF, Levesque M, Lapointe X, Jacques JF, Fournier I, Salzet M, Ouangraoua A, Scott MS, Boisvert FM, Brunet MA, Roucou X. (2024) OpenProt 2.0 builds a path to the functional characterization of alternative proteins. None. 52(D1):D522-D528. Jan 5.


Paraqindes H, Mourksi NE, Ballesta S, Hedjam J, Bourdelais F, Fenouil T, Picart T, Catez F, Combe T, Ferrari A, Kielbassa J, Thomas E, Tonon L, Viari A, Attignon V, Carrere M, Perrossier J, Giraud S, Vanbelle C, Gabut M, Bergeron D, Scott MS, Castro Vega L, Magne N, Huillard E, Sanson M, Meyronet D, Diaz JJ, Ducray F, Marcel V, Durand S. (2023) Isocitrate dehydrogenase wt and IDHmut adult-type diffuse gliomas display distinct alterations in ribosome biogenesis and 2'O-methylation of ribosomal RNA. None. 25(12):2191-2206. Dec 8.

Chowdhury MR, Hone KGMS, Prévost K, Balthazar P, Avino M, Arguin M, Beaudoin J, Malick M, Desgagné M, Robert G, Scott M, Dubé J, Laforest-Lapointe I, Massé E. (2023) Optimizing Fecal Occult Blood Test (FOBT) Colorectal Cancer Screening Using Gut Bacteriome as a Biomarker. None.

Hoang Dong N, Audrey L, Leopold MN, Javier M, Hugues AC, Luigi B, Gilles B, Scott MS, Sophie R. (2023) Osteoclast microRNA Profiling in Rheumatoid Arthritis to Capture the Erosive Factor. None. 7(8):e10776. Aug.

Bergeron D, Faucher-Giguère L, Emmerichs AK, Choquet K, Song KS, Deschamps-Francoeur G, Fafard-Couture É, Rivera A, Couture S, Churchman LS, Heyd F, Abou Elela S, Scott MS. (2023) Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences. None. 24(1):160. Jul 6.

Brand C, Deschamps-Francoeur G, Bullard-Feibelman KM, Scott MS, Geiss BJ, Bisaillon M. (2023) Kunjin Virus, Zika Virus, and Yellow Fever Virus Infections Have Distinct Effects on the Coding Transcriptome and Proteome of Brain-Derived U87 Cells. None. 15(7). Jun 23.

Fafard-Couture É, Jacques PÉ, Scott MS. (2023) Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates. None. 33(4):525-540. Apr.

Bergeron D, Paraqindes H, Fafard-Couture É, Deschamps-Francoeur G, Faucher-Giguère L, Bouchard-Bourelle P, Abou Elela S, Catez F, Marcel V, Scott MS. (2023) snoDB 2.0: an enhanced interactive database, specializing in human snoRNAs. Nucleic Acids Res. 51(D1):D291-D296. Jan 6.


Kerkhofs K, Garg J, Fafard-Couture É, Abou Elela S, Scott MS, Pearlman RE, Bayfield MA. (2022) Altered tRNA processing is linked to a distinct and unusual La protein in Tetrahymena thermophila. Nat Commun. 13(1):7332. Nov 28.

Leblanc S, Brunet MA, Jacques JF, Lekehal AM, Duclos A, Tremblay A, Bruggeman-Gascon A, Samandi S, Brunelle M, Cohen AA, Scott MS, Roucou X. (2022) Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities. Genomics Proteomics Bioinformatics. Ahead of print. Sep 29.

Malik Ghulam M, Catala M, Reulet G, Scott MS, Abou Elela S. (2022) Duplicated ribosomal protein paralogs promote alternative translation and drug resistance. Nat Commun. 13(1):4938. Aug 23.

Thibeault K, Légaré C, Desgagné V, White F, Clément AA, Scott MS, Jacques PÉ, Guérin R, Perron P, Hivert MF, Bouchard L. (2022) Maternal Body Mass Index Is Associated with Profile Variation in Circulating MicroRNAs at First Trimester of Pregnancy. Biomedicines. 10(7). Jul 18.

Deschamps-Francoeur G, Couture S, Abou-Elela S, Scott MS. (2022) The snoGloBe interaction predictor reveals a broad spectrum of C/D snoRNA RNA targets. Nucleic Acids Res. 50(11):6067-6083. Jun 24.

Zhou D, Tran Y, Abou Elela S, Scott MS. (2022) SAPFIR: A webserver for the identification of alternative protein features. BMC Bioinformatics. 23(1):250. Jun 24.

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.

Légaré C, Desgagné V, Thibeault K, White F, Clément AA, Poirier C, Luo ZC, Scott MS, Jacques PÉ, Perron P, Guérin R, Hivert MF, Bouchard L. (2022) First Trimester Plasma MicroRNA Levels Predict Risk of Developing Gestational Diabetes Mellitus. None. 13:928508


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.

. (2021) RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. None. 49(D1):D212-D220. Jan 8.

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.


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.


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.


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.


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.

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.

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


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.


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.


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.


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.


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.


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.


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


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.


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


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.


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.


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.


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.


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.