By Dr Martin Smith

Journal articles

Mercer TR; Neph S; Dinger ME; Crawford J; Smith MA; Shearwood AMJ; Haugen E; Bracken CP; Rackham O; Stamatoyannopoulos JA; Filipovska A; Mattick JS, 2011, 'The human mitochondrial transcriptome', Cell, 146, pp. 645 - 658, http://dx.doi.org/10.1016/j.cell.2011.06.051

Khaitan D; Dinger ME; Mazar J; Crawford J; Smith MA; Mattick JS; Perera RJ, 2011, 'The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion', Cancer Research, 71, pp. 3852 - 3862, http://dx.doi.org/10.1158/0008-5472.CAN-10-4460

Askarian-Amiri ME; Crawford J; French JD; Smart CE; Smith MA; Clark MB; Ru K; Mercer TR; Thompson ER; Lakhani SR; Vargas AC; Campbell IG; Brown MA; Dinger ME; Mattick JS, 2011, 'SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer', RNA, 17, pp. 878 - 891, http://dx.doi.org/10.1261/rna.2528811

Müller M; Padmanabhan PK; Rochette A; Mukherjee D; Smith M; Dumas C; Papadopoulou B, 2010, 'Rapid decay of unstable Leishmania mRNAs bearing a conserved retroposon signature 3'-UTR motif is initiated by a site-specific endonucleolytic cleavage without prior deadenylation', Nucleic Acids Research, 38, pp. 5867 - 5883, http://dx.doi.org/10.1093/nar/gkq349

Smith M; Bringaud F; Papadopoulou B, 2009, 'Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome', BMC Genomics, 10, http://dx.doi.org/10.1186/1471-2164-10-240

Rochette A; Raymond F; Ubeda JM; Smith M; Messier N; Boisvert S; Rigault P; Corbeil J; Ouellette M; Papadopoulou B, 2008, 'Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species', BMC Genomics, 9, http://dx.doi.org/10.1186/1471-2164-9-255

Smith M; Blanchette M; Papadopoulou B, 2008, 'Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania', BMC Bioinformatics, 9, http://dx.doi.org/10.1186/1471-2105-9-158

Bringaud F; Müller M; Cerqueira GC; Smith M; Rochette A; El-Sayed NMA; Papadopoulou B; Ghedin E, 2007, 'Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania', Plos Pathogens, 3, pp. 1291 - 1307, http://dx.doi.org/10.1371/journal.ppat.0030136

Working Papers

Du Q; Smith G; Luu PL; Ferguson J; Armstrong N; Caldon E; Campbell E; Nair S; Zotenko E; Gould C; Buckley M; Kaczorowski D; Barton K; Deveson I; Smith M; Powell J; Skvortsova K; Stirzaker C; Achinger-Kawecka J; Clark S, 2020, DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity, http://dx.doi.org10.1101/2020.10.15.338855

Smith M; Ersavas T; Ferguson J; Liu H; Lucas M; Begik O; Bojarski L; Barton K; Novoa EM, 2019, Barcoding and demultiplexing Oxford Nanopore native RNA sequencing reads with deep residual learning, http://dx.doi.org10.1101/864322

Preprints

Gaonac’h-Lovejoy V; Mattick JS; Sauvageau M; Smith MA, 2024, ECSfinder: Optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences, http://dx.doi.org/10.1101/2024.09.14.612549

Sagniez M; Budhraja A; Paré B; Simpson SM; Vinet-Ouellette C; Rozendaal M; Smith MA, 2024, Assembly Arena: Benchmarking RNA isoform reconstruction algorithms for nanopore sequencing, http://dx.doi.org/10.1101/2024.03.21.586080

Ersavas T; Smith MA; Mattick JS, 2024, Novel applications of Convolutional Neural Networks in the age of Transformers, http://dx.doi.org/10.21203/rs.3.rs-3868861/v1

Raad S; David A; Sagniez M; Orfi Z; Dumont N; Smith M; Faure C, 2022, Directed differentiation of EA/TEF patient-derived induced pluripotent stem cells into esophageal epithelial organoids reveal SOX2 dysregulation at the anterior foregut stage, http://dx.doi.org/10.1101/2022.02.14.480418

Sagniez M; Simpson S; Caron M; Rozendaal M; Paré B; Sontag T; Langlois S; Rouette A; Lavallée V-P; Cellot S; Sinnett D; Tran TH; Smith M, 2022, Real-time molecular classification of leukemias, http://dx.doi.org/10.1101/2022.06.22.22276550

Mostefai F; Gamache I; Huang J; N’Guessan A; Pelletier J; Pesaranghader A; Hamelin D; Murall CL; Poujol R; Grenier J-C; Smith M; Caron E; Craig M; Shapiro J; Wolf G; Krishnaswamy S; Hussin JG, 2021, Data-driven approaches for genetic characterization of SARS-CoV-2 lineages, http://dx.doi.org/10.1101/2021.09.28.462270

Hamelin DJ; Fournelle D; Grenier J-C; Schockaert J; Kovalchik K; Kubiniok P; Mostefai F; Duquette JD; Saab F; Sirois I; Smith MA; Pattijn S; Soudeyns H; Decaluwe H; Hussin J; Caron E, 2021, The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA supertype-dependent manner, http://dx.doi.org/10.1101/2021.06.03.446959

Paré B; Rozendaal M; Morin S; Poujol R; Mostefai F; Grenier J-C; Kaufmann L; Xing H; Sanchez M; Yechouron A; Racette R; Hussin J; Wolf G; Pavlov I; Smith MA, 2021, Genomic epidemiology and associated clinical outcomes of a SARS-CoV-2 outbreak in a general adult hospital in Quebec., http://dx.doi.org/10.1101/2021.05.29.21257760

Hardwick SA; Bassett SD; Kaczorowski D; Blackburn J; Barton K; Bartonicek N; Carswell SL; Tilgner HU; Loy C; Halliday G; Mercer TR; Smith MA; Mattick JS, 2019, TARGETED, HIGH-RESOLUTION RNA SEQUENCING OF NON-CODING GENOMIC REGIONS ASSOCIATED WITH NEUROPSYCHIATRIC FUNCTIONS, http://dx.doi.org/10.1101/539882

Chen Y; Prévost J; Ullah I; Romero H; Lisi V; Tolbert WD; Grover JR; Ding S; Gong SY; Beaudoin-Bussières G; Gasser R; Benlarbi M; Vézina D; Anand SP; Chatterjee D; Goyette G; Grunst MW; Yang Z; Bo Y; Zhou F; Béland K; Bai X; Zeher AR; Huang RK; Nguyen DN; Sherburn R; Wu D; Piszczek G; Paré B; Matthies D; Xia D; Richard J; Kumar P; Mothes W; Côté M; Uchil PD; Lavallée V-P; Smith MA; Pazgier M; Haddad E; Finzi A, Molecular basis for antiviral activity of pediatric neutralizing antibodies targeting SARS-CoV-2 Spike receptor binding domain, http://dx.doi.org/10.1101/2022.07.27.501708

Benoit P; Jolicoeur G; Point F; Normand K; Soucy C; Morency-Potvin P; Gagnon S; Kaufmann DE; Tremblay C; Coutlée F; Harrigan PR; Hardy I; Smith M; Savard P; Grandjean Lapierre S, On-Demand Hospital-Based SARS-CoV-2 Genomic Epidemiology to Support Nosocomial Outbreak Investigations: A Prospective Molecular Epidemiology Study in Montreal, http://dx.doi.org/10.2139/ssrn.4199208

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