By Associate Professor Martin Smith

Preprints

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

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; Lapierre SG, 2022, 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

Gamaarachchi H; Lam CW; Jayatilaka G; Samarakoon H; Simpson J; Smith M; Parameswaran S, 2019, GPU Accelerated Adaptive Banded Event Alignment for Rapid Comparative Nanopore Signal Analysis, http://dx.doi.org/10.1101/756122

Deveson I; Madala BS; Blackburn J; Barker C; Wong T; Barton K; Smith M; Watkins N; Mercer T, 2018, Chiral DNA sequences as commutable reference standards for clinical genomics, http://dx.doi.org/10.1101/404285

Gamaarachchi H; Parameswaran S; Smith M, 2018, Featherweight long read alignment using partitioned reference indexes, http://dx.doi.org/10.1101/386847

Liu H; Begik O; Lucas MC; Mason CE; Schwartz S; Mattick JS; Smith MA; Novoa EM, Accurate detection of m6A RNA modifications in native RNA sequences, http://dx.doi.org/10.1101/525741

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

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, Data-driven approaches for genetic characterization of SARS-CoV-2 lineages, http://dx.doi.org/10.1101/2021.09.28.462270

Raad S; David A; Sagniez M; Orfi Z; Dumont NA; Smith M; Faure C, 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

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, 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

Singh M; Al-Eryani G; Carswell S; Ferguson JM; Blackburn J; Barton K; Roden D; Luciani F; Phan T; Junankar S; Jackson K; Goodnow CC; Smith MA; Swarbrick A, High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes, http://dx.doi.org/10.1101/424945

Caron E; Kovalchik K; Hamelin D; Kubiniok P; Bourdin B; Mostefai F; Poujol R; Paré B; Simpson S; Sidney J; Bonneil E; Courcelles M; Saini SK; Kapoor S; Weitzen M; Grenier J-C; Gharsallaoui B; Maréchal L; Wu Z; Savoie C; Sette A; Thibault P; Sirois I; Smith M; Decaluwe H; Hussin J; Lavallée-Adam M, Integrating Machine Learning-Enhanced Immunopeptidomics and SARS-CoV-2 Population-Scale Analyses Unveils Novel Antigenic Features for Next-Generation COVID-19 Vaccines, http://dx.doi.org/10.21203/rs.3.rs-3914861/v1

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

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

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

Geoffrion N; Lawruk-Desjardins C; Langlois S; Alvarado MA; Dreyer N; Carrier AC; Lisi V; Richer C; St-Hilaire AR; Tremblay-Dauphinais P; Bataille AR; Sontag T; Landais S; Rouette A; Jouan L; Boumela I; Khakipoor B; Fong S; Vairy S; Goudie C; Jabado N; Santiago R; Shlien A; Smith MA; Sinnett D; Cellot S; Tran TH; Lavallée V-P, Single-workflow Nanopore whole genome sequencing with adaptive sampling for accelerated and comprehensive pediatric cancer profiling, http://dx.doi.org/10.1101/2025.10.02.25336569

Gamaarachchi H; Samarakoon H; Jenner S; Ferguson J; Amos T; Hammond J; Saadat H; Smith M; Parameswaran S; Deveson I, SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis, http://dx.doi.org/10.21203/rs.3.rs-668517/v1

Ferguson JM; Smith MA, SquiggleKit: A toolkit for manipulating nanopore signal data, http://dx.doi.org/10.1101/549741

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, Targeted, High-resolution RNA Sequencing of Non-coding Genomic Regions Associated with Neuropsychiatric Functions, http://dx.doi.org/10.1101/539882

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, 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

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