By Dr Martin Smith

Journal articles

Ferreira GR; Emond-Rheault JG; Alves L; Leprohon P; Smith MA; Papadopoulou B, 2024, 'Evolutionary divergent clusters of transcribed extinct truncated retroposons drive low mRNA expression and developmental regulation in the protozoan Leishmania', BMC Biology, 22, http://dx.doi.org/10.1186/s12915-024-02051-4

Kovalchik KA; Hamelin DJ; Kubiniok P; Bourdin B; Mostefai F; Poujol R; Paré B; Simpson SM; Sidney J; Bonneil É; Courcelles M; Saini SK; Shahbazy M; Kapoor S; Rajesh V; Weitzen M; Grenier JC; Gharsallaoui B; Maréchal L; Wu Z; Savoie C; Sette A; Thibault P; Sirois I; Smith MA; Decaluwe H; Hussin JG; Lavallée-Adam M; Caron E, 2024, 'Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines', Nature Communications, 15, http://dx.doi.org/10.1038/s41467-024-54734-9

Ersavas T; Smith MA; Mattick JS, 2024, 'Novel applications of Convolutional Neural Networks in the age of Transformers', Scientific Reports, 14, http://dx.doi.org/10.1038/s41598-024-60709-z

Gress V; Roussy M; Boulianne L; Bilodeau M; Cardin S; El-Hachem N; Lisi V; Khakipoor B; Rouette A; Farah A; Théret L; Aubert L; Fatima F; Audemard E; Thibault P; Bonneil E; Chagraoui J; Larameé L; Gendron P; Jouan L; Jammali S; Paré B; Simpson SM; Tran TH; Duval M; Teira P; Bittencourt H; Santiago R; Barabé F; Sauvageau G; Smith MA; Hébert J; Roux PP; Gruber TA; Lavallée VP; Wilhelm BT; Cellot S, 2024, 'CBFA2T3::GLIS2 pediatric acute megakaryoblastic leukemia is sensitive to BCL-XL inhibition by navitoclax and DT2216', Blood Advances, 8, pp. 112 - 129, http://dx.doi.org/10.1182/bloodadvances.2022008899

Barton K; Ferguson JM; Deveson IW; Falcinelli SD; James KS; Kirchherr J; Ramirez C; Gay CL; Hammond JM; Bevear B; Carswell SL; Margolis DM; Smith MA; Adimora AA; Archin NM, 2023, 'HIVepsilon-seq—scalable characterization of intact persistent proviral HIV reservoirs in women', Journal of Virology, 97, http://dx.doi.org/10.1128/jvi.00705-23

Soucy C; Normand K; Morency-Potvin P; Gagnon S; Kaufmann DE; Tremblay C; Coutlée F; Harrigan PR; Hardy I; Smith M, 2023, 'On-demand, hospital-based, severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic epidemiology to support nosocomial outbreak investigations: A prospective molecular epidemiology study', Antimicrobial Stewardship and Healthcare Epidemiology, 3, http://dx.doi.org/10.1017/ash.2023.119

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 VP; Smith MA; Pazgier M; Haddad E; Finzi A, 2023, 'Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD', iScience, 26, http://dx.doi.org/10.1016/j.isci.2022.105783

Raad S; David A; Sagniez M; Paré B; Orfi Z; Dumont NA; Smith MA; Faure C, 2022, 'iPSCs derived from esophageal atresia patients reveal SOX2 dysregulation at the anterior foregut stage', DMM Disease Models and Mechanisms, 15, http://dx.doi.org/10.1242/dmm.049541

Côté F; Bestman-Smith J; Gourdeau M; Simpson SM; Hamelin MÈ; Carbonneau J; Chiasson A; Rozendaal M; Smith MA; Boivin G, 2022, 'Reinfection with SARS-CoV-2 in a patient undergoing chemotherapy for lymphoma: Case report', JAMMI, 7, pp. 283 - 291, http://dx.doi.org/10.3138/jammi-2021-0036

Gamaarachchi H; Samarakoon H; Jenner SP; Ferguson JM; Amos TG; Hammond JM; Saadat H; Smith MA; Parameswaran S; Deveson IW, 2022, 'Fast nanopore sequencing data analysis with SLOW5', Nature Biotechnology, 40, pp. 1026 - 1029, http://dx.doi.org/10.1038/s41587-021-01147-4

Checkmahomed L; Carbonneau J; Pont VD; Riola NC; Perry JK; Li J; Paré B; Simpson SM; Smith MA; Porter DP; Boivin G, 2022, 'In Vitro Selection of Remdesivir-Resistant SARS-CoV-2 Demonstrates High Barrier to Resistance', Antimicrobial Agents and Chemotherapy, 66, http://dx.doi.org/10.1128/aac.00198-22

Mostefai F; Gamache I; N'Guessan A; Pelletier J; Huang J; Murall CL; Pesaranghader A; Gaonac'h-Lovejoy V; Hamelin DJ; Poujol R; Grenier JC; Smith M; Caron E; Craig M; Wolf G; Krishnaswamy S; Shapiro BJ; Hussin JG, 2022, 'Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages', Frontiers in Medicine, 9, http://dx.doi.org/10.3389/fmed.2022.826746

Hamelin DJ; Fournelle D; Grenier JC; Schockaert J; Kovalchik KA; Kubiniok P; Mostefai F; Duquette JD; Saab F; Sirois I; Smith MA; Pattijn S; Soudeyns H; Decaluwe H; Hussin J; Caron E, 2022, 'The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner', Cell Systems, 13, pp. 143 - 157.e3, http://dx.doi.org/10.1016/j.cels.2021.09.013

Riaz N; Leung P; Barton K; Smith MA; Carswell S; Bull R; Lloyd AR; Rodrigo C, 2021, 'Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants', BMC Genomics, 22, pp. 148, http://dx.doi.org/10.1186/s12864-021-07460-1

Paré B; Rozendaal M; Morin S; Kaufmann L; Simpson SM; Poujol R; Mostefai F; Grenier JC; Xing H; Sanchez M; Yechouron A; Racette R; Hussin JG; Wolf G; Pavlov I; Smith MA, 2021, 'Patient health records and whole viral genomes from an early SARS-CoV-2 outbreak in a Quebec hospital reveal features associated with favorable outcomes', PLoS ONE, 16, http://dx.doi.org/10.1371/journal.pone.0260714

Du Q; Smith GC; Luu PL; Ferguson JM; Armstrong NJ; Caldon CE; Campbell EM; Nair SS; Zotenko E; Gould CM; Buckley M; Chia KM; Portman N; Lim E; Kaczorowski D; Chan CL; Barton K; Deveson IW; Smith MA; Powell JE; Skvortsova K; Stirzaker C; Achinger-Kawecka J; Clark SJ, 2021, 'DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity', Cell Reports, 36, http://dx.doi.org/10.1016/j.celrep.2021.109722

Werner A; Clark JE; Samaranayake C; Casement J; Zinad HS; Sadeq S; Al-Hashimi S; Smith M; Kotaja N; Mattick JS, 2021, 'Widespread formation of double-stranded RNAs in testis', Genome Research, 31, pp. 1174 - 1186, http://dx.doi.org/10.1101/gr.265603.120

Gamaarachchi H; Samarakoon H; Jenner S; Ferguson J; Amos T; Hammond J; Saadat H; Smith M; Parameswaran S; Deveson I, 2021, 'SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis', , http://dx.doi.org/10.1101/2021.06.29.450255

Adikari TN; Riaz N; Sigera C; Leung P; Valencia BM; Barton K; Smith MA; Bull RA; Li H; Luciani F; Weeratunga P; Thein TL; Lim VWX; Leo YS; Rajapakse S; Fink K; Lloyd AR; Fernando D; Rodrigo C; Valencia Arroyo BM, 2020, 'Single molecule, near full-length genome sequencing of dengue virus', Scientific Reports, 10, pp. 18196, http://dx.doi.org/10.1038/s41598-020-75374-1

Smith MA; Ersavas T; Ferguson JM; Liu H; Lucas MC; Begik O; Bojarski L; Barton K; Novoa EM, 2020, 'Molecular barcoding of native RNAs using nanopore sequencing and deep learning', Genome Research, 30, pp. 1345 - 1353, http://dx.doi.org/10.1101/GR.260836.120

Gylling HM; Gonzalez-Aguilera C; Smith MA; Kaczorowski DC; Groth A; Lund AH, 2020, 'Repeat RNAs associate with replication forks and post-replicative DNA', RNA, 26, pp. 1104 - 1117, http://dx.doi.org/10.1261/RNA.074757.120

Gamaarachchi H; Lam CW; Jayatilaka G; Samarakoon H; Simpson JT; Smith MA; Parameswaran S, 2020, 'GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis', BMC Bioinformatics, 21, http://dx.doi.org/10.1186/s12859-020-03697-x

Ruggieri A; Naumenko S; Smith MA; Iannibelli E; Blasevich F; Bragato C; Gibertini S; Barton K; Vorgerd M; Marcus K; Wang P; Maggi L; Mantegazza R; Dowling JJ; Kley RA; Mora M; Minassian BA, 2020, 'Multiomic elucidation of a coding 99-mer repeat-expansion skeletal muscle disease', Acta Neuropathologica, 140, pp. 231 - 235, http://dx.doi.org/10.1007/s00401-020-02164-4

Field MA; Rosen BD; Dudchenko O; Chan EKF; Minoche AE; Edwards RJ; Barton K; Lyons RJ; Tuipulotu DE; Hayes VM; Omer AD; Colaric Z; Keilwagen J; Skvortsova K; Bogdanovic O; Smith MA; Aiden EL; Smith TPL; Zammit RA; Ballard JWO, 2020, 'Canfam-GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C', GigaScience, 9, http://dx.doi.org/10.1093/gigascience/giaa027

Ferguson JM; Smith MA, 2019, 'SquiggleKit: A toolkit for manipulating nanopore signal data', Bioinformatics, 35, pp. 5372 - 5373, http://dx.doi.org/10.1093/bioinformatics/btz586

Liu H; Begik O; Lucas MC; Ramirez JM; Mason CE; Wiener D; Schwartz S; Mattick JS; Smith MA; Novoa EM; Novoa Pardo EM, 2019, 'Accurate detection of m⁶A RNA modifications in native RNA sequences', Nature Communications, 10, pp. 4079, http://dx.doi.org/10.1038/s41467-019-11713-9

Deveson IW; Madala BS; Blackburn J; Barker C; Wong T; Barton KM; Smith MA; Watkins DN; Mercer TR, 2019, 'Chiral DNA sequences as commutable controls for clinical genomics', Nature Communications, 10, http://dx.doi.org/10.1038/s41467-019-09272-0

Gamaarachchi H; Parameswaran S; Smith MA, 2019, 'Featherweight long read alignment using partitioned reference indexes', Scientific Reports, 9, pp. 4318, http://dx.doi.org/10.1038/s41598-019-40739-8

Singh M; Al-Eryani G; Carswell S; Ferguson JM; Blackburn J; Barton K; Roden D; Luciani F; Giang Phan T; Junankar S; Jackson K; Goodnow CC; Smith MA; Swarbrick A, 2019, 'High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes', Nature Communications, 10, http://dx.doi.org/10.1038/s41467-019-11049-4

Corbett MA; Kroes T; Veneziano L; Bennett MF; Florian R; Schneider AL; Coppola A; Licchetta L; Franceschetti S; Suppa A; Wenger A; Mei D; Pendziwiat M; Kaya S; Delledonne M; Straussberg R; Xumerle L; Regan B; Crompton D; van Rootselaar AF; Correll A; Catford R; Bisulli F; Chakraborty S; Baldassari S; Tinuper P; Barton K; Carswell S; Smith M; Berardelli A; Carroll R; Gardner A; Friend KL; Blatt I; Iacomino M; Di Bonaventura C; Striano S; Buratti J; Keren B; Nava C; Forlani S; Rudolf G; Hirsch E; Leguern E; Labauge P; Balestrini S; Sander JW; Afawi Z; Helbig I; Ishiura H; Tsuji S; Sisodiya SM; Casari G; Sadleir LG; van Coller R; Tijssen MAJ; Klein KM; van den Maagdenberg AMJM; Zara F; Guerrini R; Berkovic SF; Pippucci T; Canafoglia L; Bahlo M; Striano P; Scheffer IE; Brancati F; Depienne C; Gecz J, 2019, 'Intronic ATTTC repeat expansions in STARD7 in familial adult myoclonic epilepsy linked to chromosome 2', Nature Communications, 10, http://dx.doi.org/10.1038/s41467-019-12671-y

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', bioRxiv, http://dx.doi.org/10.1101/756122

Liu H; Begik O; Lucas M; Mason C; Schwartz S; Mattick J; Smith M; Novoa EM, 2019, 'Accurate detection of m6A RNA modifications in native RNA sequences', Nature Communications, 10, http://dx.doi.org/10.1101/525741

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', Frontiers in Genetics, 10, pp. 309, http://dx.doi.org/10.3389/fgene.2019.00309

Hamm JN; Erdmann S; Eloe-Fadrosh EA; Angeloni A; Zhong L; Brownlee C; Williams TJ; Barton K; Carswell S; Smith MA; Brazendale S; Hancock AM; Allen MA; Raftery MJ; Cavicchioli R, 2019, 'Unexpected host dependency of Antarctic Nanohaloarchaeota', Proceedings of the National Academy of Sciences of the United States of America, 116, pp. 14661 - 14670, http://dx.doi.org/10.1073/pnas.1905179116

Ferguson J; Smith M, 2019, 'SquiggleKit: A toolkit for manipulating nanopore signal data', , http://dx.doi.org/10.1101/549741

Hardwick SA; Chen WY; Wong T; Kanakamedala BS; Deveson IW; Ongley SE; Santini NS; Marcellin E; Smith MA; Nielsen LK; Lovelock CE; Neilan BA; Mercer TR, 2018, 'Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis', Nature Communications, 9, http://dx.doi.org/10.1038/s41467-018-05555-0

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', BIORXIV, http://dx.doi.org/10.1101/404285

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

Singh M; Al-Eryani G; Carswell S; Ferguson J; Blackburn J; Barton K; Roden D; Luciani F; Phan T; Junankar S; Jackson K; Goodnow C; Smith M; Swarbrick A, 2018, 'High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes', , http://dx.doi.org/10.1101/424945

Smith MA; Seemann SE; Quek XC; Mattick JS, 2017, 'DotAligner: Identification and clustering of RNA structure motifs', Genome Biology, 18, http://dx.doi.org/10.1186/s13059-017-1371-3

Jonkhout N; Tran J; Smith MA; Schonrock N; Mattick JS; Novoa Pardo EM, 2017, 'The RNA modification landscape in human disease', RNA, 23, pp. 1754 - 1769, http://dx.doi.org/10.1261/rna.063503.117

Smith MA; Mattick JS, 2017, 'Structural and functional annotation of long noncoding RNAs', , 1526, pp. 65 - 85, http://dx.doi.org/10.1007/978-1-4939-6613-4_4

Lu Z; Zhang QC; Lee B; Flynn RA; Smith MA; Robinson JT; Davidovich C; Gooding AR; Goodrich KJ; Mattick JS; Mesirov JP; Cech TR; Chang HY, 2016, 'RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure', Cell, 165, pp. 1267 - 1279, http://dx.doi.org/10.1016/j.cell.2016.04.028

Suryani S; Carol H; Chonghaile TN; Frismantas V; Sarmah C; High L; Bornhauser B; Cowley MJ; Szymanska B; Evans K; Boehm I; Tonna E; Jones L; Manesh DM; Kurmasheva RT; Billups C; Kaplan W; Letai A; Bourquin JP; Houghton PJ; Smith MA; Lock RB, 2014, 'Cell and molecular determinants of in vivo efficacy of the BH3 mimetic ABT-263 against pediatric acute lymphoblastic leukemia xenografts', Clin Cancer Res, 20, pp. 4520 - 4531, http://dx.doi.org/10.1158/1078-0432.CCR-14-0259

Buske FA; French HJ; Smith MA; Clark SJ; Bauer DC, 2014, 'NGSANE: a lightweight production informatics framework for high-throughput data analysis', Bioinformatics, 30, pp. 1471 - 1472, http://dx.doi.org/10.1093/bioinformatics/btu036

Smith MA; Gesell T; Stadler PF; Mattick JS, 2013, 'Widespread purifying selection on RNA structure in mammals', Nucleic Acids Research, 41, pp. 8220 - 8236, http://dx.doi.org/10.1093/nar/gkt596

Clark MB; Choudhary A; Smith MA; Taft RJ; Mattick JS, 2013, 'The dark matter rises: The expanding world of regulatory RNAs', Essays in Biochemistry, 54, pp. 1 - 16, http://dx.doi.org/10.1042/BSE0540001

Shore AN; Kabotyanski EB; Roarty K; Smith MA; Zhang Y; Creighton CJ; Dinger ME; Rosen JM, 2012, 'Pregnancy-induced noncoding RNA (PINC) associates with polycomb repressive complex 2 and regulates mammary epithelial differentiation', PLoS Genetics, 8, pp. e1002840, http://dx.doi.org/10.1371/journal.pgen.1002840

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

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