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Dr Martin Smith

Dr Martin Smith

Director
Science
Ramaciotti Centre for Genomics

Martin is a computational biologist with a background in biological sciences. After majoring in microbiology and immunology at the , he undertook a Master's degree in bioinformatics at the in Quebec City, where he studied the . His interest in regulatory sequences in the non-protein coding genome brought him to Australia, where he completed a PhD in genomics and computational biology at the University of Queensland's . His thesis (UQ's lucky !) demonstrated that a substantial fraction of mammalian genomes harbours .

Dr Smith then leveraged the rise of high-throughput sequencing technologies during his postdoctoral research at the in Sydney, where he developed new computational solutions for the analysis of human transcriptomic data. As an early adopter of nanopore sequencing technology, Dr Smith then founded the Genomic Technologies Program at the for Clinical Genomics in 2017, where his group developed new genomic applications for real-time single molecule sequencing. In 2019, Dr Smith moved back to Canada to lead a research team at the (Canada's largest mother-child hospital) and teach bioinformatics at the Department of Biochemistry and Molecular Medicine at the Université de Montréal.

Dr Smith has founded two commercial nanopore sequencing platforms and is listed as an author on several patents. His research interests are focused on transcriptomics and the integration of real-time sequencing and machine learning into new clinical applications.

Location
Ramaciotti Centre for Genomics Office 2106, Biological Sciences Building South (E26)
  • Journal articles | 2024
    Ersavas T; Smith MA; Mattick JS, 2024, 'Novel applications of Convolutional Neural Networks in the age of Transformers', Scientific Reports, 14,
    Journal articles | 2024
    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,
    Journal articles | 2024
    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,
    Journal articles | 2024
    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,
    Journal articles | 2023
    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,
    Journal articles | 2023
    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,
    Journal articles | 2023
    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,
    Journal articles | 2022
    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,
    Journal articles | 2022
    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,
    Journal articles | 2022
    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,
    Journal articles | 2022
    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,
    Journal articles | 2022
    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,
    Journal articles | 2022
    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,
    Journal articles | 2021
    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,
    Journal articles | 2021
    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', ,
    Journal articles | 2021
    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,
    Journal articles | 2021
    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,
    Journal articles | 2021
    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,
    Journal articles | 2020
    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,
    Journal articles | 2020
    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,
    Journal articles | 2020
    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,
    Journal articles | 2020
    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,
    Journal articles | 2020
    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,
    Journal articles | 2020
    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,
    Journal articles | 2019
    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,
    Journal articles | 2019
    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,
    Journal articles | 2019
    Ferguson J; Smith M, 2019, 'SquiggleKit: A toolkit for manipulating nanopore signal data', ,
    Journal articles | 2019
    Ferguson JM; Smith MA, 2019, 'SquiggleKit: A toolkit for manipulating nanopore signal data', Bioinformatics, 35, pp. 5372 - 5373,
    Journal articles | 2019
    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,
    Journal articles | 2019
    Gamaarachchi H; Parameswaran S; Smith MA, 2019, 'Featherweight long read alignment using partitioned reference indexes', Scientific Reports, 9, pp. 4318,
    Journal articles | 2019
    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,
    Journal articles | 2019
    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,
    Journal articles | 2019
    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,
    Journal articles | 2019
    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,
    Journal articles | 2019
    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,
    Journal articles | 2018
    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,
    Journal articles | 2018
    Gamaarachchi H; Parameswaran S; Smith M, 2018, 'Featherweight long read alignment using partitioned reference indexes', BIORXIV,
    Journal articles | 2018
    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,
    Journal articles | 2018
    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', ,
    Journal articles | 2017
    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,
    Journal articles | 2017
    Smith MA; Mattick JS, 2017, 'Structural and functional annotation of long noncoding RNAs', , 1526, pp. 65 - 85,
    Journal articles | 2017
    Smith MA; Seemann SE; Quek XC; Mattick JS, 2017, 'DotAligner: Identification and clustering of RNA structure motifs', Genome Biology, 18,
    Journal articles | 2016
    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,
    Journal articles | 2014
    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,
    Journal articles | 2014
    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,
    Journal articles | 2013
    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,
    Journal articles | 2013
    Smith MA; Gesell T; Stadler PF; Mattick JS, 2013, 'Widespread purifying selection on RNA structure in mammals', Nucleic Acids Research, 41, pp. 8220 - 8236,
    Journal articles | 2012
    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,
    Journal articles | 2011
    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,
    Journal articles | 2011
    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,
    Journal articles | 2011
    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,
    Journal articles | 2010
    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,
    Journal articles | 2009
    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,
    Journal articles | 2008
    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,
    Journal articles | 2008
    Smith M; Blanchette M; Papadopoulou B, 2008, 'Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania', BMC Bioinformatics, 9,
    Journal articles | 2007
    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,
  • Working Papers | 2019
    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,
  • Preprints | 2024
    Gaonac’h-Lovejoy V; Mattick JS; Sauvageau M; Smith MA, 2024, ECSfinder: Optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences,
    Preprints | 2022
    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,
    Preprints | 2022
    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,
    Preprints | 2019
    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,