Martin Smith , Ph.D. , M.Sc.
    Martin Smith
    Research Axis
    Immune Diseases and Cancer Axis
    CHUSJ - Centre de Recherche Office 6.17.026

    514 345-4931 2544



    • Assistant Professor-Researcher, Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal


    • PhD in Genomics and Computational Biology, Institute for Molecular Bioscience, University of Queensland, Australia
    • MSc in Bioinformatics, Université de Montréal, Canada
    • BSc in Biological Sciences (major in Microbiology and Immunology), Université de Montréal, Canada

    Research Interests

    I am interested in genome biology and the mechanisms underlying gene expression regulation. In particular, my research focuses on improving the characterisation and profiling of transcriptomes by combining the development of bioinformatics methods with single molecule real-time sequencing.

    One of my lab's main objectives is to translate the latest genomic technologies into new clinical research applications.

    Career Summary

    After majoring in microbiology and immunology at the University of Montreal, I discovered genomics and bioinformatics during my Master’s degree, where I characterised regulatory sequences in the genome of trypoanosomatid parasites.

    I then pursued doctoral studies at the University of Queensland in Australia, using bioinformatics and comparative genomics to identify evolutionarily conserved RNA secondary structures in the human genome and facilitate the functional characterisation of long non-coding RNAs.

    During my postdoc at the Garvan Institute of Medical Research in Sydney, I developed algorithms and pipelines for the analysis of transcriptomic data, including diverse high-throughput RNA sequencing methods. Through this work, I discovered nanopore sequencing, which became a major interest of my team as leader of the genomic technologies program at the Kinghorn Centre for Clinical Genomics.

    Awards and Distinctions

    • CSIRO OnPrime accelerator prize
      Palmer Foundation innovation prize
    • MedTech’s Got Talent startup competition finalist
      Brazilian Association of Bioinformatics & Computational Biology travel award
    • Heliflite Young Explorer travel award
    • Sydney Bioinformatics Symposium, Fast-Forward Poster Prize
    • UWA and UQ bilateral research collaboration award
      University of Queensland Research Scholarship (UQRS)
      International Postgraduate Research Scholarship (IPRS)
    • Faculté des Études Supérieures bioinformatics performance award
    • Robert Cedergren Bioinformatics Colloqium, best poster Master’s level


    • « Dissecting RNA Biology, one molecule at a time »
      London Calling Nanopore Conference, London, UK
      Long Read Conference, Dunedin, New-Zealand
    • « Targeted Long-read Single Cell Sequencing of Tumour and Immune Cells »
      Nanopore Community Meeting, San Francisco, USA
      « Massively multiplexed targeted long-read single cell sequencing for deep phenotyping of tumour and immune cell repertoires »
      QMB Cancer, Queenstown, New-Zealand 2018
    • « Mapping recurring RNA structures to navigate the uncharted genome »
      Computational RNA Biology, Wellcome Trust, Hinxton, UK



    • 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. Nature Communications 10(1):4079 2019
    • Ferguson JM, Smith MA. SquiggleKit: A toolkit for manipulating nanopore signal data. Bioinformatics btz586 2019
    • 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. Nature Communications 10(1):3120 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*. Targeted, high-resolution RNA sequencing of non-coding genomic regions associated with neuropsychiatric functions. Frontiers in Genetics 10:309 2019
    • Deveson IW, Madala BS, Blackburn J, Barker C, Wong T, Barton KM, Smith MA, Watkins ND, Mercer TR. Chiral DNA sequences as commutable reference standards for clinical genomics. Nature Communications 10(1):1342 2019
    • Gamaarachchi H, Parameswaran S, Smith MA. Featherweight long read alignment using partitioned reference indexes. Scientific Reports, 9(1):4318 2019
    • Smith MA*, Seemann SE*, Quek XC, Mattick JS. DotAligner: identification and clustering of RNA structure motifs. Genome Biology 18(1):244 2017
    • Lu Z, Qiangfeng CZ, Lee B, Smith MA, Robinson J, Davidovich C, Gooding AR, Goodrich K, Mattick JS, Mesirov JP, Cech T, Chang HY. RNA duplex map in living cells reveals higher order transcriptome structure. Cell 165(5):1267-1279 2016
    • Smith MA, Gesell T, Stadler PF, Mattick JS. Widespread purifying selection for RNA structure in mammals. Nucleic Acids Res 41(17):8220-36 2013

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