Dr Martin Smith

Visiting Scientist

Dr Martin Smith

Martin is the Genomic Technologies Group Leader at the Kinghorn Centre for Clinical Genomics, located at the Garvan Institute of Medical Research in Sydney, Australia. He is a computational biologist from Canada with a background in genomics, microbiology and immunology. His work has focused on geno

Biography

Martin is the Genomic Technologies Group Leader at the Kinghorn Centre for Clinical Genomics, located at the Garvan Institute of Medical Research in Sydney, Australia. He is a computational biologist from Canada with a background in genomics, microbiology and immunology. His work has focused on genome and transcriptome annotation using comparative genomics and machine learning. He has been using nanopore sequencing since 2014, with a heavy focus on transcriptomic applications. His work aims to develop and implement new applications for precision medicine using real-time nanopore sequencing.

Presentation videos

05/2019 Dissecting RNA Biology, one molecule at a time

12/2018 High-throughput targeted nanopore sequencing of single cells

01/2018 Disruptive DNA sequencing

12/2017 'Squiggle'-cell sequencing

News articles

On-the-spot genome analysis, Science Daily

In Excess of One Million: A Milestone in DNA Sequencing, Genetic Engineering and Biotechnology News

World's longest DNA sequence decoded, BBC News

Martin is the Genomic Technologies Group Leader at the Kinghorn Centre for Clinical Genomics, located at the Garvan Institute of Medical Research in Sydney, Australia. He is a computational biologist from Canada with a background in genomics, microbiology and immunology. His work has focused on genome and transcriptome annotation using comparative genomics and machine learning. He has been using nanopore sequencing since 2014, with a heavy focus on transcriptomic applications. His work aims to develop and implement new applications for precision medicine using real-time nanopore sequencing.

Presentation videos

05/2019 Dissecting RNA Biology, one molecule at a time

12/2018 High-throughput targeted nanopore sequencing of single cells

01/2018 Disruptive DNA sequencing

12/2017 'Squiggle'-cell sequencing

News articles

On-the-spot genome analysis, Science Daily

In Excess of One Million: A Milestone in DNA Sequencing, Genetic Engineering and Biotechnology News

World's longest DNA sequence decoded, BBC News

Education

2012 - PhD Genomics and Computational Biology, Institute for Molecular Bioscience, University of Queensland - Australia
2008 - MSc Bioinformatics, Universite de Montreal & Centre de Recherche en Infectiologie, CHUL - Canada
2004 - BSc Biology, Universite de Montreal - Canada

Patents

Mandeep Singh, Ghamdan Al-Eryani, Martin Smith, Alexander Swarbrick, James Ferguson, Shaun Carswell, Katherine Jackson. Phenotypic and molecular characterisation of single cells. PCT/AU2019/050101

Martin Smith, James Ferguson, Dennis Bunadi. Processing of sequencing data streams. PCT/AU2018/050265

Selected Publications

Journal articles

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 (in press) 

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, Cavic- chioli R. Unexpected host-dependency of Antarctic Nanohaloarchaeota. Proc. Natl. Acad. Sci. U.S.A (in press)

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

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. Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis. Nature Communications, 9(1):3096 2018

Smith MA, Seemann SE, Quek XC, Mattick JS. DotAligner: identification and clustering of RNA structure motifs. Genome Biology 18(1):244 2017

Jonkhout N, Tran J, Smith MA, Schonrock N, Mattick JS, Novoa EM. The RNA modification landscape in human disease. RNA 23(12):1754-1769 2017

Smith MA, Mattick JS. Structural and functional annotation of non-coding RNAs. Bioinformatics (Humana Press, New York, NY), 65-85, 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 (cover article)

Smith MA, Gesell T, Stadler PF, Mattick JS. Widespread purifying selection for RNA structure in mammals. Nucleic Acids Res 41(17):8220-36 2013

Mercer TR, Neph S, Dinger ME, Crawford J, Smith MA, Shearwood AJ, Rackham O, Haugen E, Bracken CP, Stamatoyannopoulos JA, Filopovska A, Mattick JS. The human mitochondrial transcriptome. Cell 146:645-658 2011 (cover article)

Smith M, Bringaud F, Papadopoulou B. Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome. BMC Genomics 10:240 2009

Smith M, Blanchette M, Papadopoulou B. Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania. BMC Bioinformatics 9:158 2008

Preprint publications

Ferguson JM, Smith MA. SquiggleKit: A toolkit for manipulating nanopore signal data. bioRxiv (2019) doi: https://doi.org/10.1101/549741

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. bioRxiv (2019) doi: https://doi.org/10.1101/525741 

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. bioRxiv (2018) doi: https://doi.org/10.1101/424945