Dr Martin Smith

Head – Genomic Technologies

Conjoint/Adjunct Role(s)

Conjoint Lecturer, St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney

Martin's Personal Webpage GraphicI am a computational biologist with a strong background in biology. As a child growing up in Canada, I always dreamt of becoming a biologist. I majored as an undergraduate in microbiology and immunology at the University of Montreal, however I quickly realised this wasn’t my field. Switching to the emerging field of bioinformatics was an enthusiastic yet challenging decision for me, as it required rewiring my brain around abstract informatics concepts and discrete mathematics.

To this day, I am very passionate about bioinformatics and would recommend a cross-disciplinary career path to anyone. I have worked in 5 different cities across 3 different continents, namely Montreal (University of Montreal); Quebec City (Infectious Disease Research Centre—CHUL); Brisbane (Institute for Molecular Bioscience); Leipzig (Interdisciplinary Center for Bioinformatics); and Sydney (Garvan).

My research revolves around characterising the “regulome”, i.e. the biological mechanisms that control how genes are activated and repressed. I am particularly interested in how non-protein coding regions of the genome can regulate gene expression at the level of RNA. 

Research Interests

Oxford Nanopore Sequencing
Comparative genomics
RNA secondary structure
noncoding RNA


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

Selected Publications

p 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. RNA duplex map in living cells reveals higher order transcriptome structure. Cell, 2016, 165(5):1267-1279 (cover article)
Smith MA, Mattick JS. Functional annotation of non-coding RNAs. Bioinformations, Second Edition, Methods in Molecular Biology, Springer (in press) 

Buske FA, French HJ, Smith MA, Clark SJ, Bauer DC. NGSANE: A Lightweight Production Informatics Framework for High Throughput Data AnalysisBioinformatics (2014) 30 (10):1471-1472

Smith MA, Gesell T, Stadler PF, Mattick JS. Widespread purifying selection on RNA structure in mammals. Nucleic Acids Research, 2013, 41 (17): 8220-8236

Clark MB, Choudhary A, Smith MA, Taft RJ, Mattick JS. The dark matter rises: the expanding world of regulatory RNAsEssays Biochem, 2013, 54: 1–16
Shore AN, Kabotyanski EB, Roarty K, Smith MA, Zhang Y, Creighton CJ, Dinger ME, Rosen JM. Pregnancy-Induced Noncoding RNA (PINC) Associates with Polycomb Repressive Complex 2 and Regulates Mammary Epithelial Differentiation. PLoS Genetics, 2012, 8(7): e1002840
Mercer, Neph, Dinger, Crawford, Smith, Shearwood, Rackham, Haugen, Bracken, Stamatoyannopoulos, Filopovska, and Mattick. The human mitochondrial transcriptome. Cell,  2011, 146(4):645-658 (cover article)
Khaitan D, Dinger ME, Mazar J, Crawford J, Smith MA, Mattick JS, Perera RJ. The Melanoma-Upregulated Long Noncoding RNA SPRY4-IT1 Modulates Apoptosis and Invasion. Cancer Research, 2011, 71(11):3852-62
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.  SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA, 2011, 17(5): 878-91
Smith M, Bringaud F, Papadopoulou B. Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome. BMC Genomics, 2009, 10: 240
Rochette A, Raymond F, Ubeda JM, Smith M, Messier N, Boisvert S, Rigault P, Corbeil J, Ouellette M, Papadopoulou B. Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species. BMC Genomics, 2008, 9: 255
Smith M, Blanchette M, Papadopoulou B. Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania. BMC Bioinformatics, 2008, 9: 158
Bringaud F, Muller M, Cerqueira GC, Smith M, Rochette A, El-Sayed NM, Papadopoulou B, Ghedin E.
Members of a Large Retroposon Family Are Determinants of Post-Transcriptional Gene Expression in Leishmania. PLoS Pathogens, 2007, 3(9): 1291-307