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Research

Interests

RNA is the most polyvalent macromolecule in cells. It functions not only as a messenger that conveys digital information to analog effectors, but also as a dynamic structure capable of catalysis and regulation on its own. This duality enables a seemingly infinite web of regulatory complexity, reinforced by the quadratic preponderance of transcribed, non protein-coding sequences in the genomes of higher eukaryotes. This is why I love RNA, in particular its non-protein coding faction.

I believe most geneticists tend to have a linear perspective of the human genome and the transcriptome. This has been supported by various canonical illustrations of genetic structure in addition to the now common representation of next-generation sequencing results. Indeed, much effort is invested in observing the presence or absence of genomic sequence, while neglecting the elucidation of higher structural order and quaternary interactions.

I am currently pursuing postdoctoral research in the RNA Biology and Plasticity laboratory at the Garvan Institute of Medical Research, which is spearheaded by Prof. John S. Mattick.

Academia

When? What and where? Who?
10/2008 - 10/2012 PhD Genomics and Computational Biology.
University of Queensland
John S. Mattick
Peter F. Stadler
9/2005 - 1/2008 MSc Bioinformatics.
University of Montreal
Barbara Papadopoulou
Mathieu Blanchette
Gertraud Burger
9/2001 - 6/2004 BSc Biological Sciences: Microbiology and Immunology
University of Montreal

Publications

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure
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.
Cell, 165(5):1267-1279, 2016

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

Widespread purifying selection on RNA structure in mammals.
Smith MA, Gesell T, Stadler PF, Mattick JS
Nucleic Acids Research, 41(17):8220-8236, 2013
Click here for more details and to view the data in the UCSC genome browser

The dark matter rises: the expanding world of regulatory RNAs
Clark MB, Choudhary A, Smith MA, Taft RJ, Mattick JM.
Essays Biochem, 54:1-16, 2013

Pregnancy-Induced Noncoding RNA (PINC) Associates with Polycomb Repressive Complex 2 and Regulates Mammary Epithelial Differentiation.
Shore AN, Kabotyanski EB, Roarty K, Smith MA, Zhang Y, Creighton CJ, Dinger ME, Rosen JM.
PLoS Genetics, 8:e1002840 July 2012

The human mitochondrial transcriptome.
Tim R. Mercer, Shane Neph, Marcel E. Dinger, Joanna Crawford, Martin A. Smith, Anne-Marie J. Shearwood, Oliver Rackham, Eric Haugen, Cameron P. Bracken, John A. Stamatoyannopoulos, Aleksandra Filopovska, and John S. Mattick.
Cell, Volume 146, Issue 4, 645-658, 19 August 2011

The Melanoma-Upregulated Long Noncoding RNA SPRY4-IT1 Modulates Apoptosis and Invasion.
Khaitan D, Dinger ME, Mazar J, Crawford J, Smith MA, Mattick JS, Perera RJ
Cancer Research, May 2011

SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer.
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.
RNA, May 2011;17(5):878-91. Epub 2011 Apr 1.

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.
Müller M, Padmanabhan PK, Rochette A, Mukherjee D, Smith M, Dumas C, Papadopoulou B
Nucleic acids research. 2010 Sep 1;38(17):5867-83

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

Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species.
Rochette A, Raymond F, Ubeda JM, Smith M, Messier N, Boisvert S, Rigault P, Corbeil J, Ouellette M, Papadopoulou B.
BMC Genomics. 2008 May 29;9:255

Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania.
Smith M, Blanchette M, Papadopoulou B.
BMC Bioinformatics2008 Mar 20;9:158

Members of a Large Retroposon Family Are Determinants of Post-Transcriptional Gene Expression in Leishmania.
Bringaud F, Müller M, Cerqueira GC, Smith M, Rochette A, El-Sayed NM, Papadopoulou B, Ghedin E.
PLoS Pathog. 2007 Sep 7;3(9):1291-307

Skills

Computational

JAVA programming, BASH scripting, PBS/SGE (Portable Batch System/Sun Grid Engine), Unix/Linux, UCSC Genome Browser, R statistical programming, with a dash of perl and python.

Biological

PCR, RT-PCR, molecular cloning, cell culture, ectopic transfection, flow cytometry, fluorescent microscopy.