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Researcher

Dr Martin Smith

My Expertise

Genomics, DNA sequencing, clinical genomics, machine learning, software, bioinformatics

Keywords

Fields of Research (FoR)

Bioinformatics, Genomics, Epigenetics (incl. Genome Methylation and Epigenomics), Pattern Recognition and Data Mining, Structural Biology (incl. Macromolecular Modelling), Biomedical Engineering

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Biography

Martin is a computational biologist with a background in biological sciences. After majoring in microbiology and immunology at the Université de Montréal, he undertook a Master's degree in bioinformatics at the Infectious Disease Research Centre in Quebec City, where he studied the genomics of parasitic protists. His interest in regulatory sequences in the non-protein coding genome brought him to Australia, where he completed a PhD in...view more

Martin is a computational biologist with a background in biological sciences. After majoring in microbiology and immunology at the Université de Montréal, he undertook a Master's degree in bioinformatics at the Infectious Disease Research Centre in Quebec City, where he studied the genomics of parasitic protists. 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 Institute of Molecular Bioscience. His thesis (UQ's lucky 10,000th!) demonstrated that a substantial fraction of mammalian genomes harbours evolutionary signatures of molecular function through the conservation of RNA structures.

Dr Smith then leveraged the rise of high-throughput sequencing technologies during his postdoctoral research at the Garvan Institute for Medical Research 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 Kinghorn Centre 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 CHU Sainte-Justine Research Centre (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.


My Research Supervision


Supervision keywords


Areas of supervision

Project: Real-time genomic diagnosis with nanopore sequencing 

Whole genome sequencing (WGS) provides remarkable insights into the genetic features underlying physiology and disease. However, WGS currently requires between 4 and 12 weeks to produce a diagnosis. The latest genome sequencing technologies can produce ultra-long sequencing reads, complete with epigenetic information, in real-time. Oxford nanopore sequencing can  produce ultra-long sequencing reads (>100kb) in real-time. This platform can also observe native DNA and RNA molecules, including their epigenetic modifications. We aim to reduce the turn around time for genomic diagnoses from several weeks to less than 1 day using the latest nanopore sequencing devices. 

To achieve this, we need to further explore the idiosyncrasies of this particular technology, including both the raw electronic signal data and the derived nucleotide sequences. We are looking for an enthusiastic applicant with a background in bioinformatics, biotechnology, computer science, software engineering, or physics to join our multidisciplinary team of bioinformaticians, biologists, and clinicians. By joining the Genomic Technologies group at the Kinghorn Centre for Clinical Genomics you will gain world-class expertise in genomics, with great potential for the discovery of new biological processes and the development of next-generation genomic applications. 

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Location

Ramaciotti Centre for Genomics
Office 2106, Biological Sciences Building South (E26)

Map reference (Google map)

Videos

Exploring the electrifying field of nanopore sequencing: Algorithms and applications in signal space.
Initial impressions of RNA004 and its application for functional profiling of cancer
Functional annotation of non-coding RNA