Associate Professor Mark Cowley
| Institution | Degree | Year | Field of Study |
| UNSW Australia | PhD | 2008 | Bioinformatics, Transcriptomics, Genetics |
| University of Sydney | BSc (Hons I) | 2003 | Bioinformatics |
I am a computational biologist specialising in the analysis of genomics data to improve health outcomes in children with cancer, at the interface of diagnostics and discovery research.
I am a conjoint Associate Professor with the School of Clinical Medicine and joined the Children's Cancer Institute in 2018 as the head of the Computational Biology Group. I am also the co-head of the Luminesce Alliance Childhood Cancer Computational Biology Program and the co-head of the ACRF Childhood Cancer Liquid Biopsy Program.
My multi-disciplinary group develops novel computational approaches to make sense of genomics, transcriptomics and clinical data, predominantly applied to childhood cancer, but with lots of experience in other cancers and patients with rare genetic diseases. Much of this research is focused on developing tools to identify, understand and interpret mutations in patients, including complex, noncoding and atypical splice-altering genetic variants, which are commonly overlooked drivers of disease. By collaborating widely with clinicians and fundamental biologists, my team seeks to identify answers for patients today and make a long-term impact on our understanding of the molecular basis of disease. My team also develops the digital research architecture that underpins the Zero Childhood Cancer Program, an ambitious national research program that uses precision medicine to diagnose and treat Australian children with cancer.
- Publications
- Grants
- Awards
- Research Activities
- Teaching and Supervision
- Engagement
- Media
Since 2014, A/Prof Cowley has attracted $55.5M in research funding.
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AWARDS
2004 Australian Postgraduate Award
2005 Poster award for the intelligent use of information, presented by CSIRO at the 5th Australian Microarray Conference.
2007 Travel grant to attend the Biology of Genomes conference at Cold Spring Harbor, Long Island, New York, USA.
2008 Travel grant to attend the 8th AMATA conference at Dunedin, New Zealand
2010 Qantas Young Investigator Travel Award to attend the Biology of Genomes conference at Cold Spring Harbor, Long Island, New York, USA
2013 Best Oral Presentation, Sydney Bioinformatics Research Symposium
2013 Award for Outstanding Contribution, Garvan Institute of Medical Research
2014 Top Ranked Applicant, Cancer Institute NSW Early Career Fellowship
2014 People’s Choice Award for Best Oral Presentation, Garvan Postdoctoral Symposium
2014 Health Hack, bronze medal – Genome Pipeline Visualisation Platform
2015 Wildfire Award, Cancer Institute NSW (most highly cited paper of the year, PMID 23103869)
2016 Community Challenge Award, PrecisionFDA
2017 NSW Health Early-Mid career fellowship
2017 Health Hack, silver medal – Cancer Clinical Trials Matcher
2018 Wildfire Award, Cancer Institute NSW (most highly cited paper of the year, PMID 25719666)
2019 Wildfire Award, Cancer Institute NSW (most highly cited paper of the year, PMID 26909576)
2019 Promoting High Quality Research Papers Scheme (PHQRP; a high-impact publication award), UNSW for Bagnall et al, J Am Coll Cardiol. 2018 (PMID: 30025578)
2019 PHQRP Award, UNSW for Palmer et al, Am J Hum Genet. 2019 (PMID: 30827498)
2019 PHQRP Award, UNSW for Zammit et al, Nat Immunol. 2019 (PMID: 31534238)
2020 2020 Eberhard Mammen Seminars in Thrombosis and Haemostasis Most Popular Article Award (PMID: 31096307; URL)
2020 NSW Health 2020 ‘Health Research and Innovation Award’ for the Zero Childhood Cancer Program (URL)
2020 Mid-career researcher award, from the Australasian Bioinformatics and Computational Biology Society (ABACBS; URL)
2020 The Sydney Children’s Hospitals Network’s 2020 Annual Quality and Innovation Awards, in the Health Research and Innovation category, for the Zero Childhood Cancer Program (URL)
2021 European Association for Cancer Research (EACR)’s Top 10 Cancer Research Publications: February 2021 (PMID: 32499442; URL)
Major research questions
- Develop novel computational approaches to diagnose, prognose (risk-stratify), monitor and identify treatment options in childhood cancer patients, that is, to enable precision medicine at the national scale.
- Develop novel computational genomics approaches to understand the impact of genetic variation in coding and noncoding regions in cancer.
- To develop novel computational approaches to analyse the tumour immune microenvironment, through the development of a bioinformatic tookit and subsequent collaborations to assess their effectiveness.
- To predict the impact of coding and noncoding genetic variants on gene splicing via our software, Introme, and apply this to undiagnosed patients to drive increases in diagnostic rates and end diagnostic odysseys.
- To investigate the distribution, prevalence and composition of extrachromosomal circular DNA (ecDNA/eccDNA) as an under-appreciated oncogenic mechanism for childhood cancer tumours.
- To develop national genome data sharing infrastructure (in collaboration with AusBioCommons and intl partners CHOP) to enable ever-larger discovery research projects based on harmonised, intl datasets and collaborations.
- To develop novel approaches to extract clinical data from disparate health records – this is a significant unmet need in precision medicine, and an impediment to national-scale programs like ZERO2
- To understand how tumours evolve, why they relapse and identify early signs of relapse, through deep molecular analysis of serial solid and liquid biopsy. Single-cell approaches will become increasingly important in this area, but first we need to extract as much info as possible from bulk molecular analysis.
My Research Supervision
2 PhD students, 1 honours student
My Teaching
casual lecturer for BABS3151, PATH3206