Associate Professor Mark James Cowley

My Expertise

I am recognised nationally as a leader in computational biology research that focuses on developing genomics approaches for precision medicine. My vision is for every patient to receive an accurate, timely and cost-effective diagnosis and prognosis, to receive the best possible treatment recommendations, and to be monitored with high resolution until they are cured. We develop world-leading genome analysis tools, pipelines and resources to enable precision medicine with a major focus on children with cancer. My group supports the real-time analysis of genomic data from children enrolled on the Zero Childhood Cancer Program, where we rapidly analyse the whole genome, transcriptome and methylome of children with cancer, and distil this into medically useful information that can be actioned by the patient's clinician. This has led to a change of practice in childhood cancer, where precision medicine built on a comprehensive molecular profiling platform, provided through a clinical trial framework is rapidly becoming the standard of care. To deliver this impact, my group develops many innovative algorithms, databases, apps and web resources to allow each patient's care to be informed by all previous patients enrolled on the program.

Keywords

bioinformatics

computational biology

cancer genomics

Fields of Research (FoR)

Bioinformatics, Genomics, Cancer Genetics, Medical Genetics (excl. Cancer Genetics)

SEO tags

Cancer and Related Disorders

Human Diagnostics

Diagnostic Methods

Biography

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...view more

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.

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.

My Grants

Since 2014, A/Prof Cowley has attracted $55.5M in research funding.

Grant	Chief Investigators	Amount
Australian Research Data Commons (ARDC) Platforms Program grant (2021-2023): Global technologies and standards for sharing human genomics research data	Andrew Lonie, Oliver Hofmann, Mark Cowley, John Pearson, Warren Kaplan, Tiffany Boughtwood, Sean Smith, Heath Marks, Andrew Gilbert, Allison Heath	$ 958,080
Kids Cancer Alliance Project grant (2020-2021) WGS-MRD: a new paradigm for identifying minimal residual disease (MRD) markers and risk classification in leukaemia, using whole genome sequencing (WGS)	Mark Cowley, Rosemary Sutton, Toby Trahair, Luciano Dalla-Pozza, Dale Wright, Michelle Henderson, Marie Wong-Erasmus, Nicola Venn	$200,000
MRFF - Genomic Health Futures Mission (GHFM) Project grant (2020-2022) Returning Raw Genomic Data: Patient Autonomy or Legal Minefield?	Jane Nielsen, Amber Johns, Vanessa Tyrrell, Mark Cowley, Tracey O'Brien	$403,096
Little Legs Foundation and Charlie Teo Foundation Project grant (2020-2022) Neoantigen immunopeptidomics for the development of immunotherapies for the treatment of DIPG	Matt Dunn, Mark Cowley, Luke Hesson, Jay Horvat	$326,389
Cancer Australia Project grant (2020-2022) Functional precision medicine for aggressive childhood cancers	Maria Kavallaris, Justin Gooding, Loretta Lau, MoonSun Jung, Mark Cowley	$596,595
Cancer Institute NSW Program grant (2020-2024) Implementing novel therapeutic strategies for childhood brain cancer patients	David Ziegler, Paul Ekert, Mark Cowley, Sarah-Jane Dawson	$3.75M
ACRF Infrastructure grant (2020-2022) The ACRF Child Cancer Liquid Biopsy Program	Haber M, Norris M, Marshall G, Lock R, Cowley MJ, Ekert P, de Bock C, Ziegler D, Dawson S, Rosenfeld N, Swarbrick A, Sutton R	$3,500,000
NSW Health Project Grant (2019-2021) Paediatrio Centre for Paediatric Precision Medicine: Computational Biology Program (PPM2)	Cowley MJ, Tyrrell V	$2,497,333
NSW Health Project grant (2019-2021) Paediatrio Centre for Paediatric Precision Medicine: Paediatric Cancer Predisposition Screening Program (PPM3)	O'Brien T, Byrne J, Tyrrell V, Tucker K, Dalla Pozza L, Cowley MJ, Kirk J, Wakefield C	$3,950,000
SONY Foundation Project Grant (2019) Visualizing cancer mechanisms in VR	O’Donoghue S, Cowley MJ, Thomas D, Ballinger M	$270,000
Cancer Australia Project Grant (2019-21) Decoding the Dark Matter of the High-Risk Paediatric Cancer Genome	Cowley MJ, Pinese M, Gloss B	$577,048
PKD Foundation Project Grant (2018-9) Understanding the role of somatic variation and novel mutational mechanisms in the genetic pathogenesis of PKD	Shine J, Mallawaarachchi A, Harris P, Furlong T, Cowley MJ	$211,432 (US$160K)
BioMedTech Horizons Program Grant (2017-2018) A clinically-accredited and commercial-ready genome profiling platform to enable precision cancer medicine	Thomas D, Dinger M, Cowley M	$891,500
MTP Connect Project Grant (2017-2018) Enabling Precision Cancer Clinical Trials: A molecular profiling platform for the Australian clinical trials industry	Thomas D, Dinger M, Cowley M, Winlo M, Simes J, Joshua A, Horvath L, Lemech C, Dodds E	$400,000
Kinghorn Foundation (2017-2020) Translating genomics into the clinic	Dinger ME, Cowley MJ, Kaplan W, Groza T, Terrill B, Smith M	$20,000,000
NSW Health Early-Mid Career Fellowship (2017-2019) Translating WGS into the clinic	Cowley M	$345,000
NHMRC Project Grant (2017-2017) An international whole genome study to definitively map heritable risk in sarcomas	Thomas D, Powell J, Cowley M	$825,000
FSHD Global Project Grant (2016-2017) The next wave of whole genome sequencing based FSHD diagnostics, and clinical measures of progression	Nicholson G, Cowley M, Corbett A, Kumar K, Stoll M	$330,000
Lion’s Club International Project Grant (2016-2019) Lions Kids Cancer Genome Project	Mattick J, Palmer B, Collins J, Dziadek M, Tyrell V, Thorpe J, Marshall G, Haber M, Thomas D, Dinger M, Kaplan W, Cowley M, Botten L, Norris M, Lock R, Ziegler D, Lau L	$3,200,000
NSW Department of Health Project Grant (2016-2018) Clinical application of whole genome studies in patients with inherited cardiomyopathies	Semsarian C, Fatkin D, Dinger M, Bagnall R, Ingles J, Cowley M, Turner C, Colley A, Berman Y, Ronan A	$320,000
NSW Department of Health Project Grant (2016-2018) Discovery of Genes for Mendelian Disorders through Whole Genome Sequencing: from Clinic to Gene Identification	Roscioli T, Buckley M, Dinger M, Cowley M, Scofield D, Ewans L	$300,000
NSW Department of Health Project Grant (2016-2018) Severe infantile-onset epilepsy: Leveraging Genomic Sequencing to Identify Novel Genes Neurodevelopmental Pathways and to Determine Cost-effectiveness	Roscioli T, Sachdev R, Kirk E, Palmer E, Bye A, Schofield D, Dinger M, Cowley M, Buckley M	$180,000
NSW Department of Health Project Grant (2016-2018) Exploring the Genomic Landscape of Genetic Disorders of Bone	Zankl A, Eisman J, Croucher P, Dinger M, Cowley M, Groza T, Tam P	$180,000
NHMRC Partnership Grant APP111389 (2016-2018) The economic and social impacts of genetic sequencing for intellectual disability	Schofield D, Roscioli T, Mattick J, Dinger M, Kasparian N, Barlow-Stewart K, Cowley M, Field M, Buckley M, Shrestha R	$1,263,576
NHMRC Project Grant APP1107671 (2016-2018) Mechanistic and functional analysis of the Id4 proto-oncogene in breast and ovarian cancer	Swarbrick A, Carroll J, Cowley M, O'Toole S	$600,000
Cancer Institute NSW Infrastructure Grant #2016/REG/001 (2016) The next wave of cancer genomics: resolving complex structural variants and tumour heterogeneity with linked short-read	Dinger M, Cowley M, Thomas D, Marshall G, Clark S, Hayes V, Wilkins M, Watkins N, Swarbrick A, Gallego-Ortega D	$220,482
Qiagen Project Grant (2016) Monitoring tumour evolution through whole genome sequencing (WGS) of liquid biopsy	Cowley M	$50,000
Estate Late RT Hall Project Grant (2015-2017) Exploring personal genomes in familial forms of atrial fibrillation and dilated cardiomyopathy	Fatkin D, Dinger M, Cowley M, Martin I	$225,000
Cancer Council NSW Project Grant APP1088778 (2015-2017) Genetics stratification of tumours of the head, neck, pituitary and skull base – identifying prognostic and new therapeutic targets	Dinger ME, O’Toole S, McCormack A, Cowley M, Harvey R, Gupta R, McCabe M	$360,000
Ainsworth Foundation Project Grant (2015) Uncovering the Genetic Basis of Dystonia Affecting the Head and Neck (Craniocervical Dystonia) Using Whole Genome Sequencing	Mattick J, Kumar KR, Sue C, Cowley MJ, Dinger ME	$150,000
Cancer Institute NSW Infrastructure Grant #15/REG/1-16 (2015) Expanding basic, clinical and functional genomics cancer research at Concord Campus	van Zandwijk N, Reid G, Lin RCY, Seibel M, Cowley M, Bowden N, Cooper W, Kao S, Horvath L, Hart D	$385,470
NSW Department of Health Program Grant (2014-2018) Cancer Genome Medicine – Molecular Therapeutics Program	Thomas D, Simes J, Cowley M, Dinger M, Horvath L, Friedlander M, Epstein R, Goldstein D, Sandhu S, Meldrum C, O'Toole S, Fox S, Sjoquist K, Lee C	$6,790,082
Movember and the Prostate Cancer Foundation of Australia Project Grant(2014-2016) Adaptive response to targeting the androgen axis: exploiting the chink in the armour of resistance	Nelson C, Williams E, Russell P, Holst J, Buchanan G, Dinger M, Clements J, Hollier B, Vela I, Gunter J, Lehman M, Chopin L, Ling P (Cowley M is a co-team leader under CI Dinger)	$4,250,000
Cancer Institute NSW Fellowship #13/ECF/1-46 (2014-2016) Tumour evolution, and early detection of breast cancer empowered by massively parallel sequencing and in vivo imaging	Cowley M	$600,000
Cancer Institute NSW Infrastructure Grant #14/REG/1-07 (2014) An automated micromanipulator platform to capture viable single cells for culture and molecular analyses	Becker T, Apte M, Rasko J, Spring K, Ranson M, Gedye C, Cowley M	$270,000

My Qualifications

Institution	Degree	Year	Field of Study
UNSW Australia	PhD	2008	Bioinformatics, Transcriptomics, Genetics
University of Sydney	BSc (Hons I)	2003	Bioinformatics

My Awards

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)

My Research Activities

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.