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.


Fields of Research (FoR)

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

SEO tags


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.

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.

My Grants

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


Chief Investigators


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


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


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


Cancer Australia Project grant (2020-2022)

Functional precision medicine for aggressive childhood cancers

Maria Kavallaris, Justin Gooding, Loretta Lau, MoonSun Jung, Mark Cowley


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


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


NSW Health Project Grant (2019-2021)

Paediatrio Centre for Paediatric Precision Medicine: Computational Biology Program (PPM2)

Cowley MJ, Tyrrell V


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


SONY Foundation Project Grant (2019)
Visualizing cancer mechanisms in VR

O’Donoghue S, Cowley MJ, Thomas D, Ballinger M


Cancer Australia Project Grant (2019-21) Decoding the Dark Matter of the High-Risk Paediatric Cancer Genome

Cowley MJ, Pinese M, Gloss B


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


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


Kinghorn Foundation (2017-2020)

Translating genomics into the clinic

Dinger ME, Cowley MJ, Kaplan W, Groza T, Terrill B, Smith M


NSW Health Early-Mid Career Fellowship (2017-2019)

Translating WGS into the clinic

Cowley M


NHMRC Project Grant (2017-2017)
An international whole genome study to definitively map heritable risk in sarcomas

Thomas D, Powell J, Cowley M


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


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


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


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


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


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


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


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


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


Qiagen Project Grant (2016)

Monitoring tumour evolution through whole genome sequencing (WGS) of liquid biopsy

Cowley M


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


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


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


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


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


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)


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


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


My Qualifications

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

My 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

  1. 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.
  2. Develop novel computational genomics approaches to understand the impact of genetic variation in coding and noncoding regions in cancer.
  3. 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.
  4. 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.
  5. To investigate the distribution, prevalence and composition of extrachromosomal circular DNA (ecDNA/eccDNA) as an under-appreciated oncogenic mechanism for childhood cancer tumours.
  6. 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.
  7. 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
  8. 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

Supervision keywords

Areas of supervision


Computational Biology

Cancer Genomics

Rare disease genomics

Translational genomics

Currently supervising

2 PhD students, 1 honours student

My Teaching

casual lecturer for BABS3151, PATH3206

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Level 5, Lowy Cancer Centre (C25)


+61-2-9385 2074