Researcher

Associate Professor Mark James Cowley

Keywords

Fields of Research (FoR)

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

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Biography

A/Prof Mark Cowley is a computational biologist, whose expertise is in genomics and precision medicine. Mark joined the Children's Cancer Institute in 2018 as the head of the Computational Biology Group, co-head of the Luminesce Alliance Childhood Cancer Computational Biology Program, and now also the co-head of the ACRF Child Cancer Liquid Biopsy Program. Mark is a conjoint Associate Professor with the School of Women’s and Children’s...view more

A/Prof Mark Cowley is a computational biologist, whose expertise is in genomics and precision medicine. Mark joined the Children's Cancer Institute in 2018 as the head of the Computational Biology Group, co-head of the Luminesce Alliance Childhood Cancer Computational Biology Program, and now also the co-head of the ACRF Child Cancer Liquid Biopsy Program. Mark is a conjoint Associate Professor with the School of Women’s and Children’s Health, UNSW Medicine. 

Mark’s multi-disciplinary group develops novel computational approaches to make sense of genomics, drug screening 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 complex, noncoding and atypical splice-altering genetic variants in patients, which are commonly overlooked drivers of disease. By collaborating widely with clinicians and fundamental biologists, Mark's team seeks to identify answers for patients today and make a long-term impact on our understanding of the molecular basis of disease. His 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

  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 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 ending 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

Bioinformatics

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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Location

Level 5, Lowy Cancer Centre (C25)

Contact

+61-2-9385 2074