Researcher

Dr Mark James Cowley

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Biography

 

A/Prof Mark Cowley is a bioinformatician, whose research is focused on improving health outcomes in patients, by developing innovative computational approaches. He predominantly uses Whole Genome Sequencing to understand why patients develop cancer, how to characterise their tumours and identify optimal treatment recommendations. He leads the Computational Biology group at Children's Cancer Institute, and plays a key role in the ambitious...view more

 

A/Prof Mark Cowley is a bioinformatician, whose research is focused on improving health outcomes in patients, by developing innovative computational approaches. He predominantly uses Whole Genome Sequencing to understand why patients develop cancer, how to characterise their tumours and identify optimal treatment recommendations. He leads the Computational Biology group at Children's Cancer Institute, and plays a key role in the ambitious Zero Childhood Cancer program, Australia's most comprehensive and advanced precision medicine trial in children and adolescents with high-risk cancer. Mark also has strong expertise in rare disease diagnosis, particularly using genomics.


My Grants

Grant

Chief Investigators

Amount

Cancer Australia Project grant (2019-2021) Decoding the Dark Matter of the High-Risk Paediatric Cancer Genome

Cowley MJ, Pinese M, Gloss B

$577,048

PKD Foundation Project Grant

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, Epstein R, Goldstein D, Goodwin A, Horvath L, Jacobs C, Kirk J, Lee C, Mann G, Marshall G, Meiser B, Meldrum C, Newson A, Orchard P, O'Toole S, Roscioli T, Sjoquist K, Spigelman A

$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

Year Award
2004

Offered the 2004 Rising Star award for academic excellence (a graduate school academic supplementary stipend offered by the Medicine Faculty of UNSW)

2004-2007 Australian Postgraduate Award
2005

Poster award for the intelligent use of information, presented by CSIRO at the 5th Australian Microarray Conference, 2005.

2007

Travel grant to attend the Biology of Genomes conference at Cold Spring Harbor, Long Island, New York, USA in May 2007.

2008

Travel grant to attend the 8th AMATA conference at Dunedin, New Zealand in Nov 2008.

2010

Qantas Young Investigator Travel Award to attend the Biology of Genomes conference at Cold Spring Harbor, Long Island, New York, USA in May 2010.

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)
2016 Community Challenge Award, PrecisionFDA
2017 Health Hack, silver medal – Cancer Clinical Trials Matcher
2018 Wildfire Award, Cancer Institute NSW (most highly cited paper of the year)

My Research Activities

CONTRIBUTION TO FIELD OF RESEARCH: Dr Cowley’s translational research has resulted in the development of the world’s first ISO15189 clinically accredited WGS-based pathology test. His bioinformatics methodologies now serve as a platform for improving patient diagnosis and management in the clinic, and as a base from which to develop cutting edge approaches to understand the impact of genomic variation upon health. More recently, Dr Cowley leads the genomic analysis teams for two precision cancer genome trials, the Molecular Screening and Therapeutics Program (MoST) and Lions Kids Cancer Genome Project (LKCGP), as part of the Zero Childhood Cancer Program. Both highly translational studies are focused on rare adult or high-risk paediatric cancers, and are guiding improved patient management in real time, and generating insights into rare cancer biology.

Prior to this, Dr Cowley made seminal contributions to the understanding of pancreatic cancer (PC), by applying cancer genomics to the world’s largest, prospectively accrued cohort of PC. Initially using whole exome sequencing and functional genomics (Biankin et al, 2012, Nature), then whole genome sequencing (Waddell et al, 2015 Nature; Bailey et al, 2016, Nature), and for neuroendocrine PC (Scarpa et al, 2017, Nature). Collectively this work identified novel pathways, clinically & molecularly distinct subtypes, with significant disease management, and therapeutic implications. Mark identified a potentially treatable subtype of HER2-amplified PDAC (Chou, Waddell and Cowley et al, 2014 Genome Medicine, co-first), which was being tested in the first stratified clinical trial for PC (IMPACT; reviewed in Cowley et al, 2013).

Dr Cowley has made important contributions to bioinformatics research and methods development (PINA2, qSNP, qPure, Seave, ClinSV, mity, ROHmer, refynr, Gentian, VCFscope).

Mark’s rare disease research has resulted in the characterisation of disease genes, including PUM1, SYNGAP1, ZSWIM6, EPG5, KCNT2, ECHS1, IQSEC2, SLC39A8, applied to a range of genetic disorders, including renal, mitochondrial, cardiac, epilepsy, and movement disorders.


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

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Location

Level 5, Lowy Cancer Centre (C25)

Contact

0293852074