Dr Mark Cowley

My current research focuses on the use of bioinformatics and genomics to understand the functional impact of genetic variation. At the core of this research is the application of high throughput technologies, initially microarrays, and now massively parallel sequencing to investigate the link betwee
Visiting Scientist

Senior Bioinformatics Research Officer, Early Career Research Fellow

Conjoint/Adjunct Role(s)

Conjoint Senior Lecturer, St Vincent's Clinical School, Faculty of Medicine, UNSW Australia

My current research focuses on the use of bioinformatics and genomics to understand the functional impact of genetic variation. At the core of this research is the application of high throughput technologies, initially microarrays, and now massively parallel sequencing to investigate the link between genotype and phenotype. My current research interests include:

  • the identification of mutations underlying inherited genetic diseases;
  • implementing clinical genomics in the Australian clinic;
  • using genomic profiles to molecularly characterise tumours, for directing targeted therapeutics;
  • using next generation sequencing to facilitate the early detection of cancer from liquid biopsies (ie, from circulating tumour DNA and circulating tumour cells);
  • studying the clonal evolution of cancer;
  • characterising the roles of long noncoding RNA in cancer.

In my position with the newly established Kinghorn Centre for Clinical Genomics, we are implementing systems to apply whole exome and whole genome sequencing in an accredited, clinical setting. This involves the establishment of bioinformatic pipelines for sequence alignment, variant identification, annotation, and prioritisation to identify those genetic variants that underly inherited genetic disorders.

In addition, we are developing systems for capturing patient phenotype, to help guide variant prioritisation. In my role as a senior bioinformatics postdoc in the Genome Informatics laboratory, I am establishing methods for early detection of tumours from liquid biopsies via next generation sequencing, and using this to study tumour evolution in real time.

In my previous postdoc, I was involved in the Australian Pancreatic Cancer Initiative (APGI) and the International Cancer Genome Consortium (ICGC), where we characterised the exomes from 142 Pancreatic Ductal Adenocarcinomas. This resulted in the largest catalog of mutations and copy number alterations in PDAC, as well as the identification of a novel pathway (SLIT/ROBO signalling), and a potentially treatable subtype of HER2-amplified pancreatic cancers, which is currently being tested in the IMPACT genotype-guided clinical trial.

Prior to this, I spent three years in the Peter Wills Bioinformatics Centre (Garvan Institute), where amongst many collaborative research projects, we established the largest microarray archive in Australia, an extremely widely used GenePattern server, with ~20 of our own custom modules, and a galaxy server. During my PhD, I studied the impact of noncoding variation upon the regulation of gene expression.

I am looking for talented postdocs, PhD students, honours students and research assistants, across a range of expertise, so please contact me with your resume!

Research Interests

Clinical Genomics
Cancer Genomics
Translational Genomics
Medical Genomics
Next generation sequencing
The impact of genetic variation in the noncoding genome

Awards and Honours

2014 - Early Career Fellowship, Cancer Institute NSW
2013 - inaugural Garvan award, nominated by peers for outstanding contribution to the Garvan Institute
2013 - Australian Bioinformatics Network, best oral presentation award, at the 3rd Annual Sydney Bioinformatics Research Symposium
2012 - Cancer Institute, NSW Wildfire Award (awarded to the Pancreatic Cancer Research Group, Garvan)
2010 - Qantas Young Investigator Travel Award, to attend CSHL Biology of Genomes Meeting
2008 - Travel award to attend the 8th AMATA conference at Dunedin, New Zealand
2007 - Travel award to attend the Biology of Genomes conference at Cold Spring Harbor, Long Island, New York, USA
2005 - Poster prize for 'Intelligent use of Information' at the 5th Australian Microarray Conference (AMATA) conference, Adelaide, SA
2004 - Australian Postgraduate Award
2004 - offered The Medical Faculty of UNSW Rising Star award for academic excellence


2009 - PhD, University of New South Wales - Australia
2003 - BSc (Bioinformatics, Hons I), University of Sydney - Australia
2002 - BSc (Bioinformatics), University of Sydney - Australia

Selected Publications

Chou A ^1, Waddell N ^1, Cowley MJ ^1, Gill AJ, Chang DK, Patch A-M, et al. Clinical and molecular characterization of HER2 amplified pancreatic cancer. Genome Medicine. 2013, 5(8):78. [pubmed]

Stone A, Cowley MJ, Valdes-Mora F, McCloy RA, Sergio CM, Gallego-Ortega D, et al. BCL-2 hypermethylation is a potential biomarker of sensitivity to antimitotic chemotherapy in endocrine-resistant breast cancer. Mol Cancer Ther. 2013, 12(9):1874–85. [pubmed]

Cowley MJ, Chang DK, Pajic M, Johns AL, Waddell N, Grimmond SM, et al. Understanding pancreatic cancer genomes. J Hepato-Biliary-Pancreatic Sciences. 2013 in press. [pubmed]

Chang DK, Jamieson NB, Johns AL, Scarlett CJ, Pajic M, Chou A, et al. Histomolecular phenotypes and outcome in adenocarcinoma of the ampulla of vater. J Clin Oncol. 2013, 31(10):1348–56. [pubmed]

Nair R, Daniel L Roden WST, McFarland A, Junankar S, Ye S, Nguyen A, et al. c-Myc and Her2 cooperate to drive a stem-like phenotype with poor prognosis in breast cancer. Oncogene. 2013, in press.  [pubmed]

Kalyuga M, Gallego-Ortega D, Lee HJ, Roden DL, Cowley MJ, Caldon CE, et al. ELF5 Suppresses Estrogen Sensitivity and Underpins the Acquisition of Antiestrogen Resistance in Luminal Breast Cancer. PLoS Biol. 2012, 10(12):e1001461. [pubmed]

Biankin AV, Waddell N, Kassahn KS, Gingras M-C, Muthuswamy LB, Johns AL, et al. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature. 2012, 491(7424):399–405. [pubmed]

Song S, Nones K, Miller D, Harliwong I, Kassahn KS, Pinese M, et al. qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles. PLoS ONE. 2012, 7(9):e45835.  [pubmed]

Perez-Mancera PA, Rust AG, van der Weyden L, Kristiansen G, Li A, Sarver AL, et al. The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma. Nature. 2012, 486(7402):266–70. [pubmed]

Mann KM, Ward JM, Yew CCK, Kovochich A, Dawson DW, Black MA, et al. Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma. PNAS. 2012, 109(16):5934–41.  [pubmed]

Charchar FJ, Bloomer LDS, Barnes TA, Cowley MJ, Nelson CP, Wang Y, et al. Inheritance of coronary artery disease in men: an analysis of the role of the Y chromosome. LANCET. 2012, 379(9819):915–22.  [pubmed]

Cowley MJ, Weinberg A, Zammit N, Walters SN, Hawthorne WJ, Loudovaris T, et al. Human Islets Express a Marked Pro-Inflammatory Molecular Signature Prior to Transplantation. Cell Transplantation. 2012, 21(9):2063–78.  [pubmed]

Cowley MJ, Pinese M, Kassahn KS, Waddell N, Pearson JV, Grimmond SM, et al. PINA v2.0: mining interactome modules. Nucleic Acids Res. 2012, 40(Database issue):D862–5.  [pubmed]

Cowley MJ, Cotsapas CJ, Williams RBH, Chan EKF, Pulvers JN, Liu MY, et al. Intra- and inter-individual genetic differences in gene expression. Mamm Genome. 2009, 20(5):281–95. [pubmed

Williams RBH, Cotsapas CJ, Cowley MJ, Chan E, Nott DJ, Little PFR. Normalization procedures and detection of linkage signal in genetical-genomics experiments. Nat Genet. 2006, 38(8):855–6; [pubmed]

Person portrait

Dr Mark Cowley

Research group