• 654 Citations
  • 12 h-Index
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Personal profile

Research Interests

Research Focus 

As leader of the SAHMRI Bioinformatics Core, my group develops computational tools and workflows to enable researchers to analyse large genomics datasets, as well as working with SAHMRI research groups as a Bioinformatics consultant. Our group’s current research interests include developing methods for clinical cancer sequencing (in collaboration with the Leukaemia research group) and investigating epigenetic and structural gene regulation using multi-omic datasets, with a primary focus on reproductive systems such as the human placenta and early adaptive immune network. 

Education/Academic qualification

PhD, Murdoch University


  • RG Gynecology and obstetrics
  • Reproductive Biology
  • QH426 Genetics
  • Genomics
  • RC0254 Neoplasms. Tumors. Oncology (including Cancer)
  • Cancer Biology
  • QA76 Computer software
  • Bioinformatics

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Research Output 2007 2018

  • 654 Citations
  • 12 h-Index
  • 19 Article
  • 3 Review article
  • 1 Comment/debate

Ancient plant DNA in the genomic era

Estrada, O., Breen, J., Richards, S. M. & Cooper, A., 1 Jul 2018, In : Nature Plants. 4, 7, p. 394-396 3 p.

Research output: Contribution to journalReview article

Specific growth conditions induce a Streptococcus pneumoniae non-mucoidal, small colony variant and determine the outcome of its co-culture with Haemophilus influenzae

Tikhomirova, A., Trappetti, C., Standish, A. J., Zhou, Y., Breen, J., Pederson, S., Zilm, P. S., Paton, J. C. & Kidd, S. P., 1 Oct 2018, In : Pathogens and disease. 76, 7

Research output: Contribution to journalArticle

2 Citations (Scopus)

Unravelling the molecular basis for regulatory T-cell plasticity and loss of function in disease

Sadlon, T., Brown, C. Y., Bandara, V., Hope, C. M., Schjenken, J. E., Pederson, S. M., Breen, J., Forrest, A., Beyer, M., Robertson, S. & Barry, S. C., 2018, In : Clinical and Translational Immunology. 7, 2, 1011.

Research output: Contribution to journalReview article

2 Citations (Scopus)

Global DNA methylation patterns can play a role in defining terroir in grapevine (Vitis vinifera cv. Shiraz)

Xie, H., Konate, M., Sai, N., Tesfamicael, K. G., Cavagnaro, T., Gilliham, M., Breen, J., Metcalfe, A., Stephen, J. R., De Bei, R., Collins, C. & Lopez, C. M. R., 30 Oct 2017, In : Frontiers in Plant Science. 8, 1860.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Megafaunal isotopes reveal role of increased moisture on rangeland during late Pleistocene extinctions

Rabanus-Wallace, M. T., Wooller, M. J., Zazula, G. D., Shute, E., Jahren, A. H., Kosintsev, P., Burns, J. A., Breen, J., Llamas, B. & Cooper, A., 18 Apr 2017, In : Nature Ecology and Evolution. 1, 5, 0125.

Research output: Contribution to journalArticle