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Analytic methods for detecting and making sense of somatic genomic rearrangements

  • Full or part time
  • Application Deadline
    Applications accepted all year round
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

Bioinformatics is the application of mathematics, statistics and computational methods to the analysis of molecular biology data. Our research is focused on developing new bioinformatics methods and applying new and existing methods to analyze and make sense of complex cancer datasets. Much of our efforts are focused on next generation sequencing data.

Building on state-of-the-art methods that the lab has previously created, this project involves the development of a variety of new bioinformatics methods to cancer genome sequencing data, including copy number analysis techniques and methods for the refinement, visualisation and classification of genomic rearrangements, and their application to clinical cancer samples.

The Papenfuss laboratory uses mathematics, statistics and computing to make sense of cancer genome sequencing and other -omics data.

Prof Tony Papenfuss leads the Computational Biology Program.
This program uses mathematics, statistics and computing to generate new discoveries in cancer. We develop new models, algorithms and software tools, and apply these to make sense of cancer data. This includes whole genome, exome, transcriptome and epigenome sequencing data.
Our research interests encompass:
• bioinformatics algorithm and methods development
• computational cancer biology
• cancer evolution and genomics
• software tool development
• personalised medicine.
The program includes research laboratories, as well as the Bioinformatics Consulting Core and the Research Computing Facility. Scientists come from a range of disciplines including biology, computer science, mathematics and statistics, as well as software engineering. Many researchers in the program hold joint appointment with other programs or institutes.

Peter MacCallum Cancer Centre in Melbourne Australia’s only public hospital solely dedicated to cancer, and home to the largest cancer research group in Australia. Cancer is a complex set of diseases, and modern cancer research institutes such as Peter Mac conduct research covering a diversity of topics that range from laboratory-based studies into the fundamental mechanisms of cell growth, translational studies that seek more accurate cancer diagnosis, clinical trials with novel treatments, and research aimed to improve supportive care.

All students engaged in postgraduate studies at Peter Mac are enrolled in the Comprehensive Cancer PhD (CCPhD) program, regardless of which university they are enrolled through. The program is managed by the Sir Peter MacCallum Department of Oncology (The University of Melbourne), based at Peter Mac.

The Comprehensive Cancer PhD program builds on established conventional training for cancer research students providing a coordinated program of skills, research and career training in addition to usual PhD activities. The program is designed to complement existing PhD activities and provides opportunities to develop professional skills that will help candidates to fulfil their career ambitions.

Funding Notes

All PhD students at Peter Mac must have a scholarship from The University of Melbourne or through another government, trust or philanthropic organisation. Before applying for a scholarship, you must have agreed on a project with an institute supervisor.

For further information about the university application process, see:
View Website

For further information regarding scholarships (both local and international), see:
View Website
Closing dates for applications for scholarships to commence in 2020: Round 1 -31 October 2019; Round 2 - 31 Jan 2020; Round 3 - 15 May 2020.


Papenfuss & Thomas, Molec. and Cellular Oncology 2015, 2:4, e1000698;
Garsed et al, Cancer Cell 2014,10;26(5):653-67

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