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Mechanistic and functional drivers of cancer neochromosomes

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  • Full or part time
    Dr T. Papenfuss
  • Application Deadline
    Applications accepted all year round
  • Funded PhD Project (Students Worldwide)
    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.

Neochromosomes are massive extra chromosomes that frequently occur in certain rare cancers, such as sarcomas. They are composed of hundreds of genomic segments that are amplified, rearranged and stitched together into “Frankenstein chromosomes”. We recently discovered chaotic molecular processes which underlie their formation and evolution — chromosome shattering and breakage-fusion-bridge .

This exciting research project will involve the analysis of second and third generation DNA sequencing data (Illumina short read, Genomics 10X Chromium, Oxford Nanopore, and PacBio), integration of epigenetic, transcriptomic and proteomics data, as well as mathematical modeling, to refine our understanding of how these processes are initiated; whether they operate non-randomly; and what role they play in other cancers,

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 more information about the university application process, see:

For further information regarding scholarships (both local and international), see:
Closing dates for applications for scholarships to commence in 2017: Round 1 -31 October 2016; Round 2 - 18 Dec 2016.


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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