MSE Research Project Database

Cancer data analytics with Deep Neural Networks


Project Leader: Saman Halgamuge
Collaborators: Dr Chalini Wijetunga (Florey), Dr Jason Li (Peter MacCallum Institute for Cancer Research), Dr Kaushalya Amarasinghe (Peter MacCallum Institute for Cancer Research), Dr Marnie Shaw (Australian National University)
Sponsors: Peter MacCallum Institute for Cancer Research
Primary Contact: Saman Halgamuge (saman@unimelb.edu.au)
Keywords: bioinformatics; cancer; genomics; knowledge discovery
Disciplines: Biomedical Engineering
Domains: Convergence of engineering and IT with the life sciences

Cancer genomic data combined with image data help to identify new types of cancer, enhance the knowledge about existing cancers and develop new drugs and personalised treatments for patients. The project aims to develop new data analysis methods to extract meaningful information from multiple sources of data.

Research papers:

Kaushalya C Amarasinghe, Jason Li, Sally M Hunter, Georgina L Ryland, Prue A Cowin, Ian G Campbell and Saman K Halgamuge, Inferring copy number and genotype in tumour exome data, BMC Genomics 2014 15:732

Kaushalya C Amarasinghe, Jason Li and Saman K Halgamuge, CoNVEX: copy number variation estimation in exome sequencing data using HMM, BMC Bioinformatics 2013 14 (Suppl 2 :S2

Jason Li, Richard Lupat, Kaushalya C Amarasinghe, Ella R Thompson, Maria A Doyle, Georgina L Ryland, Richard W Tothill, Saman K Halgamuge, Ian G Campbell, Kylie L Gorringe, "CONTRA: copy number analysis for targeted resequencing", Bioinformatics, 28 (10), 1307–1313, 2012.

Further information: https://scholar.google.com.au/citations?hl=en&user=9cafqywAAAAJ&view_op=list_works