Bioinformatics

The Bioinformatics Consulting Core (BCC) in the Cancer Research Division at Peter Mac provides a range of services and know-how for data analysis.

Bioinformatics Consulting Core Facility

The aim of BCC is to provide all levels of bioinformatics support to research laboratories within Peter Mac and, more broadly, within the Victorian Comprehensive Cancer Centre (VCCC). The team of bioinformaticians and postdoctoral scientists at BCC work alongside laboratory and clinical researchers and contribute to their experimental design, grant applications and the analysis and publication of genomic and transcriptomic data. Data types analysed by the core include whole-genome and whole-exome sequencing, targeted re-sequencing, radiological images, RNA-sequencing, single-cell RNA sequencing, ChIP-sequencing, NanoString and various types of microarray data.

Cost recovery

Fees apply to project work. Support to larger projects is available via EFT (part salary) contribution, while smaller projects are charged via a fee-for-service model. The BCC has a fixed pricing structure, which is updated quarterly, for the most common analysis services. For custom or larger-scale analyses, a quotation will be provided after understanding the requirements and priorities of the project.

Consultation services are available free of charge for Peter Mac staff.

Types of services

Project work

Bioinformatics needs are often unique, and different laboratories may require different levels of support from the core. The team at BCC can help to analyse project requirements, discuss solutions with the investigators, and subsequently perform the analysis. The team also has extensive experience in generating publication-quality plots that can be used in articles, as well as publishing data as per journal requirements.

Grant applications

Bioinformaticians at BCC can contribute to grant applications by generating pilot data, and helping to describe in the application the infrastructure and bioinformatics analyses that are available to support the proposed research.

Consulting

The core can provide consultation on experimental designs and analyses options. For research groups that perform bioinformatics analyses by themselves, the core can share know-how and help troubleshoot as needed.

Methods/software development

Existing tools often fail to answer unique research questions, giving rise to the need for new bioinformatics workflows and/or methods. The team at BCC has a track record of building robust, highly cited bioinformatics software, and can discuss collaboration opportunities with research groups who are interested.

Deep machine learning

The core is committed to aiding cancer research through the development and application of deep learning (DL) and other machine learning techniques. We have been working on DL projects that involve radiological images and multi-omics data, and are keen to explore further cancer application areas. 

Pipeline development

Behind the scene, the core actively develops and maintains analysis pipelines for efficient processing of sequencing data. Bioinformatics pipelines are an integral part of high-throughput genomic facilities, and are considered by us as a fundamental software-level infrastructure. The pipelines are available to and have been extensively used by all bioinformaticians at Peter Mac, both within and outside BCC.

Partners

The BCC works closely with the Molecular Genomics Core Facility, Research Computing Facility, Papenfuss Lab, and other lab-based bioinformaticians at Peter Mac.

The team

Dr Jason Li (BCompSc, BEng(Hons), PhD): Senior Core Manager/Research Fellow.. Primary research interests in knowledge discovery from large genomic and transcriptomic datasets using machine learning techniques and software automation. Niche expertise: Bioinformatics Business Development 
[email protected]

Franco Caramia (BCompSc, MBioinf): PhD student and Senior Bioinformatician. Primary research interests in systems biology, biological network analysis and the role of chromosome X silencing in cancer. Niche expertise: Networks/Pathway analysis; Nanostring data.
[email protected]

Dr Kaushalya Amarasinghe (BSc(Hons), PhD: Bioinformatician and Data Engineer. Specialised in developing Deep Learning methods for cancer images and genomics data. Developed multiple DNA Copy Number analysis methods for next-generation sequencing data. Niche expertise: Deep Learning, Machine Learning, Copy Number Analysis  
[email protected]

Dr Niko Thio (BEng, MSc IT, PhD):  Senior Software Engineer.  Specialised in software development and management, with interests in end-to-end consolidation, analytics and visualisation.  Niche expertise: Sequencing facility LIMS; sequencing data processing. 
[email protected]

Richard Lupat (BSc): MPhil): Senior Bioinformatics Software Engineer. Specialised in bioinformatics pipeline development and automation for next generation sequencing data. Niche expertise: Clinical sequencing automation; Cloud computing.
[email protected]

Magnus Zethoven (BSc, MSc): Bioinformatician.  Primary research interests in Single-Cell RNA-seq analysis and clustering/subtyping analysis of transcriptomic datasets. Niche expertise: Single-cell RNA seq; VC pipeline validation & accreditation.
[email protected] 

Cassie Litchfield (BSc, DipMathSc, MSc): Bioinformatician. Primary research interests in analysis of ctDNA, immunogenomics and understanding cancer sex disparity. Niche expertise: LC-WGS, TCR-Seq, RNA-seq. 
[email protected] 

Michael Franklin (BSc, BCompSc): Research Software Engineer. Specialised in software development and mathematics. Niche expertise: Portable pipeline development. 
[email protected] 

Jiaan Yu (BEng, MSc): Bioinformatician. Specialised in testing and validation of next generation sequencing bioinformatics pipelines. Niche expertise: Bioinformatics pipeline testing and validation.
[email protected] 

BioInformatics Team
BioInfomatics Core Facilities Team

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