Genomics Platform Group
Researcher
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Associate Professor Oliver Hofmann
Research Overview
With a growing need for data management, analysis and research computing support – in particular due to the unprecedented growth of sequencing data – researchers and clinicians will benefit from community-driven, reusable approaches to process, analyse and aggregate large-scale sequencing data.
Associate Professor Hofmann's group is working on improved scalability and reliability of sequencing workflows, better detection of changes in cancer genomes, and aims to make tumour data, especially molecular data, from medical institutions and other organisations, accessible for research use in real time.
The group contributes to the development of a best-practice workflow system, bcbio, to fully automate high throughput sequencing analysis. They reuse existing software and solutions wherever possible to minimise redundant method development. As part of this effort the team works closely with the Global Alliance for Genomics and Health (GA4GH) on the development of the Common Workflow Language (CWL), deployment and testing of workflow execution frameworks (Cromwell, Toil, Arvados), abstraction protocols (Workflow Execution Standard, Data Object Standard) and data exchange.
As members of the Australian Genomic Health Alliance they develop a large-scale Genomics Warehouse built on community standards and support flagship projects with the management and dissemination of data.
The group is particularly focused on testing and validating new methods using community-developed benchmarks to improve the chances of detecting relevant somatic genome changes to aid in the diagnostic and treatment of cancer patients.
Staff
Associate Professor Oliver Hofmann - Group Head
Roman Valls – Senior Research Engineer
Florian Reisinger – Senior Research Engineer
Vlad Saveliev – Senior Bioinformatician
Peter Diakumis – Bioinformatician
Sehrish Kanwal – Bioinformatician
Lavinia Gordon – Project Manager / Senior Data Analyst