Bioinformatics

Bioinformatics

Gene expression in the blood cell system
The Bioinformatics division collaborates with institute and external researchers in designing, conducting and analysing genomic and molecular sequence studies to understand biology and disease. We also conduct research to improve existing methods and develop novel methods for analysing data.

Removing unwanted variation

Technologies that reveal the secrets of DNA and the genome are vital for medical research, however much of the data from these technologies – including microarray, mass spectrometry or DNA sequencing – contains variations that occur due to time, space, equipment, operators, reagents, sample source and quality and environmental conditions.

Professor Terry Speed and colleagues have developed an approach to removing unwanted variation in such data that will greatly streamline the information gained from these studies. 

Archaeology of immunity

MHC class I genes contribute to the development of longlasting immunity. These genes have evolved over time in all species of jawed vertebrates, which include humans, chickens and fish.

Associate Professor Tony Papenfuss and colleagues developed a new strategy to study the evolution of MHC class I genes in selected species of jawed vertebrates. Remarkably, they found dozens of previously undiscovered genes in several species. Most notable was a new family of MHC class I genes found in marsupials and monotremes, but missing from other mammals including humans. The role of these genes is now being investigated.

Revealing gene regulation

Chip-seq is a powerful sequencing technology that can identify sites across a whole genome used by diff erent molecules, and in different ways, to switch genes on or off . It can be used to explore transcription factors, epigenetic factors and other regulatory elements that modulate gene expression.

Professor Gordon Smyth and PhD student Mr Aaron Lun developed algorithms and software for exploring how these regulatory elements change during normal development, and in diseased cells. These tools are critical for our research teams to discover potential new targets for treating cancers, immune disorders and infectious diseases.

Health impact

Cancers: bowel cancer, breast cancer, leukaemia, lymphoma, lung cancer, myeloma, ovarian cancer, rare cancers, stomach cancer

Immune disorders: acute rheumatic fever, lupus, multiple sclerosis, rheumatoid arthritis, thyroid orbitopathy, transplantation, type 1 diabetes

Infectious disease: malaria, scabies, tuberculosis, toxoplasmosis

Other areas: congenital disease, Down syndrome, heart disease and stroke, neurodegenerative disease, personalised medicine

Division heads

Professor Gordon Smyth

Lab heads

Professor Terry Speed

Associate Professor Tony Papenfuss

Dr Melissa Davis

Dr Wei Shi

Division coordinator

Maria Markovic