Prof Smyth joined WEHI in 2001, the year the sequencing of the human genome was published, and started work on limma soon after.

Modern genomic technologies produce a vast amount of data for researchers to examine – which is where limma comes in. The software uses statistical methods to handle these massive, complex datasets, with its robust methods and ease of use making it a widely adopted tool in the genomic community.

“My team here at WEHI have, for many years, been developing the advanced computational and statistical strategies to help analyse and interpret these huge genomic datasets, headlined by limma,” said Prof Smyth.

“Our goal is ultimately to learn more about how diseases originate by examining genetic disruption and how this can be controlled – while freely providing the tools we develop to others around the world so they can do the same.”

Prof Smyth said he was thrilled to win the Eureka Prize for Excellence in Research Software, which was the result of a team effort over many years.

“I would particularly like to mention my WEHI colleagues Professor Matt Ritchie, Dr Belinda Phipson and Dr Charity Law, who made significant contributions to important limma functionalities early on and who continue to be involved in the limma project,” he said.

Understanding how genes are turned on or off, a process called gene expression, is an essential part of disease research.

By comparing, for example, how genes are expressed in healthy and diseased samples, scientists can identify genes that cause diseases like cancer, diabetes and neurological disorders, opening the door to new treatments and therapies.

Bioinformatics applies mathematics, statistics and computer science to make sense of complex biological data and systems. limma is the leading software package used in bioinformatics for statistical analysis of gene expression, and is downloaded half a million times each year.

“Software development is fundamental for modern research but has not always been fully recognised or rewarded – it is fantastic that the Australian Museum and the Australian Research Data Commons have created this prize to highlight its critical importance in driving discovery and innovation.,” said Prof Smyth.

The Eureka Prizes were announced at a ceremony in Sydney on Wednesday 4 September.

The award is the latest recognition of the significant contributions Prof Smyth has made to the fields of bioinformatics and computational biology, in a career spanning over two decades.

Prof Smyth was named an Honorary Senior Fellow of the Australian Bioinformatics and Computational Biology Society (ABACBS) in 2020, the society’s highest honour, was elected a Fellow of the Australian Academy of Science in 2021 and was awarded the Julian Wells Medal in 2023. He was won several software development awards and has been a Web of Science Highly Cited Researcher every year for over a decade.

Professor Smyth’s research has received significant support from the Australian National Health and Medical Research Council and the Chan Zuckerberg Initiative.