Dr Hasindu Gamaarachchi: resourcing researchers with accessible genomic processing technology

Who Dr Hasindu Gamaarachchi

What Modern genomic sequencing is completely changing fields such as agriculture, medicine and ecology. However, it generally requires huge supercomputers and long processing times. Dr Hasindu Gamaarachchi has developed new scalable, efficient and accessible computer processing, allowing more people to unlock the potential of genomic sequencing and democratising the whole field.

Winner of the 2025 Macquarie University Eureka Prize for Outstanding Early Career Researcher.

Your research is making genomic sequencing far more efficient, accessible and scalable. What are the key innovations in your approach to genomic data processing compared to traditional supercomputer-dependent methods?

One of the big shifts in our approach to genomic data processing is moving away from the traditional reliance on supercomputers. Instead, we’ve focused on making these methods run efficiently on everyday, low-cost hardware. The key has been combining the knowledge of computer systems with an understanding of genomics to design clever, optimised and more efficient algorithms. We’ve optimised our methods to really take advantage of the hardware, things like memory hierarchies, parallelism, and processor features. This way we get high performance without needing expensive infrastructure. It’s a very practical, systems-level approach that brings together hardware, software, and domain knowledge in genomics.

How do you see your technology changing who can participate in genomic research, especially in lower-resourced settings or developing countries?

Not everyone has access to expensive supercomputers or cutting-edge hardware. That’s why the methods we develop are designed to be more accessible, enabling researchers who lack such resources to still perform advanced analyses. Even within Australia, not every place would have access to the ultra-fast internet connections required to upload large datasets to remote supercomputers. Our methods help overcome these limitations, making high-performance genomics computing feasible in lower-resourced settings and developing countries. So, the methods we developed are undoubtedly helping lower-resourced settings or developing countries. This has already happened; some methods we developed have been adopted in countries including Indonesia, Vietnam, Indonesia, Sri Lanka and parts of Africa.

Another important angle is that even well-resourced institutions and developed countries benefit. The efficiency of our methods means that existing supercomputing infrastructure can now support much larger-scale experiments. We've seen this in practice: projects that previously could only process a few dozen samples on the NCI Gadi supercomputer can now handle hundreds, thanks to the reduced computational demands.

Has your work revealed anything surprising or unexpected?

When we first started exploring this direction of using small computers for genomics analysis, there was quite a bit of scepticism, some even thought it was simply not feasible. It was, therefore, both unexpected and surprising for many when we demonstrated that it was indeed possible. It's encouraging to see that an increasing number of researchers are now embracing the use of standard computing systems in genomics.

Do you keep track of the projects that use your technology, and if so, what stands out to you?

I don’t actively keep track of all the users of our work, as it’s open-source and often not possible to know everyone who uses it. Most of the ones I’m aware of have reached out via email, GitHub discussion threads, science-focused social media platforms like X, or through in-person interactions. This is typically when they’ve asked for help integrating the work into their projects or sometimes even kindly thanked us that they’re using it.

One particularly memorable example is a tool we developed that’s now being used for intraoperative tumour diagnostics at a hospital setting. When we created it, we never imagined it would be applied in such a critical clinical setting. Knowing that our work contributes to real-world use cases is something I’m truly proud of, it speaks to both the reliability and the practical impact of the tools we’ve built.

What are some of the larger impacts you hope to see from your work in the future?

While we’re beginning to see a gradual shift in genomics toward the use of low-cost, compact computing systems, I hope this change accelerates significantly in the near future. What’s even more exciting would be the potential for these methods to extend beyond genomics into other areas of biomedical research. That’s something I hope to see in the near future.

Another key aspect in our work is that we avoid unnecessarily complex and bloated methods. Instead, we focus on methods that are done in the most efficient and simplest way possible. If something can be done effectively with fewer resources, that is the smartest and most optimal approach. I’ve seen that there exist certain methods that are overly complicated without real need. They may look fancy on the surface, but often bring unexpected problems, require excessive resources, and complicate matters. I hope to see more intelligent approaches that truly get the job done. In my opinion, the best method for any given task is the one that is least complicated yet delivers superior results.

What does winning a Eureka Prize mean to you?

It’s truly an honour, and more than that, a great encouragement to continue doing what we’ve been doing. Over the years, we’ve been deeply passionate about our work and have invested a tremendous amount of effort into it. It’s incredibly rewarding to see that this dedication has made a significant impact and is now being recognised with an award like this. Here I prefer to use ‘we’ rather than ‘I’, as this achievement wouldn’t have been possible without the contributions of students, mentors, collaborators, and everyone who has been part of the journey. Though this is an individual award in theory, in practice I would like to share the honour with all those contributors.

The Australian Museum Eureka Prizes are the country’s most comprehensive national science awards, honouring excellence across the areas of research & innovation, leadership, science engagement, and school science.