Gyorgy Hutvagner and Alireza Ahadi. Photo by Shane Lo
Against all odds
Alireza Ahadi is an international student who began a PhD, in 2012, under the supervision of Associate Professor Gyorgy Hutvagner from the Centre of Health Technologies
Though their funding was cut, and Ahadi has since completed a different PhD in the psychology of programming, the pair continued their research and developed the online MicroRNA Target Prediction Tool, which will help biologists and clinicians identify and develop targeted treatments for disease
In 2012, international student Alireza Ahadi began a PhD under the supervision of Associate Professor Gyorgy Hutvagner from the Centre of Health Technologies. When funding for the PhD was cut, the pair nonetheless continued their research. Four years on, their work has resulted in an online tool that will help to identify and develop targeted treatments for disease.
These days, biologists generate data on a scale that was never seen before. We sequence everything – in space, soil, the sea, humans. We collect a lot of information and to try to make sense of things. For instance, if you decode the full genome of a hundred thousand people, which data could predict that you're going to get cancer? Or you're going to respond to a certain drug? So there’s a big need for advanced mathematics and bioinformatics.
Al’s background is in IT. He was an international student who had these skills, and he was interested in carrying out research in biology. He became my PhD student, and from the beginning he had a lot of input from the computational point of view.
But in biology-related subjects, producing a quality peer-reviewed paper takes time. At that point no-one was in a position to invest, so his PhD tuition was cut, our project was left in half and he had to find a new path to complete his PhD. Despite this, I still considered him as one of my lab members.
Al recognised that the set of skills he's using for his new PhD in computer science education research is perfectly applicable for biology. And he applied part of this mathematics, from a totally different subject, to what we're doing.
We're working on something called microRNAs. They're very small, but they are key for regulating the expression of most of your genes and their proper function is absolutely required for maintaining healthy cells. If something's going wrong with these guys, you can get cancer, dementia, Alzheimer's – all sorts of diseases. To understand how they work, you need to understand how they target some of your protein coding genes. And to do that, we need some very heavy bio-informatics.
Al provided the approach that combined existing data sets from the field and pulled together in a novel algorithm. He set up a website that lets you select from about 2600 microRNAs, and his prediction tool will tell you which genes are likely to be targeted by these microRNAs.
It’s for biologists mainly, but it can be used by clinicians because microRNAs are good biomarkers for diseases. If they identify microRNAs that are changing in a certain disease, they can use the tool to find the potential genes that are affected by that change. It can be a good indication of what drug you can use or develop in the future.
From this work, Al has published a paper in a very prestigious journal, which he can be proud of in any circumstances. But he had to teach, he had other jobs and he had to do a full PhD at the same time. He was going against all the odds. At some point you would give up, right? You would expect this guy to stop showing up, but he just kept coming and I kept pushing him.
I have to mentor my students, to help them prevail. It's not even a philosophy. As a supervisor, that's part of your job description. And honestly, as an academic, it’s my favourite part.
I came to UTS to do a master’s degree in information technology. I didn’t have any research background – it was a coursework degree – but I was interested in research and I started doing some along with my coursework. It was not compulsory; research was just something I was interested in moving into.
I began my research with Raymond Lister, an Associate Professor in the School of Software, who is now my PhD supervisor. But my main interest was in biology – cancer, mostly.
Something is wrong with my mother’s side of my family. I lost three aunts and one uncle to cancer, and that's too many for one family. So I have a personal interest. I always wanted to contribute to something, because it's important to me to leave something behind. I don't just want to be here, then just disappear from the planet.
When the funding was cut for my project with Gyorgy, I didn't start the new PhD straight away. I didn’t want to do just any research; I was really interested in this particular area of gene expression. Still, we kept working on it on and off for a few years. I was working in lots of different jobs – I didn’t say no to anything because I was trying to save funds for at least one more semester to work on this research.
Then I started tutoring a programming subject for Raymond. I developed a successful thesis proposal with him and began my current PhD on the psychology of programming. Sometimes all of these competing priorities made it frustrating, but if you don't give up, eventually the reward will be a juicy fruit.
In the last year, it was really tense. We were working on this paper on a daily basis. We published it at the end of last year, and I’d say the prediction tool we developed is pretty comprehensive and fills a niche in the field.
Now, I’ve just completed my PhD thesis on how novice programmers develop their critical thinking when it comes to writing a programming language or an application based on a programming language. None of this would’ve been close to possible without the faith and trust Gyorgy has in me.
You can find and use the cell-specific MicroRNA Target Prediction Tool at mirtar2go.org