Star Scientist of the Month -Dr Ralph Patrick
"It's always been the dream to develop something that as many people as possible find useful"
22 January 2021
Kicking off a new series for 2021 - Star Scientist of the Month - we interview Dr Ralph Patrick, who recently had a paper published in Genome Biology, and an eager scientist who is always looking into new areas of technological development.
Ralph, you’ve recently had a paper published in Genome Biology, congratulations!
Thank you, it was a collaborative effort, it started as a data analysis challenge at the Oz Single Cells Conference back in 2018. We were looking at developing software to analyse single-cell RNA sequencing data. Specifically, we wanted to understand the different isoforms that are being expressed between different cell types.
We came up with a software package that was able to do that. This software can detect the different isoform expression patterns between cells. For example, in the heart we found a gene that’s expressed in fibroblasts and endothelial cells, but when we applied the software, we were able to find that these cell types express different isoforms that actually control their localization to different parts of the cell.
When you publish a paper it always feels like a big achievement, I’ve been proud of all my papers for different reasons.
What do you enjoy the most about working in science?
I like the feeling of having a project to work on. I like the process of discovery or method development.
One thing I have enjoyed about working in the single cell RNA sequencing field is that it opened up new doors. We’re looking to find new cell types that haven’t been seen before. That kind of discovery is really cool.
I also enjoy the process of method development. My PhD was very focused on bioinformatics method development, trying to create a tool that’s not just comparable or better than the tools out there, but easy to use. I find some software tools can be great in theory, but then difficult to use when you’re trying to apply them to analyse data.
Is that the dream, to develop a tool that potentially scientists would use globally to benefit their research?
That’s always the dream. Develop something that as many people as possible find useful. There’s lots of commonly used bioinformatics tools out there in the market already. For example, BLAST is probably one of the most well-known computational tools for biology. In single-cell RNA sequencing analysis, Seurat is probably the most well-known.
What is your current research focused on?
This new single-cell RNA sequencing technology has allowed us to make advances in understanding the cell types in the heart and how they respond to cardiac injury.
That’s the focus of our current research, trying to identify these different cell types and understand more about them.
For example, one cell type in particular, WntX (or Wnt eXpressing), we know it exists, but we know very little about its function. We call it WntX because it almost uniquely expresses a set of genes that are involved in a particular signalling pathway called the Wnt pathway, which has been well studied in the context of development and cell differentiation and has also been implicated in heart disease.
Our hypothesis is that the WntX cells are involved in the heart’s response to injury. Specifically, that they control the timing of specific aspects of the heart’s reaction to injury.
We would love to know more about it and its role in the heart. Is it even a cell type that could be targeted to improve outcomes after a heart attack?
When did you start working at the Victor Chang Cardiac Research Institute?
I was finishing up my PhD at University of Queensland, writing my thesis and looking for jobs and I attended a bioinformatics conference at the Garvan Institute here in Sydney. I just happened to be seated with the Bioinformaticians from the Victor Chang Cardiac Research Institute. They told me that the Institute was hiring bioinformaticians and encouraged me to send in my CV. Somehow, I had totally missed the Ad, so it was a good thing I happened to be sat at that table. That’s about 4 and a half years ago now.
Was it a big move down to Sydney?
It was, obviously not as big as going overseas but still all my family are back in Brisbane. I moved down with my wife and we have two kids now. They definitely keep us busy, it’s non-stop with young kids. We always try to make time at the weekend to just play with them and spend quality time together, go to the park, see friends or go to church. We took them to the Snowy mountains this year, but because of COVID, there were limitations on what you could. Tobogganing was out of the question for example. We had to improvise and sit my daughter on my lap and just slide down the hill, we called it “daddy-bogganing.” That was a lot of fun, being a father is probably one of my greatest achievements.
Do you think you’ll encourage them to go into science?
I don’t think I would specifically push them into science but maybe they will pick it up by osmosis. I work in science and my wife is a vet so also in a science-related field, maybe that will influence them.
Who has been the biggest influences in your scientific career?
At the Institute, I would have to say Richard (Prof Richard Harvey). He is very knowledgeable; I’ve learned a lot from him. He pushes all of us to do high-quality science and really try to dig down into what’s going on.
And I would have to say my PhD supervisor, Mikael Boden. He was a really good teacher. Again, he would always push me to do more work and get my paper published in the best journal I could.
What’s next for you, where is your research headed?
I’m really interested in moving into new areas of technological development, two big new emerging areas in particular. One is called spatial transcriptomics. With normal single-cell RNA sequencing, you lose the spatial context of the cells. You have cells and you know that they express certain genes, but you don’t know where they are in the heart. The location of these cells can be so important. There are new technologies that will allow us to start answering those questions so I’m really excited to get into that space.
Another emerging area of development is something called single-cell multimodal profiling. That is, measuring multiple different types of output from a cell. We currently look at gene expression, so what genes are switched on and their different levels of expression. But with this new kind of technology another output, for example, would be measuring DNA accessibility. Essentially, what parts of the genome are accessible, which helps us understand what parts of the DNA might be active and contain regulatory elements that are controlling gene expression. What’s exciting is combining the two, and being able to improve the inference of gene regulatory networks that control the heart’s response to injury. I’m looking forward to hopefully being able to work on that.
** Dr Ralph Patrick is a member of the Developmental & Regenerational Biology Laboratory
Acknowledgement of Country
The Victor Chang Cardiac Research Institute acknowledges Traditional Owners of Country throughout Australia and recognises the continuing connection to lands, waters and communities. We pay our respect to Aboriginal and Torres Strait Islander cultures; and to Elders past and present.
