What is bioinformatics? Shred a book and put it back together

We are living in a world of ever-increasing reams of data, and biology is no exception. The relatively new field of bioinformatics is one of the jobs of the future and already it’s making waves in industries like healthcare and agriculture.

But the field doesn’t just need biologists, according to Dr Paul Wang, a senior bioinformatician at the South Australian Genomics Centre, based at the South Australian Health and Medical Research Institute (SAHMRI).

Wang spoke last week at a Cosmos Science City forum on ‘Jobs of the Future’.

“Bioinformatics is a very broad field,” Wang said at the forum. “Basically, it’s data science applied to biological data. But it covers a lot of things.”

Wang’s own research relates to understanding data-rich DNA and genomes.

“Before the turn of the millennium 20, 30 years ago, biological and medical research did not work at this scale,” said Wang.

“Researchers worked on a few genes or proteins […] But since the human genome project was completed around 2000, now you have access to this amount of data, and it becomes almost impossible to do it by hand. So a quick way of thinking about bioinformatics is: anything that you can’t really easily do in Excel, we do that stuff.”

Wang’s work revolves around genomics in particular: analysing DNA sequencing data. When you sequence a strand of DNA, the information comes back in tiny chunks.

“It’s like if you chopped up a book into tiny little pieces, inputs of 2-3 words, and then you have to somehow piece all that together,” Wang tells Cosmos.

“You can make inferences about whether or not one word comes up next, and we will use other information to do this. So for example, you’ll have lots of copies of the books and they’re chopped up in different ways – you can see the overlaps.”

This was how the human genome was first assembled, and still how researchers assemble DNA sequences – although Wang says having the human genome template to work from makes things easier.

Sequencing and comparing genomes from patients can improve their treatments. Wang cites the MoST study as an example.

“It’s a clinical diagnostic trial happening in Australia at the moment for cancer patients who fail the initial treatment: the standard treatment doesn’t work for whatever reason,” says Wang.

“[Researchers] apply those sequences and say: well, what are the most likely reasons making them not respond to the treatment?”

Genomic sequencing is also being used in agriculture research: say you have two varieties of crop that perform the same in normal conditions, says Wang.

“One of them could actually have better drought resistance, but it’s hard to know which one it is until you actually have a drought. If you know about the genome, if you have research that says this particular trait in the genome would confer drought resistance, then you can sequence the crops and figure out which one is more likely be resistant.”

But DNA isn’t the whole game in bioinformatics. Other biological substances, indicators and even photos can be rich sources of data. Wang points out South Australian company Life Whisperer, which analyses pictures of embryos with AI to improve IVF outcomes, as something that “would also be considered bioinformatics”.

And nor does the field rely on biologists alone: in fact, it needs a very diverse skillset to work.

“That’ll include physics, engineering, and chemistry, we also need an understanding of biology. And we also need lots and lots of mathematics and programming,” says Wang.

“You can enter this field from any point. I have colleagues who were trained in biology, I have colleagues who used to program for financial institute or design computer games. And many of us come from physics, where funding is a bit tricky to come by.”

Physicists, says Wang, typically have some programming and analytical skills that come in handy in bioinformatics.

“Bioinformatics doesn’t stand on its own,” he says.

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