Meet the Bioinformatics Team

 

Bioinformatics is definitively the new buzz word in medical research, despite the term being originally coined over 30 years ago.  
Back then, Paulien Hogeweg, a Dutch theoretical biologist and complex systems researcher, used it to describe ‘the study of informatic processes in biotic systems.’  
Nowadays, ‘bioinformatics’ in broad terms encompasses the branch of life science that applies information technology to the field of biology to help understand various biological processes.
It’s all about data, and lots of it.  
For a number of years, Institute researchers have been using microarray technology to rapidly screen thousands of genes at the same time.  
These microarray experiments take a snapshot of every gene in a particular cell or tissue and measure their expression levels, in some cases generating data for over 20,000 different genes.  
It’s important information that helps us to study a range of different childhood diseases, including asthma and allergy, leukaemia and brain tumours.  
But the challenge has been to combine this vast amount of biological data so that researchers can form a comprehensive picture which may help to unlock why, for example, some cells become cancerous or why the immune cells from allergic people hyper-react to harmless proteins.  
The arrival of Professor Jenefer Blackwell’s Genetics and Health team from Cambridge in 2007 heralded the beginning of another group of researchers collecting vast amounts of data.
One of the Genetics and Health team’s research interests is to use large-scale family-based genome-wide association studies to look at the causes of a number of infectious diseases including leishmaniasis and otitis media (middle-ear infections).  
Information is collected from populations as far as Brazil, Sudan and India as well as from here in Western Australia.  
Like the microarray experiments, the huge amount of data generated in these studies has proven a challenge to not only collate and store but also to analyse in order to work out which results may be biologically significant.
Professor Nick de Klerk, Head of Biostatistics and Genetic Epidemiology, explains that after consultation with senior researchers in mid-2007, the wheels were set in motion to recruit and develop a specialised bioinformatics team to assist in the management of the data sets generated by these studies.
“We got to a point where we had the samples, the technology and the expertise to generate an amazing amount of valuable data, but we were lacking the capacity to efficiently store and analyse it to get the most possible out of what had been collected,” says Nick.
“The development of a team devoted to this task seemed like the obvious next step in progressing the research at the Institute.”
So in early 2008, with funding from the State Government’s Centres of Excellence program, bioinformaticians Dr Kim Carter and Richard Francis were recruited into Senior Bioinformaticians positions at the Institute.  
Prior to joining the Institute, Kim had contributed a number of significant informatics tools to the bioinformatics and wider research communities that have generated national and international interest and are being used by research groups across the world.  
“One of the things I’m really passionate about is improving the recognition of the field of bioinformatics,” says Kim.  
“In each of the roles in my research career to date, I’ve tried to build and develop the relatively scarce human capacity within the field by collaboration, seminars and supervision and mentoring of students and so I jumped at the opportunity to continue this at the Institute.”
Richard Francis, a bioinformatician working at the Cambridge Institute for Medical Research (CIMR), was enticed to leave the green pastures of England for the sunny shores of Australia by the promise of an exciting career opportunity at the Institute.
“During my time at the CIMR, I had a dual position in that I set up the Institute’s bioinformatics facility from scratch and provided a bioinformatics support service for the building,” explains Richard.
“Whilst I thoroughly enjoyed my six years there, I was ready for a change and the opportunity to move to Australia came at the perfect time, even though it was a slightly scary prospect!”
Richard and Kim are now jointly leading and developing a program of bioinformatics at the Institute, under the supervision of Professor de Klerk.  
The majority of their work to date has been focussed in the Divisions of Genetics and Health, and Leukaemia and Cancer Research.  
However, other divisions are beginning to utilise their services in managing a number of the large population-based studies being undertaken.
“As bioinformaticians, Richard and I provide a core bioinformatics service to all research divisions, which essentially involves collaborating with researchers to enable them to better use computer technologies to improve research outcomes,” explains Kim.
Adds Richard: “It’s our job to design the databases to store the data efficiently, work with the biostatisticians when required to analyse the data effectively and develop the visualisation tools to allow researchers to more easily pull out the patterns in their data.”
Despite its rapidly emerging importance, the world of bioinformatics is still rather enigmatic to the majority of the staff at the Institute.  
Both Kim and Richard agree that the team’s main goal is to educate fellow Institute researchers on the advantages of utilising the services that they offer.
Says Kim: “We’ve still got a bit of setting up to do to get a fully comprehensive service running, so as a short term goal I’d have to say getting more of a presence in the building and increasing our usage and capacity is a definite aim.  In the long term, I would love to see the development of a large group of bioinformaticians based at the Institute who are dedicated to improving child health and child health research.”
While both admit that they are passionate about their work, in their spare time Kim and Richard indulge in their other hobbies.  
For Kim, that involves hockey (he plays for Curtin Trinity Pirates), beach volleyball and dabbling in the garden.  
Sport also plays a big part in Richard’s life, and Australia has introduced him to a couple of new ones.
“I love sport of any kind,” says Richard.  “It doesn’t matter what it is, who’s playing or where, I’ll watch it! I’ll also try my hand at anything new given the opportunity and I’m mad keen on getting into kite surfing next year.
“I also want to get back in to football (soccer) so if anyone needs new recruits for their team then give me a buzz!”