The micro-patterned surface of the MinION flow cell


, Technology

Medical research is entering an exciting phase, where new technologies are playing a critical role in revealing the causes of human disease.  Bioinformatics – the analysis of biological data to glean useful information – is one of these pioneering technologies.

Powerful new genetic sequencing techniques offer a detailed look into many biological systems but produce a vast array of data that is too large to be analysed by conventional methods. The science of bioinformatics uses computing power and people with expertise in mathematics and statistics to gain meaningful information from that data.

At the Malaghan Institute, we are growing a bioinformatics team made up of people with expertise in molecular biology and computer science, to work alongside our medical researchers. We have also invested in the computer hardware needed to process the large data sets.

The ultimate goal of bioinformatics is to uncover the wealth of biological information hidden in the mass of data and obtain a clearer insight into the fundamental biology of organisms.  It enables researchers to compare vastly greater numbers of cells at a molecular level, and with more speed and accuracy establish relevance or the need for further enquiry.

Some argue that bioinformatics is more applied and hands-on, whereas computational biology is more theoretical and fundamental.  Click here to read more about definitions at the National Institute of Health in America.  For simplicity, we use the term bioinformatics to describe all work of this nature.

Meet our team

Left Alex Smith is a British/French researcher who initially trained as a biologist specialising in applied statistics.  He went on to complete a PhD in bioinformatics at the French National Sequencing Centre in 2012, developing a method for predicting gene functions in microbes.  After following his wife to New Zealand he was recruited at the Malaghan to work as both a bioinformatician and a biostatistician post-doctoral fellow.

Alex's primary project is the investigation of transcriptional differences induced in dendritic cells (immune cells) when stimulated with different allergens.  When he's not poking RNA-seq data until it gives up its insights, he's poking other data sets from a variety of cancer- and flow cytometry-related Malaghan projects, or teaching colleagues how to master their data in the same way. Alex has also recently organised for Dr Alex Shalek, one of MIT's rising stars, to give a seminar tour on single-cell transcriptomics.

Right  David Eccles is a freelance bioinformatics research analyst based at the Malaghan Institute.  He works with computers to enable other researchers to do their research faster, cheaper, and better. He began working at the Malaghan Institute in late 2013, and thoroughly enjoys the friendly atmosphere at the Malaghan Institute.  David collaborates with a number of additional clients around the world, including The Max Planck Institute of Molecular Biomedicine (Munster, Germany), and the Queensland University of Technology (Brisbane, Australia). He works primarily on a Debian Linux system, and frequently provides support to others regarding the use and administration of free and open-source software systems. 

His long-term research aim is to study the differences in small-scale gene patterns between humans and other species, and recent projects working on mitochondrial DNA and bacterial metagenomics have helped to give some clarity to the future directions of this research.

Malaghan Institute Research Programme using Bioinformatics

Professor Franca Ronchese is already using bioinformatics to explore the role of a type of immune cells called dendritic cells, in the initiation of allergies. “I am very excited by the new opportunities we have with this technology. We know we are asking difficult questions, but we are also confident that we have the best possible set-up to find the answers.”

New Zealand has one of the highest rates of allergic disease in the developed world, so any information on how allergies might be prevented or better treated has the potential to improve the quality of life for thousands of people.

“Unfortunately, there is still a lot we don’t understand about allergies. We don’t know when or where people were first exposed to allergens, or how this first exposure develops into an allergic response and then disease. We believe that understanding the beginning of an allergic response will be useful in trying to prevent the spread of allergy, and perhaps also in finding treatments to switch it off.”

From left to right Franca Ronchese, Lisa O'Connor and Shiau Choot Tang 

Professor Ronchese and her team are researching the precise role of dendritic cells in allergies. They are sequencing the whole transcriptome (all the molecules of RNA rather than DNA) of dendritic cells in a mouse that hasn’t been exposed to an allergen and a mouse that has.

“If our research so far is correct, there is something in the dendritic cell of an allergic mouse that starts the allergy, which is not present in a normal dendritic cell. There must be some subtle difference between the dendritic cells in allergic and non-allergic mice.”

Pinpointing that difference, however, is like finding a proverbial needle in a haystack. “That’s where we rely on our bioinformatics team, who will compare the dendritic cells at a molecular level and hopefully find a result for us.”

The search for a switch to turn off unwanted immune responses has been a long-term project at the Institute. Understanding an allergic response at this molecular level has the potential to open up new areas of research as well as leads for immune therapies.