Bioinformatics of Disease

Cris Print's laboratory focuses on using bioinformatic and systems biology methods to understand disease. Currently most of our time is devoted to cancer, however we also work on diseases involving blood vessels. A major challenge facing medical science at present is the integration of vast and rapidly growing volumes of information into a holistic understanding of disease. In some cases this integration involves the generation of mathematical models such as gene regulatory networks - in other cases information can be interpreted using relatively simple bioinformatic methods. Most projects in our laboratory involve collaboration between specialists in compuational biology, applied mathematics, statistics, genetics, as well as pathologists, physicians and surgeons. We do not get much satisfaction from simply combining `omics information from different sources, or from simply generating mathematical models of the molecular aspects of a disease, no matter how elegant the methods used are! Instead, we believe that evaluation of this type of research by laboratory experiments or clinical trials is required if we are to translate `omics information into improved biological understanding or clinical practice. Please see our web site for more information website

Phylogeography

In a joint project with the Anthropology Department and several collaborators of the Allan Wilson Centre we are working on the phylogeography of the Pacific rat or kiore (Rattus exulans). Kiore are often used as proxy for human migrations because they were deliberately introduced by the first people colonising the islands of Remote Oceania. The aim of our project is to infer migration pathways of the first Lapita settlers entering Near Oceania. We use up-to-date Bayesian approaches to simulate possible pathways. If the data allows we will also incorporate time depth into the models.

Proteomics

The Bioinformatics Institute focuses on developing novel methodologies to analyse proteomics experiments and biomarker discovery. Due to the rapid expansion of proteomics, there are several unsolved technical issues. These novel methodologies allow us to close these gaps and utilise information from different proteomics experiments, including 2D gel electrophresis difference gel elctrophoresis (DIGE), and mass spectrometry (MS). We also provided bioinformatics support for the SCOPE (SCreening fOr Pregnancy Endpoints) project. Different statistical techniques are applied to identify potential protein biomarkers and utilise these protein biomarkers for disease prediction.

Genomics

We are interested in the development of new technologies for the control and operation of wastewater treatment processes. We are currently studying a strain of Acidovorax sp., a promising key organism in the wastewater treatment process. We will analyse the genome sequence to find known and hypothetical proteins then use this information to develop high-throughput functional genomics platforms that will address fundamental questions about the biology of Acidovorax and its function in activated sludge-based treatment systems.

Genetic Epidemiology

The Bioinformatics Institute has a strong programme in genetic epidemiology of retroviral diseases. Current work includes a study of the epidemiology of Feline Immunodeficiency Virus in New Zealand, and the development of mathematical models that merge the population genetics and epidemiology of virus and host.

Applied Bioinformatics

Applied Bioinformatics The Bioinformatics Institute, and its affiliate members, are involved in several general bioinformatics procedures including:

Parallelised multiple alignment with non-arbitrary gap penalties.

Support vector machines and classification of biological data.

Compression algorithms and database searching.

Systems analysis of workflows and LIMS.

GMO in silico.