Research projects

Comparative and evolutionary genomics of human parasites – identifying parasite specific genes, drug and vaccine targets

Parasitic infections by blood flukes (schistosomes) cause highly significant human diseases. Schistosomiasis, a chronic disease caused by Schistosoma spp., is considered by the World Health Organization as the second most socioeconomically devastating and second most common parasitic disease afflicting humans, affecting 200 million people worldwide. No vaccines are available and treatment relies on only one drug, praziquantel. The genomes of three Schistosoma species infecting humans have recently become publicly available. We are sequencing several further parasite genomes, which allows us to do a comprehensive comparative genome analysis of multiple parasites and free-living flatworms. Using bioinformatics methods, we identify genes important for host-parasite interaction and novel drug and vaccine targets. This project will provide important information for preventing and controlling human parasite infections by Schistosoma spp. affecting more than 200 million people every year. The study will provide novel insights into the evolution of human parasite genomes, identify gene functions and pathways important for the parasite-host interaction and reveal novel candidate drug and vaccine targets.

Biomarker discovery

We have a main interest in the discovery of biomarkers for disease onset, progression and personalised treatment. In collaboration with Dr. Andrew Barbour for example, we are aiming at developing biomarkers for prognosis, progression and personalised treatment in oesophageal adenocarcinoma. Heterogeneous datasets are used and integrated, including genomic variations, epigenetic modifications, gene expression changes and copy number variations. For the discovery of novel biomarkers we employ various machine learning and data-mining methods, such as Support Vector Machines, Cox models, generalised linear models, supervised and unsupervised clustering, and multivariate techniques.

Epigenome-wide association studies

The emerging field of epigenetics studies heritable changes of our genome, which switch genes on or off without altering the genetic code. Epigenetics allows organisms to dynamically respond to environmental factors like diet, stress or prenatal experiences. Failure of epigenetic regulation can lead to important diseases, including cancer and mental disorders. Examples of epigenetic changes are the methylation of cysteine or histone modifications. These marks can be studied on a whole genome scale using recently developed next-generation DNA sequencing techniques, for example by Chip-Seq or Medip-Seq. In light of the huge amounts of data generated and the size of the human genome, the analysis of Chip-Seq and Medip-Seq data poses a considerable computational challenge. The Bionformatics Laboratory is involved in several projects investigating the role of epigenetics in complex diseases, in particular cancer and psychological disorders.

Role of the gut microbiota in health and disease

Our gut microbiota is an integral part of our body and increasing evidence indicates that it plays an essential role in diverse diseases such as allergies, cancer, mental illness, and metabolic and gastrointestinal disorders. While considerable efforts have been dedicated to find a cure for these diseases, their causes still remain poorly understood. The Bioinformatics Laboratory is involved in various projects investigating the role of bacteria in the development of diseases and disorders, including diabetes, obesity, gastrointestinal disorders and bacterial infections. The obtained results form a valuable basis for the development of novel treatment and prevention options and for the identification of biomarkers for disease risk. We also develop novel computational tools for mining, comparing and visualising large and complex metagenomic and 16S rDNA datasets.

Cancer whole-genome sequencing

We are analysing whole-genome sequening data of cancer to identify mutations, strucutral variations and copy-number variations inovlved in tumorigenesis and response to chemotherapy.

Researcher biography

Associate Professor Lutz Krause undertook undergraduate studies in Applied Computer science and completed his PhD in Bioinformatics and Genome Research in 2007 at Bielefeld University in Germany. During his graduate studies his primary research interests were in sequence analysis, metagenomics, machine-learning and development of efficient algorithms for next-generation sequencing. He also investigated the composition and function of natural microbial communities from diverse ecosystems, including biogas fermenters, coral reefs and waste water treatment plants. Lutz joined the Nestlé Research Center in Lausanne, Switzerland in 2008, where he studied the role of the gut microbiota in health and disease, in particular in obesity and diabetes. In 2010 he moved to Brisbane to take up the role as head of the Bioinformatics laboratory at the QIMR Berghofer Medical Research Institute. His team developed and applied bioinformatics methods in the context of biomedical research with a focus on the genetics and epigenetics of complex disorders and infectious diseases.

In 2014 Lutz joined the UQ Diamantina Institute to pursue his research on cancer genetics, biomarker discovery, genetics and epigenetics of complex diseases and parasite genomics. His group analyses heterogeneous data-sets, including copy-number variations, expression data, genomic mutations, structural variations and genome-wide methylation. In collaboration with the Princess Alexandra Hospital, Lutz research aims at the identification of biomarkers that help clinicians choosing the optimal treatment for individual OAC patients. In the field of infectious diseases, he is interested in discovering novel drug and vaccine targets against human parasites, based on the sequencing and comparative analysis of multiple parasite genomes. In collaboration with the Prince Charles Hospital our group is studying the genetics of lung cancer.

Areas of research