Tools and Technologies
We develop new CRISPR gene editing tools by integrating computational approaches and validation in the laboratory using protein engineering and RNA biology. We work in the context of the CCBS and the ANU RNA Research and Development Hub to provide a discovery pipeline and a technology platform to uncover the next generation of CRISPR editing tools for diagnostics and therapeutics.
In Vivo Imaging and Therapy platforms
Quantitative biological imaging and therapy methods are central to study of complex interactions across all areas of biology and medicine. Platforms are established with a host of advanced in vivo preclinical imaging platforms (fluorescence, holographic, micro-CT, bioluminescence, microfluidics, focal therapeutic X-ray dose delivery) that can conduct quantitative experiments from single molecules up to a whole animal at single cell resolution level. Through our approach, we aim to gain a new mechanistic understanding of therapeutic pathways for disease progression in living specimens for medical research. Technologies include In vivo imaging of bioluminescent and fluorescent reporters, in vivo imaging by high resolution CT, multiphoton microscopy, and 3D volumetric image guidance for focal therapeutic X-ray dose delivery. More information about these platforms and their use can be found in the web page of the JCSMR imaging facility.
Spatial and single-cell transcriptomics
Single-cell transcriptomics enables the study of gene expression and RNA processing programs in individual cells and their dynamics across different conditions and cell types. Spatial transcriptomics makes it now possible to interrogate the regional patterns of gene expression in the original tissue context. In combination, these technologies provide spatially resolved transcriptomes at the individual cell level in their physiological context. We work closely with the experimental platforms at the JCSMR Biomolecular Resource Facility (BRF) to generate and analyse these types of datasets for the study of gene regulation in disease and during immune response in individual cells and in the context of tissues and organs.
We make intensive use of the Oxford Nanopore Technology (ONT) sequencing platforms for our research. We develop and benchmark computational tools to analyse and interpret RNA and DNA sequencing data obtained from ONT platforms. Additionally, we work closely with the JCSMR Biomolecular Resource Facility (BRF) for the use of the PromethION platform and the development of new analysis tools.
We develop deep learning methods for the analysis of multiple data types, including Nanopore signals and long reads (Eyras group, see Eyras group github page), genomic sequences and flow cytometry data (Andrews group), and high resolution bioimages: single cell to whole tissue (Lee group, see HoloUNet, low light hologram-hologram denoising tool for GPU-QPM). We have experience in the developing, training, and benchmarking of multiple architectures.
We work closely with the National Computational Infrastructure (NCI), Australia’s leading high-performance data, storage and computing organisation, which provides expert services to all areas of science, government and industry. Through this collaboration, we are able to use these services for our high-end computational requirements across our research programs and core services.