Coin Laboratory: Cancer Bioinformatics

Research Overview

The Coin Group develops genomic and transcriptomic tools to develop biomarkers for rapid characterization of disease state and prediction of drug susceptibility, with the aim of decreasing the time taken from hospital admission to administering the right treatment.   We also develop biomarkers for measuring treatment response.  We currently focus on infectious disease as well as cancer.

We utilize approaches from high-dimensional statistics, information theory and machine learning, including deep neural networks. We aim to implement streaming algorithms, which process data as soon as it is generated, providing real-time inference and visualization of both the most likely predicted disease state, as well as uncertainty in those predictions, which decrease as more data is collected.

Much of our current research utilizes real-time nanopore sequencing, based on its unique ability to generate sequence data in real-time, as well as its capability to sequence native DNA and RNA. We have emerging interests in single-cell long-read RNA and DNA sequencing, particularly as they relate to improving diagnostic and prognostic tools.

In infectious disease, we collaborate with chemists and materials scientists to develop techniques for isolating bacteria from complex biological matrices.  We apply these approaches in conjunction with real-time nanopore sequencing to sequence bacterial genomes directly from clinical sample.

We have ongoing interests in evolution of complex regions of the genome, particularly highly repetitive regions.  We are currently working utilizing long nanopore reads to characterize complex regions of tumour genomes inaccessible to short-read sequencing technologies.  We are interested in the role in which complex rearrangements in these repetitive regions can influence phenotype, including drug resistance. We have also worked on using circulating tumour DNA to non-invasively characterise copy number variation in primary tumours.

Staff

Professor Lachlan Coin:  Group leader

Dr Chenxi Zhou:  Postdoctoral researcher

Dr Devika Ganesamoorthy: Postdoctoral researcher

Dr Miranda Pitt: Postdoctoral researcher

Ms Jessie Chang:  PhD student

Mr Daniel Rawlinson: Research assistant

Collaborators

Dr Mark Blaskovich, University of Queensland

Professor Matt Cooper, University of Queensland

Dr Seweryn Bialasiewicz,  Queensland Paediatric Infectious Disease Laboratory

Dr Krispin Hajkowicz,  Royal Brisbane and Women’s Hospital

Dr Luregn Schlapbach,  Queensland Children’s Hospital

Dr Scott Bell, Prince Charles Hospital

Dr Erin Price, University of Sunshine Coast

Dr Derek Sarovich, University of Sunshine Coast

Professor Emma McBryde, James Cook University

Professor Claire Wainwright, Queensland Children’s Hospital

Dr Peter Simpson, University of Queensland

Dr Chris Coulter, Queensland Mycobacterial Reference Laboratory

Dr Arnold Bainomugisa , Queensland Mycobacterial Reference Laboratory

Dr Sushil Pandey, Queensland Mycobacterial Reference Laboratory

International

Professor Mike Levin, Imperial College London, United Kingdom

Dr Myrsini Kaforou, Imperial College London, United Kingdom

Professor John Chambers,  Nanyang Technical University, Singapore

Dr Martin Smith, University of Montreal, Canada

Dr Eva Novoa, Centre for Genomic Regulation, Spain

Dr Evelyn Lavu,  Central Public Health Laboratory at Port Moresby General Hospital

Funding

NHMRC

ARC

MRFF

Research Opportunities

This research project is available to PhD, Honours students to join as part of their thesis.
Please contact the Research Group Leader to discuss your options.