Large-scale Cancer Proteomic Analyses For Improved Prediction Of Drug Response, Patient Prognosis And Clinical Outcome
Funder
National Health and Medical Research Council
Funding Amount
$318,768.00
Summary
Proteomics is the study of all of the proteins encoded by a genome. In this project, I will use a new database of proteomic and clinical data from up to 70,000 cancer samples, and create an approach to correlate proteomic features with drug response, patient prognosis and clinical outcome. The aim of this research will be to use proteomics to better guide treatment decisions, with the potential to significantly improve the health of people with cancer, both in Australia and globally.
Improving Bioinformatic Methods For Studying Gene Regulation In Health And Disease
Funder
National Health and Medical Research Council
Funding Amount
$463,652.00
Summary
New methods for analysing genome-wide data will be developed to ease the data analysis bottleneck that currently exists in medical research. Modelling variation in gene expression from single cells, in screens designed to uncover gene function and assays that measure the factors that turn genes on or off will be the focus. Free software will be developed and made available to researchers worldwide to help them interpret the large and complex data sets that are now routine in genomic medicine.
High-throughput genetic assays are commonly used to study the molecular basis of disease and such technology requires sophisticated data analysis methods that account for significant biological and experimental complexity. Specialized methods will be developed in free public software that will greatly benefit future genetic profiling studies.
Discovering The Genetic Causes Of Congenital Heart Disease Using Systems Biology
Funder
National Health and Medical Research Council
Funding Amount
$419,180.00
Summary
Congenital heart disease (CHD) affects one in one hundred live-born babies, representing a significant health burden in Australia and worldwide. My research team is using state-of-the-art DNA sequencing technology to sequence the entire genome of hundreds of patients with CHD and their family members. My research program develops fast and reliable computer software to accelerate the discovery of the genetic causes of CHD, and make personalised genome-based medicine a reality.
Investigating Widespread Regulation Of Gene Expression Through Intron Retention
Funder
National Health and Medical Research Council
Funding Amount
$363,026.00
Summary
We recently discovered a hidden type of gene regulation that appears to be altered in diverse cancers including leukaemia, melanoma and colon cancer. We will explore this widely relevant mechanism using molecular and computational tools. We created the only computer program able to detect this type of regulation and will now share our discovery with cancer scientists through cloud computing technology.
Computational Reconstruction And Validation Of A Gene Regulatory Network Controlling Differentiation Of B Cells To Antibody-secreting Plasma Cells
Funder
National Health and Medical Research Council
Funding Amount
$618,152.00
Summary
Regulation of B cell differentiation, which occurs when our body responds to antigen infection is tightly controlled by a gene regulatory network. This project will be the first study to reconstruct a regulatory network for this process by using genome-wide expression and transcription factor binding data. The research finding from this study will elucidate the molecular mechanisms regulating this process and will shed new light on how this network is altered in lymphoma and myeloma.
Sequencing and assembling microbial community metagenomes in real-time. This project aims to assemble metagenomes directly from environmental samples using nanopore sequencing. Short-read approaches to metagenomics cannot assemble mixed genomes from an environmental sample, so focus on describing which species and genes are present. Long-read nanopore sequencing enables the assembly of full genomes of multiple species in a sample. Assembling complete genomes in important resources such as water ....Sequencing and assembling microbial community metagenomes in real-time. This project aims to assemble metagenomes directly from environmental samples using nanopore sequencing. Short-read approaches to metagenomics cannot assemble mixed genomes from an environmental sample, so focus on describing which species and genes are present. Long-read nanopore sequencing enables the assembly of full genomes of multiple species in a sample. Assembling complete genomes in important resources such as water and soil should lead to deeper understanding of the dynamics, variation and transfer of genetic material within these resources’ microbial communities, strategies to manage microbial diversity, and improved productivity and long-term sustainability for these resources.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE200101323
Funder
Australian Research Council
Funding Amount
$427,098.00
Summary
Structure guided mapping of protein interactions and their perturbation. Protein interactions are central to most biological processes, and significant effort has been devoted to trying to unravel these complicated networks. This project aims to develop new approaches to better understand these interactions, and the consequences of their perturbation. The main expected contributions will be: (i) methods to identify likely protein interaction sites using population conservation; (ii) computationa ....Structure guided mapping of protein interactions and their perturbation. Protein interactions are central to most biological processes, and significant effort has been devoted to trying to unravel these complicated networks. This project aims to develop new approaches to better understand these interactions, and the consequences of their perturbation. The main expected contributions will be: (i) methods to identify likely protein interaction sites using population conservation; (ii) computational approaches to assess the effects of any type of mutation on the interaction; and (iii) an understanding of how disruption of a specific interaction can affect the complicated biological network within a cell. Read moreRead less
Unravelling Gene Networks In Heart Development And Congenital Heart Disease
Funder
National Health and Medical Research Council
Funding Amount
$397,724.00
Summary
One in 100 Australian babies are affected by heart malformations. The heart is a complex organ and its formation is likewise orchestrated by a complex network of genes. As our current knowledge of this network is limited, I aim to employ cutting-edge bioinformatics approaches to draw a comprehensive picture of genes required to build a healthy heart and to reveal which gene interactions are altered in congenital heart disease, thereby opening new perspectives for network biology-based therapies.
Interactions Between Aberrant Transcriptional Programs And Methylation In Primary Myelodysplasia And Leukaemia.
Funder
National Health and Medical Research Council
Funding Amount
$316,449.00
Summary
Impaired development of blood stem cells leads to haematological disease such as leukaemia. State of the art next-generation sequencing and bioinformatics identified molecular pathways essential for normal blood development and a core set of these genes repressed in leukaemia. Understanding the mechanism by which these genes are re-activated by the non-specific drug azacitidine contributes to the development of new therapeutics with increased efficiency and reduced side effects.