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.
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
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.
Discovery Early Career Researcher Award - Grant ID: DE150101117
Funder
Australian Research Council
Funding Amount
$327,000.00
Summary
The functional impact of new genes acquired through retrotransposition. Novel copies of genes often arise through retrotransposition of processed messenger RNAs. Many thousands of gene copies have arisen over evolutionary time and some of these have retained functionality while diverging from the parental gene leading to new paralogs under different regulatory regimes. Through analysis of whole-genome sequence data, we are now able to identify very recent gene copies that are not present in the ....The functional impact of new genes acquired through retrotransposition. Novel copies of genes often arise through retrotransposition of processed messenger RNAs. Many thousands of gene copies have arisen over evolutionary time and some of these have retained functionality while diverging from the parental gene leading to new paralogs under different regulatory regimes. Through analysis of whole-genome sequence data, we are now able to identify very recent gene copies that are not present in the reference genomes for various species, giving us the opportunity to explore the effects of new copies on the regulation of the original gene and the surrounding genomic environment into which the new copy is inserted. This project aims to address these important open questions through computational and biochemical approaches.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE190100008
Funder
Australian Research Council
Funding Amount
$387,103.00
Summary
Exploring the evolution and ecology of non-photosynthetic Cyanobacteria. This project aims to contribute and expand our rudimentary understanding of non-photosynthetic Cyanobacteria by obtaining representative genome sequences using metagenomics. The dogma that all Cyanobacteria are photosynthetic has recently been challenged by the discovery of non-photosynthetic lineages. This project expects to obtain representative genome sequences using metagenomics to predict surface structures. The expect ....Exploring the evolution and ecology of non-photosynthetic Cyanobacteria. This project aims to contribute and expand our rudimentary understanding of non-photosynthetic Cyanobacteria by obtaining representative genome sequences using metagenomics. The dogma that all Cyanobacteria are photosynthetic has recently been challenged by the discovery of non-photosynthetic lineages. This project expects to obtain representative genome sequences using metagenomics to predict surface structures. The expected outcomes from this project includes providing insights into the function and evolution of non-photosynthetic Cyanobacteria and their viruses, and pure or enriched cultures to enable future studies.Read moreRead less
Novel Bioinformatic Methods To Determine The Link Between Genomic Complexity Of Hepatitis Viruses And Liver Disease Phenotypes
Funder
National Health and Medical Research Council
Funding Amount
$605,859.00
Summary
Bioinformatics is a discipline concerned with the study of how information is stored and used in biological systems. Here we develop bioinformatic tools to study how hepatitis viruses evolve during an infection and how these infections cause severe liver diseases.
DNA sequencing allows us to see into the microbial world in fine detail. This enables us to investigate how bugs like bacteria cause infections and other diseases. In this fellowship, I will use DNA sequencing and analysis to investigate how bacterial infections are transmitted in hospitals and cities, how bacteria become resistant to the antibiotic drugs we use to treat infected people, and how the bacteria that live in our nose and throat contribute to development of asthma in young children.
Commensal benefits: genomic basis for suppressing plant pathogens with Pseudomonas biocontrol species. Food security is an issue of mounting significance due to unpredictable climate trends and increasing global population growth. A feature of paramount importance to reliable crop production is the capacity to control plant diseases. This project investigates natural plant colonising bacteria as a tool for protecting plants from disease.