Resolving the Genetics of Grain Pigmentation Traits in Rice . New critical knowledge will enable future breeding of quality black rice cultivars that can exploit the high UV Australian growing environment to enable domestic production of high-value, healthy black rice. The demand for functional foods with health benefits, including black rice, is increasing both domestically and internationally. The concentration of key functional compounds in black rice may be increased by growing optimised cul ....Resolving the Genetics of Grain Pigmentation Traits in Rice . New critical knowledge will enable future breeding of quality black rice cultivars that can exploit the high UV Australian growing environment to enable domestic production of high-value, healthy black rice. The demand for functional foods with health benefits, including black rice, is increasing both domestically and internationally. The concentration of key functional compounds in black rice may be increased by growing optimised cultivars under high-UV radiation, making Australia well placed to produce the highest quality black rice. Utilising a unique genetic resource this project will resolve how the interaction between crop genetics and the growing environment drives the concentration of functional compounds in black rice. Read moreRead less
Characterising inheritance patterns of whole genome DNA methylation. This project aims to characterise epigenetic diversity and inheritance patterns in whole genome sequencing data from a unique human population. The project will employ the well-characterised Norfolk Island genetic isolate, cost-effective whole genome bisulphite sequencing technologies and advanced bioinformatics pipelines and statistical models. It will involve cross-discipline collaboration between human geneticists, epigeneti ....Characterising inheritance patterns of whole genome DNA methylation. This project aims to characterise epigenetic diversity and inheritance patterns in whole genome sequencing data from a unique human population. The project will employ the well-characterised Norfolk Island genetic isolate, cost-effective whole genome bisulphite sequencing technologies and advanced bioinformatics pipelines and statistical models. It will involve cross-discipline collaboration between human geneticists, epigeneticists, statistical geneticists and bioinformaticians. This project will advance our understanding of the interaction of genetics and epigenetics and their relationship to diversity and inheritance in humans.Read moreRead less
Whole-genome multivariate reaction norm model for complex traits. This project aims to develop a multivariate whole-genome genotype-covariate correlation and interaction model that can be applied to a wide range of existing genome-wide association study (GWAS) datasets. Genotype-covariate correlation and interaction (GCCI) are fundamental in biology but there is no standard approach to disentangle interaction from correlation in the whole-genome analyses. This project will address the key featur ....Whole-genome multivariate reaction norm model for complex traits. This project aims to develop a multivariate whole-genome genotype-covariate correlation and interaction model that can be applied to a wide range of existing genome-wide association study (GWAS) datasets. Genotype-covariate correlation and interaction (GCCI) are fundamental in biology but there is no standard approach to disentangle interaction from correlation in the whole-genome analyses. This project will address the key feature in biology, which relates to dissecting the complex mechanism of association and interaction. The proposed statistical model implemented in a context of a novel design based on multiple GWAS data sets is a paradigm shifting-tool with applications to multiple industries.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE220101210
Funder
Australian Research Council
Funding Amount
$451,634.00
Summary
Deciphering molecular genetic mechanisms underlying chromatin interactions. This project aims to generate the high confidence map of enhancer-promoter links in 61 tissues and cells through robust integration of novel machine learning tools with genomic and epigenomic datasets. Understanding which key elements in the genome may be important to fine-tune gene expression is essential for understanding biological pathways. The expected outcomes include i) New tools to robustly identify true chromati ....Deciphering molecular genetic mechanisms underlying chromatin interactions. This project aims to generate the high confidence map of enhancer-promoter links in 61 tissues and cells through robust integration of novel machine learning tools with genomic and epigenomic datasets. Understanding which key elements in the genome may be important to fine-tune gene expression is essential for understanding biological pathways. The expected outcomes include i) New tools to robustly identify true chromatin pairs; ii) Comperehensive maps of regulatory interactomes in 61 tissues & cells, which will provide a roadmap for interpreting & prioritising noncoding variants.
This should provide significant benefit to Australia's capacity for cutting-edge genomics research through fundamental understanding of gene regulation mechanism.Read moreRead less
Identification of causal variants for complex traits. The aim of this project is to identify causal variants for complex traits in cattle and humans. Although most important traits in agriculture, medicine and evolution are complex traits, very few of the genetic variants affecting these traits are known and this undermines our understanding of how genetic variants affect a trait and practical uses of this knowledge. Huge datasets of individuals with genome sequence and phenotypes and new statis ....Identification of causal variants for complex traits. The aim of this project is to identify causal variants for complex traits in cattle and humans. Although most important traits in agriculture, medicine and evolution are complex traits, very few of the genetic variants affecting these traits are known and this undermines our understanding of how genetic variants affect a trait and practical uses of this knowledge. Huge datasets of individuals with genome sequence and phenotypes and new statistical methods provide the opportunity to close this gap. The outcome will be identification of many genomic variants causing variation in complex traits. This will benefit scientific understanding of complex traits and the ability to predict traits for individuals from their genome sequence.Read moreRead less
High Dimensional Approximation, Learning, and Uncertainty. This project aims to develop next-generation computational methods for complex problems in science and engineering that have many uncertain parameters, using advanced high-dimensional strategies and deep learning to enhance computational speed. The significance of the project is that these methods will help address important applications that at present are not feasible or at the edge of feasibility. The expected outcomes are powerful me ....High Dimensional Approximation, Learning, and Uncertainty. This project aims to develop next-generation computational methods for complex problems in science and engineering that have many uncertain parameters, using advanced high-dimensional strategies and deep learning to enhance computational speed. The significance of the project is that these methods will help address important applications that at present are not feasible or at the edge of feasibility. The expected outcomes are powerful methods that will be mathematically rigorous and suitable for a wide variety of applications. The benefits are that the project will boost Australia’s position as a leader in innovation, and contribute to future developments over a wide area, from aerospace engineering to personalised computational oncology.Read moreRead less
Large dynamic time-varying models for structural macroeconomic inference. This project aims to broaden the range of macroeconomic models that have an integrated capacity for both greater realism and efficiency in analysis. This approach will be applied to two contexts at the forefront of current macroeconomic research, the effects of noisy productivity signals on business cycles and the effects of fiscal policy shocks. Flexible macro-econometric models underpin accurate inference by economists ....Large dynamic time-varying models for structural macroeconomic inference. This project aims to broaden the range of macroeconomic models that have an integrated capacity for both greater realism and efficiency in analysis. This approach will be applied to two contexts at the forefront of current macroeconomic research, the effects of noisy productivity signals on business cycles and the effects of fiscal policy shocks. Flexible macro-econometric models underpin accurate inference by economists and policymakers and the project outputs should provide widespread and significant benefits by improving policy and boosting Australia’s comparative advantage.Read moreRead less
Bayesian inference for psychological theories with intractable likelihood. This project pursues breakthroughs which allow important questions of basic and applied science to be addressed using mathematical theories from cognitive psychology. Advances are made through an interdisciplinary effort, combining recent developments in econometric and statistical methods and cognitive science. The outcomes will advance knowledge and open up new avenues for applied research in important aspects of psych .... Bayesian inference for psychological theories with intractable likelihood. This project pursues breakthroughs which allow important questions of basic and applied science to be addressed using mathematical theories from cognitive psychology. Advances are made through an interdisciplinary effort, combining recent developments in econometric and statistical methods and cognitive science. The outcomes will advance knowledge and open up new avenues for applied research in important aspects of psychology. This research will result in new methods available to the wider scientific community which open up new horizons for understanding basic cognition, and human behavior in many domains. Read moreRead less
Flexible models and methods for cognitive model-based decision-making. This project aims to apply mathematical decision models to important questions of basic and applied science. Advances will be pursued through an interdisciplinary effort, combining recent developments in econometric and statistical methods, cognitive science and computing. The expected outcomes will bring a proven and powerful approach to a new range of questions investigating psychological aspects of choices about health c ....Flexible models and methods for cognitive model-based decision-making. This project aims to apply mathematical decision models to important questions of basic and applied science. Advances will be pursued through an interdisciplinary effort, combining recent developments in econometric and statistical methods, cognitive science and computing. The expected outcomes will bring a proven and powerful approach to a new range of questions investigating psychological aspects of choices about health care and consumer purchases. This project will provide significant benefits to the wider scientific community to understand basic cognition, and human behaviour in many domains.Read moreRead less
High Dimensional Computation and Uncertainty. This project aims to establish powerful computational methods for high-dimensional problems - methods that are rigorous, and carefully tailored to specific applications, from physics, environment, manufacturing and finance, and often driven by uncertainty. The project will generate new knowledge in the area of high-dimensional computation, and develop technological innovations in key areas of science and industry. Expected outcomes include improved c ....High Dimensional Computation and Uncertainty. This project aims to establish powerful computational methods for high-dimensional problems - methods that are rigorous, and carefully tailored to specific applications, from physics, environment, manufacturing and finance, and often driven by uncertainty. The project will generate new knowledge in the area of high-dimensional computation, and develop technological innovations in key areas of science and industry. Expected outcomes include improved control of uncertainty in industry, enhanced international and interdisciplinary collaborations, and significant publications and presentations in international forums. The technological advancements will help boost Australia's position as a world leader in innovation.Read moreRead less