Demographic and evolutionary inferences from large, whole-genome datasets. A new data structure for genome-wide datasets has allowed great improvements in the efficiency of genomic data storage and in population genomics simulations, which are crucial to developing and testing mathematical models of population history and species evolution. We will take these advances in new directions, using efficient data structures to dramatically improve inferences about: the demographic histories of popul .... Demographic and evolutionary inferences from large, whole-genome datasets. A new data structure for genome-wide datasets has allowed great improvements in the efficiency of genomic data storage and in population genomics simulations, which are crucial to developing and testing mathematical models of population history and species evolution. We will take these advances in new directions, using efficient data structures to dramatically improve inferences about: the demographic histories of populations, rates of genome change, and phylogenetic networks, and we will develop the first inference methods for the multispecies coalescent with recombination. Outcomes will include advances in understanding the evolutionary histories of humans and other species, including pathogens of importance for global health.Read moreRead less
Determining features that separate groups of protein sequences. This project aims to develop mathematical approaches for determining features that distinguish one group of proteins from another, based on their amino acid sequences. The groups of sequences will reflect different outcomes, so that identifying the fundamental features can result in targeted interventions against the poorer outcome. A simple comparison at each position or of known features can fail to determine robust differentiator ....Determining features that separate groups of protein sequences. This project aims to develop mathematical approaches for determining features that distinguish one group of proteins from another, based on their amino acid sequences. The groups of sequences will reflect different outcomes, so that identifying the fundamental features can result in targeted interventions against the poorer outcome. A simple comparison at each position or of known features can fail to determine robust differentiators and so more complex methods are required. The project will, for example, help identify HIV vaccine targets by comparing early HIV transmission sequences from those in chronic infection. The methods will be applicable to viral proteins where high mutation rates make this task even more complex.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE200101791
Funder
Australian Research Council
Funding Amount
$427,082.00
Summary
Mathematically optimal R&D for coral reef conservation. This project aims to develop mathematical methodologies for optimising Research & Development (R&D) of technologies that will secure complex and uncertain ecosystems into the future. Current conventional management approaches will not prevent the degradation of threatened ecosystems like the Great Barrier Reef, so new technologies are needed. The biggest challenge in choosing these technologies is the long delay between development and depl ....Mathematically optimal R&D for coral reef conservation. This project aims to develop mathematical methodologies for optimising Research & Development (R&D) of technologies that will secure complex and uncertain ecosystems into the future. Current conventional management approaches will not prevent the degradation of threatened ecosystems like the Great Barrier Reef, so new technologies are needed. The biggest challenge in choosing these technologies is the long delay between development and deployment, in which time ecosystem function may collapse and complex, dynamic ecological and social systems will change. The mathematical methods and theory developed will inform a Great Barrier Reef case study, and will be ready for rapid application to other ecosystems as the urgent need arises.Read moreRead less
Optimising progress towards elimination of malaria. The project aims to advance mathematical knowledge by developing novel tools appropriate for modelling disease elimination. We will apply these new mathematical tools to the significant problem of malaria elimination in Vietnam. The expected outcomes are new tools for modelling disease elimination on a fine spatial resolution with heterogeneities in individual patient characteristics, calibrating models to household level data on disease transm ....Optimising progress towards elimination of malaria. The project aims to advance mathematical knowledge by developing novel tools appropriate for modelling disease elimination. We will apply these new mathematical tools to the significant problem of malaria elimination in Vietnam. The expected outcomes are new tools for modelling disease elimination on a fine spatial resolution with heterogeneities in individual patient characteristics, calibrating models to household level data on disease transmission and designing intervention strategies for maximum effect on disease transmission. The innovative combination of modelling, inference and optimisation ensures that the mathematical methods developed will be broadly applicable to modelling elimination strategies for other infectious diseases.
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Discovery Early Career Researcher Award - Grant ID: DE190101416
Funder
Australian Research Council
Funding Amount
$329,538.00
Summary
The value of model complexity for fisheries management. This project aims to quantify the benefits of using dynamic multi-species models for harvest decisions in the fishing industry. More than 99.8 per cent of fisheries are assessed using single-species models. Since fishers harvest multiple interacting species, not considering these interactions can lead to negative outcomes that reduce food security, eliminate human livelihoods, decrease economic production, and harm the environment. The proj ....The value of model complexity for fisheries management. This project aims to quantify the benefits of using dynamic multi-species models for harvest decisions in the fishing industry. More than 99.8 per cent of fisheries are assessed using single-species models. Since fishers harvest multiple interacting species, not considering these interactions can lead to negative outcomes that reduce food security, eliminate human livelihoods, decrease economic production, and harm the environment. The project is expected to provide guidance for fisheries scientists on when to use multi-species models for management, improved decision making capacity to reduce the risk of fishery collapse, a new method for dynamic model validation in the face of limited data, and enhanced collaboration between modellers and applied agencies. By reducing the risk of ecosystem collapse through better use of complex and simple models. The project will provide major benefits for the environment, humans, and the economy, at national and global scales.Read moreRead less
ARC Centre of Excellence for Plant Success in Nature and Agriculture. The ARC CoE for Plant Success in Nature and Agriculture will discover the adaptive strategies underpinning productivity and resilience in diverse plants and deepen knowledge of the genetic and physiological networks driving key traits. Using novel quantitative and computational approaches, the Centre will link gene networks with traits across biological levels, giving breeders an unparalleled predictive capacity. The Centre wi ....ARC Centre of Excellence for Plant Success in Nature and Agriculture. The ARC CoE for Plant Success in Nature and Agriculture will discover the adaptive strategies underpinning productivity and resilience in diverse plants and deepen knowledge of the genetic and physiological networks driving key traits. Using novel quantitative and computational approaches, the Centre will link gene networks with traits across biological levels, giving breeders an unparalleled predictive capacity. The Centre will accelerate technologies to transfer successful networks into crops and build legal frameworks to secure this knowledge. With a uniquely multidisciplinary team, the Centre will deliver new strategies to address the problems of food security and climate change, establishing Australia as a global leader in these areas.Read moreRead less