Creating new stochastic models to understand the evolution of gene families. This project aims to extend stochastic modelling techniques in order to develop mathematically rigorous and biologically relevant models for the evolution of gene families. The project expects to model evolutionary processes such as gene retention, duplication and loss, and the generation of new gene functions. The duplication and subsequent re-purposing of genes is thought to be a key mechanism for generating evolution ....Creating new stochastic models to understand the evolution of gene families. This project aims to extend stochastic modelling techniques in order to develop mathematically rigorous and biologically relevant models for the evolution of gene families. The project expects to model evolutionary processes such as gene retention, duplication and loss, and the generation of new gene functions. The duplication and subsequent re-purposing of genes is thought to be a key mechanism for generating evolutionary novelty. By applying these models to genome data, the project expects to be able to quantify the importance of these different evolutionary mechanisms. The project will strengthen collaborative links between researchers in stochastic modelling and molecular evolutionary biology.Read moreRead less
Algebraically informed models of biological sequence evolution. To make sense of the patterns they see in the natural world, biologists across fields as diverse as genetics, epidemiology and biogeography need an accurate picture of evolutionary history. DNA sequences provide an exciting means to establish this picture of the past, but to decode it successfully requires mathematical models of how DNA evolves. Mathematical inconsistencies have been identified with current approaches. In particular ....Algebraically informed models of biological sequence evolution. To make sense of the patterns they see in the natural world, biologists across fields as diverse as genetics, epidemiology and biogeography need an accurate picture of evolutionary history. DNA sequences provide an exciting means to establish this picture of the past, but to decode it successfully requires mathematical models of how DNA evolves. Mathematical inconsistencies have been identified with current approaches. In particular, understanding the effect of natural selection in different parts of the tree of life requires models that behave robustly in the face of shifting evolutionary processes. This project aims to use insights from algebraic methods to construct mathematically consistent models of wide biological utility.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE130100423
Funder
Australian Research Council
Funding Amount
$369,061.00
Summary
Group theory and phylogenetics: exploiting symmetry to uncover evolutionary history. Using advanced algebra, structural symmetries inherent in phylogenetic methods will be studied and improved approaches will be derived. DNA sequences contain a wealth of information about evolutionary events that occurred millions of years ago, but extracting this information requires the application of robust methods.
Advanced matrix-analytic methods with applications. Over the last twenty-five years, matrix-analytic methods have proved to be very successful in formulating and analysing certain classes of stochastic models. Motivated by applications, this project will investigate more advanced matrix-analytic methods than have hitherto been studied.
An efficient approach to the computation of bacterial evolutionary distance. This project aims to apply advanced mathematical tools to improve our understanding of bacterial evolution. Bacteria account for as much total Earth biomass as all plant species put together, and have an unparalleled ability to evolve quickly and adapt to changing environments. Unfortunately, the existing mathematical models used to model bacterial evolution are generally computationally intractable. This project will r ....An efficient approach to the computation of bacterial evolutionary distance. This project aims to apply advanced mathematical tools to improve our understanding of bacterial evolution. Bacteria account for as much total Earth biomass as all plant species put together, and have an unparalleled ability to evolve quickly and adapt to changing environments. Unfortunately, the existing mathematical models used to model bacterial evolution are generally computationally intractable. This project will rectify this situation by using representation theory to transform combinatorial group theory into linear algebra, allowing for the application of advanced methods of numeric approximation. This will provide a better understanding of how bacteria evolve and improve our ability to manage their impact.Read moreRead less
Outflows, Jets and Plumes. This project studies how fluid flows out from a small concentrated object into a second surrounding fluid. New solution methods will be provided, and new results about how these fluid flows evolve will be obtained. These are important problems with significance in modelling underwater explosions. They are also important in astrophysics, and will help explain the shapes of outflows from some stars or galaxies. The outcomes of the project will be a deeper mathematical un ....Outflows, Jets and Plumes. This project studies how fluid flows out from a small concentrated object into a second surrounding fluid. New solution methods will be provided, and new results about how these fluid flows evolve will be obtained. These are important problems with significance in modelling underwater explosions. They are also important in astrophysics, and will help explain the shapes of outflows from some stars or galaxies. The outcomes of the project will be a deeper mathematical understanding of which outflow shapes are stable, and under what circumstances they might become unstable. This will provide valuable information about galaxy shapes, and a new suite of computational methods for solving such problems.Read moreRead less
Turning back the clock on brain cell aging. This proposal aims to determine the role of fundamental epigenetic mechanisms in the process of aging and whether modulation of the epi-genome underpins an improvement in cognitive function. It combines the fields of epigenetics, neurosciences and mathematics to delineate the dynamics of DNA methylation and histone modification marking on the transcriptome during normal, healthy aging. The outcomes will provide significant new knowledge of the variable ....Turning back the clock on brain cell aging. This proposal aims to determine the role of fundamental epigenetic mechanisms in the process of aging and whether modulation of the epi-genome underpins an improvement in cognitive function. It combines the fields of epigenetics, neurosciences and mathematics to delineate the dynamics of DNA methylation and histone modification marking on the transcriptome during normal, healthy aging. The outcomes will provide significant new knowledge of the variable cognitive decline that occurs in healthy aging and why some populations age less successfully than others do. Better understanding of the impact of environmental change on the biology of aging has potential community benefits.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
Special Research Initiatives - Grant ID: SR120200004
Funder
Australian Research Council
Funding Amount
$30,000,000.00
Summary
Australian Synchrotron Access Program. The Australian Synchrotron epitomises scientific research excellence in Australian and New Zealand. Its impact spans nearly every research sector. This proposal brings together over 30 Australian universities working together to ensure that world-class peer-reviewed science continues to be performed at the Australian Synchrotron.
Linking wave–sea ice feedbacks to rapid ice retreat. Antarctic sea ice extent has been in sharp decline since 2016, which is stressing the fragile Southern Ocean and Antarctic environments so vital to the global climate. This project aims to investigate a crucial candidate mechanism of sea ice loss by predicting rapid ice retreat in response to large Southern Ocean waves. New theory and modelling capabilities that account for wave–ice feedbacks will underpin the predictions, leveraging on recent ....Linking wave–sea ice feedbacks to rapid ice retreat. Antarctic sea ice extent has been in sharp decline since 2016, which is stressing the fragile Southern Ocean and Antarctic environments so vital to the global climate. This project aims to investigate a crucial candidate mechanism of sea ice loss by predicting rapid ice retreat in response to large Southern Ocean waves. New theory and modelling capabilities that account for wave–ice feedbacks will underpin the predictions, leveraging on recent research breakthroughs, including novel datasets derived from satellite and field observations. The outcomes are expected to quantify sea ice retreat due to ocean waves for the first time, with potentially major implications for coupled wave–sea ice modelling in climate studies.Read moreRead less