Mathematical Methods for Next Generation Sequencing. The emergence of a new generation of high throughput genomic sequencing technologies is providing unprecedented opportunities for biological research. Hidden within the huge amounts of data generated by this technology is information about the expression and regulation of genes, and the complex functional purpose of non-coding, so called 'junk', DNA. Development of mathematical and statistical tools is essential to interpreting these data. The ....Mathematical Methods for Next Generation Sequencing. The emergence of a new generation of high throughput genomic sequencing technologies is providing unprecedented opportunities for biological research. Hidden within the huge amounts of data generated by this technology is information about the expression and regulation of genes, and the complex functional purpose of non-coding, so called 'junk', DNA. Development of mathematical and statistical tools is essential to interpreting these data. The proposed research will enhance Australia's reputation for developing novel quantitative techniques at the cutting edge of modern biology. The proposed project has a broad range of potential applications in biotechnology, particularly in the medical and agricultural industries.Read moreRead less
Decision-making in social insects and nature-inspired optimisation algorithms. Insect societies are ideal for the study of complex systems. Contrary to other complex systems, insect colonies can be modified without destroying the system. Computer scientists have found a source of inspiration in the behaviour of social insects for solving optimisation problems. Here we will study the influence of information flow on decision-making in real insect societies using:
1) Experiments aimed at investig ....Decision-making in social insects and nature-inspired optimisation algorithms. Insect societies are ideal for the study of complex systems. Contrary to other complex systems, insect colonies can be modified without destroying the system. Computer scientists have found a source of inspiration in the behaviour of social insects for solving optimisation problems. Here we will study the influence of information flow on decision-making in real insect societies using:
1) Experiments aimed at investigating how storage and transfer of information affects individual decision-making within a honey bee colony (University of Sydney)
2) Design of a new class of 'bee' algorithms that incorporate direct information transfer and are aimed at solving dynamic multicriterion optimisation problems (University of Leipzig).
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Bio-inspired speech analysis: Specialised information processing of vocalisations in the auditory brainstem. This project has the potential to benefit bionic ear and hearing aid users through the development of signal processing methods that mimic the amazing abilities of the brain. Speech perception performance by bionic ear users has reached a plateau and these new strategies could produce the breakthrough needed to provide the next increase in performance. The benefit for greater improved hea ....Bio-inspired speech analysis: Specialised information processing of vocalisations in the auditory brainstem. This project has the potential to benefit bionic ear and hearing aid users through the development of signal processing methods that mimic the amazing abilities of the brain. Speech perception performance by bionic ear users has reached a plateau and these new strategies could produce the breakthrough needed to provide the next increase in performance. The benefit for greater improved hearing has enormous benefit and potential for improving the quality of life of the hearing impaired, especially those with severe and profound hearing loss. In addition, the algorithms may provide more robust automatic speech recognition, making this technology more useful in everyday situations; the markets that this would open up are enormous.Read moreRead less
Alternative Splicing in the Mouse Transcriptome. Although the human genome completion is cause for excitement we do not have any firm indication of precisely how many protein-coding genes exist in a mammalian genome. We have even less indication of the extent to which these genes generate alternative gene products, through a process termed alternative splicing. The detection and sequencing of these full-length alternative gene products is the focus of this application. This application details t ....Alternative Splicing in the Mouse Transcriptome. Although the human genome completion is cause for excitement we do not have any firm indication of precisely how many protein-coding genes exist in a mammalian genome. We have even less indication of the extent to which these genes generate alternative gene products, through a process termed alternative splicing. The detection and sequencing of these full-length alternative gene products is the focus of this application. This application details the opportunity to participate in the identification of the full transcriptome of the mouse and is part of a collaborative effort with The RIKEN Genome Sciences Center in Japan.Read moreRead less
Mathematical models and bioinformatic analyses of bacterial genome evolution. Bacteria are vital agents in earth's biosphere, breaking down and synthesising a wide variety of compounds. Some bacteria cause disease; others are exploited for a range of biotechnological applications. Bacteria have a remarkable ability to survive and thrive in changing conditions. For example, pathogenic bacteria confronted by antibiotics easily evolve resistance to them. With the reality of climate change, we expec ....Mathematical models and bioinformatic analyses of bacterial genome evolution. Bacteria are vital agents in earth's biosphere, breaking down and synthesising a wide variety of compounds. Some bacteria cause disease; others are exploited for a range of biotechnological applications. Bacteria have a remarkable ability to survive and thrive in changing conditions. For example, pathogenic bacteria confronted by antibiotics easily evolve resistance to them. With the reality of climate change, we expect more rapid shifts in the structure of bacterial communities, possibly leading to the emergence of new pathogens. The benefits of this project are to discover how the genetic structure of bacteria confer this flexibility, and to help keep Australia at the forefront of research in bioinformatics and mathematical biology.
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A new theory for retinotectal map formation. How brains become wired up during development is a question of
importance to both biology and computing. In this project we adopt a
novel computational approach to understanding the development of
topographic maps, a wiring pattern that is ubiquitous in biological
nervous systems. This project will build capacity for research in
computational neuroscience in Australia. It may also lead to
technological benefits such as new ideas for the design o ....A new theory for retinotectal map formation. How brains become wired up during development is a question of
importance to both biology and computing. In this project we adopt a
novel computational approach to understanding the development of
topographic maps, a wiring pattern that is ubiquitous in biological
nervous systems. This project will build capacity for research in
computational neuroscience in Australia. It may also lead to
technological benefits such as new ideas for the design of self-wiring
computing devices, and new insights into
the causes of wiring defects both during normal development and
rewiring after injury.
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Statistical methods for detection of non-coding RNAs in eukaryote genomes. Understanding how eukaryotic cells work is a major goal of 21st century biology. A crucial step will be to catalogue the functional components of eukaryotic genomes. Australian researchers must be involved in this process at an early stage, in order to maximise commercial opportunities, attract quality researchers and position ourselves for further advances. This project will make major contributions to international effo ....Statistical methods for detection of non-coding RNAs in eukaryote genomes. Understanding how eukaryotic cells work is a major goal of 21st century biology. A crucial step will be to catalogue the functional components of eukaryotic genomes. Australian researchers must be involved in this process at an early stage, in order to maximise commercial opportunities, attract quality researchers and position ourselves for further advances. This project will make major contributions to international efforts in this area, via the development of statistical methods for segmenting genomes, classification of those segments, and study of the resulting classes. In the long term, enhanced understanding of eukaryotic cells will lead to breakthroughs in biology, and to medical, pharmaceutical, agricultural and scientific advances.Read moreRead less
Multi-scale modelling of cell migration in developmental biology. Interpretative and predictive tools are needed for the comprehensive understanding of directed cell migration in the medical sciences. Mathematical models and modelling methodologies developed in this project will make a significant contribution to the investigation of cell migration and the testing and generation of hypotheses. Such models are needed to understand observed cellular patterns. This project will contribute to knowle ....Multi-scale modelling of cell migration in developmental biology. Interpretative and predictive tools are needed for the comprehensive understanding of directed cell migration in the medical sciences. Mathematical models and modelling methodologies developed in this project will make a significant contribution to the investigation of cell migration and the testing and generation of hypotheses. Such models are needed to understand observed cellular patterns. This project will contribute to knowledge of normal and abnormal developmental processes, especially in embryonic growth. Understanding these processes should lead to prediction and treatment of congenital disorders and contribute to a healthy start to life.Read moreRead less
Nonlinear Dynamics of Pulse Coupled Oscillators. A mathematical model of the heart pacemaker system will be created, based on simple interacting units. These units have been shown to be good models of physiological information e.g. the discrimination of different influences on heart rate. We will firstly look at the interaction of the units in simple combinations and then tune the model to mimic the behaviour of the cardiac pacemaker.
Potential benefits may arise from elucidating the mechanis ....Nonlinear Dynamics of Pulse Coupled Oscillators. A mathematical model of the heart pacemaker system will be created, based on simple interacting units. These units have been shown to be good models of physiological information e.g. the discrimination of different influences on heart rate. We will firstly look at the interaction of the units in simple combinations and then tune the model to mimic the behaviour of the cardiac pacemaker.
Potential benefits may arise from elucidating the mechanisms underlying arrhythmias which contribute to ?sudden cardiac death? in young men, and suggesting strategies for artificial pacemakers to effectively arrest abnormal rhythms before they convert to potentially fatal fibrillation.Read moreRead less
Markov invariants and phylogenetic tree reconstruction. The project will assist Australia to progress as an innovator in the production phylogenetic tree reconstruction techniques.
Identifying species is a difficult task with environmental, social and economic benefits to Australia. DNA evidence and phylogenetic methods clearly achieve this task. Conservation of rare species depends upon identification and hence robust phylogenetic analysis. Phylogenetically identifying fish species has econom ....Markov invariants and phylogenetic tree reconstruction. The project will assist Australia to progress as an innovator in the production phylogenetic tree reconstruction techniques.
Identifying species is a difficult task with environmental, social and economic benefits to Australia. DNA evidence and phylogenetic methods clearly achieve this task. Conservation of rare species depends upon identification and hence robust phylogenetic analysis. Phylogenetically identifying fish species has economic importance as different fish species are all managed separately, having different catch limits, catch areas and market values. Using effective phylogenetic methods, epidemiologists can track the spread of a disease through a population. Read moreRead less