Computational Modeling of RNA Control Networks. One of the most exciting new ideas for understanding the regulation of gene expression involves the contribution of intronic and other non-protein coding RNAs to regulatory networks within cells. This novel role for intronic RNA is currently making headlines within the molecular biology community but has not yet been modelled computationally. The network of genetic regulatory interactions forms a complex system which is amenable to computational ....Computational Modeling of RNA Control Networks. One of the most exciting new ideas for understanding the regulation of gene expression involves the contribution of intronic and other non-protein coding RNAs to regulatory networks within cells. This novel role for intronic RNA is currently making headlines within the molecular biology community but has not yet been modelled computationally. The network of genetic regulatory interactions forms a complex system which is amenable to computational analysis. This project aims to extend current models to incorporate intronic RNA feedback control, complementing parallel studies in vivo, and computationally testing ideas essential to the theoretical understanding of the basis of life.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
Spontaneous activity and neural decoding in the developing brain. This project aims to investigate how patterns of neural activity emerge in the developing brain, using the zebrafish as a model system. This project expects to generate new knowledge regarding the functional significance of spontaneously generated activity, and how it interacts with sensory experience. The expected outcomes of this project include enhanced capacity at the interface between neuroscience and computation. This should ....Spontaneous activity and neural decoding in the developing brain. This project aims to investigate how patterns of neural activity emerge in the developing brain, using the zebrafish as a model system. This project expects to generate new knowledge regarding the functional significance of spontaneously generated activity, and how it interacts with sensory experience. The expected outcomes of this project include enhanced capacity at the interface between neuroscience and computation. This should provide significant benefits including greater insight into normal brain development, and the formulation of new concepts potentially relevant for brain-inspired computing.Read moreRead less
How does environmental enrichment affect brain development? This project aims to use brain imaging and advanced computational analyses to investigate how early sensory experience affects brain development. It adopts the larval zebrafish as a model system, since they display sophisticated behaviours from an early age, and neural activity can be recorded at whole-brain scale with single neuron resolution. The project aims to generate new knowledge regarding environmental effects on brain developme ....How does environmental enrichment affect brain development? This project aims to use brain imaging and advanced computational analyses to investigate how early sensory experience affects brain development. It adopts the larval zebrafish as a model system, since they display sophisticated behaviours from an early age, and neural activity can be recorded at whole-brain scale with single neuron resolution. The project aims to generate new knowledge regarding environmental effects on brain development and behaviour. This will provide significant benefits including greater insight into normal brain development, and the formulation of new concepts potentially relevant for brain-inspired computing. The expected outcomes also include enhanced capacity at the interface between neuroscience and computation.Read moreRead less
How do patterns of brain activity emerge during early life? This project uses theory and experiment to investigate how neural coding emerges in the developing brain. It adopts the larval zebrafish as a model system, because neural activity can be recorded at whole-brain scale but with single neuron resolution. The project expects to generate new knowledge regarding how neural activity comes to represent sensory stimuli, and new statistical models for interpreting large-scale patterns of neural a ....How do patterns of brain activity emerge during early life? This project uses theory and experiment to investigate how neural coding emerges in the developing brain. It adopts the larval zebrafish as a model system, because neural activity can be recorded at whole-brain scale but with single neuron resolution. The project expects to generate new knowledge regarding how neural activity comes to represent sensory stimuli, and new statistical models for interpreting large-scale patterns of neural activity. This will provide significant benefits including greater insight into normal brain development, and the formulation of new concepts potentially relevant for brain-inspired computing. The expected outcomes also include enhanced capacity at the interface between neuroscience and computation.Read moreRead less
A Novel Framework for Optimised Ensemble Classifier. The project aims to develop a novel framework for creating an optimised ensemble classifier that will improve data analysis and the accuracy of many real-world applications such as document analysis, robotics and medical diagnosis. The project plans to develop and investigate novel methods for generating diverse training environment layers, base classifiers and fusion of classifiers. It also plans to design a multi-objective evolutionary algor ....A Novel Framework for Optimised Ensemble Classifier. The project aims to develop a novel framework for creating an optimised ensemble classifier that will improve data analysis and the accuracy of many real-world applications such as document analysis, robotics and medical diagnosis. The project plans to develop and investigate novel methods for generating diverse training environment layers, base classifiers and fusion of classifiers. It also plans to design a multi-objective evolutionary algorithm-based search obtain the optimal number of layers, clusters and base classifiers. The expected outcomes of the proposed framework are advances in classifier learning. The final outcome may be novel methods which will bring in diversity during the learning of the base classifiers and provide an optimal ensemble classifier for real-world applications.Read moreRead less
Mechanisms of nerve fibre guidance by molecular gradients. Brain wiring is crucial for brain function. The project will investigate the basic principles underlying the development of brain wiring, using both experiments and mathematical models. This will lead a predictive model of how wiring develops, both in normal and abnormal situations.
Deep Learning Architecture with Context Adaptive Features for Image Parsing. This project aims to develop a novel deep learning network architecture with contextual adaptive features for image parsing that can improve the object detection accuracy in real-world applications. A number of innovative methods for deep learning, contextual features and network parameter selection will be developed and investigated. The impact of the proposed architecture and features will be improved object-detection ....Deep Learning Architecture with Context Adaptive Features for Image Parsing. This project aims to develop a novel deep learning network architecture with contextual adaptive features for image parsing that can improve the object detection accuracy in real-world applications. A number of innovative methods for deep learning, contextual features and network parameter selection will be developed and investigated. The impact of the proposed architecture and features will be improved object-detection accuracy and advances in deep learning network architecture for image parsing. The intended outcomes are deep learning network architecture, contextual feature extraction techniques and network parameter optimisation techniques for image parsing.Read moreRead less
A new paradigm of gene regulation - implications in embryogenesis and disease. The proposed analysis of a new paradigm of gene regulation will provide a new key to understanding genome function and inform some of the most compelling biological issues of our time such as stem cell biology, tissue and organ regeneration and genetic programming. The insights and technologies developed in this program will be widely applicable in biotechnological and pharmacogenomic research in Australia and worldwi ....A new paradigm of gene regulation - implications in embryogenesis and disease. The proposed analysis of a new paradigm of gene regulation will provide a new key to understanding genome function and inform some of the most compelling biological issues of our time such as stem cell biology, tissue and organ regeneration and genetic programming. The insights and technologies developed in this program will be widely applicable in biotechnological and pharmacogenomic research in Australia and worldwide, and assert Australia's leadership in this area of research.Read moreRead less
Organisation, expression and diversity of the sub-telomeric regions of the ancient eukaryote, Giardia duodenalis. We propose to extend our findings on the extreme plasticity of the structure and organisation of the sub-telomeric region of the complete genome of Giardia by more extensive chromosome walking, and comparison of different isolates. These regions are subject to gene conversion, transcriptional silencing, gene mobility, recombination, variable surface protein expression, subtelomeric i ....Organisation, expression and diversity of the sub-telomeric regions of the ancient eukaryote, Giardia duodenalis. We propose to extend our findings on the extreme plasticity of the structure and organisation of the sub-telomeric region of the complete genome of Giardia by more extensive chromosome walking, and comparison of different isolates. These regions are subject to gene conversion, transcriptional silencing, gene mobility, recombination, variable surface protein expression, subtelomeric instability and the insertion of transposable elements, a dynamic balance between structural conservation and rapid evolution. This is a rare opportunity to understand the forces at work in moulding eukaryotic sub-telomeric sequences because Giardia is not constrained by sexual homogenisation and the dynamic variability is retained.Read moreRead less