Structure and informatics of the genetic code. Recent advances in biotechnology have seen its emergence as a highly
quantitative, numerically-based discipline. To exploit the available
data to the full will require, alongside computing power, new
analytical techniques. This project aims to develop such techniques,
by handling the systematics of the genetic code with methods derived
from theoretical physics and chemistry. Expected outcomes include a
dynamical (quantum field theory) model ....Structure and informatics of the genetic code. Recent advances in biotechnology have seen its emergence as a highly
quantitative, numerically-based discipline. To exploit the available
data to the full will require, alongside computing power, new
analytical techniques. This project aims to develop such techniques,
by handling the systematics of the genetic code with methods derived
from theoretical physics and chemistry. Expected outcomes include a
dynamical (quantum field theory) model of phylogenetic branching,
analyses of nucleic acid structure and content (spin chain models of
RNA binding and of DNA open reading frames), and insights into the
origin of the code itself (via numerical codon similarity measures).
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Quantitative dynamics of functional magnetic resonance imaging. By modeling and verifying the dynamics of brain activity and blood flow that underlie functional magnetic resonance imaging (fMRI), this project will yield improved scientific outcomes and imaging sensitivity. The new data analysis techniques and technologies that result will yield potentially patentable intellectual property, and will increase the standing of Australia in this rapidly developing field, including via links being bu ....Quantitative dynamics of functional magnetic resonance imaging. By modeling and verifying the dynamics of brain activity and blood flow that underlie functional magnetic resonance imaging (fMRI), this project will yield improved scientific outcomes and imaging sensitivity. The new data analysis techniques and technologies that result will yield potentially patentable intellectual property, and will increase the standing of Australia in this rapidly developing field, including via links being built to leading international workers. The National Research Priority Goals of Frontier Technologies, Breakthrough Science, Smart Information Use, and Promoting an Innovation Economy will thus be advanced.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
Neural spike variability: unifying conflicting views of neural dynamics. The project aims to improve our understanding of neural dynamics. The brain represents and processes information by means of neural voltage spikes, which show great variability in their timing. Understanding the origin of such variable neural dynamics is a long-standing problem in neuroscience. The aim of this project is to develop a novel account of variable neural dynamics, unravelling their computational principles in th ....Neural spike variability: unifying conflicting views of neural dynamics. The project aims to improve our understanding of neural dynamics. The brain represents and processes information by means of neural voltage spikes, which show great variability in their timing. Understanding the origin of such variable neural dynamics is a long-standing problem in neuroscience. The aim of this project is to develop a novel account of variable neural dynamics, unravelling their computational principles in the brain, and unifying current leading but conflicting theories. The model developed in this project would be used to explain a range of empirical observations, and the principles unravelled would be applied to understand spike-timing based neural coding. The new knowledge gained in this project may have profound implications for designing brain-like computing devices.Read moreRead less
Mutagenesis and combinatorial algorithms for sequencing problematic genomic regions. This project will develop a remarkable and original approach to DNA sequencing with potential to radically improve the speed, accuracy and effectiveness of existing sequencing technologies. It is especially useful for dealing with difficult-to-sequence genomic regions and has implications for all sequencing projects, including completion of the Human Genome Project. The approach involves generating, and wholly o ....Mutagenesis and combinatorial algorithms for sequencing problematic genomic regions. This project will develop a remarkable and original approach to DNA sequencing with potential to radically improve the speed, accuracy and effectiveness of existing sequencing technologies. It is especially useful for dealing with difficult-to-sequence genomic regions and has implications for all sequencing projects, including completion of the Human Genome Project. The approach involves generating, and wholly or partially sequencing, mutated copies of problematic regions of the target genome. Advanced combinatorial algorithms are then used to form highly probable alignments between strings and determine the unknown sequence. The approach has additional benefits in detecting single-nucleotide polymorphisms and sequencing errors.Read moreRead less
Statistical methods for analysing multi-source microarray data and building gene regulatory networks. I will devise a statistical learning technique that does not force a gene to be assigned to exactly one category. This technique reflects the biological reality that a gene can belong to two or more functional categories. Therefore, the new technique will improve a model's ability to identify regulatory genes in different types of cancer; these regulatory genes can be targeted by new anti-cancer ....Statistical methods for analysing multi-source microarray data and building gene regulatory networks. I will devise a statistical learning technique that does not force a gene to be assigned to exactly one category. This technique reflects the biological reality that a gene can belong to two or more functional categories. Therefore, the new technique will improve a model's ability to identify regulatory genes in different types of cancer; these regulatory genes can be targeted by new anti-cancer drugs resulting in a more effective treatment. I will model gene regulatory networks using microarray data from multiple sources. These networks will be used to identify regulatory cliques - a group of genes that are vital for a cellular function. This will improve our understanding of debilitating conditions such as asthma.Read moreRead less
Emerging applications of advanced computational methods and discrete mathematics. Ongoing improvements in computer performance are revolutionising research in combinatorial discrete mathematics, and leading to exciting new applications in information technology and the biological and chemical sciences. As a result, substantial international research effort, both at universities and in commercial and industrial organisations, is being channelled into high-performance computation and theoretical p ....Emerging applications of advanced computational methods and discrete mathematics. Ongoing improvements in computer performance are revolutionising research in combinatorial discrete mathematics, and leading to exciting new applications in information technology and the biological and chemical sciences. As a result, substantial international research effort, both at universities and in commercial and industrial organisations, is being channelled into high-performance computation and theoretical problems in combinatorial mathematics. Our aim is to develop and apply advanced computational methods through the study of several unsolved theoretical problems in design theory and practical problems in exact matrix computation and drug design.Read moreRead less
Mathematical models of cell migration in three-dimensional living tissues. This project aims to develop mathematical models of cell migration in crowded, living tissues. Existing models rely solely on stochastic simulations, and therefore provide no general mathematical insight into how properties of the crowding environment (obstacle shape, size, density) affect the migration of cells through that environment. This project will produce mathematical analysis, mathematical calculations and exact ....Mathematical models of cell migration in three-dimensional living tissues. This project aims to develop mathematical models of cell migration in crowded, living tissues. Existing models rely solely on stochastic simulations, and therefore provide no general mathematical insight into how properties of the crowding environment (obstacle shape, size, density) affect the migration of cells through that environment. This project will produce mathematical analysis, mathematical calculations and exact analytical tools that quantify how the crowding environment in three-dimensional living tissues affects the migration of cells within these tissues. Long term effects will be the translation of this new mathematical knowledge into decision support tools for researchers from the life sciences.Read moreRead less
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
Statistical methods and tools for integrative microarray analysis. Tools used for biological and medical research have been evolving and there has been an increase in high-throughput technologies such as genome sequencing and DNA microarray. The growing number of entries and the increasing availability of public microarray repositories and other sequence databases have generated the new challenge of developing tools to efficiently integrate data by different research groups. This research provi ....Statistical methods and tools for integrative microarray analysis. Tools used for biological and medical research have been evolving and there has been an increase in high-throughput technologies such as genome sequencing and DNA microarray. The growing number of entries and the increasing availability of public microarray repositories and other sequence databases have generated the new challenge of developing tools to efficiently integrate data by different research groups. This research provides new statistical methods to integrate different data sets. Its application in the biomedical field will allow researchers to effectively interpret the myriad of data generated within the community.Read moreRead less