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
Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0347727
Funder
Australian Research Council
Funding Amount
$400,000.00
Summary
Computational infrastructure for high-throughput genome bioinformatics. We propose a high-performance computing and web facility for genome bioinformatics. It will provide a common software development environment in support of molecular biosciences, systems biology and complex systems modelling at the Institute for Molecular Bioscience at University of Queensland, and at Queensland University of Technology. The platform will support Australia's first genome-scale bioinformatics research website ....Computational infrastructure for high-throughput genome bioinformatics. We propose a high-performance computing and web facility for genome bioinformatics. It will provide a common software development environment in support of molecular biosciences, systems biology and complex systems modelling at the Institute for Molecular Bioscience at University of Queensland, and at Queensland University of Technology. The platform will support Australia's first genome-scale bioinformatics research website, with unique software and mirrors of the IBM Biological Pattern Discovery, UC San Diego MEME/MetaMEME/MAST, and NGI comparative genomics websites. Australian/NZ researchers will access the facility at no cost for high-throughput use of unique software, website mirrors and other important tools for genome bioinformatics.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).
Read moreRead less
Trans-dimensional and Approximate Bayesian Computation. Many applied scientists in Australia, particularly those in the biological, medical and environmental sciences are now interested in incorporating Bayesian statistical methodologies into their research.
The development of more generic and efficient Bayesian statistical methods will not only benefit applied statisticians but also the more occasional users of statistics in other disciplinary areas. The success of this project will enhance Au ....Trans-dimensional and Approximate Bayesian Computation. Many applied scientists in Australia, particularly those in the biological, medical and environmental sciences are now interested in incorporating Bayesian statistical methodologies into their research.
The development of more generic and efficient Bayesian statistical methods will not only benefit applied statisticians but also the more occasional users of statistics in other disciplinary areas. The success of this project will enhance Australia's reputation as a strong contributor to the development of Bayesian methodologies. Two PhD students will also be provided training in computational Bayesian statistics.Read moreRead less
The prediction of sleep/wake behaviour based on physiological and social factors. The prevalence of shiftwork has increased in Australia over the last few decades. Shiftworkers obtain less sleep, have greater difficulty maintaining good relationships, have poorer health, and are more likely to be injured at work than others. Using the largest dataset of its kind, we will substantially contribute to understanding the relationships between work hours, sleep, performance and safety. Ultimately, the ....The prediction of sleep/wake behaviour based on physiological and social factors. The prevalence of shiftwork has increased in Australia over the last few decades. Shiftworkers obtain less sleep, have greater difficulty maintaining good relationships, have poorer health, and are more likely to be injured at work than others. Using the largest dataset of its kind, we will substantially contribute to understanding the relationships between work hours, sleep, performance and safety. Ultimately, the project will answer a question critical to workplace safety - how much time off between shifts is needed to be alert and safe at work? The project will also produce tools to help industry design fatigue-friendly rosters, improving the safety, productivity and general well-being of shiftworkers in Australia and overseas.Read moreRead less
Quantum Information and Entanglement: a new framework for Science and Technology with quantum many-body systems. The expected outcome of the research program is a significant boost in the understanding of quantum many-body systems, which will reinforce Australia's competitiveness and international profile in aspects of breakthrough science and frontier technologies. By developing both the underpinning theory and innovative computational tools, and by applying them to problems of recognised impor ....Quantum Information and Entanglement: a new framework for Science and Technology with quantum many-body systems. The expected outcome of the research program is a significant boost in the understanding of quantum many-body systems, which will reinforce Australia's competitiveness and international profile in aspects of breakthrough science and frontier technologies. By developing both the underpinning theory and innovative computational tools, and by applying them to problems of recognised importance, this program will have direct implications in areas of condensed matter physics, quantum statistical mechanics, particle physics, complex systems, quantum information science and technology, quantum computation, engineered quantum systems and nanotechnology. Read moreRead less
Adaptiveness of self-organised decision making. Complex systems are an important international research focus in many disciplines, and their engineering applications are plentiful. The new mathematical approach developed by this project will enable different disciplines for the first time to communicate using a common formal framework. This will open the path to a generalized understanding of self-organized systems in dynamic environments. Creating the tools for a unified interdisciplinary a ....Adaptiveness of self-organised decision making. Complex systems are an important international research focus in many disciplines, and their engineering applications are plentiful. The new mathematical approach developed by this project will enable different disciplines for the first time to communicate using a common formal framework. This will open the path to a generalized understanding of self-organized systems in dynamic environments. Creating the tools for a unified interdisciplinary approach will allow Australia to gain a stronger position in biomimetic engineering and to take a lead in international research on collective behavior.
Read moreRead less
The geometry of impossible, or contradictory objects and its applications to computing and cognition. The principal aim is pure research, the increase of knowledge within the Theory of Inconsistency and particularly its mathematical aspects, to be available to the national and world community. Additionally, a new stock of hitherto-unseen images (still, moving and three-dimensional) will be constructed in a virtual reality environment. In addition to enhancing Australia's strong reputation in log ....The geometry of impossible, or contradictory objects and its applications to computing and cognition. The principal aim is pure research, the increase of knowledge within the Theory of Inconsistency and particularly its mathematical aspects, to be available to the national and world community. Additionally, a new stock of hitherto-unseen images (still, moving and three-dimensional) will be constructed in a virtual reality environment. In addition to enhancing Australia's strong reputation in logic, there are spin-offs for mathematics, cognitive science, computer studies, and the arts and entertainment industries.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