Searching for near-exact protein models. This project aims to develop novel and efficient heuristic-based algorithms leading to near accurate protein tertiary structure models. Knowledge about protein structures is fundamental to our understanding of living systems. The progress on experimental determination of these structures has been extremely limited and remains an open challenge in molecular biology. Computational prediction of protein structures from sequences is emerging as a promising ap ....Searching for near-exact protein models. This project aims to develop novel and efficient heuristic-based algorithms leading to near accurate protein tertiary structure models. Knowledge about protein structures is fundamental to our understanding of living systems. The progress on experimental determination of these structures has been extremely limited and remains an open challenge in molecular biology. Computational prediction of protein structures from sequences is emerging as a promising approach, but its accuracy is far from satisfactory. The software systems developed in this project will be used in structural identification of target proteins in drug design. This will make drug design process more efficient, saving time and cost, potentially saving lives.Read moreRead less
RNA structure prediction by deep learning and evolution-derived restraints. This project addresses the long-standing structure-folding problem of Ribonucleic acids (RNA) whose solution is essential for elucidating the roles of noncoding RNAs in living organisms. The proposed approach will detect hidden homologous sequences and enhance evolutionary covariation signals by developing new algorithms for search and smarter neural networks for deep learning. The project expects to generate new tools ....RNA structure prediction by deep learning and evolution-derived restraints. This project addresses the long-standing structure-folding problem of Ribonucleic acids (RNA) whose solution is essential for elucidating the roles of noncoding RNAs in living organisms. The proposed approach will detect hidden homologous sequences and enhance evolutionary covariation signals by developing new algorithms for search and smarter neural networks for deep learning. The project expects to generate new tools for structure-based probing of RNA evolutional and functional mechanisms. The outcomes should provide significant benefits by high-accuracy computational modelling of RNA structures that are difficult and costly to solve by current structural biology techniques but important for enabling biotech and clinical applications.Read moreRead less
Mapping the Effectiveness of Automated Software Testing. This project aims to help software engineers build complex software systems in far more reliable and cost-effective ways. It takes an interdisciplinary approach by applying machine learning techniques to automatically test complex software systems. Expected outcomes include a novel methodology for assessing the strengths and weaknesses of test suites generated by automated software testing techniques and the approaches required for generat ....Mapping the Effectiveness of Automated Software Testing. This project aims to help software engineers build complex software systems in far more reliable and cost-effective ways. It takes an interdisciplinary approach by applying machine learning techniques to automatically test complex software systems. Expected outcomes include a novel methodology for assessing the strengths and weaknesses of test suites generated by automated software testing techniques and the approaches required for generating high-quality test cases. Such advances are urgently needed to avoid disasters when deploying software systems in the real world.Read moreRead less
The role of gene isoforms in human brain development. This project aims to investigate how genes vary their products to control human brain development, by creating new methods to study gene activity in individual brain cells. Using these innovative methods, this project expects to generate fundamental new knowledge of how the human brain forms. Expected outcomes of this project include widely applicable techniques, strengthened international (UK) research collaborations and highly trained perso ....The role of gene isoforms in human brain development. This project aims to investigate how genes vary their products to control human brain development, by creating new methods to study gene activity in individual brain cells. Using these innovative methods, this project expects to generate fundamental new knowledge of how the human brain forms. Expected outcomes of this project include widely applicable techniques, strengthened international (UK) research collaborations and highly trained personnel in genomics and neuroscience. This should deliver many benefits, including a better understanding of how the brain forms, training of higher degree by research students, as well as tools and methods of benefit to the academic research and biotechnology sectors.Read moreRead less
Ownership-based Alias Analysis for Securing Unsafe Rust Programs. This project aims to develop an ownership-based alias analysis as a complement to Rust's ownership type system for improving Rust's memory safety. This project, therefore, expects to deliver an alias analysis foundation that can provide stronger memory safety guarantees than the state-of-the-art in detecting memory-safety violations and security vulnerabilities in real-world Rust programs that use unsafe language features. The exp ....Ownership-based Alias Analysis for Securing Unsafe Rust Programs. This project aims to develop an ownership-based alias analysis as a complement to Rust's ownership type system for improving Rust's memory safety. This project, therefore, expects to deliver an alias analysis foundation that can provide stronger memory safety guarantees than the state-of-the-art in detecting memory-safety violations and security vulnerabilities in real-world Rust programs that use unsafe language features. The expected outcomes are a deployable ownership-based alias analysis in the Rust compiler and an industrial-strength open-source framework. These outcomes are expected to provide significant benefits in improving software quality and security in Rust, an emerging language that offers both performance and safety.Read moreRead less
Formation of boundaries in the developing embryo. This project aims to decipher how the boundaries between the different organs are established in the developing embryo. The project aims to identify the components of the gene regulatory network that controls lateral plate mesoderm formation, develop a mathematical model that can explain how the domains are formed within this region, and validate novel interactions in vivo in zebrafish. The expected outcome of the project is to reveal how the pro ....Formation of boundaries in the developing embryo. This project aims to decipher how the boundaries between the different organs are established in the developing embryo. The project aims to identify the components of the gene regulatory network that controls lateral plate mesoderm formation, develop a mathematical model that can explain how the domains are formed within this region, and validate novel interactions in vivo in zebrafish. The expected outcome of the project is to reveal how the progenitors of our body parts are instructed to be positioned at the right time and at the right place in the embryo. This project should provide significant benefit such as the expansion of Australia's knowledge base and research capability in cross-disciplinary science.Read moreRead less
Values-oriented Defect Fixing for Mobile Software Applications. This project aims to address critical problems with mobile applications that exhibit human values-based defects, by advancing our understanding, detection and fixing of such defects. Many mobile apps do not operate according to the essential values of their human users - e.g. inclusivity, accessibility, privacy, ethical behaviour, due care, emotions, etc - making them ineffective, underused, unfit for purpose or even dangerous. Exp ....Values-oriented Defect Fixing for Mobile Software Applications. This project aims to address critical problems with mobile applications that exhibit human values-based defects, by advancing our understanding, detection and fixing of such defects. Many mobile apps do not operate according to the essential values of their human users - e.g. inclusivity, accessibility, privacy, ethical behaviour, due care, emotions, etc - making them ineffective, underused, unfit for purpose or even dangerous. Expected outcomes include new theories, techniques and prototype tools for developers and end users to detect and help fix values-based defects in mobile apps. Benefits include better, safer mobile apps for people and organisations and improved app developer productivity and competitiveness.Read moreRead less
Scalable Stream Processing in Hybrid Edge-Cloud Infrastructures. This project aims to develop a new computational paradigm to ensure low-latency services for streaming applications across heterogeneous Edge devices while satisfying high-throughput and scalability requirements. This project is of high significance for generating new knowledge in the area of real-time streaming using innovative algorithms that overcome the limitations of remote Cloud and distributed Edge computing. Expected outcom ....Scalable Stream Processing in Hybrid Edge-Cloud Infrastructures. This project aims to develop a new computational paradigm to ensure low-latency services for streaming applications across heterogeneous Edge devices while satisfying high-throughput and scalability requirements. This project is of high significance for generating new knowledge in the area of real-time streaming using innovative algorithms that overcome the limitations of remote Cloud and distributed Edge computing. Expected outcomes include novel programming abstractions, performance models, and control mechanisms to address complex problems for incremental and iterative computations in hybrid Edge-Cloud infrastructures. This should provide significant benefits, one of which is the optimised utilisation of limited computing resources.Read moreRead less
How novel ribosomal RNA gene repeat variants drive cellular function. The hundreds of ribosomal RNA gene repeat copies are a remarkable part of our genomes, as they encode the machinery responsible for all cellular protein synthesis and shape the structure of the nucleus. However, due to their high degree of sequence similarity, they still have not been assembled into the human genome reference. This project will resolve this impasse and furthermore uncover the functional impacts of a newly iden ....How novel ribosomal RNA gene repeat variants drive cellular function. The hundreds of ribosomal RNA gene repeat copies are a remarkable part of our genomes, as they encode the machinery responsible for all cellular protein synthesis and shape the structure of the nucleus. However, due to their high degree of sequence similarity, they still have not been assembled into the human genome reference. This project will resolve this impasse and furthermore uncover the functional impacts of a newly identified molecular diversity in the ribosomal RNA gene repeats. Outcomes include new paradigms for how the ribosomal RNA gene repeats drive protein synthesis and genome structure, and a blueprint to develop novel genomics applications for human health, biotechnology, and agriculture.Read moreRead less
Genome evolution & adaptation of the multinuclear wheat stripe rust fungus. Animals and plants package their genomes into a single nucleus within each cell. In contrast, millions of fungal species accommodate multiple nuclei containing individual haploid genomes. It is currently unknown what the evolutionary implications are for this unusual genome division into multiple nuclei. Here we explore the evolutionary consequences of genome division into multiple nuclei for the first time by applying c ....Genome evolution & adaptation of the multinuclear wheat stripe rust fungus. Animals and plants package their genomes into a single nucleus within each cell. In contrast, millions of fungal species accommodate multiple nuclei containing individual haploid genomes. It is currently unknown what the evolutionary implications are for this unusual genome division into multiple nuclei. Here we explore the evolutionary consequences of genome division into multiple nuclei for the first time by applying cutting edge genome biology tools and algorithms. The economically significant study system is the devastating wheat stripe rust fungus. This pathogen costs Australian farmers over $100 million a year. New understanding is expected to lead to better disease management, reduced fungicide applications, and increased yields.Read moreRead less