Motivation: A rapid technological development in the biosciences and in computer science in the last decade has enabled the analysis of high-dimensional biological datasets on standard desktop computers. However, in spite of these technical advances, common properties of the new…
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Tropical peatlands play an important role in the global carbon cycle, but little is known about the factors which regulate carbon dioxide (CO2) and methane (CH4) fluxes from these ecosystems. To improve our understanding of the potential impact of future changes in climate and/o…
The Notch signalling pathway is pivotal in ensuring that the processes of arterial specification, angiogenic sprouting and haematopoietic stem cell (HSC) specification are correctly carried out in the dorsal aorta (DA), a primary arterial blood vessel in developing vertebrate em…
Given the ever increasing quantity of sequence data, functional annotation of new gene sequences persists as being a significant challenge for bioinformatics. This is a particular problem for transcriptomics studies in crop plants where large genomes and evolutionarily distant m…
Protein Structure Comparison (PSC) is at the core of many important structural biology problems. PSC is used to infer the evolutionary history of distantly related proteins; it can also help in the identification of the biological function of a new protein by comparing it with o…
This thesis concerns two areas of bioinformatics related by their role in protein structure and function: protein structure prediction and post translational modification of proteins. The dihedral angles Ψ and Φ are predicted using support vector regression. For the prediction o…
The complex environment of a living cell contains many molecules interacting in a variety of ways. Examples include the physical interaction between two proteins, or the biochemical interaction between an enzyme and its substrate. A challenge of systems biology is to understand …
In this thesis, a series of mathematical models suitable for describing biological tissue growth are developed. The motivation for this work is a bioreactor system which provides perfusion and compressive mechanical stimulation to a cell-seeded scaffold; however, the formulation…