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Metabolic engineering is increasingly being used for the production of industrial products such as pharmaceuticals and enzymes. These chemicals have traditionally been chemically synthesized, but the application of synthetic biology techniques to microbes facilitates faster, cheaper production. Modelling and the integration of existing data can help inform the design of synthetic pathways. We applied...
Populations of bacteria acting in collaboration can produce complex behaviors which are not achievable by individual cells. There has, consequently, been considerable interest in the engineering of bacterial populations. Here we describe an approach for the engineering of aspects of bacterial quorum communication, using Standard Virtual Parts, a synthetic biology programming language, dubbed SVPWrite,...
Biological systems are inherently stochastic, a fact which is often ignored when simulating genetic circuits. Synthetic biology aims to design genetic circuits de novo, and cannot therefore afford to ignore the effects of stochastic behavior. Since computational design tools will be essential for large-scale synthetic biology, it is important to develop an understanding of the role of stochasticity...
Many biological systems can be modeled as networks. Hence, network analysis is of increasing importance to systems biology. We describe an evolutionary algorithm for selecting clusters of nodes within a large network based upon network topology together with a measure of the relevance of nodes to a set of independently identified genes of interest. We apply the algorithm to a previously published...
The concept of a network motif-a small set of interacting genes which produce a predictable behaviour at the network level-has attracted considerable attention amongst network analysts. It is of particular interest to synthetic biology, a new discipline which aims to apply engineering principles to biological systems. The modular nature of network motifs would make them ideal candidates for the basic...
The integration of diverse data sets into probabilistic functional networks is an active and important area of research in systems biology. In this paper we fracture a previously published integrated network into its component networks, and investigate the overlap between the information provided by each data set to the final network. Using three-node network motifs as a surrogate for information...
The analysis of microbial genome sequences can identify protein families that provide potential drug targets for new antibiotics. With the rapid accumulation of newly sequenced genomes, this analysis has become a computationally intensive and data-intensive problem. This paper describes the development of a Web-service-enabled, component-based, architecture to support the large-scale comparative analysis...
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