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Computational biology approaches for studying gene regulatory network discovery and modelling

Salama, Rafik A (2011)
Ph.D. thesis, University of Birmingham.

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Abstract

The advent of next generation sequencing has increased the gap between genome sequence data and knowledge, enhancing the need for faster means to fill this gap. The development of efficient computational biology methods to handle this gap has never been so important. Gene regulatory networks in particular have been studied widely for their role in controlling cellular behaviour, resulting in manifold phenotypic characteristics. In this thesis, I present novel techniques contributing to the discovery of gene regulatory network connections, through enhanced binding site prediction, binding site multiple sequence alignment and binding site specificity. Another major advantage of computational biology is the ability to simulate the behaviour of gene regulatory networks, in order to study the governing dynamics of such networks. In this thesis, I also introduce a new modelling language bringing computational modelling capabilities into the biological domain to simplify the process of writing a model that can be simulated in silico. I have proved through this work that: first, the devised computational biology techniques can provide cheap yet powerful and efficient techniques to study gene regulatory networks; and second, the techniques presented have novel superiority over current research in this domain.

Type of Work:Ph.D. thesis.
Supervisor(s):Stekel, Dov
School/Faculty:Colleges (2008 onwards) > College of Life & Environmental Sciences
Department:School of Biosciences
Subjects:QA Mathematics
QR Microbiology
Institution:University of Birmingham
ID Code:3039
This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder.
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