Rafik Salama’s PhD thesis

Rafik Salama’s PhD thesis and abstract have now been posted for public view on the University of Birmingham web site:



Computational biology approaches for studying gene regulatory network discovery and modelling


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.

International Scholarships Available for MRes or PhD at University of Nottingham

Are you an international student interested in studying for an MRes or PhD in Bioinformatics or Systems Biology? Would you like to join my group at the University of Nottingham? We have a wide range of projects available looking at microbial gene regulation.

Details of all Masters and PhD scholarships can be found here:


In particular, for potential PhD students, there are

If you are interested in coming to study with us and applying for one of these scholarships, please be in touch, sending CV and short paragraph describing your research ambitions.