Example PhD

Information extraction for systems biology applications

Supervisor: Dr I. Spasić

Keywords: Natural language processing, Information extraction, Bioinformatics, Systems biology.

Systems biology has emerged as an approach to studying biological systems by understanding how the heterogeneous parts combine to form the whole through systematic integration of technology, biology and computation. A principal goal of systems biology is to develop and exploit appropriate methods for detailed, genome-scale, metabolic modelling: the virtual cell, which can be used to simulate biological systems in silico. While the structure of such systems is now relatively well-known, access to the required kinetic parameters such as the Michaelis constant, K(m), and the catalytic constant, k(cat), remains a big challenge. Most experimental evidence on kinetic parameters remains buried in the literature, whose manual searching is complex, time-consuming and partial. Information extraction, which selectively structures and combines data from text, can be used to facilitate access to this type of biological information. The aim of the current project would be populate metabolic models automatically with extracted kinetic parameters as part of systematic integration of experimental data and mathematical models in systems biology.

Key Skills/Background: Open to Computing Graduates and postgraduates.

Contact: Dr I. Spasić to discuss this research topic.