Doctoral student in theComputational Biology Group, Department of Computer Science, Oxford
Industrial partner organisationMicrosoft Research Cambridge, Biological Computation Group
I started out as an undergraduate at Cambridge, where I studied maths for three years. Because of a long standing interest in the Life Sciences I transferred into the relatively new Masters in Systems Biology course, then decided to persue a DPhil at Oxford in the same spirit. My current scientific interest is the development of computer models that include both cell mechanics and a decision making "program" embedded in each cell. The hope is to test hypotheses about cell behaviour by looking at whether they lead to correct properties at the whole tissue or organ level.
My current work involves using a cell based model of the C. elegans germ line to try and better understand the behaviour of individual germ cells. I am particularly interested in how the cell cycle and the mitosis/meiosis decision are regulated. For this project I am based most of the time at MSR Cambridge, where I am supervised by Dr James Osborne and Dr Hillel Kugler, and this work is done in collaboration with the Hubbard lab at NYU. The example simulation in the video below shows a C. elegans gonad being formed behind a leader cell with a migration defect.
This was a 12 week project, also based at MSR Cambridge, that led into my DPhil. The goal was to write a model of the C. elegans germ line using the software tool Chaste (Cancer Heart and Soft Tissue Environment); a C++ library for biological modelling developed at Oxford. The behaviour of each germ cell in the simulation is controlled by an internal Statechart, which determines whether the cell should proliferate or differentiate based on the signals it receives. This project built on previous work by Setty et al., especially for the sub cellular model.
Over 12 weeks, the aim of this short project was to develop a 1D PDE model of wound healing, to include both oxygen partial pressure and bacterial load. By adding burts of high oxygen supply it is possible to mimic the effect of a supplemental oxygen treatment, and see whether that intervention is enough prevent an infection. I was particularly interested in whether the different response to oxygen of various bacterial species might affect the outcome. The hope was to eventually determine when supplemental oxygen is an appropriate measure post-surgery, although no firm conclusions were reached within the short time frame.
My MSci project aimed to describe the healthy process of targeted bone remodelling. A system of delay differential equations was used to model how bone density changes over time, depending on the chemical signals and cell numbers present. Using a method of lines solver written in C, I also simulated the migration of the cells responsible for bone resorption and suggested a way that resorption might be localised to microfractures. Supervised by Dr Pietro Liò.
This 10 week project involved modelling wound healing in healthy and diabetic individuals. I used a reaction diffusion equation to describe the movement and proliferation of cells dependent on a growth factor, and wrote a method of lines solver in MATLAB to produce an animation of wound closure (see below). The model was used to determine where a limited number of bFGF doses should be injected for optimal healing. Supervised by Prof. Philip Maini and Dr Helen Byrne.