Wolfson Building, Parks Road, Oxford OX1 3QD
My research primarily involves development of cell-based models for colorectal cancer (CRC), working at the subcellular and cellular scales of interest.
- Development of dynamical systems models for several key biochemical pathways implicated in CRC, and their impact upon mitotic mechanisms via the cell cycle;
- Emphasis upon crosstalk between the Notch and Wnt pathways and the effect of such interaction on local and global cell behaviour within the colorectal epithelium;
- Development of a multiscale framework coupling cellular behaviour with the subcellular reaction networks mentioned above;
- Application of this framework to in silico translation experiments, exploring the impact of tissue geometry upon the expression of subcellular biochemistry;
- Application of these techniques to drug discovery problems, for example studying drug synergies within the intestinal crypt.
The biochemical modelling aspects of this work have drawn on opinions from the experimental research community, including clinicians and biologists from the Weatherall Institute for Molecular Medicine (WIMM). Meanwhile, the computational aspects of my DPhil involve developing the cell-based side of Chaste (http://www.cs.ox.ac.uk/chaste/), an open-source, C++ based framework for cell and tissue simulation.
My previous work in computational biology includes:
Fluid Dynamics of the Eye (MSc thesis, supervised by Dr. Andrew Hazel,
Manchester 2008): Finite element methods for modelling the flow of liquefied vitreous humour within the human eye;
Cellular Potts Modelling of the Colorectal Crypt (supervised by Prof. David Gavaghan and Dr. James Osborne, Oxford 2009): Application of the cellular Potts model to modelling the colorectal crypt, examining its suitability for representing intestinal tissue;
Perineural Tumour Invasion (supervised by Prof. Philip Maini and Dr. Alex Fletcher, Oxford 2009): Examination of discrete versus continuum approaches for modelling migration of tumour cells towards the perineural sheath in cancers of the head and neck.
I am also a Research Assistant for the Networks Cluster of the Keble Advanced Studies Centre, which aims to promote and facilitate interdisciplinary research into all aspects of network theory and its applications.
In 2012-13 I worked with the Open Knowledge Foundation as one of their inaugural Panton
Fellows. My fellowship work examined the role open practice might take in addressing reproducibility issues in scientific
research; this work culminated in the founding of the Open Science Training
Initiative (OSTI), a graduate scheme designed to provide integrated training in open science through a novel approach
known as Rotation Based Learning.
Aside from my academic work, I am also interested in educational initiatives in mathematics and science and am involved in several Open Day, Women in Science and Access initiatives.
Hybridised Open Educational Resources and Rotation Based Learning
In Open Education 2030. JRC−IPTS Vision Papers. Part III: Higher Education. 2013.
Colorectal Cancer Through Simulation and Experiment
Sophie K Kershaw‚ Helen M Byrne‚ David J Gavaghan and James M Osborne
In IET Systems Biology. 2013.
A hybrid approach to multi−scale modelling of cancer
J. M. Osborne‚ A. Walter‚ S. K. Kershaw‚ G. R. Mirams‚ A. G. Fletcher‚ P. Pathmanathan‚ D. Gavaghan‚ O. E. Jensen‚ P. K. Maini and H. M. Byrne
In Philosophical Transactions of the Royal Society A: Mathematical‚ Physical and Engineering Sciences. Vol. 368. No. 1930. Pages 5013–5028. November, 2010.