My Research History

 

Current

I currently have research interests around the broad theme of Complex Systems Science (in particular Cybernetics), with specific focus on the Operational Research of Health and Illness (both hard and soft approaches), and Computational Social Systems. Particular emphasis is currently applied to the use of computational, mathematical and statistical approaches to understand how to harness the complexity that arises in large multi-vendor Enterprise Systems implementations. This is because, without a clear understanding of the emergent behaviours of large projects, it is difficult to predict the likelihood of successful implementation.


Agent-Based Modelling and Simulation of the NF-kB Signalling Pathway

The transcription factor NF-kB is a biological component which is central to the regulation of genes involved in the innate immune system. Dysregulation of the NF-kB signalling pathway is known to be involved in a large number of inflammatory diseases, including arthritis and atherosclerosis, and more recently has been associated with various cancers. Although considerable research has been performed since discovery in 1986, we are still not in a position to control the signalling pathway, and thus limit effects of NF-kB within the promotion of inflammatory diseases.


This PhD research project utilised computational modelling and simulation approaches to facilitate a more comprehensive understanding of the role of NF-kB in promotion of inflammatory diseases. I took a principled approach to design and development of an agent-based model using the FLAME simulation framework, which focused at the level of single cell data.


In Silico Experimentation of Experimental Autoimmune Encephalomyelitis









I have supervised a number of PhD students:

Mr Chris Lawrence (Oct 2022 - Present) - Agent-Based Modelling of Competitive Signalling and Competitive Dynamics

Mr Shayan Rashidi (Oct 2021 - Present) - The Role of Artificial Intelligence within Organisational Innovation Practices

Mr Drupad Parmar (Jun 2019 - Present) - Input Uncertainty Quantification for Large-Scale Simulation Models

Mr Abdulrahman Aldogiher (Oct 2018 - Submitted) - The Role of Identity in Resistance to Health Information System Implementations

Miss April Zhou (Oct 2018 - Present) - Agent-Based Modelling of Ecosystems

Dr Nicola Platt (Mar 2017 - Accepted pending minor revisions) - Boundary Spanning across Interdependent Boundaries

Dr Fred Ingram (Awarded Sept 2021) - An Agent-Based Classroom Lessons Model and Simulation.

 

My M.Res. Computational Biology degree had a 4-month summer placement. I negotiated a place with Prof. Jon Timmis (who is now my Ph.D. supervisor) within the Computer Science Department at York, and was co-supervised by Paul Andrews (Post Doc in the group), and Mark Read, a Ph.D. student who had developed a Java-based simulator of an autoimmune disease. The domain (subject matter) expert was Vipin Kumar, based at the Torrey Pines Institute for Molecular Studies (TPIMS), La Jolla, California.


Experimental Autoimmune Encephalomyelitis (EAE) is an animal model of human autoimmune diseases in general, and Multiple Sclerosis in particular. The disease is mediated by CD4 and CD8 T cells, which facilitate the activation of dendritic cells in the periphery and subsequent demyelination of neurons within the central nervous

system.


In this work I augmented the previously developed model and simulator to test a number of hypotheses, one of which involved mutually exclusive antigen presentation of dendritic cells. The results provide evidence that mutually exclusive antigen presentation of dendritic cells decreases the CD8 Treg mediated apoptosis of CD4 Th1 cells.