Kieran Alden
PhD student

Profile

Career

  • Centre for Immunology and Infection
    PhD student

Research

Overview

  • Simulation modelling of lymphoid tissue organogenesis

Lymphoid tissue develops during embryonic development and as a result of chronic infections. This consists of networks of specialised mesenchymal-derived stromal cells that support and organize the adaptive immune system. Development of these tissues is a result of dynamic cellular interactions between haematopoietic cells and stromal cells.  Gene-targeted mice have provided insight into the cellular interactions involved but have failed to lead to a complete understanding of lymph node organogenesis. Thus we wish to utilise simulation modelling to determine the role of deterministic forces in lymphoid tissue organogenesis.  This project will involve the development of an agent based simulation of lymphoid tissue development utilizing primary data sets that we have collected; going through both the design of a model of lymphoid organogenesis in UML (primarily using state diagrams) and implementation of this to generate a functional model which will be utilised to test our hypothesis that deterministic forces (including the role of fluidic pressure, physical geometry and oxygen levels (physiological forces)) are critical in lymphoid tissue formation.

Kieran is also involved the development and maintenance of the dConsensus bioinformatic tool with collaborators at the University of California, San Diego. This is a web resource, used by those working in the structural biology field, that displays the results of calculations from multiple protein domain assignment algorithms and generates a domain assignment consensus with an associated reliability score. This provides insights into the fundamental units of protein structure so important to the study of evolutionary and functional relationships.

There will be two components to the PhD project.

  1. Biology, Coles research group
    The project will involve the analysis and interpretation of primary imaging data sets used in the construction of simulation models of lymphoid tissue organogenesis.  This will involve determining important parameters required to successfully implement the model.  As we obtain output from the simulation, we will utilise this to design and implement “wet biology” experiments. 
  2. Computer science, Timmis Laboratory
    The project will involve the development of simulation models based on UML state and activity diagrams that can be used simulate the role of physiological forces on the biological process of tissue formation.  Key to these simulations is the generation of biologically meaningful models that can be used to generate predictions of how physiological forces may impact on the process of organogenesis.


Research group(s)

Publications

Selected publications

Contact details

Kieran Alden
PhD student
Centre for Immunology and Infection

Tel: 01904 328857