Genome Design
: Computational Methods and Multi-scale Analysis

  • Sophie Landon

Student thesis: Doctoral ThesisDoctor of Philosophy (PhD)


Biological modelling has increased in use dramatically over the past few years, due to
greater availability of computational power and an increase in interdisciplinary research.
This opens more possibilities of coupling modelling with experiment design, with the
end goal of using models to discover interesting and relevant pathways for experiments, thus
making biological research more efficient. In this thesis, we describe the structure and use of the
two existing whole-cell models, and how they relate to genome design. We use the two existing
whole-cell models to demonstrate that their output, after processing, can be used to understand
metabolic behaviour and further understanding of the relationship between cell and external
environment in the case of Mycoplasma genitalium, and uncover modular structure which could
be used for metabolic engineering in Escherichia coli. Finally, we speculate on the future of
whole-cell modelling, and how it will improve with advances in both modelling and biological
data collection
Date of Award12 May 2022
Original languageEnglish
Awarding Institution
  • University of Bristol
SupervisorLucia Marucci (Supervisor) & Claire S Grierson (Supervisor)

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