School of BioSciences - Research Publications

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    Bayesian and Algebraic Strategies to Design in Synthetic Biology
    Araujo, RP ; Vittadello, ST ; Stumpf, MPH (IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2021-12-07)
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    Turing pattern design principles and their robustness
    Vittadello, ST ; Leyshon, T ; Schnoerr, D ; Stumpf, MPH (ROYAL SOC, 2021-12-27)
    Turing patterns have morphed from mathematical curiosities into highly desirable targets for synthetic biology. For a long time, their biological significance was sometimes disputed but there is now ample evidence for their involvement in processes ranging from skin pigmentation to digit and limb formation. While their role in developmental biology is now firmly established, their synthetic design has so far proved challenging. Here, we review recent large-scale mathematical analyses that have attempted to narrow down potential design principles. We consider different aspects of robustness of these models and outline why this perspective will be helpful in the search for synthetic Turing-patterning systems. We conclude by considering robustness in the context of developmental modelling more generally. This article is part of the theme issue 'Recent progress and open frontiers in Turing's theory of morphogenesis'.
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    Model comparison via simplicial complexes and persistent homology
    Vittadello, ST ; Stumpf, MPH (ROYAL SOC, 2021-10-13)
    In many scientific and technological contexts, we have only a poor understanding of the structure and details of appropriate mathematical models. We often, therefore, need to compare different models. With available data we can use formal statistical model selection to compare and contrast the ability of different mathematical models to describe such data. There is, however, a lack of rigorous methods to compare different models a priori. Here, we develop and illustrate two such approaches that allow us to compare model structures in a systematic way by representing models as simplicial complexes. Using well-developed concepts from simplicial algebraic topology, we define a distance between models based on their simplicial representations. Employing persistent homology with a flat filtration provides for alternative representations of the models as persistence intervals, which represent model structure, from which the model distances are also obtained. We then expand on this measure of model distance to study the concept of model equivalence to determine the conceptual similarity of models. We apply our methodology for model comparison to demonstrate an equivalence between a positional-information model and a Turing-pattern model from developmental biology, constituting a novel observation for two classes of models that were previously regarded as unrelated.