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DTSTART;TZID=America/New_York:20260416T104000
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DTSTAMP:20260413T092241
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SUMMARY:Simon Martina-Perez (University of Oxford\, Mathematics)
DESCRIPTION:Biologically grounded mechanistic modelling from single-cell transcriptomics: case studies in neuroblastoma developmental dynamics and tubular injury in kidney rejection\nOrdinary differential equation models are ubiquitous in mathematical biology due to their interpretability and tractability. At the same time\, their construction relies on substantial a priori assumptions about the relevant variables and their interactions. These assumptions can lead to model misspecification. A bottom-up approach using single-cell transcriptomics can guide the identification of biologically meaningful structure before formal model construction. In this talk\, I will argue that transcriptomic data can be used to define the appropriate state space for ODE-based mechanistic modelling. In the first case study\, we consider neuroblastoma\, where transcriptomic structure reveals a disrupted developmental programme. A phenotypically structured mathematical model\, informed by the data\, captures differentiation dynamics and links altered developmental trajectories to tumour growth and relapse risk. In the second case study\, we apply a similar philosophy to spatial transcriptomics of biopsies from human kidney allograft rejection. By analysing transcriptomic coherence at the level of individual tubules\, we identify structured patterns of gene expression that cannot be explained by spatial proximity alone. This reveals feedback loops between tubular epithelial cells and infiltrating immune populations\, suggesting that tubules act as coherent\, interacting units of injury. Together\, these examples illustrate how transcriptomics can provide a starting point for mechanistic modelling\, enabling the construction of biologically realistic models that better capture the true organisational structure of disease.
URL:https://biomath.math.ufl.edu/event/simon-martina-perez-university-of-oxford-mathematics/
LOCATION:Zoom\, To obtain the Zoom link\, please contact Youngmin Park at park.y@ufl.edu or Kyle Adams at adams.k@ufl.edu.
CATEGORIES:Spring 2026
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