Stochastic networks theory to model single-cell genomic count data

We propose a novel way of representing and analysing single-cell genomic count data, by modelling the observed data count matrix as a network adjacency matrix. This perspective enables theory from stochastic networks modelling to be applied in a principled way to this type of data, providing new ways to view and analyse these data, and giving first-principles theoretical justification to established, successful methods. We show the success of this approach in the context of three cell-biological contexts, from the epiblast/epithelial/neural lineage. New technology has made it possible to gather genomic data from single cells at unprecedented scale, and this brings with it new challenges to deal with much higher levels of heterogeneity than expected between individual cells. Novel, tailored, computational-statistical methodology is needed to make the most of these new types of data, involving collaboration between mathematical and biomedical scientists.