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The ability to profile the expression profile, genome and epigenome of individual cells is transforming our ability to answer questions about cell type heterogeneity, cell fate decisions in early development and the regulation of variability in gene expression levels. In this presentation, I will discuss some of the computational methods we have developed to analyse such data and discuss their application in the context of early mammalian development. I will also discuss how we are integrating information about genetic differences between individuals into our analyses.