Collide-seq

We reprogrammed fibroblasts through combinatorial over expression of transcription factors and used single-cell RNA-sequencing as a read-out of the resulting phenotype. We used this transcriptomic snapshot to understand how cell fates are resolved if conflicting lineages, represented as transcription factors, “collide“.

Bob A. Hersbach, , David S. Fischer, et al. Probing cell identity hierarchies by fate titration and collision during direct reprogramming. Molecular Systems Biology 18:e11129 (2022).

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Inferring cell-cell communication with graph neural networks

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Connecting snapshots of T cell clones across time