Eliza Barkan

Abstract Improvements in single-cell sequencing protocols have democratized their use for phenotyping at organism-scale and molecular resolution, but interpreting such experiments poses computational challenges. Identifying the genes and cell types directly impacted by genetic, chemical, or environmental perturbations requires explicit modeling of lineage relationships amongst many cell types, over time, from datasets with millions of cells collected from thousands of specimens.

Abstract Organogenesis is a highly organized process that is conserved across vertebrates and is heavily dependent on intercellular signaling to achieve cell type identity. We lack a comprehensive understanding of how developing cell types in each organ and tissue depend on developmental signaling pathways.

Localizing gene expression Single-cell RNA sequencing can provide information about cellular relationships based on shared transcriptomes, but most methods lose spatial information. Those methods that do retain spatial information can be limited to a specific set of genes and/or a small area. Srivatsan et al.