Research Focus:

The Applied Genomics team works on projects in the Cell Type program, where the goal is to define the diversity of cell types in the mouse and human brains.  Multimodal techniques must be used to correlate the transcriptomically-defined cell types with structural, physiological and functional neuronal properties.  Dr. Levi’s team is involved in establishing both prospective and retrospective methods for identifying cell types at the Allen Institute.  These techniques include multiplexed FISH and Patch-seq for retrospective marking of cell types, and building live-cell viral reporters to prospectively mark and manipulate transcriptomically-defined cell types in mouse and human tissues. Dr. Levi’s team was also involved in the characterization of neural cell types differentiated from human embryonic stem cells. hESC-derived forebrain excitatory, inhibitory, and mid/hindbrain cell types, and their lineages were characterized by single cell RNA-Seq. Those cell types were compared to single cells form primary human fetal cells to determine genes that were conserved or divergent in the hESC derived cell types.  This work helped establish more precisely what cell types are generated in some of the most commonly used neural differentiation protocols, and what cell types these culture systems succeed and fail to model.