About Us

Located in the UC San Diego Bioengineering department, we develop high-throughput technologies to profile single cell genomes/transcriptomes/epigenomes, map the spatial gene expression of diverse tissues and organs, trace the lineages of single cells, and perform functional genomics screens. We apply these novel technologies to build quantitative maps of human cell types (brain, kidney, lung, cancer) and then use machine learning methods to analyze and interpret these maps. If you're interested in working at the intersection of high-throughput genomics and machine learning please contact us for openings!

Single cell technology development

  • Measuring gene expression and chromatin accessibility in the same cell using single cell multi-omics (SNARE-seq [v1, v2])
  • Measuring gene expression in tissues while retaining spatial context (Dartfish)
  • Tracing the lineages of single cells (RETrace)
  • Assessing the role of key developmental regulators across cell types and across developmental time using functional genomics screens and novel developmental models (Teratoma Project)
  • Generating interpretable visualizations of single cell datasets (SWNE)

Creating quantitative maps of human cell types

  • Profiling the single cell expression and regulatory landscape of the human brain (BRAIN initiative)
  • Understanding normal kidney cell types and the progression of kidney disease with single cell gene expression, gene regulation, and spatial expression (HuBMAP; KPMP)
  • Mapping single cell expression and regulatory landscape of both the developing and adult human lung (HuBMAP; CZI)
  • Dissecting the heterogeneity of gene expression and gene regulation in pediatric gliomas and neuroblastomas (Human Tumor Atlas Network)