Our research
Cell identity.
At single-cell resolution.
How does a cell establish its identity—and what drives it from one state to another? We develop and apply genomic technologies to investigate the circuitry behind cell fate.
Scalable single-cell technologies
We develop combinatorial indexing strategies that make it possible to profile large numbers of cells. Our methods measure DNA methylation, chromatin accessibility, and whole genomes, with an emphasis on improving coverage, throughput, and accessibility.
Platforms include sciMET for DNA methylation, single-cell ATAC-seq for accessible chromatin, and whole-genome approaches for genetic variation.
Explore sciMET publications ↗Epigenetic programs in the brain
We use single-cell methods to study how epigenetic patterns emerge during neural development. Cerebral organoids provide models of the developing brain, while single-cell methylation and chromatin measurements help distinguish cell types and trace changes in cell state.
Recent work examines postnatal DNA methylation dynamics and the effects of MECP2 loss in the context of Rett syndrome.
Read the neurodevelopment preprint ↗Heterogeneity, genomes & disease
Individual cells within a tumor can differ in their genomes, regulatory landscapes, and responses to treatment. We apply single-cell genomic and epigenomic methods to investigate these differences, including copy-number variation and changes in chromatin accessibility.
Explore related publications ↗Tools for exploring complex data
We develop software alongside our experimental methods. Amethyst supports analysis and exploration of single-cell DNA methylation data; scitools provides tools for processing and investigating single-cell datasets.