Department of Electrical Engineering & Computer Sciences, Center for Computational Biology, UC Berkeley
The broad goals of the research in the lab are to understand:
- How transcription is regulated in immune cells.
- How changes in transcription affect cell- and tissue-level phenotypes.
Beyond a basic scientific drive to study these fundamental questions, we are motivated by the translational potential of identifying and modulating the causes of transcriptional shifts. Our contribution to this wide area of research is in developing and applying computational tools (algorithms, software) to design, integrate and interpret large molecular data sets that can teach us about the regulation and the downstream effects of the transcriptional process. Some of the software we have developed includes:
- scvi-tools for end-to-end analysis of single-cell omics data with deep generative models
- cassiopeia for single cell lineage tracing tree reconstruction
- vision for functional interpretation for scRNA-seq data
- epitome for prediction of epigenetic events using chromatin accessibility
The lab currently focuses on two related areas of research:
- Modeling and interpreting the effects of heterogeneity between immune cells based on single-cell genomics, with a focus on mRNA profiling.
- Exploring regulatory factors that govern cell state transitions based on large-scale chromatin profiling assays and massively parallel reporter assays.