Technology and Computation

Our methods combine:

  1. quantitative precision in each measurement, especially during dynamic responses, to empower the development of sophisticated models
  2. genomic breadth, to ensure the unbiased discovery of circuits and their components
  3. massive scale, commensurate with the processing of large numbers of samples essential for analyzing the effects of many perturbations
  4. sample sparing input requirement, enabling analyses of precious primary cells and rare tissue samples.

Computationally, we have developed ways to infer molecular models from genomic profiles reflecting different regulatory layers in the cell, including signaling pathways, transcriptional regulation, chromatin control and the RNA and protein life cycle.  We have also developed methods to analyze single cell profiles to infer cell types and their positions in complex tissues.

Areas of Focus:

Epigenomic Profiling

  • Methods development for measuring DNA methylation
  • Technologies for mapping histone modifications and chromatin proteins
  • Single cell and low input epigenetic analysis
  • Higher order chromosomal organization
  • Microfluidic for epigenomic measurements

Bulk and Single Cell Transcriptome Analysis

  • Assembly (Trinity, etc.)
  • Single cell RNA Seq

Genetic Perturbation for Circuit Dissection

  • CRISPR
  • Epigenome engineering
  • In vivo genetic screens

Algorithms for Circuit Reconstruction

Tools to Enable Clinical Sample Analysis

  • Mint-ChIP
  • Microfluidic-ChIP
  • Single-cell RNA seq