Dr. Elizabeth Read is Assistant Professor of Chemical & Biomolecular Engineering at the University of California, Irvine. She holds undergraduate degrees in Chemistry and Mathematics from the University of Colorado and a PhD in Chemistry from the University of California, Berkeley. Prof. Read is a member of the UC Irvine Center for Complex Biological Systems and the NSF-Simons Center for Multiscale Cell Fate.

Title: Stochastic dynamics of gene regulatory networks: numerical techniques to bridge models and experiments

Abstract:

Cell biological data is increasingly available at single-cell, single-nucleotide, and single-molecule resolution. Such experiments reveal often-unexpected levels of heterogeneity at these scales. In the Read lab, we use stochastic modeling to quantitatively describe this heterogeneity and infer mechanistic insights from data.

I will present recent work in the area of stochastic dynamics of gene regulatory networks. First, stochastic modeling of gene regulatory networks can inform our understanding of cell-to-cell heterogeneity, but integrating such models with data is challenging. We propose a framework for integrating single cell RNA sequencing datasets with Chemical Master Equation models. We find that such model-based analysis can reveal new insights on cell differentiation and gene regulation mechanisms. If time permits, I will also discuss numerical techniques to characterize metastability in discrete stochastic models.

Suggested Reading or Key Publications:

• • a
  • b
  • c
  • d

Links to Relevant Software: 

• • e
  • f
  • g
  • h

• • Question 1
  • Question 2