TCBG Seminar

Computational understanding of biological patterns: 3D genome folding and landscape of stochastic cellular fate

Jie Liang
Biomedical Engineering
University of Illinois at Chicago
Chicago, Illinois

Monday, October 23, 2023
3:00 pm (CT)


Experimental measurements of chromosome conformation, epigenetic modifications, and stochastic cellular behavior present new opportunities for understanding fundamental biology. We first discuss how 3D polymer models using the CHROMATIX method and Hi-C chromosome conformation capture studies can identify a small set of non-random polymer interactions, which can drive chromatin folding. Large ensemble models of independently folded chromatin conformations can uncover hubs of many-body interactions, revealing novel mechanisms of promoter-enhancer interactions and gene regulation. We then discuss recent development of the ACME (accurate chemical master equation) method that can construct the exact time-evolving probabilistic landscapes of stochastic reaction networks by solving the underlying discrete chemical master equation. Examples of how these landscapes can be used to study cellular fate will be given. We also discuss how to meet the rising challenges of decipher these newly computable high-dimensional probability landscapes and quantify their exact topological structures of peaks and cycles of various dimensions through persistent homology.

3269 Beckman Institute or Zoom link

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