karthik-d / maxent-parameter-inference

Maximum Entropy (MaxEnt) parameter inference in biological networks.

Maximum Entropy Parameter Inference in Biological Networks

Quick links

• Project Summary Report [PDF].
• Analysis Code Notebook [Matlab LiveScript PDF].
• Synthetic Datasets [CSVs].

Overview

• Overarching Goal: Appoximate biological process networks - such as molecular signaling and protein inetractions - as Markov birth-death processes and infer their parameters using MaxEnt to quantitatively characterize and predict cell` population response heterogeneity.

  

• Analysis of Bistability in the Lactose Utilization Network of E.coli as a model network.

  

• Infer molecular abundance time-evolution trajectories using MaxEnt in the E.coli lactose utilization network.

  

Primary References

• Dixit, Purushottam D., et al. "Maximum entropy framework for predictive inference of cell population heterogeneity and responses in signaling networks." Cell systems 10.2 (2020): 204-212.
• Kim, Dae Wook, et al. "Systematic inference identifies a major source of heterogeneity in cell signaling dynamics: The rate-limiting step number." Science advances 8.11 (2022): eabl4598.