William Poole

A Physics-based Model Reveals Mechanisms of Epigenetic Memory

This paper introduces a physics-based model explaining how cells maintain histone methylation patterns after division, validated by simulations and experimental data.

Metabolomics-informed coarse-grained model enables prediction of cell-free protein expression dynamics

The paper develops a coarse-grained model of cell-free protein synthesis using metabolomics data and Bayesian inference to predict expression dynamics across novel conditions.

Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline

The paper presents a pipeline for modeling and parameter identification in biological systems, applied to characterize integrase and excisionase activity in cell-free systems.

Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape

The paper introduces bioscrape, a Python package for fast and flexible simulation and parameter estimation of chemical reaction networks in synthetic biology.

BioCRNpyler: Compiling Chemical Reaction Networks from Biomolecular Parts in Diverse Contexts

BioCRNpyler compiles chemical reaction networks from modular biochemical parts, enabling rapid model development and exploration across diverse contexts.

Vivarium: an interface and engine for integrative multiscale modeling in computational biology

This paper introduces Vivarium, a software tool for building integrative multiscale models in computational biology, demonstrating its utility by combining multiple modeling frameworks.