Zane R. Thornburg

Spatially Resolved Reaction-Diffusion Modeling Reveals Effects of Intracellular Spatial Heterogeneity on Yeast Galactose Network Dynamics

The paper develops spatially-resolved models of the yeast galactose switch to show how intracellular organization affects regulatory dynamics.

Full-length transcriptomics and proteomics reveal how genome minimization reshapes gene expression in synthetic bacteria

The paper characterizes RNA and protein expression in synthetic bacteria Syn1.0 and Syn3A, showing genome minimization alters gene expression and resource allocation.

Predicting Human mRNA Isoform Levels from Site-Specific Splicing Kinetics in silico

This paper develops a stochastic kinetic model of splicing to predict mRNA isoform levels from site-specific splicing kinetics and validates it under normoxia and hypoxia.

Bringing the Genetically Minimal Cell to Life on a Computer in 4D

A hybrid 4D whole-cell simulation of the minimal bacterium JCVI-syn3A integrates spatial reaction-diffusion, metabolism, polymer chromosome dynamics, and division across a complete 105-minute cell cycle.

Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell

The paper integrates the assembly of 21 macromolecular complexes into a whole-cell kinetic model of JCVI-syn3A, improving efficiency and consistency with experimental data.

COTree: A Statistical Framework for Deciphering Cell-Resolved Multi-Omics Trajectories

COTree is a statistical framework that analyzes multi-omic simulation trajectories to identify cellular progression patterns and key driver species in a whole-cell model.

Unraveling the Transcriptional Landscape within a Minimized Bacterium via Comparative Analysis

This study compares transcriptomes of two minimized bacteria to understand gene expression patterns and highlights limitations of bioinformatics alone.