David B. Bernstein

The paper integrates flux balance analysis with diffusion equations to simulate spatio-temporal microbial community metabolism, showing optimal interaction distances for metabolite production.

The paper evaluates the accuracy of E. coli genome-scale metabolic models using mutant fitness data and identifies improvements to enhance prediction accuracy.

This paper develops a Python tool for studying string chemistries and introduces a network-pruning algorithm to generate minimal metabolic networks.

The paper quantifies biosynthetic network robustness in the human oral microbiome using a probabilistic metric to identify metabolic interdependences and uncultivated taxa.