Jeffrey D. Varner

The paper develops a dynamic constraint-based model of E. coli cell-free protein synthesis to analyze metabolic flux and protein production with and without electron transport chain inhibitors.

This study develops and models a D-gluconate biosensor in a cell-free system, showing its dose response and kinetics across concentrations.

The paper develops a biophysical modeling approach to simulate transcription and translation in cell-free synthetic circuits, showing it captures expression dynamics for two tested circuits.

This study develops a dynamic model of E. coli cell-free protein synthesis, showing that oxidative phosphorylation, glycolysis, and amino acid biosynthesis are key for productivity.

This study uses metabolic modeling to design E. coli strains that overproduce glycan precursors for glycoprotein production.

This paper introduces DOPS, a hybrid meta-heuristic for parameter estimation in biochemical models, which outperforms existing methods on test functions and real-world models.

This paper uses sequence-specific constraint-based modeling to estimate the performance of E. coli cell-free protein synthesis systems using limited parameters.

The paper develops a reduced order mathematical model of the human complement system that is predictive and computationally efficient, showing that multiple therapeutic targets are needed to disrupt complement activation.

This study develops an effective model of ATRA-induced HL-60 differentiation, identifying key feedback mechanisms and critical genes involved in the process.

The paper develops a mathematical model of EMT regulation, identifies NFAT and phosphorylated Sp1 as master regulators, and shows that dual TGF-{beta} and VEGF-A exposure leads to phenotypic heterogeneity.