4 papers
Rethinking the Choice Behavior of Sugar Metabolism in Bacteria
Jeffrey D. Varner
The paper reformulates bacterial sugar metabolism as an economic consumer choice problem, showing that cells allocate a limited proteome budget to enzymes via a linear program that…
Computational framework for multistep metabolic pathway design
Peter Zhiping Zhang, Jeffrey D. Varner
In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been…
ParetoEnsembles.jl: A Julia Package for Multiobjective Parameter Estimation Using Pareto Optimal Ensemble Techniques
Jeffrey D. Varner
Mathematical models of natural and man-made systems often have many adjustable parameters that must be estimated from multiple, potentially conflicting datasets. Rather than report…
BSTModelKit.jl: A Julia Package for Constructing, Solving, and Analyzing Biochemical Systems Theory Models
Sandra Vadhin, Jeffrey D. Varner
We present BSTModelKit.jl, an open-source Julia package for constructing, solving, and analyzing Biochemical Systems Theory (BST) models of biochemical networks. The package implem…