Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …

Engineering cell metabolism for bioproduction not only consumes building blocks and
energy molecules (eg, ATP) but also triggers energetic inefficiency inside the cell. The …

Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic
framework for integrative analysis of experimental molecular systems biology data and …

For thousands of years, the yeast Saccharomyces cerevisiae (S. cerevisiae) has served as a
cell factory for the production of bread, beer, and wine. In more recent years, this yeast has …

Constraint-based reconstruction and analysis (COBRA) methods at the genome scale have
been under development since the first whole-genome sequences appeared in the mid …

The turnover number k cat, a measure of enzyme efficiency, is central to understanding
cellular physiology and resource allocation. As experimental k cat estimates are unavailable …

Growth is a fundamental process of life. Growth requirements are well‐characterized
experimentally for many microbes; however, we lack a unified model for cellular growth …

Genome-scale metabolic models (GEMs) enable the mathematical simulation of the
metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a …

Knowing the catalytic turnover numbers of enzymes is essential for understanding the
growth rate, proteome composition, and physiology of organisms, but experimental data on …

Metabolism is highly complex and involves thousands of different connected reactions; it is
therefore necessary to use mathematical models for holistic studies. The use of …