93 citations · 95 across the 4 of their papers we have counts for
5 papers
Scalable computation of intracellular metabolite concentrations
Amir Akbari, Bernhard O. Palsson
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direc…
Estimating Cellular Goals from High-Dimensional Biological Data
Laurence Yang, Michael A. Saunders, Jean-Christophe Lachance +2
Optimization-based models have been used to predict cellular behavior for over 25 years. The constraints in these models are derived from genome annotations, measured macro-molecul…
Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0
Laurent Heirendt, Sylvain Arreckx, Thomas Pfau +52
COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physico…
Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
Ding Ma, Laurence Yang, Ronan M. T. Fleming +3
Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-s…
A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks
Ronan M. T. Fleming, Christopher M. Maes, Michael A. Saunders +2
We derive a convex optimization problem on a steady-state nonequilibrium network of biochemical reactions, with the property that energy conservation and the second law of thermody…