An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems.

By Prit Pharkya, Costas D. Maranas. Metabolic Engineering, 2006

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OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities (2012, unknown): “Taking a step further, OptCom can be readily modified to identify the minimal number of direct interventions (i.e., knock-up/down/outs) to the community leading to the elevated production of a desired compound (e.g., by considering the overproduction of desired compound as the outer problem objectiv”
OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions (2010, methodology): “coli [22,38,39] and Saccharomyces cerevisiae [40] and bioelectricity in Geobacter sulfurreducens [41].”
Genome-scale models of bacterial metabolism: reconstruction and applications (2008, methodology): “A more systematic approach was introduced with the OptReg method, which identiﬁes at genome-scale the relative changes of ﬂux values with respect to the wild-type ﬂux distribution that provide the best production yield (Pharkya & Maranas, 2006).”
Computationally efficient flux variability analysis (2010, background): “Applications of FVA for molecular systems biology include, but are not limited to, the exploration of alternative optima of (1) [3], studying flux distributions under suboptimal growth [4], investigating network flexibility and network redundancy [5], optimization of process feed formulation for ant”