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During the "design phase", the GDLS strain design algorithm [ 9] was used to generate a set of knockout strains that coupled succinate production to biomass synthesis (see Methods).
The dataset consisted of the phenotypic outcomes from a set of knockout mutants of single genes and was used to define the classes "essential" and "non-essential" for our reactions.
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OptKnock was used to find a set of knockouts that led to coupling between biofuel and growth.
Otherwise, searching the huge number of possible knockout sets without target production makes finding a set of knockouts with non-zero target production extremely difficult.
Furthermore, all the aforementioned methods can be used to investigate how a set of knockouts is reflected on the flux distribution.
Measurements over a set of double knockout mutants are given in a sparse matrix G ∈ ℝ n × n and those of single knockout mutants in a vector S ∈ ℝ n.
To investigate the role of the gene products encoded from the open reading frames 101, 142, and 144 of Autographa californica multiple nucleopolyhedrovirus (AcMNPV), a set of bacmid knockout and repair constructs were generated.
In order to assess the relevance of the BL31 system to LCLs, we analysed the transcriptome of a set of EBNA3B knockout (3BKO) LCLs.
We also compared the compensatory performances of a set of invertase knockout mutants to the Columbia-4 wild type.
A second study measured gene expression in a set of four knockout human cell lines across ten laboratories using three different microarray platforms [ 18].
The goal of these authors was to infer the structure of the signaling network that best explains a set of gene knockout pairs, given a protein protein interaction network.
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