Sentence examples for based on gene essentiality from inspiring English sources

Constraint-based model improvement and gap-filling based on gene essentiality predictions derived from the work of Baba et al. have been examined for the COBRA family of constraint-based models of E. coli metabolism by Reed et al.[ 140], Kumar et al.[ 141], Kumar and Maranas [ 142], Barua et al.[ 143], Orth and Palsson [ 73, 144], and Tervo and Reed [ 145].

Based on gene essentiality analysis, the genome-scale metabolic model of B. cenocepacia was further refined.

In few instances, they considered some druggability prediction (including in some cases structural aspects), a role in dormancy based on gene expression data, essentiality and off-target criteria to avoid potential unwanted side effects.

For example, physical interaction studies in yeast have allowed comparison of connectivity to gene essentiality based on gene deletion.

Unfortunately, the knowledge on gene essentiality in other high animals is still very limited.

Information on gene essentiality (lethal phenotypes upon single gene-KO or KD) was taken from publications [ 25, 35, 36, 40- 46].

Information on gene essentiality from a transposon site hybridisation (TraSH) mutagenesis study for Mtb [ 23] has also been incorporated in the decision criteria.

Data on gene essentiality were downloaded from the SHIGEN Profiling of E. coli Chromosome database (Hashimoto et al. 2005; Kato and Hashimoto 2007).

Among these models, the simplest one is prediction of essential genes based on the known essentiality of homologous genes [ 18- 21].

We developed a systematic set of procedures to optimally modify an existing metabolic network based on discrepancies in gene essentiality between computational predictions and experimental data.

In the original iNJ661 network, 16 vitamins and cofactors were included as part of the biomass based on in vitro gene essentiality data but without any experimental verification [ 15], suggesting that these metabolites might not be part of the biomass when M. tuberculosis grows in a different nutritional environment.