4 papers
A Gene Ranking Framework Enhances the Design Efficiency of Genome-Scale Constraint-Based Metabolic Networks under Time Limits
Yier Ma, Takeyuki Tamura
The design of genome-scale constraint-based metabolic networks has steadily advanced, with an increasing number of successful cases achieving growth-coupled production, in which th…
GraphGDel: Constructing and Learning Graph Representations of Genome-Scale Metabolic Models for Growth-Coupled Gene Deletion Prediction
Ziwei Yang, Takeyuki Tamura
In genome-scale constraint-based metabolic models, gene deletion strategies are essential for achieving growth-coupled production, where cell growth and target metabolite synthesis…
DBgDel: Database-Enhanced Gene Deletion Framework for Growth-Coupled Production in Genome-Scale Metabolic Models
Ziwei Yang, Takeyuki Tamura
When simulating metabolite productions with genome-scale constraint-based metabolic models, gene deletion strategies are necessary to achieve growth-coupled production, which means…
RatGene: Gene deletion-addition algorithms using growth to production ratio for growth-coupled production in constraint-based metabolic networks
Yier Ma, Takeyuki Tamura
In computational metabolic design, it is often necessary to modify the original constraint-based metabolic networks to lead to growth-coupled production, where cell growth forces t…