1 citations · 1 across the 5 of their papers we have counts for
5 papers
Decoding enzyme-substrate interaction topology reveals principles underlying catalytic efficiency and mutational outcomes
Weiren Zhao, Takeyuki Tamura
The enzyme turnover number (kcat) defines catalytic efficiency and constrains quantitative models of metabolism, yet the molecular determinants governing kcat and its response to m…
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…
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…
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…