GeNETop: Context-Specific Genome-Scale Constrained Models Using Network Topology, Flux Variability, and Transcriptomics

Abstract

Context-specific genome-scale metabolic models are critical tools for studying cellular metabolism under dynamic conditions. However, most existing methods for deriving these models are designed for steady-state settings and may fail to preserve reactions required for transient metabolic shifts, thereby limiting their compatibility with dynamic FBA. Here, we present GeNETop, a methodology for deriving context-specific GEMs designed to preserve dynamic compatibility. GeNETop integrates flux variability analysis (FVA), network topology metrics based on the Integrated Value of Influence (IVI), and transcriptomic data to identify reactions that are both flux-flexible and structurally influential. Reactions are prioritized based on variability and maximality indices, while topology and gene expression guide further refinement, reducing dependence on fixed expression thresholds. Using batch fermentation of Saccharomyces cerevisiae as a case study, we evaluate GeNETop against established methods for context-specific metabolic reconstruction. The resulting networks remain dynamically feasible across growth phases, capture key metabolic transitions, reduce non-essential reactions, and maintain computational tractability. Overall, GeNETop enables context-specific metabolic reconstructions that are compatible with dynamic simulations while maintaining computational efficiency. By overcoming key limitations of existing approaches, the method supports a more accurate representation of time-dependent metabolic processes in biotechnology and systems biology. Author summaryCellular metabolism relies on complex networks of reactions to process nutrients, generate energy, and build essential compounds for biomass. Context-specific metabolic models aim to represent only the reactions active under a given condition, improving biological realism and reducing computational complexity in flux balance analysis simulations. However, metabolic activity adapts dynamically to changing environmental conditions, and reactions that are inactive at one stage may become essential at another. Many current reconstruction methods are designed for steady-state conditions and may exclude reactions that are required during metabolic transitions, thereby limiting their ability to describe dynamic behavior. Here, we introduce GeNETop, a novel approach that refines context-specific networks by integrating multiple layers of information. GeNETop identifies the most relevant reactions by considering their flexibility, importance within the network topology, and gene activity levels. In this way, the method generates biologically meaningful models that focus on metabolic pathways relevant under dynamic conditions. We tested GeNETop on yeast fermentation, a key process in food and biofuel production. The resulting models capture metabolic changes over time and enable stable dynamic simulations, supporting improved flux balance analysis of time-dependent metabolic processes.