Extending combinatorial regulatory network modeling to include activity control and decay modulation

TL;DR

This paper extends the DSGRN network modeling platform to incorporate activity control and decay modulation, enabling more accurate and versatile analysis of complex biological and signed directed networks.

Contribution

The authors introduce new types of network edges in DSGRN that model activity level and decay rate control, broadening its applicability beyond traditional abundance rate control.

Findings

Extended DSGRN to include activity and decay control edges

Applicable to diverse signed directed networks

Provides more accurate network dynamics summaries

Abstract

Understanding how the structure of within-system interactions affects the dynamics of the system is important in many areas of science. We extend a network dynamics modeling platform DSGRN, which combinatorializes both dynamics and parameter space to construct finite but accurate summaries of network dynamics, to new types of interactions. While the standard DSGRN assumes that each network edge controls the rate of abundance of the target node, the new edges may control either activity level or a decay rate of its target. While motivated by processes of post-transcriptional modification and ubiquitination in systems biology, our extension is applicable to the dynamics of any signed directed network.