The paper has two goals:(1) It presents basic ideas, notions, and methods for reduction of
reaction kinetics models: quasi-steady-state, quasi-equilibrium, slow invariant manifolds …

In the plethora of conceptual and algorithmic developments supporting data analytics and
system modeling, humancentric pursuits assume a particular position owing to ways they …

Biological experiments have verified that EIciRNAs (a class of circRNA) produced from pre‐
mRNA can regulate gene expression, but the effect of regulation remains unexplored. Here …

Boolean networks are a mathematical model that has been widely used since decades in
the context of biological regulation networks' qualitative modelling. They consist in …

We extend the notion of compositional associative rewriting as recently studied in the rule
algebra framework literature to the setting of rewriting rules with conditions. Our …

We develop a novel method to analyze the dynamics of stochastic rewriting systems
evolving over finitary adhesive, extensive categories. Our formalism is based on the so …

Intrinsic noise, which arises in gene expression at low copy numbers, can be controlled by
diverse regulatory motifs, including feedforward loops. Here, we study an example of a …

This study addresses a problem of correspondence between dynamics of a parameterized
system and the structure of interactions within that system. The structure of interactions is …

This chapter presents the formalism of Boolean networks and their relation to classic models
from fundamental computer science, in particular with Petri nets with different update …

Cells use various regulatory motifs, including feedforward loops, to control the intrinsic noise
that arises in gene expression at low copy numbers. Here we study one such system, which …