The logical (or logic) formalism is increasingly used to model regulatory and signaling
networks. Complementing these applications, several groups contributed various methods …

Computational models are increasingly used to analyze the operation of complex
biochemical networks, including those involved in cell signaling networks. Here we review …

Large‐scale protein signalling networks are useful for exploring complex biochemical
pathways but do not reveal how pathways respond to specific stimuli. Such specificity is …

Motivation: In silico modeling of gene regulatory networks has gained some momentum
recently due to increased interest in analyzing the dynamics of biological systems. This has …

Background The understanding of regulatory and signaling networks has long been a core
objective in Systems Biology. Knowledge about these networks is mainly of qualitative …

The lac operon in Escherichia coli has been studied extensively and is one of the earliest
gene systems found to undergo both positive and negative control. The lac operon is known …

This paper addresses the problem of finding attractors in synchronous Boolean networks.
The existing Boolean decision diagram-based algorithms have limited capacity due to the …

Abstract Gene Regulatory Networks (GRNs) represent the interactions among genes
regulating the activation of specific cell functionalities, such as reception of (chemical) …

Alternative cell differentiation pathways are believed to arise from the concerted action of
signalling pathways and transcriptional regulatory networks. However, the prediction of …

Motivation Molecular interaction maps have emerged as a meaningful way of representing
biological mechanisms in a comprehensive and systematic manner. However, their static …