Reductionist science produces causal models of small fragments of complicated systems.
Causal models of entire systems can be hard to construct because what is known of them is …

In this paper, we present DiSH, a simulator for large discrete models of biological signal
transduction pathways, capable of simulating networks with multi-valued elements in both …

Wound healing is a well-coordinated concerted event in response to injury and its
microenvironment, which aims at reinstating normal tissue homeostasis. Being a well …

Systems Biology pose computational challenges that surpass the capabilities of current
computing platforms. A particular challenge in this regard is simulating the dynamics of …

A reaction system is a modeling framework for investigating the functioning of the living cell,
focused on capturing cause–effect relationships in biochemical environments. Biochemical …

In medical research it is of great importance to be able to quickly obtain answers to inquiries
about system response to different stimuli. Modeling the dynamics of biological regulatory …

Recent work has presented logical models and showed the benefits of applying logical
approaches to studying the dynamics of biological networks. In this work, we develop a …

We describe our approach to modeling timing of cell signaling systems in which existing
information about the system spans from detailed mechanistic knowledge to much coarser …

Boolean models are a powerful abstraction for qualitative modeling of gene regulatory
networks. With the recent availability of advanced high-throughput technologies, Boolean …

In Systems Biology, Boolean models are gaining popularity in modeling and analysis of
qualitative dynamics of gene regulatory mechanisms. With the development of advanced …