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 …

The biomolecules inside or near cells form a complex interacting system. Cellular
phenotypes and behaviors arise from the totality of interactions among the components of …

Highly complex molecular networks, which play fundamental roles in almost all cellular
processes, are known to be dysregulated in a number of diseases, most notably in cancer …

A central goal of systems biology is the construction of predictive models of bio-molecular
networks. Cellular networks of moderate size have been modeled successfully in a …

Despite the current wealth of high-throughput data, our understanding of signal transduction
is still incomplete. Mathematical modeling can be a tool to gain an insight into such …

Background A central goal of Systems Biology is to model and analyze biological signaling
pathways that interact with one another to form complex networks. Here we introduce …

Motivation: Logic modeling is a useful tool to study signal transduction across multiple
pathways. Logic models can be generated by training a network containing the prior …

Rule‐based modeling was developed to address the limitations of traditional approaches for
modeling chemical kinetics in cell signaling systems. These systems consist of multiple …

Understanding of the logic and dynamics of gene-regulatory and biochemical networks is a
major challenge of systems biology. To facilitate this research topic, we have developed a …