Background Mathematical modelling of cellular networks is an integral part of Systems
Biology and requires appropriate software tools. An important class of methods in Systems …

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

Clinical responses to anticancer therapies are often restricted to a subset of patients. In some
cases, mutated cancer genes are potent biomarkers for responses to targeted agents. Here…

Systematic studies of cancer genomes have provided unprecedented insights into the
molecular nature of cancer. Using this information to guide the development and application of …

The growing availability of single-cell data, especially transcriptomics, has sparked an
increased interest in the inference of cell-cell communication. Many computational tools were …

Background Structural analysis of cellular interaction networks contributes to a deeper
understanding of network-wide interdependencies, causal relationships, and basic functional …

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 critical for …

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

In Rspondin-based 3D cultures, Lgr5 stem cells from multiple organs form ever-expanding
epithelial organoids that retain their tissue identity. We report the establishment of tumor …

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 nature…