The advancements in “omics”(proteomics, genomics, lipidomics, and metabolomics)
technologies have yielded large inventories of genes, transcripts, proteins, and metabolites …

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 …

Dynamics of complex systems is often driven by large and intricate networks of microscopic
interactions, whose sheer size obfuscates understanding. With limited experimental data …

Rule-based modeling involves the representation of molecules as structured objects and
molecular interactions as rules for transforming the attributes of these objects. The approach …

Signalling pathway activation analysis is a powerful approach for extracting biologically
relevant features from large-scale transcriptomic and proteomic data. However, modern …

Modelers of molecular signaling networks must cope with the combinatorial explosion of
protein states generated by posttranslational modifications and complex formation. Rule …

Clinically used RAF inhibitors are ineffective in RAS mutant tumors because they enhance
homo-and heterodimerization of RAF kinases, leading to paradoxical activation of ERK …

We propose a new biomathematical method, OncoFinder, for both quantitative and
qualitative analysis of the intracellular signaling pathway activation (SPA). This method is …

Ordinary differential equations (ODEs) with polynomial derivatives are a fundamental tool for
understanding the dynamics of systems across many branches of science, but our ability to …

Abstract Models that capture the chemical kinetics of cellular regulatory networks can be
specified in terms of rules for biomolecular interactions. A rule defines a generalized …