Abstract Bigraphs are graphs whose nodes may be nested, representing locality, independently of the edges connecting them. They may be equipped with reaction rules, forming a bigra...
Transcriptional regulation is a key mechanism that allows cells to make the appropriate amount of proteins at the right time. This is mediated by transcription factors that respond...
Clustered graph is a very useful model for drawing large and complex networks. This paper presents a new method for drawing clustered graphs in three dimensions. The method uses a ...
Background: Mathematical modeling is being applied to increasingly complex biological systems and datasets; however, the process of analyzing and calibrating against experimental ...
Kyoung Ae Kim, Sabrina L. Spencer, John G. Albeck,...
Constructing quantitative dynamic models of signaling pathways is an important task for computational systems biology. Pathway model construction is often an inherently incremental...