Rapid progress in the development of next-generation sequencing (NGS) technologies in
recent years has provided many valuable insights into complex biological systems, ranging …

Boolean network models are one of the simplest models to study complex dynamic behavior
in biological systems. They can be applied to unravel the mechanisms regulating the …

Background Understanding the interaction among different species within a community and
their responses to environmental changes is a central goal in ecology. However, defining …

Despite considerable progress in genome-and proteome-based high-throughput screening
methods and in rational drug design, the increase in approved drugs in the past decade did …

Mathematical modeling of biological processes provides deep insights into complex cellular
systems. While quantitative and continuous models such as differential equations have been …

In order to understand the functioning of organisms on the molecular level, we need to know
which genes are expressed, when and where in the organism, and to which extent. The …

In recent years gene regulatory networks (GRNs) have attracted a lot of interest and many
methods have been introduced for their statistical inference from gene expression data …

Until recently, understanding the regulatory behavior of cells has been pursued through
independent analysis of the transcriptome or the proteome. Based on the central dogma, it …

▪ Abstract Systems biology studies biological systems by systematically perturbing them
(biologically, genetically, or chemically); monitoring the gene, protein, and informational …

Motivation: Our goal is to construct a model for genetic regulatory networks such that the
model class:(i) incorporates rule-based dependencies between genes;(ii) allows the …