With the emergence of metabolic networks, novel mathematical pathway concepts were
introduced in the past decade, aiming to go beyond canonical maps. However, the use of …

Context: Computational modeling involves the use of computer simulations and models to
study and understand real-world phenomena. Its application is particularly relevant in the …

Algorithms for active module identification (AMI) are central to analysis of omics data. Such
algorithms receive a gene network and nodes' activity scores as input and report …

Toxic liver injury causes necrosis and fibrosis, which may lead to cirrhosis and liver failure.
Despite recent progress in understanding the mechanism of liver fibrosis, our knowledge of …

Background Over the last decade network enrichment analysis has become popular in
computational systems biology to elucidate aberrant network modules. Traditionally, these …

Motivation Analysis of differential expression of genes is often performed to understand how
the metabolic activity of an organism is impacted by a perturbation. However, because the …

De novo pathway enrichment is a systems biology approach in which OMICS data are
projected onto a molecular interaction network to identify subnetworks representing …

In silico approaches are increasingly considered to improve breast cancer treatment. One of
these treatments, neoadjuvant TFAC chemotherapy, is used in cases where application of …

State of the art high-throughput technologies allow comprehensive experimental studies of
organism metabolism and induce the need for a convenient presentation of large …

Algorithms for active module identification (AMI) are central to analysis of omics data. Such
algorithms receive a gene network and nodes' activity scores as input and report sub …