Background Identifying perturbed pathways in a given condition is crucial in understanding
biological phenomena. In addition to identifying perturbed pathways individually, pathway …

Pathway analysis has become popular as a secondary analysis strategy for genome-wide
association studies (GWAS). Most of the current pathway analysis methods aggregate …

Pathway enrichment analysis is the most common approach for understanding which
biological processes are affected by altered gene activities under specific conditions …

Background In biological systems, pathways coordinate or interact with one another to
achieve a complex biological process. Studying how they influence each other is essential …

In human physiological conditions like complex diseases, a large number of genes/proteins,
as well as their interactions, are involved. Thus, detecting the biochemical pathways …

Background Pathways in biological system often cooperate with each other to function.
Changes of interactions among pathways tightly associate with alterations in the properties …

Background Pathway analysis combining multiple types of high-throughput data, such as
genomics and proteomics, has become the first choice to gain insights into the pathogenesis …

Integration of pathway and protein-protein interaction (PPI) data can provide more
information that could lead to new biological insights. PPIs are usually represented by a …

Motivation: Cells communicate with their environment via signal transduction pathways. On
occasion, the activation of one pathway can produce an effect downstream of another …

Recognition of indirect interactions is instrumental to in silico reconstruction of signaling
pathways and sheds light on the exploration of unknown physical paths between two …