Networks are one of the most common ways to represent biological systems as complex sets
of binary interactions or relations between different bioentities. In this article, we discuss the …

Cytoscape is open-source software for integration, visualization and analysis of biological
networks. It can be extended through Cytoscape plugins, enabling a broad community of …

The composition of the gut microbiome can control innate and adaptive immunity and has
emerged as a key regulator of tumor growth, especially in the context of immune checkpoint …

Protein networks have become a popular tool for analyzing and visualizing the often long
lists of proteins or genes obtained from proteomics and other high-throughput technologies …

Despite remarkable strides in microbiome research, the viral component of the microbiome
has generally presented a more challenging target than the bacteriome. This gap persists …

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by
unexplained debilitating fatigue, cognitive dysfunction, gastrointestinal disturbances, and …

To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma
(ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic …

A system-wide understanding of cellular function requires knowledge of all functional
interactions between the expressed proteins. The STRING database aims to collect and …

Transcriptional recording by CRISPR spacer acquisition from RNA endows engineered
Escherichia coli with synthetic memory, which through Record-seq reveals transcriptome …

Biological networks are often used to represent complex biological systems, which can
contain several types of entities. Analysis and visualization of such networks is supported by …