Bipartite graphs in systems biology and medicine: a survey of methods and applications

Abstract

The latest advances in high-throughput techniques during the past decade allowed the systems biology field to expand significantly. Today, the focus of biologists has shifted from the study of individual biological components to the study of complex biological systems and their dynamics at a larger scale. Through the discovery of novel bioentity relationships, researchers reveal new information about biological functions and processes. Graphs are widely used to represent bioentities such as proteins, genes, small molecules, ligands, and others such as nodes and their connections as edges within a network. In this review, special focus is given to the usability of bipartite graphs and their impact on the field of network biology and medicine. Furthermore, their topological properties and how these can be applied to certain biological case studies are discussed. Finally, available methodologies and software are presented, and useful insights on how bipartite graphs can shape the path toward the solution of challenging biological problems are provided.

Ophidiomycosis surveillance of snakes in Georgia, USA reveals new host species and taxonomic associations with disease

“…While this approach is extremely challenging in wild snakes, whose movements and interactions are difficult to track, bipartite networks can be used to examine connections between two sets of data, such as species and disease traits, and illuminate overall trends. These networks are defined by having two sets of nodes and no two nodes within the same set adjacent 30 . A bipartite network analysis conducted to look for associations with chytridiomycosis in frogs observed that skin sloughing rate varied with phylogenetic group, but there was no evidence that sloughing was associated with Bd-driven population declines 31 .…”

Bipartite Competency Schemas on Polish Labor Market

“…Species belonging to the "higher" group correspond always to columns, and species belonging to "lower" group always correspond to rows of the matrix. Using this convention, competencies are equivalent to species belonging to the "higher" group, and values of the set correspond to species from the "lower" group (Pavlopoulos et al, 2018).…”

NORMA-The network makeup artist: a web tool for network annotation visualization

“…proteins, genes, small molecules, metabolites, ligands, diseases, drugs) in order to unravel how complex systems operate. Despite the great variety of visualization tools to efficiently represent such networks [1][2][3][4][5][6] , visualization still remains a bottleneck as views often become incomprehensive due to the large number of nodes and edges. Therefore, ways to visually focus on the important parts of a network emerge.…”