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

Creative Commons License

Pavlopoulos G. A., Kontou P. I., Pavlopoulou A., Bouyioukos C., Markou E., Bagos P. G.

GigaScience, cilt.7, sa.4, ss.1-31, 2018 (SCI-Expanded) identifier identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 7 Sayı: 4
  • Basım Tarihi: 2018
  • Doi Numarası: 10.1093/gigascience/giy014
  • Dergi Adı: GigaScience
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Sayfa Sayıları: ss.1-31
  • Anahtar Kelimeler: biological networks, graph theory, systems biology, bipartite graphs, ecological networks, network medicine, PROTEIN-PROTEIN INTERACTIONS, ANIMAL MUTUALISTIC NETWORKS, COMMUNITY STRUCTURE, LINK PREDICTION, INTERACTION MAP, DRAWING GRAPHS, SMALL WORLD, RNA-SEQ, VISUALIZATION, NESTEDNESS
  • Dokuz Eylül Üniversitesi Adresli: Evet

Özet

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.