skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: 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.

Authors:
ORCiD logo [1];  [2];  [3];  [4];  [2]; ORCiD logo [2]
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Univ. of Thessaly, Thessaly (Greece)
  3. Dokuz Eylül Univ., Izmire (Turkey). Izmir International Biomedicine and Genome Inst. (iBG-Izmir)
  4. Univ. Paris Diderot, Paris (France)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1432564
Alternate Identifier(s):
OSTI ID: 1543958
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
GigaScience
Additional Journal Information:
Journal Volume: 7; Journal Issue: 4; Journal ID: ISSN 2047-217X
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
Life Sciences & Biomedicine - Other Topics; Science & Technology - Other Topics

Citation Formats

Pavlopoulos, Georgios A., Kontou, Panagiota I., Pavlopoulou, Athanasia, Bouyioukos, Costas, Markou, Evripides, and Bagos, Pantelis G. Bipartite graphs in systems biology and medicine: a survey of methods and applications. United States: N. p., 2018. Web. doi:10.1093/gigascience/giy014.
Pavlopoulos, Georgios A., Kontou, Panagiota I., Pavlopoulou, Athanasia, Bouyioukos, Costas, Markou, Evripides, & Bagos, Pantelis G. Bipartite graphs in systems biology and medicine: a survey of methods and applications. United States. doi:10.1093/gigascience/giy014.
Pavlopoulos, Georgios A., Kontou, Panagiota I., Pavlopoulou, Athanasia, Bouyioukos, Costas, Markou, Evripides, and Bagos, Pantelis G. Mon . "Bipartite graphs in systems biology and medicine: a survey of methods and applications". United States. doi:10.1093/gigascience/giy014.
@article{osti_1432564,
title = {Bipartite graphs in systems biology and medicine: a survey of methods and applications},
author = {Pavlopoulos, Georgios A. and Kontou, Panagiota I. and Pavlopoulou, Athanasia and Bouyioukos, Costas and Markou, Evripides and Bagos, Pantelis G.},
abstractNote = {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.},
doi = {10.1093/gigascience/giy014},
journal = {GigaScience},
number = 4,
volume = 7,
place = {United States},
year = {2018},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1093/gigascience/giy014

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

A novel genetic system to detect protein–protein interactions
journal, July 1989

  • Fields, Stanley; Song, Ok-kyu
  • Nature, Vol. 340, Issue 6230, p. 245-246
  • DOI: 10.1038/340245a0

mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
journal, March 2004