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Biclique: an R package for maximal biclique enumeration in bipartite graphs

Journal Article · · BMC Research Notes
 [1];  [2];  [2]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Univ. of Tennessee, Knoxville, TN (United States)
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Bipartite graphs are widely used to model relationships between pairs of heterogeneous data types. Maximal bicliques are foundational structures in such graphs, and their enumeration is an important task in systems biology, epidemiology and many other problem domains. Thus, there is a need for an efficient, general purpose, publicly available tool to enumerate maximal bicliques in bipartite graphs. The statistical programming language R is a logical choice for such a tool, but until now no R package has existed for this purpose. Our objective is to provide such a package, so that the research community can more easily perform this computationally demanding task. Biclique is an R package that takes as input a bipartite graph and produces a listing of all maximal bicliques in this graph. Input and output formats are straightforward, with examples provided both in this paper and in the package documentation. Biclique employs a state-of-the-art algorithm previously developed for basic research in functional genomics.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC); National Institutes of Health (NIH); USEPA
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1766481
Journal Information:
BMC Research Notes, Journal Name: BMC Research Notes Journal Issue: 1 Vol. 13; ISSN 1756-0500
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

References (12)

Bicliques in Graphs I: Bounds on Their Number journal January 2000
Ontological discovery environment: A system for integrating gene–phenotype associations journal December 2009
The maximum edge biclique problem is NP-complete journal September 2003
Discovering statistically significant biclusters in gene expression data journal July 2002
Obtaining Maximal Concatenated Phylogenetic Data Sets from Large Sequence Databases journal April 2003
A graph-theoretical approach for pattern discovery in epidemiological research journal January 2007
On finding bicliques in bipartite graphs: a novel algorithm and its application to the integration of diverse biological data types journal January 2014
The maximum edge biclique problem is NP-complete journal September 2003
Discovering statistically significant biclusters in gene expression data journal July 2002
A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data journal January 2007
KONECT: the Koblenz network collection conference January 2013
Clustering by pattern similarity in large data sets conference January 2002

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Related Subjects

97 MATHEMATICS AND COMPUTING
R package
biclique
bipartite graph
graph algorithms
maximality