@article{Shannon01112003,
author = {Shannon, Paul and Markiel, Andrew and Ozier, Owen and Baliga, Nitin S. and Wang, Jonathan T. and Ramage, Daniel and Amin, Nada and Schwikowski, Benno and Ideker, Trey}, 
title = {Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks},
volume = {13}, 
number = {11}, 
pages = {2498-2504}, 
year = {2003}, 
doi = {10.1101/gr.1239303}, 
abstract ={Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.}, 
URL = {http://genome.cshlp.org/content/13/11/2498.abstract}, 
eprint = {http://genome.cshlp.org/content/13/11/2498.full.pdf+html}, 
journal = {Genome Research} 
}