TY  - JOUR
A1  - Shannon, Paul
A1  - Markiel, Andrew
A1  - Ozier, Owen
A1  - Baliga, Nitin S.
A1  - Wang, Jonathan T.
A1  - Ramage, Daniel
A1  - Amin, Nada
A1  - Schwikowski, Benno
A1  - Ideker, Trey
T1  - Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Y1  - 2003/11/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 2498 
EP  - 2504 
DO  - 10.1101/gr.1239303 
VL  - 13 
IS  - 11 
UR  - http://genome.cshlp.org/content/13/11/2498.abstract 
N2  - 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. 
ER  -