Cytoscape: a software environment for integrated models of biomolecular interaction networks. Export

@article{citeulike:920055, 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.}, address = {Institute for Systems Biology, Seattle, Washington 98103, USA.}, 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}, citeulike-article-id = {920055}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.1239303}, citeulike-linkout-1 = {http://genome.cshlp.org/content/13/11/2498.full.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/13/11/2498.full.full.pdf}, citeulike-linkout-3 = {http://www.genome.org/cgi/content/abstract/13/11/2498}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/14597658}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=14597658}, doi = {10.1101/gr.1239303}, issn = {1088-9051}, journal = {Genome research}, keywords = {bioinformatics, book-chapter, cytoscape}, month = {November}, number = {11}, pages = {2498--2504}, posted-at = {2009-03-24 17:18:41}, priority = {2}, title = {Cytoscape: a software environment for integrated models of biomolecular interaction networks.}, url = {http://dx.doi.org/10.1101/gr.1239303}, volume = {13}, year = {2003} }

TY - JOUR ID - citeulike:920055 L3 - citeulike-article-id:920055 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. IS - 11 JF - Genome research SN - 1088-9051 AD - Institute for Systems Biology, Seattle, Washington 98103, USA. EP - 2504 TI - Cytoscape: a software environment for integrated models of biomolecular interaction networks. VL - 13 SP - 2498 KW - bioinformatics KW - book-chapter KW - cytoscape AU - Shannon, Paul AU - Markiel, Andrew AU - Ozier, Owen AU - Baliga, Nitin AU - Wang, Jonathan AU - Ramage, Daniel AU - Amin, Nada AU - Schwikowski, Benno AU - Ideker, Trey PY - 2003/11// UR - http://dx.doi.org/10.1101/gr.1239303 ER -