Cytoscape swMATH ID: 9080 Software Authors: Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T Description: Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. 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. Homepage: http://genome.cshlp.org/content/13/11/2498.short Related Software: KEGG; R; IntAct; Bioconductor; Gephi; BioGRID; MetaCyc; NetworkX; igraph; UniProt; STRING; TRANSFAC; DAVID; Pajek; MCODE; BiNGO; DrugBank; GeneMANIA; CFinder; ClueGO Cited in: 43 Publications all top 5 Cited by 132 Authors 2 Kelemen, Arpad G. 2 Li, Min 2 Liang, Yulan 1 Ambroise, Christophe 1 Anbarasu, Anand 1 Bacic, Antony 1 Bag, Susmita 1 Baths, Veeky 1 Chang, Chang 1 Chen, Xinren 1 Chitra, Uthsav 1 Cui, Yuehua 1 Curme, Chester 1 De Niz, Carlos 1 Delahaye-Duriez, Andrée 1 Delgado, Alberto Santos 1 Ding, Yanjun 1 Domico, Kelly 1 Dryden, Ian L. 1 Elloumi, Mourad 1 Elyanow, Rebecca 1 Fire, Michael 1 Galbraith, Sally 1 Golden, Bruce L. 1 Gollini, Isabella 1 Hashemi, Zahra Sadat 1 He, Dongxiao 1 Heath, Allison P. 1 Hinow, Peter 1 Hu, Guang 1 Huang, Chien-Hung 1 Indhumathy, M. 1 Jafarisani, Moslem 1 Jahangiri, Abolfazl 1 Jatana, Nidhi 1 Jin, Di 1 Kavraki, Lydia E. 1 Keith, Jonathan M. 1 Kelemen, Adam 1 Khalili, Saeed 1 Kinable, Joris 1 Kong, Yan 1 Latha, N. 1 Li, Gaoshi 1 Li, Hui 1 Li, Huijia 1 Li, Jianming 1 Li, Shaoyu 1 Li, Yaohang 1 Likić, Vladimir A. 1 Lithgow, Trevor 1 Liu, Chonghui 1 Liu, Chunmei 1 Liu, Dayou 1 Liu, Hsiang-Chuan 1 Liu, Hsueh-Chuan 1 Liu, Huaping 1 Lum, Oliver 1 Lv, Hongchao 1 Mahesh, K. B. 1 Martínez-Antonio, Agustino 1 Martinez de Aguiar, Marcus Aloizio 1 Mcconville, Malcolm J. 1 Michail, Dimitrios 1 Miele, Vincent 1 Moreira, Carolina A. 1 Murphy, Thomas Brendan 1 Nahálková, Jarmila 1 Naveh, Barak 1 Ng, Kalok 1 Olivera, Beatriz Carely Luna 1 Omar, Sara Ibrahim 1 Pal, Ranadip 1 Pan, Yi 1 Pardy, Christopher 1 Payandeh, Zahra 1 Peng, Wei 1 Picard, Franck 1 Pinter, Ron Yair 1 Podder, Avijit 1 Preston, Simon P. 1 Puzis, Rami 1 Rahbar, Mohammad Reza 1 Rahman, Raziur 1 Rajendra, Rangaswamy 1 Ramaiah, Sudha 1 Raphael, Benjamin J. 1 Rasaee, Mohammad Javad 1 Réda, Clémence 1 Reddy, P. Siva Kota 1 Ren, Xianwen 1 Reyna, Matthew A. 1 Rietman, Edward A. 1 Salter-Townshend, Michael 1 Severn, Katie E. 1 Shen, Bairong 1 Sichi, John V. 1 Singh, Tarkeshwar 1 Singhal, Mudita 1 Song, Wei ...and 32 more Authors all top 5 Cited in 23 Serials 9 Journal of Theoretical Biology 4 The Annals of Applied Statistics 2 New Journal of Physics 2 Statistical Applications in Genetics and Molecular Biology 2 Computational Biology and Chemistry 2 Journal of Statistical Mechanics: Theory and Experiment 2 Methods in Molecular Biology 1 Physica A 1 Bulletin of Mathematical Biology 1 ACM Transactions on Mathematical Software 1 Russian Journal of Mathematical Physics 1 INFORMS Journal on Computing 1 International Journal of Theoretical and Applied Finance 1 Journal of Systems Science and Complexity 1 Journal of Discrete Algorithms 1 Networks and Spatial Economics 1 Mathematical Biosciences and Engineering 1 Proyecciones 1 Computational & Mathematical Methods in Medicine 1 Statistical Analysis and Data Mining 1 Algorithms 1 1 Computer Science Review all top 5 Cited in 11 Fields 28 Biology and other natural sciences (92-XX) 10 Statistics (62-XX) 7 Computer science (68-XX) 6 Combinatorics (05-XX) 6 Game theory, economics, finance, and other social and behavioral sciences (91-XX) 3 Operations research, mathematical programming (90-XX) 2 General and overarching topics; collections (00-XX) 2 Statistical mechanics, structure of matter (82-XX) 1 Probability theory and stochastic processes (60-XX) 1 Numerical analysis (65-XX) 1 Information and communication theory, circuits (94-XX) Citations by Year