The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
A travel guide to Cytoscape plugins
Open accessAbstract
Cytoscape is open-source software for integration, visualization and analysis of biological networks. It can be extended through Cytoscape plugins, enabling a broad community of scientists to contribute useful features. This growth has occurred organically through the independent efforts of diverse authors, yielding a powerful but heterogeneous set of tools. We present a travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5–2.8. We also describe ongoing efforts to distribute, organize and maintain the quality of the collection.
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Cytoscape: A software Environment for integrated models of biomolecular interaction networks
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Self-citationGene Ontology: tool for the unification of biology
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Self-citationNetwork‐based classification of breast cancer metastasis
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Self-citationPathway Commons, a web resource for biological pathway data
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Self-citationHigh-throughput generation, optimization and analysis of genome-scale metabolic models
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The BioPAX community standard for pathway data sharing
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“Cytoscape imports interaction data in various generic tabular formats including CSV (comma-separated values), TSV (tab-separated values) and Excel, along with network-specific formats such as SIF (simple interaction file, originally developed for Cytoscape), XGMML (Extensible Graph Markup and Modeling Language), GML (…”
BackgroundSelf-citationWikiPathways: Pathway Editing for the People
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Self-citationThe Edinburgh human metabolic network reconstruction and its functional analysis
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Cited by
Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N. T., Roth, A., Bork, P., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw937 · Cited by 6,980
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations
Hornbeck, P. V., Zhang, B., Murray, B., Kornhauser, J. M., Latham, V., & Skrzypek, E. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1267 · Cited by 3,411
New genetic loci link adipose and insulin biology to body fat distribution
The ADIPOGen Consortium, Shungin, D., The CARDIOGRAMplusC4D Consortium, The CKDGen Consortium, The GEFOS Consortium, The GENIE Consortium, The, G. L. G. C., The, I. C. B. P., The International Endogene Consortium, Study, T. L. C., et al. (2015) · Nature · doi:10.1038/nature14132 · Cited by 1,580
FunRich: An open access standalone functional enrichment and interaction network analysis tool
Pathan, M., Keerthikumar, S., Ang, C., Gangoda, L., Quek, C. Y. J., Williamson, N. A., Mouradov, D., Sieber, O. M., Simpson, R. J., Salim, A., et al. (2015) · PROTEOMICS · doi:10.1002/pmic.201400515 · Cited by 1,316
Probiotics, gut microbiota, and their influence on host health and disease
Sánchez, B., Delgado, S., Blanco‐Míguez, A., Lourenço, A., Gueimonde, M., & Margolles, A. (2017) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201600240 · Cited by 1,104
Metadata
- Authors
- Saito, R., Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P.-L., Lotia, S., Pico, A. R., Bader, G. D., & Ideker, T.
- Venue
- Nature Methods
- Published
- 2012-11
- Volume
- 9
- Issue
- 11
- Pages
- 1069-1076
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2000860171
- Cited by
- 1,500
- References
- 12
- FWCI
- 47.75
- Type
- journal article
- Language
- en
- Open access
- green
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