The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
Open accessAbstract
Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)--in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics). Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools.
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Cites
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Edgar, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.207 · Cited by 13,288
A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011
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Self-citationThe UCSC Genome Browser database: 2014 update
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Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction
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Self-citationJSBML 1.0: providing a smorgasbord of options to encode systems biology models
Rodriguez, N., Thomas, A., Watanabe, L., Vazirabad, I. Y., Kofia, V., Gómez, H. F., Mittag, F., Matthes, J., Rudolph, J., Wrzodek, F., et al. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv341 · Cited by 37
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Cited by
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
King, Z. A., Lu, J., Dräger, A., Miller, P., Federowicz, S., Lerman, J. A., Ebrahim, A., Palsson, B. O., & Lewis, N. E. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1049 · Cited by 938
Self-citationArts, R. J. W., Novakovic, B., ter Horst, R., Carvalho, A., Bekkering, S., Lachmandas, E., Rodrigues, F., Silvestre, R., Cheng, S.-C., Wang, S.-Y., et al. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.10.008 · Cited by 930
Systems biology and multi-omics integration: viewpoints from the metabolomics research community
Pinu, F. R., Beale, D. J., Paten, A. M., Kouremenos, K., Swarup, S., Schirra, H. J., & Wishart, D. (2019) · Metabolites · doi:10.3390/metabo9040076 · Cited by 723
da Silveira, W. A., Fazelinia, H., Rosenthal, S. B., Laiakis, E. C., Kim, M. S., Meydan, C., Kidane, Y., Rathi, K. S., Smith, S. M., Stear, B., et al. (2020) · Cell · doi:10.1016/j.cell.2020.11.002 · Cited by 402
Essential metabolism for a minimal cell
Breuer, M., Earnest, E. E., Merryman, C., Wise, K. S., Sun, L., Lynott, M. R., Hutchison, C. A., Smith, H. O., Lapek, J. D., Gonzalez, D. J., et al. (2019) · eLife · doi:10.7554/elife.36842 · Cited by 190
“Overview of the metabolic reconstruction of JCVI-syn3A, drawn with Escher (King et al., 2015).”
Method
Metadata
- Authors
- King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O.
- Venue
- PLOS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2015-08-27
- Volume
- 11
- Issue
- 8
- Pages
- e1004321
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- OpenAlex
- W1665355332
- Cited by
- 385
- References
- 6
- FWCI
- 8.88
- Type
- journal article
- Language
- en
- Open access
- gold
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- King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1004321
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