ArticlePLoS computational biology2015
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 193 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
193 citing papers in PubMed.
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- Causal AI digital twin for bioprocess bottleneck diagnosis via metabolic flexibility and rigidification maps.iScience · 2026Article
- Early EGFR Inhibition Triggers Actionable Tumor and Microenvironmental Remodeling in Lung Cancer.Cancer research communications · 2026Article
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- NAViFluX: a visualization‑centric platform for interactive analysis, refinement and design of genome‑scale metabolic networks.Bioinformatics (Oxford, England) · 2026Article
- Metabolic reconstruction reveals ATP salvage as a key response to trimethoprim treatment.iScience · 2026Article
- Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages.bioRxiv : the preprint server for biology · 2026Article
- Aryl hydrocarbon receptor in the kidney regulates metabolic cross-talk with the liver and gut microbiome.Scientific reports · 2026Article
- The loss of peroxiredoxin 2 in mice disrupts the biochemical aging phenotype in erythrocytes.iScience · 2026Article
- COBRAxy: constraint-based metabolic modeling in Galaxy.Bioinformatics (Oxford, England) · 2026Article
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- Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models.mSystems · 2026Article
- Drug-tolerant persister cells reallocate carbon sources to fuel antioxidant metabolism for survival.bioRxiv : the preprint server for biology · 2026Article
- Fermentative growth decreases the iron demand of Staphylococcus aureus.Journal of inorganic biochemistry · 2026Article
- Python-Based Interactive Notebooks for Teaching AI and Data Science to Undergraduate Students in the Life Sciences.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Dynamic Constrained Allocation Flux Balance Analysis (dCAFBA).Methods in molecular biology (Clifton, N.J.) · 2026Article
133 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.