ArticleNature methods2012
A travel guide to Cytoscape plugins.
Article in Nature methods, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 835 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
835 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Treatment of liver fibrosis in hepatolenticular degeneration with traditional Chinese medicine: systematic review of meta-analysis, network pharmacology and molecular dynamics simulation.Frontiers in medicine · 2023Pooled it
- Global Meta-analysis of Airborne Bacterial Communities and Associations with Anthropogenic Activities.Environmental science & technology · 2022Pooled it
- Identification of cancer-associated fibroblast biomarkers in cutaneous squamous cell carcinoma.Oncology letters · 2026Article
- Conserved signaling pathways and transcriptional regulators drive ovarian aging across species.Poultry science · 2026Article
- Biocontrol potential of endophytic fungal-derived 3-Hydroxy-1,2-dimethyl-4 (1H)-pyridone against Venturia inaequalis.Archives of microbiology · 2026Article
- Dynamic effects of radioactive iodine therapy on gut microbiota and metabolites in patients with papillary thyroid cancer.Microbiology spectrum · 2026Article
- A proteome-driven strategy to discover novel therapeutic targets in Orientia tsutsugamushi.Antonie van Leeuwenhoek · 2026Article
- Irisquinone exerts anti-osteosarcoma activity by regulating the PI3K/AKT signaling pathway.Scientific reports · 2026Article
- A diverse gut virome in natural populations of Drosophila melanogaster.Animal microbiome · 2026Article
- Curation of Mass Spectrometry Reference Data for Improved Identification and Dereplication of Cyanobacterial Specialized Metabolites.Journal of natural products · 2026Article
- Multi-tissue analysis identifies mitochondrial genes in chicken aging-induced productivity decline.Journal of animal science and biotechnology · 2026Article
- Article
- Additive and Partially Dominant Effects from Genomic Variation Contribute to Rice Heterosis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Unraveling the molecular landscape of clear cell renal cell carcinoma through integrative transcriptomic analysis and validation using clinical samples.Biochemistry and biophysics reports · 2026Article
- A Narrative Review on Integrative Bioinformatics Approaches for microRNA Research in Familial Mediterranean Fever: Current Insights and Future Directions.Health science reports · 2026Article
- Multi-omics mapping identifies CYBA-mediated mitochondrial dysfunction driving macrophage polarization and ferroptosis via Nrf2 pathway in atherosclerosis.APL bioengineering · 2026Article
- Naked cuticle is essential for Drosophila wing development beyond Wingless signaling.FEBS open bio · 2026Article
- Chondrogenic potential of mesenchymal progenitors from somatic and cartilage-derived iPSCs is predicted by their transcriptomic signatures.Genes & diseases · 2026Article
- Short Ileal Microvillus Length Phenotype Associates with Progression from Inflammatory to Complicated Disease Behavior in Pediatric Crohn's Disease.Inflammatory bowel diseases · 2026Article
- Experimental Validation of miR-4443, miR-572, and miR-150-5p in Serum and Tissue of Breast Cancer Patients as a Potential Diagnostic Biomarker: A Study Based on Bioinformatics Prediction.Biochemical genetics · 2026Article
775 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
9 authors.
Funding
Abstract
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.
Indexed as
Identifiers
What OpenQuestion holds
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.