ArticleCurrent protocols in bioinformatics2014
Biological network exploration with Cytoscape 3.
Article in Current protocols in bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 579 papers, 1 of them a synthesis 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
579 citing papers in PubMed, 1 synthesis or guideline pooled it.
- MicroRNAs and Cellular Senescence in Melanoma: An Underexplored Link to Tumor Progression-A Systematic Review with Bioinformatics Analyses.International journal of molecular sciences · 2026Pooled it
- Progressive suppression of regulated cell death defines terminal macrophage states in liver cirrhosis.Annals of medicine · 2026Article
- Type III secretion system diversity in the Pseudomonas fluorescens species complex.The New phytologist · 2026Article
- Multi-Layer Transcriptome Analysis Uncovers Molecular Signatures of Coliform Mastitis in Lactating Cows.International journal of molecular sciences · 2026Article
- Hawaiian geothermal fumaroles contain diverse and novel viruses.Microbiology spectrum · 2026Article
- Spatiotemporal Metabolome and Single-Nucleus Transcriptome Integration Illuminates an Auxin Gradient Orchestrated by NtTAC1 Underlying Leaf Angle Regulation in Tobacco.Plant biotechnology journal · 2026Article
- Ethylene-responsive CmERF3-CmMYB4 cascade suppresses anthocyanin biosynthesis inHorticulture research · 2026Article
- Transcriptomic Insights into Developmental Toxicity of Per- and polyfluoroalkyl Substances (PFAS) inEnvironment & health (Washington, D.C.) · 2026Article
- Investigation of the Potential Neuroprotective Mechanisms ofInternational journal of molecular sciences · 2026Article
- MicroRNA-597 Suppresses Gastric Cancer Invasion and Progression viaInternational journal of molecular sciences · 2026Article
- Inducible CRISPRi enables efficient and high-fidelity genome editing in Streptomyces.Nucleic acids research · 2026Article
- A telomere-to-telomere genome assembly ofHorticulture research · 2026Article
- Multi-faceted characterization of the gut microbiome and metabolome in patients with primary Sjögren syndrome.Cell reports. Medicine · 2026Article
- Genome-Wide Identification and Characterization of theInternational journal of molecular sciences · 2026Article
- Dual-channel graph learning reveals similarity and complementarity in protein-protein interaction networks.PLoS computational biology · 2026Article
- Hawaiian Geothermal Fumaroles Contain Diverse and Novel Viruses.bioRxiv : the preprint server for biology · 2026Article
- Integrated network toxicology and immune profiling identify ESR1 as a potential hub linking Benzo[a]pyrene exposure to gastric cancer risk.Discover oncology · 2026Article
- Short-term effects of biochar amendment on root-microbe interactions in natural and peri-urban soils.Scientific reports · 2026Article
- Aging Reprograms the Signaling, Metabolic, and Gene Regulatory Dynamics in Murine Bone Marrow-Derived Mesenchymal Stem Cells.Applied sciences (Basel, Switzerland) · 2026Article
- Serum metabolic signatures of cognitive resilience in a longitudinal aging cohort.bioRxiv : the preprint server for biology · 2026Article
519 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
4 authors.
Funding
Abstract
Cytoscape is one of the most popular open-source software tools for the visual exploration of biomedical networks composed of protein, gene, and other types of interactions. It offers researchers a versatile and interactive visualization interface for exploring complex biological interconnections supported by diverse annotation and experimental data, thereby facilitating research tasks such as predicting gene function and constructing pathways. Cytoscape provides core functionality to load, visualize, search, filter, and save networks, and hundreds of Apps extend this functionality to address specific research needs. The latest generation of Cytoscape (version 3.0 and later) has substantial improvements in function, user interface, and performance relative to previous versions. This protocol aims to jump-start new users with specific protocols for basic Cytoscape functions, such as installing Cytoscape and Cytoscape Apps, loading data, visualizing and navigating the networks, visualizing network associated data (attributes), and identifying clusters. It also highlights new features that benefit experienced users.
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.