ArticleNature protocols2012
Topological analysis and interactive visualization of biological networks and protein structures.
Article in Nature protocols, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 238 papers, 3 of them syntheses that pooled it.
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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.
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
238 citing papers in PubMed, 3 syntheses or guidelines pooled it.
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- Exploring proteins and protein-ligand complexes through residue interaction networks.Nature protocols · 2026Review
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- Host Species Mediate Distinct Seed Microbiome Responses to Restoration.Microbial ecology · 2026Article
- Exploring the mechanism of Dieda Qili Tablet on fracture healing based on network pharmacology combined with machine learning models.Scientific reports · 2026Article
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- Metabolic profiles of squamous cell lung carcinoma and diagnostic model construction.Scientific reports · 2025Article
- Decoding the relationship between oxidative stress and antiseizure medications using network pharmacology and molecular docking.Scientific reports · 2025Article
- A systems approach for elucidating the role of the microbiome in epigenetic cellular memory.mSystems · 2025Review
- QMRInternational journal of molecular sciences · 2025Article
- Elucidating PTEN conformational dynamics and phosphatase regulation via integrative modeling and mutation prediction.Structure (London, England : 1993) · 2025Article
- Generalists and keystone species drive rhizosphere microbial diversity and stability in feral Brassica napus.Scientific reports · 2025Article
- Blooming resilience: transcriptomic insights into cotton flower responses to boll weevil infestation.Plant cell reports · 2025Article
- Temporal dynamics and tissue-specific variations of the blueberry phyllosphere mycobiome.Horticulture research · 2025Article
178 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
No grant is acknowledged in the PubMed record.
Abstract
Computational analysis and interactive visualization of biological networks and protein structures are common tasks for gaining insight into biological processes. This protocol describes three workflows based on the NetworkAnalyzer and RINalyzer plug-ins for Cytoscape, a popular software platform for networks. NetworkAnalyzer has become a standard Cytoscape tool for comprehensive network topology analysis. In addition, RINalyzer provides methods for exploring residue interaction networks derived from protein structures. The first workflow uses NetworkAnalyzer to perform a topological analysis of biological networks. The second workflow applies RINalyzer to study protein structure and function and to compute network centrality measures. The third workflow combines NetworkAnalyzer and RINalyzer to compare residue networks. The full protocol can be completed in ∼2 h.
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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.