ArticleBioinformatics (Oxford, England)2015
The Cyni framework for network inference in Cytoscape.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Longitudinal deep multi-omics profiling in a CLN3Communications medicine · 2026Article
- Global expression profiling of CD10 + /CD19 + pre-B lymphoblasts from Hispanic B-ALL patients correlates with comparative TARGET database analysis.Discover oncology · 2022Article
- Temporal transcriptome analysis of neuronal commitment reveals the preeminent role of the divergent lncRNA biotype and a critical candidate gene during differentiation.Cell death discovery · 2020Article
- Leveraging User-Friendly Network Approaches to Extract Knowledge From High-ThroughputFrontiers in genetics · 2019Review
- Alternative splicing complexity contributes to genetic improvement of drought resistance in the rice maintainer HuHan2B.Scientific reports · 2017Article
- Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa.Planta · 2017Article
- Inferring causal molecular networks: empirical assessment through a community-based effort.Nature methods · 2016Article
- Enabling network inference methods to handle missing data and outliers.BMC bioinformatics · 2015Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
motivationResearch on methods for the inference of networks from biological data is making significant advances, but the adoption of network inference in biomedical research practice is lagging behind. Here, we present Cyni, an open-source 'fill-in-the-algorithm' framework that provides common network inference functionality and user interface elements. Cyni allows the rapid transformation of Java-based network inference prototypes into apps of the popular open-source Cytoscape network analysis and visualization ecosystem. Merely placing the resulting app in the Cytoscape App Store makes the method accessible to a worldwide community of biomedical researchers by mouse click. In a case study, we illustrate the transformation of an ARACNE implementation into a Cytoscape app. AVAILABILITY AND IMPLEMENTATION: Cyni, its apps, user guides, documentation and sample code are available from the Cytoscape App Store http://apps.cytoscape.org/apps/cynitoolbox CONTACT: benno.schwikowski@pasteur.fr.
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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.