ArticleF1000Research2016
CoNet app: inference of biological association networks using Cytoscape.
Article in F1000Research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 314 papers, 2 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.
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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.
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Who cites it
314 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Gut Bacteroides act in a microbial consortium to cause susceptibility to severe malaria.Nature communications · 2023Pooled it
- Meta-analysis of microbiome association networks reveal patterns of dysbiosis in diseased microbiomes.Scientific reports · 2022Pooled it
- Methanogenesis associated with altered microbial production of short-chain fatty acids and human-host metabolizable energy.The ISME journal · 2025Trial
- Stable Bacterial Cores and Patchy Eukaryotic Communities Shape the Summer Microbiomes of Patagonian Fjord Ecosystems Across Spatial, Functional and Temporal Gradients.Environmental microbiology reports · 2026Article
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- Gut Microbiota Signatures and Ecological Network Alterations Associated with Hemodialysis.Microorganisms · 2026Article
- Chronic Nitrogen Deposition Alters Diazotrophic Community Composition, Reduces Biological Nitrogen Fixation, and Restructures Fungal-Diazotroph CO-Occurrence Networks in Deadwood.Microbial ecology · 2026Article
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- Effects of an Isolate ofPlants (Basel, Switzerland) · 2026Article
- Molecular insights into avocado grafting: the role of chitinase-like genes.Plant physiology · 2026Article
- Municipal Solid Waste (MSW)-Compost Amendment Increases Diversity, Functional Activities, and Network Connectivity of a Vineyard Soil Microbiota.Microorganisms · 2026Article
- Evaluating microbial network inference methods: moving beyond synthetic data with reproducibility-driven benchmarks.BMC bioinformatics · 2026Article
- Host Species Mediate Distinct Seed Microbiome Responses to Restoration.Microbial ecology · 2026Article
- Host genotype and environmental factors differentially shape the black piranha's gill microbiota.Microbiology spectrum · 2026Article
- Metagenomic surveillance of tick-borne pathogens and microbiomes in Huntingdon County, Pennsylvania.One health (Amsterdam, Netherlands) · 2026Article
- Bacillus megaterium strain KGA3 increases saline-alkaline tolerance of maize by recruiting keystone taxa in rhizosphere soil.Scientific reports · 2026Article
- Comparative Analysis of the Intestinal Microbiota in Wild and Aquaculture Populations ofMicroorganisms · 2026Article
- Bacterial Community Structure and Environmental Adaptation in the Endorhizosphere and Rhizosphere Soils ofMicroorganisms · 2026Article
- Shipped and shifted: modeling collection-induced bias in microbiome multi-omics using a tractable fermentation system.NPJ biofilms and microbiomes · 2026Article
- Spatial organization of cutaneous microbiomes reveals putative microbial contributions to host chemical defenses in the American toad.Frontiers in microbiology · 2026Article
254 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
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here we present the Cytoscape app version of our association network inference tool CoNet. Though CoNet was developed with microbial community data from sequencing experiments in mind, it is designed to be generic and can detect associations in any data set where biological entities (such as genes, metabolites or species) have been observed repeatedly. The CoNet app supports Cytoscape 2.x and 3.x and offers a variety of network inference approaches, which can also be combined. Here we briefly describe its main features and illustrate its use on microbial count data obtained by 16S rDNA sequencing of arctic soil samples. The CoNet app is available at: http://apps.cytoscape.org/apps/conet.
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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.