ArticleThe ISME journal2017
iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure.
Article in The ISME journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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
63 citing papers in PubMed, 117 citations in OpenAlex.
- Trial
- Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient.Nature communications · 2025Article
- Node role of wild boars in virus circulation among wildlife and domestic animals.Nature communications · 2025Article
- Co-Occurrence of Toxic Bloom-Forming CyanobacteriaToxins · 2025Article
- A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics.Nature microbiology · 2025Article
- Temporal dynamics of microbial transcription in wetted hyperarid desert soils.FEMS microbiology ecology · 2024Article
- Review
- MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets.ISME communications · 2023Article
- VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models.PLoS computational biology · 2023Article
- Depth-driven patterns in lytic viral diversity, auxiliary metabolic gene content, and productivity in offshore oligotrophic waters.Frontiers in microbiology · 2023Article
- Characterization of the human gut virome in metabolic and autoimmune diseases.Inflammation and regeneration · 2022Review
- Individuality and ethnicity eclipse a short-term dietary intervention in shaping microbiomes and viromes.PLoS biology · 2022Article
- Life and death in the soil microbiome: how ecological processes influence biogeochemistry.Nature reviews. Microbiology · 2022Review
- A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens.iScience · 2022Review
- Microbial metabolites in the marine carbon cycle.Nature microbiology · 2022Review
- Freshwater macrophytes harbor viruses representing all five major phyla of the RNA viral kingdomPeerJ · 2022Article
- iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology.ISME communications · 2021Review
- High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome.Scientific reports · 2021Article
- Spatial and Temporal Dynamics of Prokaryotic and Viral Community Assemblages in a Lotic System (Manatee Springs, Florida).Applied and environmental microbiology · 2021Article
- Revisiting the rules of life for viruses of microorganisms.Nature reviews. Microbiology · 2021Review
3 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
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbes affect nutrient and energy transformations throughout the world's ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as 'Apps') for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.
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.