ArticleFrontiers in microbiology2015
Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes.
Article in Frontiers in microbiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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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
23 citing papers in PubMed, 37 citations in OpenAlex.
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- The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies.Microbial genomics · 2024Article
- Virome release of an invasive exotic plant species in southern France.Virus evolution · 2024Article
- How Metagenomics Has Transformed Our Understanding of Bacteriophages in Microbiome Research.Microorganisms · 2022Review
- Metagenomic sequencing reveals time, host, and body compartment-specific viral dynamics after lung transplantation.Microbiome · 2022Article
- Isolation and characterization of two homolog phages infectingFrontiers in microbiology · 2022Article
- LABRADOR-A Computational Workflow for Virus Detection in High-Throughput Sequencing Data.Viruses · 2021Article
- Traces of SARS-CoV-2 RNA in Peripheral Blood Cells of Patients with COVID-19.Omics : a journal of integrative biology · 2021Article
- Mycobacteriophages as Potential Therapeutic Agents against Drug-Resistant Tuberculosis.International journal of molecular sciences · 2021Review
- Characterization of the Bacteriophage vB_VorS-PVo5 Infection onFrontiers in microbiology · 2020Article
- UPΦ phages, a new group of filamentous phages found in several members ofVirus evolution · 2020Article
- MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples.BMC genomics · 2019Article
- Minimum Information about an Uncultivated Virus Genome (MIUViG).Nature biotechnology · 2019Article
- Temperature, by Controlling Growth Rate, Regulates CRISPR-Cas Activity in Pseudomonas aeruginosa.mBio · 2018Article
- A fast and reliable method for monitoring of prophage-activating chemicals.Microbial biotechnology · 2018Article
- Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data.Nature protocols · 2017Article
- Insertion sequences enrichment in extreme Red sea brine pool vent.Extremophiles : life under extreme conditions · 2017Article
- Benchmarking viromics: anPeerJ · 2017Article
- Article
- Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments.Scientific reports · 2016Article
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 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. We propose adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.
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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.