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IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1007/s00705-018-3723-zopenalex-snapshot
Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee
inferredcites →https://doi.org/10.1007/s00705-020-04577-8openalex-snapshot
Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee
inferredcites →https://doi.org/10.1016/j.cell.2019.03.040openalex-snapshot
Marine DNA Viral Macro- and Microdiversity from Pole to Pole
inferredcites →https://doi.org/10.1016/j.chom.2019.01.017openalex-snapshot
Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome
inferredcites →https://doi.org/10.1016/j.chom.2019.08.019openalex-snapshot
A Phage Protein Aids Bacterial Symbionts in Eukaryote Immune Evasion
inferredcites →https://doi.org/10.1016/j.chom.2020.08.003openalex-snapshot
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut
inferredcites →https://doi.org/10.1021/acs.est.7b04203openalex-snapshot
Diversity of DNA and RNA Viruses in Indoor Air As Assessed via Metagenomic Sequencing
inferredcites →https://doi.org/10.1038/ismej.2015.48openalex-snapshot
Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton
inferredcites →https://doi.org/10.1038/ismej.2016.89openalex-snapshot
iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure
inferredcites →https://doi.org/10.1038/ismej.2017.126openalex-snapshot
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
inferredcites →https://doi.org/10.1038/nbt.4163openalex-snapshot
KBase: The United States Department of Energy Systems Biology Knowledgebase
inferredcites →https://doi.org/10.1038/nbt.4306openalex-snapshot
Minimum Information about an Uncultivated Virus Genome (MIUViG)
inferredcites →https://doi.org/10.1038/ncomms5498openalex-snapshot
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
inferredcites →https://doi.org/10.1038/nprot.2017.063openalex-snapshot
Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data
inferredcites →https://doi.org/10.1038/nrmicro.2016.177openalex-snapshot
Virus taxonomy in the age of metagenomics
inferredcites →https://doi.org/10.1038/nrmicro1750openalex-snapshot
Marine viruses — major players in the global ecosystem
inferredcites →https://doi.org/10.1038/nrmicro3404openalex-snapshot
Rising to the challenge: accelerated pace of discovery transforms marine virology
inferredcites →https://doi.org/10.1038/s41396-019-0450-8openalex-snapshot
Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches
inferredcites →https://doi.org/10.1038/s41396-020-0705-4openalex-snapshot
Insights into the dynamics between viruses and their hosts in a hot spring microbial mat
inferredcites →https://doi.org/10.1038/s41564-018-0166-yopenalex-snapshot
Phage puppet masters of the marine microbial realm
inferredcites →https://doi.org/10.1038/s41564-019-0510-xopenalex-snapshot
Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes
inferredcites →https://doi.org/10.1038/s41564-019-0612-5openalex-snapshot
A jumbo phage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity
inferredcites →https://doi.org/10.1038/s41586-020-1957-xopenalex-snapshot
Giant virus diversity and host interactions through global metagenomics
inferredcites →https://doi.org/10.1038/s41587-020-00774-7openalex-snapshot
CheckV assesses the quality and completeness of metagenome-assembled viral genomes
inferredcites →https://doi.org/10.1038/s41587-020-0718-6openalex-snapshot
A genomic catalog of Earth’s microbiomes
inferredcites →https://doi.org/10.1093/bioinformatics/btaa490openalex-snapshot
Metaviral SPAdes : assembly of viruses from metagenomic data
inferredcites →https://doi.org/10.1093/bioinformatics/btab222openalex-snapshot
SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts
inferredcites →https://doi.org/10.1093/femsre/fuv048openalex-snapshot
Computational approaches to predict bacteriophage–host relationships
inferredcites →https://doi.org/10.1093/nar/gkv1189openalex-snapshot
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
inferredcites →https://doi.org/10.1093/nar/gkw1030openalex-snapshot
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses
inferredcites →https://doi.org/10.1093/nar/gkx1124openalex-snapshot
MVP: a microbe–phage interaction database
inferredcites →https://doi.org/10.1093/nar/gky1127openalex-snapshot
IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes
inferredcites →https://doi.org/10.1093/nar/gky901openalex-snapshot
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
inferredcites →https://doi.org/10.1093/nar/gky977openalex-snapshot
Genomes OnLine database (GOLD) v.7: updates and new features
inferredcites →https://doi.org/10.1093/nar/gky995openalex-snapshot
The Pfam protein families database in 2019
inferredcites →https://doi.org/10.1093/nargab/lqaa044openalex-snapshot
A network-based integrated framework for predicting virus–prokaryote interactions
inferredcites →https://doi.org/10.1101/2020.05.06.081778openalex-snapshot
CheckV: assessing the quality of metagenome-assembled viral genomes
inferredcites →https://doi.org/10.1111/j.1462-2920.2010.02270.xopenalex-snapshot
A call for standardized classification of metagenome projects
inferredcites →https://doi.org/10.1128/aem.00992-19openalex-snapshot
Potential Interactions between Clade SUP05 Sulfur-Oxidizing Bacteria and Phages in Hydrothermal Vent Sponges
inferredcites →https://doi.org/10.1128/jvi.01340-15openalex-snapshot
Dark Matter of the Biosphere: the Amazing World of Bacteriophage Diversity
inferredcites →https://doi.org/10.1128/jvi.03289-14openalex-snapshot
Viromes, Not Gene Markers, for Studying Double-Stranded DNA Virus Communities
inferredcites →https://doi.org/10.1128/mmbr.00061-19openalex-snapshot
Global Organization and Proposed Megataxonomy of the Virus World
inferredcites →https://doi.org/10.1128/mmbr.68.3.560-602.2004openalex-snapshot
Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion
inferredcites →https://doi.org/10.1146/annurev-micro-092412-155633openalex-snapshot
The Wonderful World of Archaeal Viruses
inferredcites →https://doi.org/10.1146/annurev-virology-092818-015851openalex-snapshot
Expanding the RNA Virosphere by Unbiased Metagenomics
inferredcites →https://doi.org/10.1146/annurev-virology-101416-041639openalex-snapshot
Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/s40168-017-0283-5openalex-snapshot
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
inferredcites →https://doi.org/10.1186/s40168-018-0452-1openalex-snapshot
Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes
inferredcites →https://doi.org/10.1186/s40168-019-0768-5openalex-snapshot
Diversity, evolution, and classification of virophages uncovered through global metagenomics
inferredcites →https://doi.org/10.1371/journal.pcbi.1002195openalex-snapshot
Accelerated Profile HMM Searches
inferredcites →https://doi.org/10.1371/journal.pone.0234636openalex-snapshot
Genomic diversity of bacteriophages infecting Microbacterium spp
inferredcites →https://doi.org/10.3389/fmicb.2017.00005openalex-snapshot
Identification and Antifungal Susceptibility Profiles of Candida nivariensis and Candida bracarensis in a Multi-Center Chinese Collection of Yeasts
inferredcites →https://doi.org/10.3389/fmicb.2017.01710openalex-snapshot
Editorial: Virus Discovery by Metagenomics: The (Im)possibilities
inferredcites →https://doi.org/10.3389/fmicb.2019.00806openalex-snapshot
The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes
inferredcites →https://doi.org/10.3389/fmicb.2019.01951openalex-snapshot
Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea
inferredcites →https://doi.org/10.3390/genes10030194openalex-snapshot
Halobacterium salinarum virus ChaoS9, a Novel Halovirus Related to PhiH1 and PhiCh1
inferredcites →https://doi.org/10.7554/elife.03125openalex-snapshot
Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics
inferredcites →https://doi.org/10.7554/elife.08490openalex-snapshot
Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
inferredcites →https://doi.org/10.7717/peerj.6800openalex-snapshot
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands
inferredcites →https://doi.org/10.7717/peerj.985openalex-snapshot
VirSorter: mining viral signal from microbial genomic data
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.2139/ssrn.4047248openalex-extracted
A Five-Fold Expansion of the Global RNA Virome Reveals Multiple New Clades of RNA Bacteriophages
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Oligonucleotide‐Linked Lipid Nanoparticles as a Versatile mRNA Nanovaccine Platform
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Long‐Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage‐Encoded Methyltransferases
inferred← citeshttps://doi.org/10.1002/advs.202516916openalex-snapshot
Alternating High‐Fat and Polysaccharide Diets Modulates Gut Phage‐Bacterial Interplay
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Diversity, transfer potential, and transcriptional activity of virus‐carried antibiotic resistance genes in global estuaries
inferred← citeshttps://doi.org/10.1002/imt2.118openalex-snapshot
ViWrap: A modular pipeline to identify, bin, classify, and predict viral–host relationships for viruses from metagenomes
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MicroEXPERT: Microbiome profiling platform with cross‐study metagenome‐wide association analysis functionality
inferred← citeshttps://doi.org/10.1002/imt2.188openalex-snapshot
A panoramic view of the virosphere in three wastewater treatment plants by integrating viral‐like particle‐concentrated and traditional non‐concentrated metagenomic approaches
inferred← citeshttps://doi.org/10.1002/imt2.59openalex-snapshot
Over two decades of research on the marine RNA virosphere
inferred← citeshttps://doi.org/10.1002/mlf2.12088openalex-snapshot
Sequence‐discrete species for prokaryotes and other microbes: A historical perspective and pending issues
inferred← citeshttps://doi.org/10.1002/prot.26569openalex-snapshot
Prediction of protein assemblies by structure sampling followed by interface‐focused scoring
inferred← citeshttps://doi.org/10.1007/978-1-0716-3072-3_17openalex-snapshot
Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data
inferred← citeshttps://doi.org/10.1007/s00248-022-02167-6openalex-snapshot
Significant Differences in Planktonic Virus Communities Between “Cellular Fraction” (0.22 ~ 3.0 µm) and “Viral Fraction” (< 0.22 μm) in the Ocean
inferred← citeshttps://doi.org/10.1007/s00705-022-05498-4openalex-snapshot
Genomic analysis of a novel active prophage of Hafnia paralvei
inferred← citeshttps://doi.org/10.1007/s10123-023-00476-5openalex-snapshot
Genome analysis of vB_SupP_AX, a novel N4-like phage infecting Sulfitobacter
inferred← citeshttps://doi.org/10.1007/s11104-026-08395-wopenalex-snapshot
Linking soil organic carbon and viral communities in alpine grasslands
inferred← citeshttps://doi.org/10.1007/s11783-026-2217-6openalex-snapshot
Antibiotic resistance genes in food wastes: diversity, dynamics, and interactions with prokaryotes and viruses in centralized biogas plants
inferred← citeshttps://doi.org/10.1007/s42995-022-00160-zopenalex-snapshot
Genomic diversity and ecological distribution of marine Pseudoalteromonas phages
inferred← citeshttps://doi.org/10.1007/s44370-025-00015-yopenalex-snapshot
Understanding the roles of viruses as key players in environmental dynamics and ecosystem functioning
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Virus-prokaryote interactions assist pollutant removal in constructed wetlands
inferred← citeshttps://doi.org/10.1016/j.cell.2022.08.023openalex-snapshot
Expansion of the global RNA virome reveals diverse clades of bacteriophages
inferred← citeshttps://doi.org/10.1016/j.cell.2024.12.035openalex-snapshot
Structure-guided discovery of viral proteins that inhibit host immunity
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Arbitrium phages can manipulate each other’s lysis/lysogeny decisions
inferred← citeshttps://doi.org/10.1016/j.celrep.2021.110204openalex-snapshot
Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts
inferred← citeshttps://doi.org/10.1016/j.celrep.2022.110984openalex-snapshot
Thousands of small, novel genes predicted in global phage genomes
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Biological warfare between two bacterial viruses in a defense archipelago sheds light on the spread of CRISPR-Cas systems
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Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential
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Large-scale phage cultivation for commensal human gut bacteria
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Commensal enteric virome regulates intestinal carbohydrate digestion and absorption
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RVvictor: Virus RNA-directed molecular interactions for RNA virus infection
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Global overview and major challenges of host prediction methods for uncultivated phages
inferred← citeshttps://doi.org/10.1016/j.coviro.2021.05.008openalex-snapshot
Fishing for phages in metagenomes: what do we catch, what do we miss?
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Current challenges to virus discovery by meta-transcriptomics
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Perspective on taxonomic classification of uncultivated viruses
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Virus genomics: what is being overlooked?
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Predicting the capsid architecture of phages from metagenomic data
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Identification of over ten thousand candidate structured RNAs in viruses and phages
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Visualizing metagenomic and metatranscriptomic data: A comprehensive review
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Viral community structure and functional potential vary with lifestyle and altitude in soils of Mt. Everest
inferred← citeshttps://doi.org/10.1016/j.envint.2024.109155openalex-snapshot
Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas
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Viral diversity and biogeochemical potential revealed in different prawn-culture sediments by virus-enriched metagenome analysis
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From sewage to genomes: Expanding our understanding of the urban and semi-urban wastewater RNA virome
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Saline lakes on the Qinghai-Tibet Plateau harbor unique viral assemblages mediating microbial environmental adaption
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A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens
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Dynamic nature of viral and bacterial communities in human faeces
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Comparative genomic segmental abundance of southern rice black-streaked dwarf virus in rice and weeds reveals host-dependent accumulation and variation post first outbreak in India
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Environmental viromes reveal the global distribution signatures of deep-sea DNA viruses
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Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants
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Metagenomic analysis reveals ecological and functional signatures of oral phageome associated with severe early childhood caries
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Distinct adaptive strategies and microbial interactions of soil viruses under different metal(loid) contaminations
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Effects of vegetation cover and aquaculture pollution on viral assemblages in mangroves sediments
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Unveiling the dynamic viral landscape across developmental stages of cold seep ecosystems: Implications for global marine biogeochemistry
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Comparative metagenomic analyses of viral genomic diversity and ecosystem functions in extremely acidic copper mine tailings
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Promises of microbiome-based therapies
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“What I cannot create, I do not understand": elucidating microbe–microbe interactions to facilitate plant microbiome engineering
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Type III CRISPR-Cas provides resistance against nucleus-forming jumbo phages via abortive infection
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Diversity and function of mountain and polar supraglacial DNA viruses
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Agricultural practices drive biological loads, seasonal patterns and potential pathogens in the aerobiome of a mixed-land-use dryland
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phoH-carrying virus communities responded to multiple factors and their correlation network with prokaryotes in sediments along Bohai Sea, Yellow Sea, and East China Sea in China
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Ecological drivers and potential functions of viral communities in flooded arsenic-contaminated paddy soils
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Soil viral community dynamics over seven years of heat disturbance: Spatial variation exceeds temporal in annually sampled soils
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Inverted microbial community stratification and spatial–temporal stability in hypersaline anaerobic sediments from the S’Avall solar salterns
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Diversity in the soil virosphere: to infinity and beyond?
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Early life dynamics of ARG and MGE associated with intestinal virome in neonatal piglets
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Genomic and functional characterization of Bacillus phage BCE1 targeting a key gut bacterium in Aedes albopictus larvae
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Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India
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Tracing the fate of wastewater viruses reveals catchment-scale virome diversity and connectivity
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CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter
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Metagenomic analysis unveils the underexplored roles of prokaryotic viruses in a full-scale landfill leachate treatment plant
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Narrow host range phages infect essential bacteria for water purification reactions in groundwater-fed rapid sand filters
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Identifying ARG-carrying bacteriophages in a lake replenished by reclaimed water using deep learning techniques
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Decrypting the viral community in aerobic activated sludge reactors treating antibiotic production wastewater
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Viruses in human-impacted estuarine ecotones: Distribution, metabolic potential, and environmental risks
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Predicting norovirus contamination and antimicrobial resistance in coastal waters from community and hospital-derived sources
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Unlocking the PirAB Pandora's box: Genomic epidemiology and phage biocontrol of an emerging waterborne One Health crisis
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Viral and Bacterial Community Dynamics in Food Waste and Digestate from Full-Scale Biogas Plants
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From Field Metagenomes to Mutant Genomes: Coevolution of Cyanophages and Synechococcus in Estuarine Ecosystems
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Water Safety Consideration of the Dual Nature of Virus in Global Urban Water Cycle: From Source to Reuse
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Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity
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Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot
inferred← citeshttps://doi.org/10.1038/s41396-023-01404-1openalex-snapshot
Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting
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Virus–pathogen interactions improve water quality along the Middle Route of the South-to-North Water Diversion Canal
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Ecology and molecular targets of hypermutation in the global microbiome
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Genome binning of viral entities from bulk metagenomics data
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Structural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanase
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Response of soil viral communities to land use changes
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Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut
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Interrogating the viral dark matter of the rumen ecosystem with a global virome database
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A systematic analysis of marine lysogens and proviruses
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Structure-guided discovery of anti-CRISPR and anti-phage defense proteins
inferred← citeshttps://doi.org/10.1038/s41467-024-45653-wopenalex-snapshot
Identification of HDV-like theta ribozymes involved in tRNA-based recoding of gut bacteriophages
inferred← citeshttps://doi.org/10.1038/s41467-024-50777-0openalex-snapshot
Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage
inferred← citeshttps://doi.org/10.1038/s41467-024-51101-6openalex-snapshot
Global diversity and ecological functions of viruses inhabiting oil reservoirs
inferred← citeshttps://doi.org/10.1038/s41467-024-51230-yopenalex-snapshot
Unveiling the unknown viral world in groundwater
inferred← citeshttps://doi.org/10.1038/s41467-024-53787-0openalex-snapshot
Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination
inferred← citeshttps://doi.org/10.1038/s41467-025-62406-5openalex-snapshot
Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome
inferred← citeshttps://doi.org/10.1038/s41467-025-63565-1openalex-snapshot
Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae
inferred← citeshttps://doi.org/10.1038/s41467-025-66049-4openalex-snapshot
Protein Set Transformer: a protein-based genome language model to power high-diversity viromics
inferred← citeshttps://doi.org/10.1038/s41559-024-02347-2openalex-snapshot
Biogeographic patterns and drivers of soil viromes
inferred← citeshttps://doi.org/10.1038/s41564-021-01039-yopenalex-snapshot
Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes
inferred← citeshttps://doi.org/10.1038/s41564-022-01178-wopenalex-snapshot
Viral biogeography of the mammalian gut and parenchymal organs
inferred← citeshttps://doi.org/10.1038/s41564-022-01297-4openalex-snapshot
Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome
inferred← citeshttps://doi.org/10.1038/s41564-023-01347-5openalex-snapshot
Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats
inferred← citeshttps://doi.org/10.1038/s41564-023-01485-wopenalex-snapshot
A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment
inferred← citeshttps://doi.org/10.1038/s41564-023-01564-yopenalex-snapshot
The gut virome is associated with stress-induced changes in behaviour and immune responses in mice
inferred← citeshttps://doi.org/10.1038/s41564-023-01584-8openalex-snapshot
Large language models improve annotation of prokaryotic viral proteins
inferred← citeshttps://doi.org/10.1038/s41564-023-01598-2openalex-snapshot
COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes
inferred← citeshttps://doi.org/10.1038/s41564-024-01686-xopenalex-snapshot
A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts
inferred← citeshttps://doi.org/10.1038/s41564-024-01876-7openalex-snapshot
Unravelling viral ecology and evolution over 20 years in a freshwater lake
inferred← citeshttps://doi.org/10.1038/s41564-026-02352-0openalex-snapshot
Functional diversity of phage sponge proteins that sequester host immune signals
inferred← citeshttps://doi.org/10.1038/s41579-022-00755-4openalex-snapshot
Mutualistic interplay between bacteriophages and bacteria in the human gut
inferred← citeshttps://doi.org/10.1038/s41579-022-00811-zopenalex-snapshot
Soil viral diversity, ecology and climate change
inferred← citeshttps://doi.org/10.1038/s41579-023-00963-6openalex-snapshot
The oral microbiome: diversity, biogeography and human health
inferred← citeshttps://doi.org/10.1038/s41586-023-06376-yopenalex-snapshot
Small protein modules dictate prophage fates during polylysogeny
inferred← citeshttps://doi.org/10.1038/s41586-023-06583-7openalex-snapshot
Unraveling the functional dark matter through global metagenomics
inferred← citeshttps://doi.org/10.1038/s41586-023-06612-5openalex-snapshot
Bacteriophages suppress CRISPR–Cas immunity using RNA-based anti-CRISPRs
inferred← citeshttps://doi.org/10.1038/s41587-023-01844-2openalex-snapshot
Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification
inferred← citeshttps://doi.org/10.1038/s41587-023-01953-yopenalex-snapshot
Identification of mobile genetic elements with geNomad
inferred← citeshttps://doi.org/10.1038/s41589-023-01269-7openalex-snapshot
Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins
inferred← citeshttps://doi.org/10.1038/s41597-024-03210-6openalex-snapshot
Phylogenomics and genetic analysis of solvent-producing Clostridium species
inferred← citeshttps://doi.org/10.1038/s41598-024-52626-yopenalex-snapshot
Community ecology and functional potential of bacteria, archaea, eukarya and viruses in Guerrero Negro microbial mat
inferred← citeshttps://doi.org/10.1038/s42003-024-06798-yopenalex-snapshot
Metagenomic analysis reveals high diversity of gut viromes in yaks (Bos grunniens) from the Qinghai-Tibet Plateau
inferred← citeshttps://doi.org/10.1038/s43705-021-00083-3openalex-snapshot
iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology
inferred← citeshttps://doi.org/10.1038/s43705-022-00112-9openalex-snapshot
Viral diversity is linked to bacterial community composition in alpine stream biofilms
inferred← citeshttps://doi.org/10.1038/s43705-022-00135-2openalex-snapshot
Potential metabolic and genetic interaction among viruses, methanogen and methanotrophic archaea, and their syntrophic partners
inferred← citeshttps://doi.org/10.1038/s43705-022-00179-4openalex-snapshot
Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater
inferred← citeshttps://doi.org/10.1038/s43705-023-00249-1openalex-snapshot
The association of prokaryotic antiviral systems and symbiotic phage communities in drinking water microbiomes
inferred← citeshttps://doi.org/10.1038/s43705-023-00295-9openalex-snapshot
MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets
inferred← citeshttps://doi.org/10.1039/d3ew00015jopenalex-snapshot
Highly sensitive detection and quantification of dissolved free extracellular DNA using colloid adsorption and foam concentration
inferred← citeshttps://doi.org/10.1073/pnas.2522060123openalex-snapshot
Uncovering ParB-dependent and -independent subclasses of T-dioxygenases from bacteriophage
inferred← citeshttps://doi.org/10.1080/19490976.2025.2501194openalex-snapshot
The influence of early life exposures on the infant gut virome
inferred← citeshttps://doi.org/10.1089/phage.2021.0007openalex-snapshot
INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes
inferred← citeshttps://doi.org/10.1089/phage.2021.0008openalex-snapshot
From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs
inferred← citeshttps://doi.org/10.1093/bib/bbac258openalex-snapshot
Accurate identification of bacteriophages from metagenomic data using Transformer
inferred← citeshttps://doi.org/10.1093/bib/bbac487openalex-snapshot
PhaTYP: predicting the lifestyle for bacteriophages using BERT
inferred← citeshttps://doi.org/10.1093/bib/bbac505openalex-snapshot
Virus classification for viral genomic fragments using PhaGCN2
inferred← citeshttps://doi.org/10.1093/bib/bbaf065openalex-snapshot
A review of neural networks for metagenomic binning
inferred← citeshttps://doi.org/10.1093/bib/bbaf084openalex-snapshot
VITALdb: to select the best viroinformatics tools for a desired virus or application
inferred← citeshttps://doi.org/10.1093/bioadv/vbag149openalex-snapshot
vClassifier: a toolkit for high-resolution phylogenetic classification of prokaryotic viruses
inferred← citeshttps://doi.org/10.1093/gigascience/giac110openalex-snapshot
What the Phage: a scalable workflow for the identification and analysis of phage sequences
inferred← citeshttps://doi.org/10.1093/ismeco/ycad011openalex-snapshot
Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components
inferred← citeshttps://doi.org/10.1093/ismeco/ycaf129openalex-snapshot
Solar radiation shapes viral ecology in an alpine lake at 4700 meters
inferred← citeshttps://doi.org/10.1093/ismejo/wrae124openalex-snapshot
Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles
inferred← citeshttps://doi.org/10.1093/nar/gkaa1216openalex-snapshot
The 2021 Nucleic Acids Research database issue and the online molecular biology database collection
inferred← citeshttps://doi.org/10.1093/nar/gkab859openalex-snapshot
CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids
inferred← citeshttps://doi.org/10.1093/nar/gkac1037openalex-snapshot
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata
inferred← citeshttps://doi.org/10.1093/nar/gkac1168openalex-snapshot
Genome-scale top-down strategy to generate viable genome-reduced phages
inferred← citeshttps://doi.org/10.1093/nar/gkac467openalex-snapshot
UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions
inferred← citeshttps://doi.org/10.1093/nar/gkad800openalex-snapshot
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes
inferred← citeshttps://doi.org/10.1093/nar/gkae016openalex-snapshot
Innate programmable DNA binding by CRISPR-Cas12m effectors enable efficient base editing
inferred← citeshttps://doi.org/10.1093/nar/gkaf1283openalex-snapshot
Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes
inferred← citeshttps://doi.org/10.1093/nargab/lqae185openalex-snapshot
vClean: assessing virus sequence contamination in viral genomes
inferred← citeshttps://doi.org/10.1093/ve/veae104openalex-snapshot
Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics
inferred← citeshttps://doi.org/10.1099/jgv.0.001744openalex-snapshot
HBV induced the discharge of intrinsic antiviral miRNAs in HBV-replicating hepatocytes via extracellular vesicles to facilitate its replication
inferred← citeshttps://doi.org/10.1099/mgen.0.001198openalex-snapshot
The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies
inferred← citeshttps://doi.org/10.1099/mgen.0.001423openalex-snapshot
Bacteriophages in Pseudomonas aeruginosa evade the CRISPR-Cas I-F system by depletion of PAM sequences
inferred← citeshttps://doi.org/10.1101/2020.11.25.398248openalex-snapshot
Generating complex patterns of gene expression without regulatory circuits
inferred← citeshttps://doi.org/10.1101/2021.04.21.440840openalex-snapshot
Virulent but not temperate bacteriophages display hallmarks of rapid translation initiation
inferred← citeshttps://doi.org/10.1101/2021.05.31.446456openalex-snapshot
Viruses roam the wheat phyllosphere
inferred← citeshttps://doi.org/10.1101/2021.07.07.451412openalex-snapshot
Genome binning of viral entities from bulk metagenomics data
inferred← citeshttps://doi.org/10.1101/2021.07.30.454538openalex-snapshot
Plant-associated microbiomes promote nutrient turnover in impoverished substrates of a biodiversity hotspot
inferred← citeshttps://doi.org/10.1101/2021.12.14.472558openalex-snapshot
Elevation drives activity of soil bacteria, but not of bacterial viruses
inferred← citeshttps://doi.org/10.1101/2022.01.20.477139openalex-snapshot
Parallel multicopy-suppressor screens reveal convergent evolution of phage-encoded single gene lysis proteins
inferred← citeshttps://doi.org/10.1101/2022.01.27.478124openalex-snapshot
Genomic and phylogenetic analysis of the first myovirus isolated from Oceanospirillaceae , representing a novel viral cluster prevalent in polar oceans
inferred← citeshttps://doi.org/10.1101/2022.03.03.482774openalex-snapshot
De-heterogeneity of the eukaryotic viral reference database (EVRD) improves the accuracy and efficiency of viromic analysis
inferred← citeshttps://doi.org/10.1101/2022.04.13.488139openalex-snapshot
Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities
inferred← citeshttps://doi.org/10.1101/2022.05.20.492862openalex-snapshot
Lysogenized phages of methanotrophic bacteria show a broad and untapped genetic diversity
inferred← citeshttps://doi.org/10.1101/2022.08.31.505936openalex-snapshot
An RNA sequence that reprograms ribosomes to bypass a 50 nucleotide coding gap is encoded by a mobile element whose sequence conservation illuminates its bypass mechanisms
inferred← citeshttps://doi.org/10.1101/2022.10.12.504627openalex-snapshot
CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter
inferred← citeshttps://doi.org/10.1101/2022.11.22.517103openalex-snapshot
Host translation machinery is not a barrier to phages that infect both CPR and non-CPR bacteria
inferred← citeshttps://doi.org/10.1101/2023.03.10.532047openalex-snapshot
VirRep: accurate identification of viral genomes from human gut metagenomic data via a hybrid language representation learning framework
inferred← citeshttps://doi.org/10.1101/2023.08.29.555303openalex-snapshot
Phylogeny and disease links of a widespread and ancient gut phage lineage
inferred← citeshttps://doi.org/10.1101/2023.09.19.558540openalex-snapshot
Diversity and ecological functions of viruses inhabiting the oil reservoirs
inferred← citeshttps://doi.org/10.1101/2023.09.26.559499openalex-snapshot
Progressive community, biogeochemical and evolutionary remodeling of the soil microbiome underpins long-term desert ecosystem restoration
inferred← citeshttps://doi.org/10.1101/2024.05.25.595874openalex-snapshot
Microbial species exist and are maintained by ecological cohesiveness coupled to high homologous recombination
inferred← citeshttps://doi.org/10.1101/2024.05.28.596318openalex-snapshot
vClassifier: a toolkit for species-level classification of prokaryotic viruses
inferred← citeshttps://doi.org/10.1101/2025.07.12.664507openalex-snapshot
Structural modeling reveals viral proteins that manipulate host immune signaling
inferred← citeshttps://doi.org/10.1101/2025.09.01.673544openalex-snapshot
PanGene-O-Meter: Intra-Species Diversity Based on Gene-Content
inferred← citeshttps://doi.org/10.1101/2025.10.13.681967openalex-snapshot
Arbitrium phages can manipulate each other’s lysis - lysogeny decisions
inferred← citeshttps://doi.org/10.1111/1462-2920.15630openalex-snapshot
Ancient saltern metagenomics: tracking changes in microbes and their viruses from the underground to the surface
inferred← citeshttps://doi.org/10.1111/1462-2920.15802openalex-snapshot
Virus diversity in metagenomes of a lichen symbiosis ( Umbilicaria phaea ): complete viral genomes, putative hosts and elevational distributions
inferred← citeshttps://doi.org/10.1111/1462-2920.16665openalex-snapshot
Virus ecology and 7‐year temporal dynamics across a permafrost thaw gradient
inferred← citeshttps://doi.org/10.1111/1462-2920.70017openalex-snapshot
Insights Into Phylogeny, Diversity and Functional Potential of Poseidoniales Viruses
inferred← citeshttps://doi.org/10.1111/1758-2229.12912openalex-snapshot
Viral discovery in the ‘realm’ of COVID ‐19
inferred← citeshttps://doi.org/10.1111/jeb.14203openalex-snapshot
Open questions in the social lives of viruses
inferred← citeshttps://doi.org/10.1111/mec.16756openalex-snapshot
Metatranscriptomics reveals contrasting effects of elevation on the activity of bacteria and bacterial viruses in soil
inferred← citeshttps://doi.org/10.1126/sciadv.add8911openalex-snapshot
Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems
inferred← citeshttps://doi.org/10.1126/sciadv.adg4015openalex-snapshot
The phageome in normal and inflamed human skin
inferred← citeshttps://doi.org/10.1126/science.aea1761openalex-snapshot
Structural modeling reveals phage proteins that manipulate bacterial immune signaling
inferred← citeshttps://doi.org/10.1128/aem.00367-24openalex-snapshot
A novel flavobacterial phage abundant during green tide, representing a new viral family, Zblingviridae
inferred← citeshttps://doi.org/10.1128/aem.01160-21openalex-snapshot
Viral Characteristics of the Warm Atlantic and Cold Arctic Water Masses in the Nordic Seas
inferred← citeshttps://doi.org/10.1128/aem.01581-23openalex-snapshot
A rumen virosphere with implications of contribution to fermentation and methane production, and endemism in cattle breeds and individuals
inferred← citeshttps://doi.org/10.1128/aem.01896-22openalex-snapshot
Discovery of an Abundant Viral Genus in Polar Regions through the Isolation and Genomic Characterization of a New Virus against Oceanospirillaceae
inferred← citeshttps://doi.org/10.1128/aem.01973-22openalex-snapshot
Viruses Regulate Microbial Community Assembly Together with Environmental Factors in Acid Mine Drainage
inferred← citeshttps://doi.org/10.1128/mbio.00651-22openalex-snapshot
Virus-Host Interactions and Genetic Diversity of Antarctic Sea Ice Bacteriophages
inferred← citeshttps://doi.org/10.1128/mbio.01766-23openalex-snapshot
Host translation machinery is not a barrier to phages that interact with both CPR and non-CPR bacteria
inferred← citeshttps://doi.org/10.1128/mbio.02135-25openalex-snapshot
The evolutionary replacement of restriction-modification by Ssp antiviral systems is associated with the distribution of prophages in the major clonal group of Acinetobacter baumannii
inferred← citeshttps://doi.org/10.1128/mbio.02938-21openalex-snapshot
Cargo Genes of Tn 7 -Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes
inferred← citeshttps://doi.org/10.1128/mbio.03009-22openalex-snapshot
Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming
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