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2024
Active prokaryotic and eukaryotic viral ecology across spatial scale in a deep-sea brine pool
ISME Communications
2024
Long-read powered viral metagenomics in the oligotrophic Sargasso Sea
Nature Communications
2024
Methods in Molecular Biology
2024
Microbial evolution through horizontal gene transfer by mobile genetic elements
Microbial Biotechnology
2024
Bacteriophages: Vectors of or weapons against the transmission of antibiotic resistance genes in hospital wastewater systems?
Water Research
2024
Xanthomonas Phage PBR31: Classifying the Unclassifiable
Viruses
2024
Phenotypic characterization and genomic analysis of a Salmonella phage L223 for biocontrol of Salmonella spp. in poultry
Scientific Reports
2024
Molecular Medical Microbiology
2024
How to introduce a new bacteriophage on the block: a short guide to phage classification
Journal of Virology
2024
Genomic and biological characteristics of a novel phage induced from Limosilactobacillus fermentum
Food Bioscience
2024
Diversity and ecological potentials of viral assemblages from the seamount sediments of the Northwest Pacific Ocean
The Innovation Geoscience
2024
Characterization of the novel phage vB_BceP_LY3 and its potential role in controlling Bacillus cereus in milk and rice
International Journal of Food Microbiology
2024
Viral potential to modulate microbial methane metabolism varies by habitat
Nature Communications
2024
Diversity of Salmonella enterica phages isolated from chicken farms in Kenya
Microbiology Spectrum
2024
Targeted phage hunting to specific Klebsiella pneumoniae clinical isolates is an efficient antibiotic resistance and infection control strategy
Microbiology Spectrum
2024
Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost
mSphere
2024
A novel flavobacterial phage abundant during green tide, representing a new viral family, Zblingviridae
Applied and Environmental Microbiology
2024
Targeted viromes and total metagenomes capture distinct components of bee gut phage communities
Microbiome
2024
Temperate Stutzerimonas Phage Encoding Toxin-Antitoxin System Genes Represents a Novel Genus
Journal of Ocean University of China
2024
Isolation and Characterization of a Novel Aeromonas salmonicida-Infecting Studiervirinae Bacteriophage, JELG-KS1
Microorganisms
2024
Methods in Molecular Biology
2024
Exploring pangenomic diversity and CRISPR-Cas evasion potential in jumbo phages: a comparative genomics study
Microbiology Spectrum
2023
Viral diversity and dynamics and CRISPR-Cas-mediated immunity in a robust alkaliphilic cyanobacterial consortium
Microbiology Spectrum
2023
Three Phages One Host: Isolation and Characterization of Pantoea agglomerans Phages from a Grasshopper Specimen
International Journal of Molecular Sciences
2023
With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities
Applied and Environmental Microbiology
2023
Genomic Analysis and Taxonomic Characterization of Seven Bacteriophage Genomes Metagenomic-Assembled from the Dishui Lake
Viruses
2023
Lytic bacteriophage vB_KmiS-Kmi2C disrupts biofilms formed by members of the Klebsiella oxytoca complex, and represents a novel virus family and genus
Journal of Applied Microbiology
2023
Four principles to establish a universal virus taxonomy
PLOS Biology
2023
Potential Auxiliary Metabolic Capabilities and Activities Reveal Biochemical Impacts of Viruses in Municipal Wastewater Treatment Plants
Environmental Science & Technology
2023
Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick
ISME Communications
2023
Characterization and genomic analysis of a novel lytic phage vB_PstM_ZRG1 infecting Stutzerimonas stutzeri, representing a new viral genus, Elithevirus
Virus Research
2023
Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles
Nature Communications
2023
Isolation and infection cycle of a polinton-like virus virophage in an abundant marine alga
Nature Microbiology
2023
Characterization of prophages in bacterial genomes from the honey bee (Apis mellifera) gut microbiome
PeerJ
2023
ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis
Gut Microbes
2023
PhaGenus: genus-level classification of bacteriophages using a Transformer model
Briefings in Bioinformatics
2023
Impact of antibiotic perturbation on fecal viral communities in mice
G3
2023
Characterization and genomic analysis of phage vB_ValR_NF, representing a new viral family prevalent in the Ulva prolifera blooms
Frontiers in Microbiology
2023
VirClust—A Tool for Hierarchical Clustering, Core Protein Detection and Annotation of (Prokaryotic) Viruses
Viruses
2023
Enhanced Bacterium–Phage Symbiosis in Attached Microbial Aggregates on a Membrane Surface Facing Elevated Hydraulic Stress
Environmental Science & Technology
2023
Broad-range capsule-dependent lytic Sugarlandvirus against Klebsiella sp.
Microbiology Spectrum
2023
Burkholderia contaminans Bacteriophage CSP3 Requires O-Antigen Polysaccharides for Infection
Microbiology Spectrum
2023
Revisiting evolutionary trajectories and the organization of the Pleolipoviridae family
PLOS Genetics
2023
Marine viruses disperse bidirectionally along the natural water cycle
Nature Communications
2023
A predicted CRISPR-mediated symbiosis between uncultivated archaea
Nature Microbiology
2023
Investigating the Human Intestinal DNA Virome and Predicting Disease-Associated Virus–Host Interactions in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
International Journal of Molecular Sciences
2023
Identification and genomic analysis of temperate Halomonas bacteriophage vB_HmeY_H4907 from the surface sediment of the Mariana Trench at a depth of 8,900 m
Microbiology Spectrum
2023
A Genome of Temperate Enterococcus Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences
Viruses
2023
Combine thermal processing with polyvalent phage LPEK22 to prevent the Escherichia coli and Salmonella enterica contamination in food
Food Research International
2022
Characterization of the human gut virome in metabolic and autoimmune diseases
Inflammation and Regeneration
2022
Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater
ISME Communications
2022
Ecological Studies
2022
2022 IEEE/WIC/ACM International Joint Conference on Web Intelligence and Intelligent Agent Technology (WI-IAT)
2022
Unravelling the ecological complexity of soil viromes: Challenges and opportunities
Science of The Total Environment
2022
Characterization and In Vitro Testing of Newly Isolated Lytic Bacteriophages for the Biocontrol of Pseudomonas Aeruginosa
Future Microbiology
2022
Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing
Microorganisms
2022
A Novel Inovirus Reprograms Metabolism and Motility of Marine Alteromonas
Microbiology Spectrum
2022
The First Cbk-Like Phage Infecting Erythrobacter, Representing a Novel Siphoviral Genus
Frontiers in Microbiology
2022
Mobile Genetic Elements Drive Antimicrobial Resistance Gene Spread in Pasteurellaceae Species
Frontiers in Microbiology
2022
Structural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanase
Nature Communications
2022
Record-Breaking Rain Event Altered Estuarine Viral Assemblages
Microorganisms
2022
Bioinformatics of virus taxonomy: foundations and tools for developing sequence-based hierarchical classification
Current Opinion in Virology
2022
Viral tag and grow: a scalable approach to capture and characterize infectious virus–host pairs
ISME Communications
2022
Characterization and genomic Analysis of a novel Pseudomonas phage vB_PsaP_M1, representing a new viral family, Psaeviridae
Frontiers in Marine Science
2022
ViBE: a hierarchical BERT model to identify eukaryotic viruses using metagenome sequencing data
Briefings in Bioinformatics
2022
Molecular dissection of the first Staphylococcus cohnii temperate phage IME1354_01
Virus Research
2022
Broad host range may be a key to long-term persistence of bacteriophages infecting intestinal Bacteroidaceae species
Scientific Reports
2022
Characterization of the Novel Phage vB_VpaP_FE11 and Its Potential Role in Controlling Vibrio parahaemolyticus Biofilms
Viruses
2022
Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts
Microbiome
2022
Accurate identification of bacteriophages from metagenomic data using Transformer
Briefings in Bioinformatics
2022
Advances and challenges in cataloging the human gut virome
Cell Host & Microbe
2022
Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework
Frontiers in Microbiology
2022
Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere
Microbiome
2022
Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica
Applied and Environmental Microbiology
2022
Comparative Genomics of Xylella fastidiosa Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems
Microorganisms
2022
CHERRY: a Computational metHod for accuratE pRediction of virus–pRokarYotic interactions using a graph encoder–decoder model
Briefings in Bioinformatics
2022
Optimized Metavirome Analysis of Marine DNA Virus Communities for Taxonomic Profiling
Ocean Science Journal
2022
Sheep in wolves’ clothing: Temperate T7-like bacteriophages and the origins of the Autographiviridae
Virology
2022
Identification of Novel Viruses and Their Microbial Hosts from Soils with Long-Term Nitrogen Fertilization and Cover Cropping Management
mSystems
2022
A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria
Applied and Environmental Microbiology
2022
Prediction of Prophages and Their Host Ranges in Pathogenic and Commensal Neisseria Species
mSystems
2022
Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures
The ISME Journal
2021
Isolation and Characterisation of the Bundooravirus Genus and Phylogenetic Investigation of the Salasmaviridae Bacteriophages
Viruses
2021
Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils
mSphere
2021
Phage Genome Annotation: Where to Begin and End
PHAGE
2021
Lytic archaeal viruses infect abundant primary producers in Earth’s crust
Nature Communications
2021
Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing
Environmental Microbiology
2021
Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions
The ISME Journal
2021
Isolation and Characterization of Klebsiella Phages for Phage Therapy
PHAGE
2021
iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology
ISME Communications
2021
Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil
mSystems
2021
Bacteriophage classification for assembled contigs using graph convolutional network
Bioinformatics
2021
Biogeochemistry Goes Viral: towards a Multifaceted Approach To Study Viruses and Biogeochemical Cycling
mSystems
2021
Genome Characterization of Nocturne116, Novel Lactococcus lactis-Infecting Phage Isolated from Moth
Microorganisms
2021
DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes
mBio
2021
VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families
Bioinformatics
2021
Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life
ISME Communications
2021
The human virome: assembly, composition and host interactions
Nature Reviews Microbiology
2021
Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations
Microbiome
2021
Genome Sequence of Streptomyces sp. Strain HB-N217, Isolated from the Marine Sponge Forcepia sp.
Microbiology Resource Announcements
2021
High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome
Scientific Reports
2021
The Fennoscandian Shield deep terrestrial virosphere suggests slow motion ‘boom and burst’ cycles
Communications Biology
2021
Unveiling Ecological and Genetic Novelty within Lytic and Lysogenic Viral Communities of Hot Spring Phototrophic Microbial Mats
Microbiology Spectrum
2021
DNase Treatment Improves Viral Enrichment in Agricultural Soil Viromes
mSystems
2021
Predicting the hosts of prokaryotic viruses using GCN-based semi-supervised learning
BMC Biology
2021
PHROG: families of prokaryotic virus proteins clustered using remote homology
NAR Genomics and Bioinformatics
2021
The human oral phageome
Periodontology 2000
2021
INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes
PHAGE
2021
Genome‐resolved viral ecology in a marine oxygen minimum zone
Environmental Microbiology
2021
Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome
Viruses
2021
Draft Genome Sequences of Pelagimyophage Mosig EXVC030M and Pelagipodophage Lederberg EXVC029P, Isolated from Devil’s Hole, Bermuda
Microbiology Resource Announcements
2021
A Roadmap for Genome-Based Phage Taxonomy
Viruses
2021
Characterization and Genomic Analysis of PALS2, a Novel Staphylococcus Jumbo Bacteriophage
Frontiers in Microbiology
2021
Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies
PeerJ
2021
Novel Siphoviridae Bacteriophages Infecting Bacteroides uniformis Contain Diversity Generating Retroelement
Microorganisms
2021
Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance
mSystems
2021
Genome and Ecology of a NovelAlteromonasPodovirus, ZP6, Representing a New Viral Genus,Mareflavirus
Microbiology Spectrum
2021
Ecogenomics and Adaptation Strategies of Southern Ocean Viral Communities
mSystems
2021
Cyanophage Diversity and Community Structure in Dead Zone Sediments
mSphere
2021
Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents
The ISME Journal
2021
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters
The ISME Journal
2020
Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems
mSystems
2020
Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages
Systematic Biology
2020
Discovery of several thousand highly diverse circular DNA viruses
eLife
2020
Clades of huge phages from across Earth’s ecosystems
Nature
2020
Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee
Archives of Virology
2020
Setting a baseline for global urban virome surveillance in sewage
Scientific Reports
2020
Shining Light on Human Gut Bacteriophages
Frontiers in Cellular and Infection Microbiology
2020
Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages
Environmental Microbiology
2020
Tara Oceans: towards global ocean ecosystems biology
Nature Reviews Microbiology
2020
Phage diversity, genomics and phylogeny
Nature Reviews Microbiology
2020
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut
Cell Host & Microbe
2020
Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota
Proceedings of the National Academy of Sciences
2020
Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice
mSystems
2020
Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone
Viruses
2019
Charting the diversity of uncultured viruses of Archaea and Bacteria
BMC Biology
2019
Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses
mSphere
2019
Gut Bacteriophage: Current Understanding and Challenges
Frontiers in Endocrinology
2019
Integrated mobile genetic elements in Thaumarchaeota
Environmental Microbiology
2019
Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses
Genes
2019
Marine DNA Viral Macro- and Microdiversity from Pole to Pole
Cell
2019
Viral taxonomy derived from evolutionary genome relationships
PLOS ONE
2019
Marine DNA Viral Macro-and Micro-Diversity From Pole to Pole
SSRN Electronic Journal
2019
Evolution and ecology of plant viruses
Nature Reviews Microbiology
2019
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
Nature Biotechnology
2019
Prevalence of viral photosynthesis genes along a freshwater to saltwater transect in Southeast USA
Environmental Microbiology Reports
2019
Classifying the Unclassified: A Phage Classification Method
Viruses
2019
IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes
Nucleic Acids Research
2019
Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
Microbiome
2019
Reference Module in Biomedical Sciences
2019
A viral reckoning: viruses emerge as essential manipulators of global ecosystems
Environmental Microbiology Reports
2019
Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome
Cell Host & Microbe
2019
Minimum Information about an Uncultivated Virus Genome (MIUViG)
Nature Biotechnology
2019
iMicrobe: Tools and data-driven discovery platform for the microbiome sciences
GigaScience
2019
Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust
mBio
2019
Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales
Nature Microbiology
2019
Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters
Viruses
2019
Towards a genome-based virus taxonomy
Nature Microbiology
2019
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands
PeerJ
2018
The lytic Myoviridae of Enterobacteriaceae form tight recombining assemblages separated by discontinuities in genome average nucleotide identity and lateral gene flow
Microbial Genomics
2018
Deciphering the Human Virome with Single-Virus Genomics and Metagenomics
Viruses
2018
Virus classification – where do you draw the line?
Archives of Virology
2018
New insight into the RNA aquatic virosphere via viromics
Virus Research
2018
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing
mSystems
2018
High-Resolution Temporal and Spatial Patterns of Virome in Wastewater Treatment Systems
Environmental Science & Technology
2018
Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy
Journal of General Virology
2018
Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems
Microbiome
2018
Biogeography and taxonomic overview of terrestrial hot spring thermophilic phages
Extremophiles
2018
Bacteriophage research – What we have learnt and what still needs to be addressed
Research in Microbiology
2018
Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing
Nature Microbiology
2018
The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification
Microbiome
2018
Host-linked soil viral ecology along a permafrost thaw gradient
Nature Microbiology
2018
Biological species in the viral world
Proceedings of the National Academy of Sciences
2018
Lysogeny is prevalent and widely distributed in the murine gut microbiota
The ISME Journal
2018
Multiple mechanisms drive phage infection efficiency in nearly identical hosts
The ISME Journal
2018
Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee
Archives of Virology
2018
Finer-Scale Phylosymbiosis: Insights from Insect Viromes
mSystems
2017
Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
PeerJ
2017
Single-virus genomics reveals hidden cosmopolitan and abundant viruses
Nature Communications
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