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2024
Exploring viral particle, soil, and extraction buffer physicochemical characteristics and their impacts on extractable viral communities
Soil Biology and Biochemistry
2024
Methods in Molecular Biology
2024
Frontiers of lake microbial ecology opened up by new technologies.
Japanese Journal of Limnology (Rikusuigaku Zasshi)
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
Optimization and evaluation of viral metagenomic amplification and sequencing procedures toward a genome-level resolution of the human fecal DNA virome
Journal of Advanced Research
2023
Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria
Microbiome
2023
Microviruses: A World Beyond phiX174
Annual Review of Virology
2023
Novel RNA viruses from the Atlantic Ocean: Ecogenomics, biogeography, and total virioplankton mass contribution from surface to the deep ocean
Environmental Microbiology
2023
Impact of antibiotic perturbation on fecal viral communities in mice
G3
2023
Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community
Journal of Virology
2023
Decoding the DNA and RNA viromes of a tropical urban lagoon
Environmental Microbiology
2023
Viral Diversity in Benthic Abyssal Ecosystems: Ecological and Methodological Considerations
Viruses
2023
Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles
Nature Communications
2023
The impact of storage buffer and storage conditions on fecal samples for bacteriophage infectivity and metavirome analyses
Microbiome
2023
KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
Bioinformatics
2023
Investigating the genetic diversity of CRESS DNA viruses in cats identifies a novel feline circovirus and unveils exposure of cats to canine circovirus
Research in Veterinary Science
2023
Capturing variation in metagenomic assembly graphs with MetaCortex
Bioinformatics
2023
Expanding known viral diversity in the healthy infant gut
Nature Microbiology
2022
Microbiome-Gut-Brain Axis
2022
Phages in the Gut Ecosystem
Frontiers in Cellular and Infection Microbiology
2022
Predicting the capsid architecture of phages from metagenomic data
Computational and Structural Biotechnology Journal
2022
HoPhage: an ab initio tool for identifying hosts of phage fragments from metaviromes
Bioinformatics
2022
Female reproduction and viral infection in a long‐lived mammal
Journal of Animal Ecology
2022
Unravelling the ecological complexity of soil viromes: Challenges and opportunities
Science of The Total Environment
2022
Viral biogeography of the mammalian gut and parenchymal organs
Nature Microbiology
2022
Bacteriophages and their potential for treatment of gastrointestinal diseases
Nature Reviews Gastroenterology & Hepatology
2022
Characterization of the human gut virome in metabolic and autoimmune diseases
Inflammation and Regeneration
2022
Novel lineages of single-stranded DNA phages that coevolved with the symbiotic bacteria Rhizobium
Frontiers in Microbiology
2022
The Viral Fraction Metatranscriptomes of Lake Baikal
Microorganisms
2022
Diversity of CRESS DNA Viruses in Squamates Recapitulates Hosts Dietary and Environmental Sources of Exposure
Microbiology Spectrum
2021
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters
The ISME Journal
2021
Probing the “Dark Matter” of the Human Gut Phageome: Culture Assisted Metagenomics Enables Rapid Discovery and Host-Linking for Novel Bacteriophages
Frontiers in Cellular and Infection Microbiology
2021
Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens
Microbiome
2021
Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils
Environmental Microbiology
2021
The human virome: assembly, composition and host interactions
Nature Reviews Microbiology
2021
Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants
Nature Communications
2021
A library preparation optimized for metagenomics of RNA viruses
Molecular Ecology Resources
2021
Challenges of Studying the Human Virome – Relevant Emerging Technologies
Trends in Microbiology
2021
Application of machine learning in bacteriophage research
BMC Microbiology
2021
iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology
ISME Communications
2021
Phage Annotation Guide: Guidelines for Assembly and High-Quality Annotation
PHAGE
2021
Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types
PeerJ
2021
Analysis of viromes and microbiomes from pig fecal samples reveals that phages and prophages rarely carry antibiotic resistance genes
ISME Communications
2021
Functional Restoration of Bacteriomes and Viromes by Fecal Microbiota Transplantation
Gastroenterology
2021
Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics
Microorganisms
2021
Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review
Microorganisms
2021
Bacteriophages
2021
Adaptation of the polony technique to quantify Gokushovirinae, a diverse group of single‐stranded DNA phage
Environmental Microbiology
2021
Glacier ice archives nearly 15,000-year-old microbes and phages
Microbiome
2021
Encyclopedia of Life Sciences
2021
Integrating Viral Metagenomics into an Ecological Framework
Annual Review of Virology
2021
Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads
DNA Research
2020
Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics
Soil Systems
2020
Resurrection of a global, metagenomically defined gokushovirus
eLife
2020
Autochthonous faecal viral transfer (FVT) impacts the murine microbiome after antibiotic perturbation
BMC Biology
2020
Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts
Cell Host & Microbe
2020
Circular Rep encoding single stranded (CRESS) DNA virus-like sequences detected in quagga mussels (Dreissena rostriformis bugensis) and sediments from the central Lake Michigan benthos
Journal of Great Lakes Research
2020
Quantification of T4-Like and T7-Like Cyanophages Using the Polony Method Show They Are Significant Members of the Virioplankton in the North Pacific Subtropical Gyre
Frontiers in Microbiology
2020
Shining Light on Human Gut Bacteriophages
Frontiers in Cellular and Infection Microbiology
2020
Global Organization and Proposed Megataxonomy of the Virus World
Microbiology and Molecular Biology Reviews
2020
Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities
Genome Research
2020
Bacteriophages
2020
Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization
Cell Host & Microbe
2020
Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface
Frontiers in Cellular and Infection Microbiology
2020
Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA
mBio
2020
Single-gene lysis in the metagenomic era
Current Opinion in Microbiology
2020
Coral Bleaching Phenotypes Associated With Differential Abundances of Nucleocytoplasmic Large DNA Viruses
Frontiers in Marine Science
2019
The smallest ssDNA phage infecting a marine bacterium
Environmental Microbiology
2019
Classifying the Unclassified: A Phage Classification Method
Viruses
2019
Viral abundance and diversity vary with depth in a southeastern United States agricultural ultisol
Soil Biology and Biochemistry
2019
Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters
Viruses
2019
A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach
Scientific Reports
2019
Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome
Cell Host & Microbe
2019
Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease
Cell Host & Microbe
2019
A Protocol for Extraction of Infective Viromes Suitable for Metagenomics Sequencing from Low Volume Fecal Samples
Viruses
2019
Studying the gut virome in the metagenomic era: challenges and perspectives
BMC Biology
2019
Metagenomic Analysis of Virioplankton from the Pelagic Zone of Lake Baikal
Viruses
2019
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands
PeerJ
2019
The Virome of Cerebrospinal Fluid: Viruses Where We Once Thought There Were None
Frontiers in Microbiology
2019
The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific
Cell Host & Microbe
2019
Gut Bacteriophage: Current Understanding and Challenges
Frontiers in Endocrinology
2019
Estimate of the diversity of viral and bacterial assemblage in the coastal water of Lake Baikal
FEMS Microbiology Letters
2019
Contrasting distributions of bacteriophages and eukaryotic viruses from contaminated coastal sediments
Environmental Microbiology
2019
Human cytomegalovirus genomics and transcriptomics through the lens of next-generation sequencing: revision and future challenges
Virus Genes
2019
Optimizing de novo genome assembly from PCR-amplified metagenomes
PeerJ
2019
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
PeerJ
2019
Advances in Virus Research
2019
Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
PeerJ
2019
Choice of assembly software has a critical impact on virome characterisation
Microbiome
2019
Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes
Nature Communications
2019
Diversities and potential biogeochemical impacts of mangrove soil viruses
Microbiome
2018
Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis
Virology Journal
2018
A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria
Nature
2018
Metavirome Sequencing of the Termite Gut Reveals the Presence of an Unexplored Bacteriophage Community
Frontiers in Microbiology
2018
Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan
Frontiers in Microbiology
2018
Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses
Microbiome
2018
The ‘Neglected’ Soil Virome – Potential Role and Impact
Trends in Microbiology
2018
Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism (Ciona robusta)
Viruses
2018
Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions
Viruses
2018
A Virus Infecting Marine Photoheterotrophic Alphaproteobacteria (Citromicrobium spp.) Defines a New Lineage of ssDNA Viruses
Frontiers in Microbiology
2018
Reproducible protocols for metagenomic analysis of human faecal phageomes
Microbiome
2018
Viral Communities of Shark Bay Modern Stromatolites
Frontiers in Microbiology
2018
Phage puppet masters of the marine microbial realm
Nature Microbiology
2018
Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome
Respiratory Research
2018
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing
mSystems
2018
Interrogating marine virus‐host interactions and elemental transfer with BONCAT and nanoSIMS‐based methods
Environmental Microbiology
2018
Diversity of DNA and RNA Viruses in Indoor Air As Assessed via Metagenomic Sequencing
Environmental Science & Technology
2018
Lysogeny is prevalent and widely distributed in the murine gut microbiota
The ISME Journal
2018
Viromes of one year old infants reveal the impact of birth mode on microbiome diversity
PeerJ
2018
Methods in Molecular Biology
2018
Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses
Trends in Microbiology
2017
Quantification of diverse virus populations in the environment using the polony method
Nature Microbiology
2017
Distribution of circular single‐stranded DNA viruses associated with benthic amphipods of genus Diporeia in the Laurentian Great Lakes
Freshwater Biology
2017
Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches
Viruses
2017
Review article: the human intestinal virome in health and disease
Alimentary Pharmacology & Therapeutics
2017
From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments
Scientific Reports
2017
Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters
PLOS Genetics
2017
Current Advances on Virus Discovery and Diagnostic Role of Viral Metagenomics in Aquatic Organisms
Frontiers in Microbiology
2017
Gene expression of benthic amphipods (genus:Diporeia) in relation to a circular ssDNA virus across two Laurentian Great Lakes
PeerJ
2017
Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
PeerJ
2017
The Number of Target Molecules of the Amplification Step Limits Accuracy and Sensitivity in Ultradeep-Sequencing Viral Population Studies
Journal of Virology
2017
Viral coinfection is shaped by host ecology and virus–virus interactions across diverse microbial taxa and environments
Virus Evolution
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