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2025
Making sense of the virome in light of evolution and ecology
Proceedings of the Royal Society B: Biological Sciences
2025
A sensitive sample preparation pipeline for adventitious virus detection using Oxford Nanopore sequencing
Molecular Therapy Methods & Clinical Development
2025
Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome
Nature Communications
2025
Unveiling the viral diversity in coastal sediments: Metagenomic insights along the Kerala coast, Southern India
Journal of Earth System Science
2025
Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses
Nucleic Acids Research
2025
Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations
Nature Communications
2024
Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners
Microbiome
2024
Long-read powered viral metagenomics in the oligotrophic Sargasso Sea
Nature Communications
2024
Nanopore and Illumina sequencing reveal different viral populations from human gut samples
Microbial Genomics
2024
Improving Bacterial Metagenomic Research through Long-Read Sequencing
Microorganisms
2024
The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies
Microbial Genomics
2024
Tools and methodology to in silico phage discovery in freshwater environments
Frontiers in Microbiology
2024
Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing
Nature Methods
2024
Virus ecology and 7‐year temporal dynamics across a permafrost thaw gradient
Environmental Microbiology
2024
Metagenomic time series reveals a Western English Channel viral community dominated by members with strong seasonal signals
The ISME Journal
2023
VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data
Briefings in Bioinformatics
2023
Functional ecology of bacteriophages in the environment
Current Opinion in Microbiology
2023
Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India
Virus Research
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
Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines
Microbiome
2023
Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment
Genomics, Proteomics & Bioinformatics
2023
Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes
The ISME Journal
2022
MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research
Water
2022
Revolutionized virome research using systems microbiology approaches
Experimental Biology and Medicine
2022
Influence of short and long term processes on SAR11 communities in open ocean and coastal systems
ISME Communications
2022
Phascinating Phages
Microorganisms
2022
Virus genomics: what is being overlooked?
Current Opinion in Virology
2022
Microbiome Analysis Using Next-Generation Sequencing in Urinary Tract Infections
Urogenital Tract Infection
2022
Coupling Imaging and Omics in Plankton Surveys: State-of-the-Art, Challenges, and Future Directions
Frontiers in Marine Science
2022
Long-Read Metagenomics Improves the Recovery of Viral Diversity from Complex Natural Marine Samples
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
RNA Viruses in Aquatic Ecosystems through the Lens of Ecological Genomics and Transcriptomics
Viruses
2022
Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome
Microorganisms
2022
Microbiome-Gut-Brain Axis
2022
VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data
Frontiers in Bioinformatics
2022
viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data
Genome Biology
2022
Uncovering 1058 Novel Human Enteric DNA Viruses Through Deep Long-Read Third-Generation Sequencing and Their Clinical Impact
Gastroenterology
2022
Uncovering novel human gut virome using ultra-deep metagenomic sequencing
Chinese Medical Journal
2022
Computational Tools for the Analysis of Uncultivated Phage Genomes
Microbiology and Molecular Biology Reviews
2022
Advances in Virus Research
2022
Newly identified HMO-2011-type phages reveal genomic diversity and biogeographic distributions of this marine viral group
The ISME Journal
2022
Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth
The ISME Journal
2022
Improved Mobilome Delineation in Fragmented Genomes
Frontiers in Bioinformatics
2022
MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations
Microbiome
2022
Recent insights into aquatic viruses: Emerging and reemerging pathogens, molecular features, biological effects, and novel investigative approaches
Water Biology and Security
2022
Diversity in the soil virosphere: to infinity and beyond?
Trends in Microbiology
2022
Emerging technologies in the study of the virome
Current Opinion in Virology
2022
Dynamic impact of virome on colitis and colorectal cancer: Immunity, inflammation, prevention and treatment
Seminars in Cancer Biology
2021
A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses
Microorganisms
2021
Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria
Nature Communications
2021
Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities
mSystems
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
The gut virome in Irritable Bowel Syndrome differs from that of controls
Gut Microbes
2021
Challenges of Studying the Human Virome – Relevant Emerging Technologies
Trends in Microbiology
2021
Illuminating the Virosphere Through Global Metagenomics
Annual Review of Biomedical Data Science
2021
Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens
Microbiome
2021
Interaction dynamics and virus–host range for estuarine actinophages captured by epicPCR
Nature Microbiology
2021
Probing the Mobilome: Discoveries in the Dynamic Microbiome
Trends in Microbiology
2021
iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology
ISME Communications
2021
Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads
DNA Research
2021
Phage Genome Annotation: Where to Begin and End
PHAGE
2021
Alpha-synuclein alters the faecal viromes of rats in a gut-initiated model of Parkinson’s disease
Communications Biology
2021
A library preparation optimized for metagenomics of RNA viruses
Molecular Ecology Resources
2021
Metagenomic tools in microbial ecology research
Current Opinion in Biotechnology
2021
Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay
Viruses
2021
Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types
PeerJ
2021
CheckV assesses the quality and completeness of metagenome-assembled viral genomes
Nature Biotechnology
2021
Genomic diversity, life strategies and ecology of marine HTVC010P-type pelagiphages
Microbial Genomics
2021
Glacier ice archives nearly 15,000-year-old microbes and phages
Microbiome
2021
Efficient dilution-to-extinction isolation of novel virus–host model systems for fastidious heterotrophic bacteria
The ISME Journal
2021
Reconstruction of plasmids by shotgun sequencing from environmental DNA: which bioinformatic workflow?
Briefings in Bioinformatics
2021
Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology
Applied and Environmental Microbiology
2021
The Power of Using Novel Nanopore Sequencing Technology for Diagnosis, Genomic and Pathological Studies of Covid-19
E3S Web of Conferences
2021
VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature
PeerJ
2020
Shining Light on Human Gut Bacteriophages
Frontiers in Cellular and Infection Microbiology
2020
Evaluation of a portable nanopore-based sequencer for detection of viruses in water
Journal of Virological Methods
2020
Single-virus genomics and beyond
Nature Reviews Microbiology
2020
Tara Oceans: towards global ocean ecosystems biology
Nature Reviews Microbiology
2020
Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice
mSystems
2020
Current Trends in Diagnostics of Viral Infections of Unknown Etiology
Viruses
2020
MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics
Microbiome
2020
Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities
Genome Research
2020
Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system
Environmental Microbiology
2020
High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method
Microbiome
2020
Microbiomes of Soils, Plants and Animals
2020
High-throughput sequencing (HTS) for the analysis of viral populations
Infection, Genetics and Evolution
2019
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
PeerJ
2019
Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
Genome Research
2019
PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning
GigaScience
2019
Studying the gut virome in the metagenomic era: challenges and perspectives
BMC Biology
2019
Gut Bacteriophage: Current Understanding and Challenges
Frontiers in Endocrinology
2019
Identification of Histoplasma causing an unexplained disease cluster in Matthews Ridge, Guyana
Biosafety and Health
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