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2025
Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes
Nature Biotechnology
2025
Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses
Nucleic Acids Research
2025
Clinical metagenomics for diagnosis and surveillance of viral pathogens
Nature Reviews Microbiology
2025
Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome
Environmental Microbiome
2025
Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation
PeerJ
2024
Varroa destructor economic injury levels and pathogens associated with colony losses in Western Canada
Frontiers in Bee Science
2024
Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security
Microorganisms
2024
Identification and classification of the genomes of novel microviruses in poultry slaughterhouse
Frontiers in Microbiology
2024
SnakeLines: integrated set of computational pipelines for sequencing reads
Journal of Integrative Bioinformatics
2024
Virome analyses of Amblyomma cajennense and Rhipicephalus microplus ticks collected in Colombia
Acta Tropica
2024
Blood virome research in myalgic encephalomyelitis/chronic fatigue syndrome: challenges and opportunities
Current Opinion in Virology
2023
Exploring the Potential of Bacteriophages on Earth and Beyond
Journal of the Indian Institute of Science
2023
Giant Virus Infection Signatures Are Modulated by Euphotic Zone Depth Strata and Iron Regimes of the Subantarctic Southern Ocean
mSystems
2023
Disturbed gut virome with potent interferonogenic property in systemic lupus erythematosus
Science Bulletin
2023
Evaluation of tools for taxonomic classification of viruses
Briefings in Functional Genomics
2023
FastViromeExplorer-Novel: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data
Journal of Computational Biology
2023
Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach
Viruses
2023
A remarkably diverse and well-organized virus community in a filter-feeding oyster
Microbiome
2023
ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis
Gut Microbes
2023
Breeding honey bees (Apis mellifera L.) for low and high Varroa destructor population growth: Gene expression of bees performing grooming behavior
Frontiers in Insect Science
2023
Methods in Molecular Biology
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
Characterization of the Urinary Metagenome and Virome in Healthy Children
Biomedicines
2022
Virome studies of food production systems: time for ‘farm to fork’ analyses
Current Opinion in Biotechnology
2022
Revolutionized virome research using systems microbiology approaches
Experimental Biology and Medicine
2022
Computational Tools for the Analysis of Uncultivated Phage Genomes
Microbiology and Molecular Biology Reviews
2022
Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies
Gut Pathogens
2022
Resolving the structure of phage–bacteria interactions in the context of natural diversity
Nature Communications
2022
Knowledge and perception of breast cancer among women of reproductive age in Chattogram, Bangladesh: A cross‐sectional survey
Health Science Reports
2022
Effects of Dietary Antimicrobial Growth Promoters on Performance Parameters and Abundance and Diversity of Broiler Chicken Gut Microbiome and Selection of Antibiotic Resistance Genes
Frontiers in Microbiology
2022
Development and Validation of a Bioinformatic Workflow for the Rapid Detection of Viruses in Biosecurity
Viruses
2022
Surveillance of Viruses in Varroa destructor Samples Collected from Honey Bee Colonies in Ontario, Canada, between 2015 and 2019
Journal of Apicultural Science
2022
A Metagenomic Investigation of Spatial and Temporal Changes in Sewage Microbiomes across a University Campus
mSystems
2022
Ecological Studies
2021
The human virome: assembly, composition and host interactions
Nature Reviews Microbiology
2021
Characterizing Enterotypes in Human Metagenomics: A Viral Perspective
Frontiers in Microbiology
2021
Role of human Pegivirus infections in whole Plasmodium falciparum sporozoite vaccination and controlled human malaria infection in African volunteers
Virology Journal
2021
Double-Stranded DNA Virus Assemblages in Groundwater in Three Informal Urban Settlements in Sub-Saharan Africa Differ from Each Other
ACS ES&T Water
2021
ViralRecall—A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in ‘Omic Data
Viruses
2021
Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria
Nature Communications
2021
Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade
eLife
2021
High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System
mSystems
2021
High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome
Scientific Reports
2021
Rapid screening and identification of viral pathogens in metagenomic data
BMC Medical Genomics
2020
A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level
GigaScience
2020
Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution
Nature Communications
2020
Experimental approaches to tracking mobile genetic elements in microbial communities
FEMS Microbiology Reviews
2019
Giant viral genomic signatures in the previously reported gut metagenomes of pre-school children in rural India
Archives of Virology
2019
Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications
2019
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands
PeerJ
2019
Long-term stability and Red Queen-like strain dynamics in marine viruses
Nature Microbiology
2019
virMine: automated detection of viral sequences from complex metagenomic samples
PeerJ
2019
Phage Therapy: A Practical Approach
2019
Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut
Viruses
2019
VFM: Identification of Bacteriophages From Metagenomic Bins and Contigs Based on Features Related to Gene and Genome Composition
IEEE Access
2019
The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes
Frontiers in Microbiology
2018
Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum
mBio
2018
Expansion of the metazoan virosphere: progress, pitfalls, and prospects
Current Opinion in Virology
2018
Maximal viral information recovery from sequence data using VirMAP
Nature Communications
2018
Proceedings of the International Conference "Mathematical Biology and Bioinformatics"
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