Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework

Constructing benchmark test sets for biological sequence analysis using independent set algorithms

(2022) Samantha Petti et al.   PLoS Computational Biology

Accurate identification of bacteriophages from metagenomic data using Transformer

(2022) Jiayu Shang et al.   BRIEFINGS IN BIOINFORMATICS

VPF-Class: Taxonomic assignment and host prediction of uncultivated viruses based on viral protein families

(2021) Joan Carles Pons et al.   BIOINFORMATICS

Fast and sensitive taxonomic assignment to metagenomic contigs

(2021) M Mirdita et al.   BIOINFORMATICS

Bacteriophage classification for assembled contigs using graph convolutional network

(2021) Jiayu Shang et al.   BIOINFORMATICS

Phage diversity, genomics and phylogeny

(2020) Moïra B. Dion et al.   NATURE REVIEWS MICROBIOLOGY

Seeker: alignment-free identification of bacteriophage genomes by deep learning

(2020) Noam Auslander et al.   NUCLEIC ACIDS RESEARCH

Phage Therapy in Gastrointestinal Diseases

(2020) Beatriz Gutiérrez et al.   Microorganisms

CAMISIM: simulating metagenomes and microbial communities

(2019) Adrian Fritz et al.   Microbiome

Classifying the Unclassified: A Phage Classification Method

(2019) Cynthia Maria Chibani et al.   Viruses-Basel

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales

(2019) Soo Jen Low et al.   Nature Microbiology

Genetic transduction by phages and chromosomal islands: The new and noncanonical

(2019) Yin Ning Chiang et al.   PLoS Pathogens

Gut Bacteriophage: Current Understanding and Challenges

(2019) Thomas D. S. Sutton et al.   Frontiers in Endocrinology

The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

(2018) Pakorn Aiewsakun et al.   Microbiome

A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria

(2018) Kathryn M. Kauffman et al.   NATURE

Applicability of commercial phage-based products against Listeria monocytogenes for improvement of food safety in Spanish dry-cured ham and food contact surfaces

(2017) Diana Gutiérrez et al.   FOOD CONTROL

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Lysogeny in nature: mechanisms, impact and ecology of temperate phages

(2017) Cristina Howard-Varona et al.   ISME Journal

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

(2017) Elliot J Lefkowitz et al.   NUCLEIC ACIDS RESEARCH

The Human Gut Phage Community and Its Implications for Health and Disease

(2017) Pilar Manrique et al.   Viruses-Basel

Jumbo Bacteriophages: An Overview

(2017) Yihui Yuan et al.   Frontiers in Microbiology

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

(2017) Benjamin Bolduc et al.   PeerJ

Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory

(2017) Kurt E. Williamson et al.   Annual Review of Virology

Bacteriophages to reduce gut carriage of antibiotic resistant uropathogens with low impact on microbiota composition

(2016) Matthieu Galtier et al.   ENVIRONMENTAL MICROBIOLOGY

Viruses as Winners in the Game of Life

(2016) Ana Georgina Cobián Güemes et al.   Annual Review of Virology

Piggyback-the-Winner in host-associated microbial communities

(2016) Cynthia B Silveira et al.   npj Biofilms and Microbiomes

Bacteriophage Combinations Significantly Reduce Clostridium difficile GrowthIn Vitroand ProliferationIn Vivo

(2015) Janet Y. Nale et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Early life dynamics of the human gut virome and bacterial microbiome in infants

(2015) Efrem S Lim et al.   NATURE MEDICINE

Transfer of antibiotic-resistance genes via phage-related mobile elements

(2015) Maryury Brown-Jaque et al.   PLASMID

Biogeography of Viruses in the Sea

(2015) Cheryl-Emiliane T. Chow et al.   Annual Review of Virology

Characterization of virus-like particles associated with the human faecal and caecal microbiota

(2014) Lesley Hoyles et al.   RESEARCH IN MICROBIOLOGY

Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses

(2013) Jennifer R Brum et al.   ISME Journal

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

(2013) Pascal Hingamp et al.   ISME Journal

Understanding Bacteriophage Specificity in Natural Microbial Communities

(2013) Britt Koskella et al.   Viruses-Basel

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

(2012) D. M. Kristensen et al.   JOURNAL OF BACTERIOLOGY

Efficacy of cocktail phage therapy in treating Vibrio cholerae infection in rabbit model

(2012) Abhishek Jaiswal et al.   MICROBES AND INFECTION

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

(2011) M. Krupovic et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Phage and Their Lysins as Biocontrol Agents for Food Safety Applications

(2010) Brid Cof fey et al.   Annual Review of Food Science and Technology

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Bacteriophage genomics

(2008) Graham F Hatfull   CURRENT OPINION IN MICROBIOLOGY

Bacteriophages and their application in food safety

(2008) P. García et al.   LETTERS IN APPLIED MICROBIOLOGY