Knowing and Naming: Phage Annotation and Nomenclature for Phage Therapy

Fast and accurate protein structure search with Foldseek

(2023) Michel van Kempen et al.   NATURE BIOTECHNOLOGY

MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes

(2023) Aaron Pfennig et al.   JOURNAL OF MOLECULAR BIOLOGY

Corrigendum: VirionFinder: Identification of Complete and Partial Prokaryote Virus Virion Protein From Virome Data Using the Sequence and Biochemical Properties of Amino Acids

(2022) Zhencheng Fang et al.   Frontiers in Microbiology

ColabFold: making protein folding accessible to all

(2022) Milot Mirdita et al.   NATURE METHODS

Phage-antibiotic combination is a superior treatment against Acinetobacter baumannii in a preclinical study

(2022) Fernando L. Gordillo Altamirano et al.   EBioMedicine

Identification of Phage Receptor-Binding Protein Sequences with Hidden Markov Models and an Extreme Gradient Boosting Classifier

(2022) Dimitri Boeckaerts et al.   Viruses-Basel

Detection of nucleotide modifications in bacteria and bacteriophages: Strengths and limitations of current technologies and software

(2022) Tue Kjærgaard Nielsen et al.   MOLECULAR ECOLOGY

Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

(2021) Dimitri Boeckaerts et al.   Scientific Reports

Phage φAB6-Borne Depolymerase Combats Acinetobacter baumannii Biofilm Formation and Infection

(2021) Md. Shahed-Al-Mahmud et al.   Antibiotics-Basel

MultiPhATE2: code for functional annotation and comparison of phage genomes

(2021) Carol L Ecale Zhou et al.   G3-Genes Genomes Genetics

BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains

(2021) Adam J. Hockenberry et al.   PeerJ

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes

(2021) Patricia P Chan et al.   NUCLEIC ACIDS RESEARCH

AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

(2021) Michael Feldgarden et al.   Scientific Reports

VFDB 2022: a general classification scheme for bacterial virulence factors

(2021) Bo Liu et al.   NUCLEIC ACIDS RESEARCH

Double-Layer Agar (DLA) Modifications for the First Step of the Phage-Antibiotic Synergy (PAS) Identification

(2021) Xymena Stachurska et al.   Antibiotics-Basel

Diversity and Function of Phage Encoded Depolymerases

(2020) Leandra E. Knecht et al.   Frontiers in Microbiology

PVPred-SCM: Improved Prediction and Analysis of Phage Virion Proteins Using a Scoring Card Method

(2020) Phasit Charoenkwan et al.   Cells

The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks

(2020)   Nature Microbiology

Metaviral SPAdes: assembly of viruses from metagenomic data

(2020) Dmitry Antipov et al.   BIOINFORMATICS

Standardized bacteriophage purification for personalized phage therapy

(2020) Tiffany Luong et al.   Nature Protocols

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

Bacteriophages as Environmental Reservoirs of Antibiotic Resistance

(2019) William Calero-Cáceres et al.   TRENDS IN MICROBIOLOGY

PHANOTATE: a novel approach to gene identification in phage genomes

(2019) Katelyn McNair et al.   BIOINFORMATICS

MyDGR: a server for identification and characterization of diversity-generating retroelements

(2019) Fatemeh Sharifi et al.   NUCLEIC ACIDS RESEARCH

Viruses as key reservoirs of antibiotic resistance genes in the environment

(2019) Didier Debroas et al.   ISME Journal

A Novel Polysaccharide Depolymerase Encoded by the Phage SH-KP152226 Confers Specific Activity Against Multidrug-Resistant Klebsiella pneumoniae via Biofilm Degradation

(2019) Yunqiang Wu et al.   Frontiers in Microbiology

PVP-SVM: Sequence-Based Prediction of Phage Virion Proteins Using a Support Vector Machine

(2018) Balachandran Manavalan et al.   Frontiers in Microbiology

A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage

(2018) Sean Benler et al.   Microbiome

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

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

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

How to Name and Classify Your Phage: An Informal Guide

(2017) Evelien Adriaenssens et al.   Viruses-Basel

Bacteriophages Contribute to the Spread of Antibiotic Resistance Genes among Foodborne Pathogens of the Enterobacteriaceae Family – A Review

(2017) Anna Colavecchio et al.   Frontiers in Microbiology

Bacteriophage evolution differs by host, lifestyle and genome

(2017) Travis N. Mavrich et al.   Nature Microbiology

Two T7-like Bacteriophages, K5-2 and K5-4, Each Encodes Two Capsule Depolymerases: Isolation and Functional Characterization

(2017) Pei-Fang Hsieh et al.   Scientific Reports

PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data

(2017) Julian R. Garneau et al.   Scientific Reports

Prophages mediate defense against phage infection through diverse mechanisms

(2016) Joseph Bondy-Denomy et al.   ISME Journal

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

(2016) François Enault et al.   ISME Journal

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

(2016) Ana Laura Grazziotin et al.   NUCLEIC ACIDS RESEARCH

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

(2016) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

The Tailocin Tale: Peeling off Phage Tails

(2015) Maarten G.K. Ghequire et al.   TRENDS IN MICROBIOLOGY

Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9

(2015) Alexandra L. Bryson et al.   mBio

Stop codon reassignments in the wild

(2014) N. N. Ivanova et al.   SCIENCE

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

(2013) Sheetal R. Modi et al.   NATURE

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

(2013) J. H. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of the ELPhiS Prophage from Salmonella enterica Serovar Enteritidis Strain LK5

(2012) L. Farris Hanna et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PHACTS, a computational approach to classifying the lifestyle of phages

(2012) Katelyn McNair et al.   BIOINFORMATICS

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS