Mining of Thousands of Prokaryotic Genomes Reveals High Abundance of Prophages with a Strictly Narrow Host Range

A novel vieuvirus from multidrug-resistant Acinetobacter baumannii

(2021) Gamaliel López-Leal et al.   ARCHIVES OF VIROLOGY

Massive expansion of human gut bacteriophage diversity

(2021) Luis F. Camarillo-Guerrero et al.   CELL

Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins

(2021) Sean Carim et al.   ISME Journal

Common Oral Medications Lead to Prophage Induction in Bacterial Isolates from the Human Gut

(2021) Steven G. Sutcliffe et al.   Viruses-Basel

Analysis of a Novel Bacteriophage vB_AchrS_AchV4 Highlights the Diversity of Achromobacter Viruses

(2021) Laura Kaliniene et al.   Viruses-Basel

Prophages Encode Antibiotic Resistance Genes in Acinetobacter baumannii

(2020) Gamaliel López-Leal et al.   Microbial Drug Resistance

Metaviral SPAdes: assembly of viruses from metagenomic data

(2020) Dmitry Antipov et al.   BIOINFORMATICS

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter

(2019) Valeria Mateo-Estrada et al.   Genome Biology and Evolution

Lysogeny is prevalent and widely distributed in the murine gut microbiota

(2018) Min-Soo Kim et al.   ISME Journal

Phage morons play important roles in controlling Pseudomonas aeruginosa phenotypes

(2018) Yu-Fan Tsao et al.   JOURNAL OF BACTERIOLOGY

Genomic analysis of Acinetobacter baumannii prophages reveals remarkable diversity and suggests profound impact on bacterial virulence and fitness

(2018) Ana Rita Costa et al.   Scientific Reports

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

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

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

(2017) Kazuma Nakano et al.   Human Cell

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

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

Cryptic prophages as targets for drug development

(2016) Xiaoxue Wang et al.   DRUG RESISTANCE UPDATES

Genetic and life-history traits associated with the distribution of prophages in bacteria

(2016) Marie Touchon et al.   ISME Journal

Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction

(2016) Ovidiu Popa et al.   ISME Journal

Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences

(2016) Marie A. Chattaway et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences

(2016) Nathan A. Ahlgren et al.   NUCLEIC ACIDS RESEARCH

Temperate phages both mediate and drive adaptive evolution in pathogen biofilms

(2016) Emily V. Davies et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lifemap: Exploring the Entire Tree of Life

(2016) Damien M. de Vienne   PLOS BIOLOGY

Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation

(2016) Emily A. Pettengill et al.   Frontiers in Microbiology

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla

(2015) Kema Malki et al.   Virology Journal

Independent Co-Option of a Tailed Bacteriophage into a Killing Complex in Pseudomonas

(2015) Kevin L. Hockett et al.   mBio

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Pervasive domestication of defective prophages by bacteria

(2014) L.-M. Bobay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linking the lytic and lysogenic bacteriophage cycles to environmental conditions, host physiology and their variability in coastal lagoons

(2013) C. F. Maurice et al.   ENVIRONMENTAL MICROBIOLOGY

Filamentous phages of Ralstonia solanacearum: double-edged swords for pathogenic bacteria

(2013) Takashi Yamada   Frontiers in Microbiology

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens

(2012) Ben Busby et al.   ENVIRONMENTAL MICROBIOLOGY

The proportional lack of archaeal pathogens: Do viruses/phages hold the key?

(2011) Erin E. Gill et al.   BIOESSAYS

Sequencing technologies and genome sequencing

(2011) Chandra Shekhar Pareek et al.   JOURNAL OF APPLIED GENETICS

The Filamentous Phage ϕRSS1 Enhances Virulence of PhytopathogenicRalstonia solanacearumon Tomato

(2011) Hardian S. Addy et al.   PHYTOPATHOLOGY

Metagenomic signatures of 86 microbial and viral metagenomes

(2009) Dana Willner et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles

(2008) David Vallenet et al.   PLoS One

Host recognition and integration of filamentous phage ϕRSM in the phytopathogen, Ralstonia solanacearum

(2008) Ahmed Askora et al.   VIROLOGY