Bacteria have numerous distinctive groups of phage–plasmids with conserved phage and variable plasmid gene repertoires

Protein-Mediated and RNA-Based Origins of Replication of Extrachromosomal Mycobacterial Prophages

(2020) Katherine S. Wetzel et al.   mBio

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

(2020) Guillaume Gautreau et al.   PLoS Computational Biology

Mosaic plasmids are abundant and unevenly distributed across prokaryotic taxa

(2019) Mitchell W. Pesesky et al.   PLASMID

Evolution of Superinfection Immunity in Cluster A Mycobacteriophages

(2019) Travis N. Mavrich et al.   mBio

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

(2019) Yin Ning Chiang et al.   PLoS Pathogens

Diversity of P1 phage-like elements in multidrug resistant Escherichia coli

(2019) Carola Venturini et al.   Scientific Reports

Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements

(2018) Jean Cury et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome sequence of Escherichia coli tailed phage D6 and the diversity of Enterobacteriales circular plasmid prophages

(2018) Eddie B. Gilcrease et al.   VIROLOGY

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis

(2018) Andrey N. Shkoporov et al.   Nature Communications

ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R

(2017) Marvin N. Wright et al.   Journal of Statistical Software

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

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Integrative and conjugative elements and their hosts: composition, distribution and organization

(2017) Jean Cury et al.   NUCLEIC ACIDS RESEARCH

Characterization of a P1-like bacteriophage carrying CTX-M-27 in Salmonella spp. resistant to third generation cephalosporins isolated from pork in China

(2017) Ling Yang et al.   Scientific Reports

Large Preferred Region for Packaging of Bacterial DNA by phiC725A, a Novel Pseudomonas aeruginosa F116-Like Bacteriophage

(2017) Christine Pourcel et al.   PLoS One

A Phage-Like IncY Plasmid Carrying the mcr-1 Gene in Escherichia coli from a Pig Farm in China

(2016) Chunping Zhang et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements

(2016) Jaime Iranzo et al.   JOURNAL OF VIROLOGY

Function, expression, specificity, diversity and incompatibility of actinobacteriophageparABSsystems

(2016) Rebekah M. Dedrick et al.   MOLECULAR MICROBIOLOGY

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

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

Virus Variation Resource – improved response to emergent viral outbreaks

(2016) Eneida L. Hatcher et al.   NUCLEIC ACIDS RESEARCH

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Why Be Temperate: Lessons from Bacteriophage λ

(2016) Sylvain Gandon   TRENDS 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

Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy

(2015) Masaki Shintani et al.   Frontiers in Microbiology

Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals

(2015) Lukasz Dziewit et al.   Frontiers in Microbiology

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

The Legacy of Nat Sternberg: The Genesis of Cre-loxTechnology

(2015) Michael Yarmolinsky et al.   Annual Review of Virology

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Beyond the Chromosome: The Prevalence of Unique Extra-Chromosomal Bacteriophages with Integrated Virulence Genes in Pathogenic Staphylococcus aureus

(2014) Bryan Utter et al.   PLoS One

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

(2014) Sophie S. Abby et al.   PLoS One

Phages Preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis: Past, Present and Future

(2014) Annika Gillis et al.   Viruses-Basel

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

Narrow-Host-Range Bacteriophages That Infect Rhizobium etli Associate with Distinct Genomic Types

(2013) Rosa Isela Santamaría et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Core Lipopolysaccharide-Specific Phage SSU5 as an Auxiliary Component of a Phage Cocktail for Salmonella Biocontrol

(2013) Minsik Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization and complete genome sequence of a virulent bacteriophage B4 infecting food-borne pathogenic Bacillus cereus

(2013) Ju-Hoon Lee et al.   ARCHIVES OF VIROLOGY

Genome sequence and analysis of a broad-host range lytic bacteriophage that infects the Bacillus cereus group

(2013) Tarek F El-Arabi et al.   Virology Journal

Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses

(2013) Mart Krupovic   Current Opinion in Virology

Prokaryote viruses studied by electron microscopy

(2012) H.-W. Ackermann et al.   ARCHIVES OF VIROLOGY

A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T

(2012) Shivakumara Siddaramappa et al.   BMC GENOMICS

Pilus biogenesis at the outer membrane of Gram-negative bacterial pathogens

(2012) William J Allen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Complete Genome Sequence of Bacteriophage SSU5 Specific for Salmonella enterica serovar Typhimurium Rough Strains

(2012) M. Kim et al.   JOURNAL OF VIROLOGY

The Adaptation of Temperate Bacteriophages to Their Host Genomes

(2012) Louis-Marie Bobay et al.   MOLECULAR BIOLOGY AND EVOLUTION

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Prevalence and Significance of Plasmid Maintenance Functions in the Virulence Plasmids of Pathogenic Bacteria

(2011) Manjistha Sengupta et al.   INFECTION AND IMMUNITY

Characterization of a novel temperate phage originating from a cereulide-producing Bacillus cereus strain

(2011) Pierre R. Smeesters et al.   RESEARCH IN MICROBIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

The SPO1-related bacteriophages

(2010) Jochen Klumpp et al.   ARCHIVES OF VIROLOGY

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex

(2010) Karlene H Lynch et al.   BMC GENOMICS

Plasmid segregation: how to survive as an extra piece of DNA

(2010) Jeanne Salje   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Mobility of Plasmids

(2010) C. Smillie et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

N15: The linear phage–plasmid

(2010) Nikolai V. Ravin   PLASMID

Introducing the bacterial ‘chromid’: not a chromosome, not a plasmid

(2010) Peter W. Harrison et al.   TRENDS IN MICROBIOLOGY

Characterization of a New Plasmid-Like Prophage in a Pandemic Vibrio parahaemolyticus O3:K6 Strain

(2009) S.-F. Lan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT