Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment

Xenogeneic silencing relies on temperature-dependent phosphorylation of the host H-NS protein in Shewanella

(2021) Xiaoxiao Liu et al.   NUCLEIC ACIDS RESEARCH

Isolation of an archaeon at the prokaryote–eukaryote interface

(2020) Hiroyuki Imachi et al.   NATURE

Discovery of several thousand highly diverse circular DNA viruses

(2020) Michael J Tisza et al.   eLife

Lysogenic host–virus interactions in SAR11 marine bacteria

(2020) Robert M. Morris et al.   Nature Microbiology

Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts

(2020) Kosuke Fujimoto et al.   Cell Host & Microbe

Bacterial chemolithoautotrophy via manganese oxidation

(2020) Hang Yu et al.   NATURE

Identification of bacteria-derived urease in the coral gastric cavity

(2020) Yiqing Zhou et al.   Science China-Earth Sciences

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

(2020) Noam Auslander et al.   NUCLEIC ACIDS RESEARCH

Bacterial Retrons Function In Anti-Phage Defense

(2020) Adi Millman et al.   CELL

Coupling S-adenosylmethionine–dependent methylation to growth: Design and uses

(2019) Hao Luo et al.   PLOS BIOLOGY

Prophage LambdaSo uses replication interference to suppress reproduction of coexisting temperate phage MuSo2 in Shewanella oneidensis MR‐1

(2019) Qinggong Guo et al.   ENVIRONMENTAL MICROBIOLOGY

Origin of viruses: primordial replicators recruiting capsids from hosts

(2019) Mart Krupovic et al.   NATURE REVIEWS MICROBIOLOGY

Prophage Hunter: an integrative hunting tool for active prophages

(2019) Wenchen Song et al.   NUCLEIC ACIDS RESEARCH

Symbiosis of a P2‐family phage and deep‐sea Shewanella putrefaciens

(2019) Xiaoxiao Liu et al.   ENVIRONMENTAL MICROBIOLOGY

Unstable chromosome rearrangements in Staphylococcus aureus cause phenotype switching associated with persistent infections

(2019) Romain Guérillot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire

(2019) Eugene V. Koonin et al.   NATURE REVIEWS GENETICS

Antagonism between coral pathogen Vibrio coralliilyticus and other bacteria in the gastric cavity of scleractinian coral Galaxea fascicularis

(2019) Kaihao Tang et al.   Science China-Earth Sciences

Cross-resistance to phage infection in Listeria monocytogenes serotype 1/2a mutants

(2019) Danielle M. Trudelle et al.   FOOD MICROBIOLOGY

Contemporary Phage Biology: From Classic Models to New Insights

(2018) Gal Ofir et al.   CELL

Reef invertebrate viromics: diversity, host specificity and functional capacity

(2018) Patrick W. Laffy et al.   ENVIRONMENTAL MICROBIOLOGY

Lysogeny is prevalent and widely distributed in the murine gut microbiota

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

Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis

(2018) Natalya Yutin et al.   Virology Journal

A Virus Infecting Marine Photoheterotrophic Alphaproteobacteria (Citromicrobium spp.) Defines a New Lineage of ssDNA Viruses

(2018) Qiang Zheng et al.   Frontiers in Microbiology

Spontaneously induced prophages are abundant in a naturally evolved bacterial starter culture and deliver competitive advantage to the host

(2018) Svetlana Alexeeva et al.   BMC MICROBIOLOGY

The smallest ssDNA phage infecting a marine bacterium

(2018) Yuanchao Zhan et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2018) Kathryn M. Kauffman et al.   NATURE

Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum

(2018) Mélanie Massonnet et al.   Frontiers in Microbiology

Excisionase in Pf filamentous prophage controls lysis‐lysogeny decision‐making in Pseudomonas aeruginosa

(2018) Yangmei Li et al.   MOLECULAR MICROBIOLOGY

Virus found in a boreal lake links ssDNA and dsDNA viruses

(2017) Elina Laanto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2017) Jie Ren et al.   Microbiome

Cold adaptation regulated by cryptic prophage excision in Shewanella oneidensis

(2016) Zhenshun Zeng et al.   ISME Journal

Lytic to temperate switching of viral communities

(2016) B. Knowles et al.   NATURE

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

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

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

(2016) Jana Trifinopoulos et al.   NUCLEIC ACIDS RESEARCH

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

The Significance of Mutualistic Phages for Bacterial Ecology and Evolution

(2016) Nancy Obeng et al.   TRENDS IN MICROBIOLOGY

Piggyback-the-Winner in host-associated microbial communities

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

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Filamentous Bacteriophage Promote Biofilm Assembly and Function

(2015) Patrick R. Secor et al.   Cell Host & Microbe

A new perspective on lysogeny: prophages as active regulatory switches of bacteria

(2015) Ron Feiner et al.   NATURE REVIEWS MICROBIOLOGY

Physiological Function of Rac Prophage During Biofilm Formation and Regulation of Rac Excision in Escherichia coli K-12

(2015) Xiaoxiao Liu et al.   Scientific Reports

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

(2015) Simon Roux et al.   eLife

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Genome-Based Identification of Active Prophage Regions by Next Generation Sequencing in Bacillus licheniformis DSM13

(2015) Robert Hertel et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

BREX is a novel phage resistance system widespread in microbial genomes

(2014) T. Goldfarb et al.   EMBO JOURNAL

Impact of Spontaneous Prophage Induction on the Fitness of Bacterial Populations and Host-Microbe Interactions

(2014) Arun M. Nanda et al.   JOURNAL OF BACTERIOLOGY

Bacterial Genome Instability

(2014) E. Darmon et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Potential role of viruses in white plague coral disease

(2013) Nitzan Soffer et al.   ISME Journal

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rapid evolution of the human gut virome

(2013) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Twelve previously unknown phage genera are ubiquitous in global oceans

(2013) K. Holmfeldt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

Structure Unifies the Viral Universe

(2012) Nicola G.A. Abrescia et al.   Annual Review of Biochemistry

GemSIM: general, error-model based simulator of next-generation sequencing data

(2012) Kerensa E McElroy et al.   BMC GENOMICS

Prophage Excision Activates Listeria Competence Genes that Promote Phagosomal Escape and Virulence

(2012) Lev Rabinovich et al.   CELL

Uncoupled viral and bacterial distributions in coral reef waters of Tuamotu Archipelago (French Polynesia)

(2012) Marc Bouvy et al.   MARINE POLLUTION BULLETIN

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

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism

(2011) L. R. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic analysis of the coral holobiont during a natural bleaching event on the Great Barrier Reef

(2011) Raechel Littman et al.   Environmental Microbiology Reports

A Holistic Approach to Marine Eco-Systems Biology

(2011) Eric Karsenti et al.   PLOS BIOLOGY

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Cryptic prophages help bacteria cope with adverse environments

(2010) Xiaoxue Wang et al.   Nature Communications

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms

(2009) Xiaoxue Wang et al.   ISME Journal

Prophinder: a computational tool for prophage prediction in prokaryotic genomes

(2008) Gipsi Lima-Mendez et al.   BIOINFORMATICS