Prophage Genomics and Ecology in the Family Rhodobacteraceae

clinker & clustermap.js: automatic generation of gene cluster comparison figures

(2021) Cameron L M Gilchrist et al.   BIOINFORMATICS

The genomic content and context of auxiliary metabolic genes in roseophages

(2021) Xingyu Huang et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes

(2020) Cynthia B. Silveira et al.   BMC GENOMICS

Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column

(2020) Elaine Luo et al.   ISME Journal

Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom

(2020) Xiao-Peng Du et al.   Microorganisms

Genetically similar temperate phages form coalitions with their shared host that lead to niche-specific fitness effects

(2020) Jonelle T. R. Basso et al.   ISME Journal

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

From Orphan Phage to a Proposed New Family–The Diversity of N4-Like Viruses

(2020) Johannes Wittmann et al.   Antibiotics-Basel

Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages

(2020) Amjad Khan et al.   PLoS Computational Biology

Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean

(2020) Hiroto Kaneko et al.   iScience

Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems

(2019) Vera Bischoff et al.   ISME Journal

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea

(2019) Yantao Liang et al.   Frontiers in Microbiology

Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems

(2019) Amy E. Zimmerman et al.   NATURE REVIEWS MICROBIOLOGY

Charting the diversity of uncultured viruses of Archaea and Bacteria

(2019) F. H. Coutinho et al.   BMC BIOLOGY

Diverse, Abundant, and Novel Viruses Infecting the Marine Roseobacter RCA Lineage

(2019) Zefeng Zhang et al.   mSystems

Scaling read aligners to hundreds of threads on general-purpose processors

(2018) Ben Langmead et al.   BIOINFORMATICS

Microarray analysis of gene expression of Dinoroseobacter shibae DFL12 T in response to phage R2C infection

(2018) Yunlan Yang et al.   Marine Genomics

Screening and characterization of prophages in Desulfovibrio genomes

(2018) Josicelli Souza Crispim et al.   Scientific Reports

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

(2018) Qiang Zheng et al.   Frontiers in Microbiology

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

Profiles of quorum sensing (QS)-related sequences in phycospheric microorganisms during a marine dinoflagellate bloom, as determined by a metagenomic approach

(2018) Xinqing Huang et al.   MICROBIOLOGICAL RESEARCH

Bacteriophages That Infect Marine Roseobacters: Genomics and Ecology

(2018) Yuanchao Zhan et al.   ENVIRONMENTAL MICROBIOLOGY

Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function

(2017) Sheila Roitman et al.   ISME Journal

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats

(2017) Meinhard Simon et al.   ISME Journal

Not a barrier but a key: How bacteriophages exploit host's O-antigen as an essential receptor to initiate infection

(2017) Nina K. Broeker et al.   MOLECULAR MICROBIOLOGY

Seasonal Dynamics and Metagenomic Characterization of Marine Viruses in Goseong Bay, Korea

(2017) Jinik Hwang et al.   PLoS One

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Pneumococcal prophages are diverse, but not without structure or history

(2017) Angela B. Brueggemann et al.   Scientific Reports

Characterization and Complete Genome Sequences of Three N4-Like Roseobacter Phages Isolated from the South China Sea

(2016) Baolian Li et al.   CURRENT MICROBIOLOGY

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

(2016) Marie Touchon et al.   ISME Journal

Biofilm plasmids with a rhamnose operon are widely distributed determinants of the ‘swim-or-stick’ lifestyle in roseobacters

(2016) Victoria Michael et al.   ISME Journal

Impact of Microalgae-Bacteria Interactions on the Production of Algal Biomass and Associated Compounds

(2016) Juan Fuentes et al.   Marine Drugs

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

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

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

Metagenomic Analysis of Virioplankton of the Subtropical Jiulong River Estuary, China

(2016) Lanlan Cai et al.   Viruses-Basel

A novel roseobacter phage possesses features of podoviruses, siphoviruses, prophages and gene transfer agents

(2016) Yuanchao Zhan et al.   Scientific Reports

Piggyback-the-Winner in host-associated microbial communities

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

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

(2015) Jessica M Labonté et al.   ISME Journal

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Plasmid curing and the loss of grip – The 65-kb replicon of Phaeobacter inhibens DSM 17395 is required for biofilm formation, motility and the colonization of marine algae

(2015) Oliver Frank et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

The green impact: bacterioplankton response toward a phytoplankton spring bloom in the southern North Sea assessed by comparative metagenomic and metatranscriptomic approaches

(2015) Bernd Wemheuer et al.   Frontiers in Microbiology

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Complete Genome Sequence Analysis of Two Pseudomonas plecoglossicida Phages, Potential Therapeutic Agents

(2014) Yasuhiko Kawato et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Host-dependent differences in abundance, composition and host range of cyanophages from the Red Sea

(2014) Naama P. Dekel-Bird et al.   ENVIRONMENTAL MICROBIOLOGY

Evolutionary Ecology of the Marine Roseobacter Clade

(2014) Haiwei Luo et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

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

Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes

(2014) Jacqueline Z.-M. Chan et al.   Frontiers in Microbiology

Extrachromosomal, extraordinary and essential—the plasmids of the Roseobacter clade

(2013) Jörn Petersen et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition

(2013) Nana Yaw D Ankrah et al.   ISME Journal

Evolution of Divergent Life History Strategies in Marine Alphaproteobacteria

(2013) H. Luo et al.   mBio

Enterococcus faecalis Prophage Dynamics and Contributions to Pathogenic Traits

(2013) Renata C. Matos et al.   PLoS Genetics

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

(2012) Limin Fu et al.   BIOINFORMATICS

Competition and the origins of novelty: experimental evolution of niche-width expansion in a virus

(2012) L. M. Bono et al.   Biology Letters

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

(2012) Lev Rabinovich et al.   CELL

Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes

(2012) Sabine Lenk et al.   ISME Journal

The Adaptation of Temperate Bacteriophages to Their Host Genomes

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Evolution and Diversity of the Microviridae Viral Family through a Collection of 81 New Complete Genomes Assembled from Virome Reads

(2012) Simon Roux et al.   PLoS One

Metagenomes of Mediterranean Coastal Lagoons

(2012) Rohit Ghai et al.   Scientific Reports

Influence of vitamin B auxotrophy on nitrogen metabolism in eukaryotic phytoplankton

(2012) Erin M. Bertrand et al.   Frontiers in Microbiology

The Role of B Vitamins in Marine Biogeochemistry

(2011) Sergio A. Sañudo-Wilhelmy et al.   Annual Review of Marine Science

Host responses of a marine bacterium, Roseobacter denitrificans OCh114, to phage infection

(2011) Yongyu Zhang et al.   ARCHIVES OF MICROBIOLOGY

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

Roseobacticides: Small Molecule Modulators of an Algal-Bacterial Symbiosis

(2011) Mohammad R. Seyedsayamdost et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Insights into the Evolution of Vitamin B12 Auxotrophy from Sequenced Algal Genomes

(2011) K. E. Helliwell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Microviridae Goes Temperate: Microvirus-Related Proviruses Reside in the Genomes of Bacteroidetes

(2011) Mart Krupovic et al.   PLoS One

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

Complete genome sequence of a marine roseophage provides evidence into the evolution of gene transfer agents in alphaproteobacteria

(2011) Sijun Huang et al.   Virology Journal

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Molecular mechanisms underlying roseobacter–phytoplankton symbioses

(2010) Haifeng Geng et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

Molecular and physiological analysis of three Pseudomonas aeruginosa phages belonging to the “N4-like viruses”

(2010) Pieter-Jan Ceyssens et al.   VIROLOGY

Searching for a "Hidden" Prophage in a Marine Bacterium

(2009) Y. Zhao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial Diversity and Bioprospecting for Cold-Active Lipases, Amylases and Proteases, from Culturable Bacteria of Kongsfjorden and Ny-Ålesund, Svalbard, Arctic

(2009) T. N. R. Srinivas et al.   CURRENT MICROBIOLOGY

Distribution ofRoseobacterRCA and SAR11 lineages and distinct bacterial communities from the subtropics to the Southern Ocean

(2009) Helge-Ansgar Giebel et al.   ENVIRONMENTAL MICROBIOLOGY

Genome sequences of two novel phages infecting marine roseobacters

(2009) Yanlin Zhao et al.   ENVIRONMENTAL MICROBIOLOGY