Diversity and Host Interactions among Virulent and Temperate Baltic Sea Flavobacterium Phages

Host-hijacking and planktonic piracy: how phages command the microbial high seas

(2019) Joanna Warwick-Dugdale et al.   Virology Journal

PHANOTATE: a novel approach to gene identification in phage genomes

(2019) Katelyn McNair et al.   BIOINFORMATICS

Genomic and seasonal variations among aquatic phages infecting the Baltic Sea Gammaproteobacteria Rheinheimera sp. BAL341

(2019) E. Nilsson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Multiple mechanisms drive phage infection efficiency in nearly identical hosts

(2018) Cristina Howard-Varona et al.   ISME Journal

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature 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

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

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

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

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

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

How to Name and Classify Your Phage: An Informal Guide

(2017) Evelien Adriaenssens et al.   Viruses-Basel

An Anthropocentric View of the Virosphere-Host Relationship

(2017) Rodrigo A. L. Rodrigues et al.   Frontiers in Microbiology

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

(2017) Simon Roux et al.   PeerJ

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

(2017) Natalya Yutin et al.   Nature Microbiology

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

(2016) Leighton Pritchard et al.   Analytical Methods

Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems

(2016) Karin Holmfeldt et al.   ENVIRONMENTAL MICROBIOLOGY

Viruses of microorganisms in the Baltic Sea: current state of research and perspectives

(2016) Sigitas Šulčius et al.   Marine Biology Research

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

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Comparative Genome Analysis Provides Insights into the Pathogenicity of Flavobacterium psychrophilum

(2016) Daniel Castillo et al.   PLoS One

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Variably lytic infection dynamics of largeBacteroidetespodovirus phi38:1 against twoCellulophaga balticahost strains

(2015) Vinh T. Dang et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics

(2015) Jennifer R Brum et al.   ISME Journal

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1.

(2015) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Simon Roux et al.   eLife

Detection and Quantification of Flavobacterium psychrophilum-Specific BacteriophagesIn Vivoin Rainbow Trout upon Oral Administration: Implications for Disease Control in Aquaculture

(2014) Rói Hammershaimb Christiansen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacteriophage Resistance Mechanisms in the Fish Pathogen Flavobacterium psychrophilum: Linking Genomic Mutations to Changes in Bacterial Virulence Factors

(2014) Daniel Castillo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Contrasting genomic patterns and infection strategies of two co-existingBacteroidetespodovirus genera

(2014) Karin Holmfeldt et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

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

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

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

(2014) Simon Roux et al.   eLife

Temperature dependent bacteriophages of a tropical bacterial pathogen

(2014) Jinyu Shan et al.   Frontiers in Microbiology

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

Isolation and characterization of phage–host systems from the Baltic Sea ice

(2013) Anne-Mari Luhtanen et al.   EXTREMOPHILES

Genomic structure of bacteriophage 6H and its distribution as prophage inFlavobacterium psychrophilumstrains

(2013) Daniel Castillo et al.   FEMS MICROBIOLOGY LETTERS

Ecology of marine Bacteroidetes: a comparative genomics approach

(2013) Beatriz Fernández-Gómez et al.   ISME Journal

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

Understanding Bacteriophage Specificity in Natural Microbial Communities

(2013) Britt Koskella et al.   Viruses-Basel

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic

(2012) Lisa Zeigler Allen et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Diversity of Flavobacterium psychrophilum and the potential use of its phages for protection against bacterial cold water disease in salmonids

(2012) D Castillo et al.   JOURNAL OF FISH DISEASES

Complete Genome Sequences of Two Persicivirga Bacteriophages, P12024S and P12024L

(2012) Ilnam Kang et al.   JOURNAL OF VIROLOGY

Complete Genome Sequence of Croceibacter Bacteriophage P2559S

(2012) Ilnam Kang et al.   JOURNAL OF VIROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups

(2012) Joakim Ågren et al.   PLoS One

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

Phage–bacteria infection networks

(2012) Joshua S. Weitz et al.   TRENDS IN MICROBIOLOGY

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

Easyfig: a genome comparison visualizer

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

Community Variability of Bacteria in Alpine Snow (Mont Blanc) Containing Saharan Dust Deposition and Their Snow Colonisation Potential

(2011) Maria S. Chuvochina et al.   MICROBES AND ENVIRONMENTS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Comparative Genomic Analysis of 60 Mycobacteriophage Genomes: Genome Clustering, Gene Acquisition, and Gene Size

(2010) Graham F. Hatfull et al.   JOURNAL OF MOLECULAR BIOLOGY

Bacteriophage resistance mechanisms

(2010) Simon J. Labrie et al.   NATURE REVIEWS MICROBIOLOGY

Cryptic prophages help bacteria cope with adverse environments

(2010) Xiaoxue Wang et al.   Nature Communications

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Position paper: The creation of a rational scheme for the nomenclature of viruses ofBacteriaandArchaea

(2009) Andrew M. Kropinski et al.   ENVIRONMENTAL MICROBIOLOGY

Bacteriophages drive strain diversification in a marineFlavobacterium: implications for phage resistance and physiological properties

(2009) Mathias Middelboe et al.   ENVIRONMENTAL MICROBIOLOGY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Molecular Taxonomy of Phytopathogenic Fungi: A Case Study in Peronospora

(2009) Markus Göker et al.   PLoS One

Isolation and Characterization of Bacteriophages Infecting the Fish Pathogen Flavobacterium psychrophilum

(2008) A. R. Stenholm et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?

(2008) John H Paul   ISME Journal

Elevated Lytic Phage Production as a Consequence of Particle Colonization by a Marine Flavobacterium (Cellulophaga sp.)

(2008) Lasse Riemann et al.   MICROBIAL ECOLOGY