Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay

Enterococcus phage Nonaheksakonda infecting clinical isolates of Enterococcus faecalis represents a new lineage in the family Siphoviridae

(2021) Nikoline S. Olsen et al.   ARCHIVES OF VIROLOGY

Efficient dilution-to-extinction isolation of novel virus–host model systems for fastidious heterotrophic bacteria

(2021) Holger H. Buchholz et al.   ISME Journal

A Case of Phage Therapy against Pandrug-Resistant Achromobacter xylosoxidans in a 12-Year-Old Lung-Transplanted Cystic Fibrosis Patient

(2021) David Lebeaux et al.   Viruses-Basel

SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts

(2021) Ruoshi Zhang et al.   BIOINFORMATICS

Clades of huge phages from across Earth’s ecosystems

(2020) Basem Al-Shayeb et al.   NATURE

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Isolation and Characterization of Lactobacillus brevis Phages

(2019) Feyereisen et al.   Viruses-Basel

Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands

(2019) Joanna Warwick-Dugdale et al.   PeerJ

A Protocol for Extraction of Infective Viromes Suitable for Metagenomics Sequencing from Low Volume Fecal Samples

(2019) Ling Deng et al.   Viruses-Basel

Bacteriophages in Natural and Artificial Environments

(2019) Batinovic et al.   Pathogens

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Passage and community changes of filterable bacteria during microfiltration of a surface water supply

(2019) Jie Liu et al.   ENVIRONMENT INTERNATIONAL

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses

(2018) Marcos Parras-Moltó et al.   Microbiome

A mathematical model of marine bacteriophage evolution

(2018) Silvia Pagliarini et al.   Royal Society Open Science

Second Correction for Henson et al., “Artificial Seawater Media Facilitate Cultivating Members of the Microbial Majority from the Gulf of Mexico”

(2018) Michael W. Henson et al.   mSphere

Stochastic Modeling and Simulation of Viral Evolution

(2018) Luiza Guimarães Fabreti et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Virus taxonomy in the age of metagenomics

(2017) Peter Simmonds et al.   NATURE REVIEWS MICROBIOLOGY

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

(2017) Sergey A. Shmakov et al.   mBio

Effect of bacterial growth rate on bacteriophage population growth rate

(2017) Dominik Nabergoj et al.   MicrobiologyOpen

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Membrane filtration immobilization technique-a simple and novel method for primary isolation and enrichment of bacteriophages

(2016) G.S. Ghugare et al.   JOURNAL OF APPLIED MICROBIOLOGY

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

More Is Better: Selecting for Broad Host Range Bacteriophages

(2016) Alexa Ross et al.   Frontiers in Microbiology

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

(2016) Christian Rinke et al.   PeerJ

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

(2015) Josué L. Castro-Mejía et al.   Microbiome

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Pseudomonas syringae pv. tomato DC3000: A Model Pathogen for Probing Disease Susceptibility and Hormone Signaling in Plants

(2013) Xiu-Fang Xin et al.   Annual Review of Phytopathology

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method

(2012) Melissa B. Duhaime et al.   ENVIRONMENTAL MICROBIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Pseudomonas syringaepv.tomatoDC3000 Uses Constitutive and Apoplast-Induced Nutrient Assimilation Pathways to Catabolize Nutrients That Are Abundant in the Tomato Apoplast

(2008) Arantza Rico et al.   MOLECULAR PLANT-MICROBE INTERACTIONS