Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

(2015) Manuel Kleiner et al.   BMC GENOMICS

Rising to the challenge: accelerated pace of discovery transforms marine virology

(2015) Jennifer R. Brum et al.   NATURE REVIEWS MICROBIOLOGY

The use of ionic liquids for cracking viruses for isolation of nucleic acids

(2015) S. Fister et al.   SEPARATION AND PURIFICATION TECHNOLOGY

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

(2015) Simon Roux et al.   eLife

Bacteriophage and their potential roles in the human oral cavity

(2015) Anna Edlund et al.   Journal of Oral Microbiology

Accurate viral population assembly from ultra-deep sequencing data

(2014) S. Mangul et al.   BIOINFORMATICS

Characterization of bacteriophage communities and CRISPR profiles from dental plaque

(2014) Mayuri Naidu et al.   BMC MICROBIOLOGY

Kingdom-Agnostic Metagenomics and the Importance of Complete Characterization of Enteric Microbial Communities

(2014) Jason M. Norman et al.   GASTROENTEROLOGY

NCBI Viral Genomes Resource

(2014) J. Rodney Brister et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA

(2014) Shahzad Shaukat et al.   Virology Journal

Altered Oral Viral Ecology in Association with Periodontal Disease

(2014) M. Ly et al.   mBio

Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome

(2014) Rachel Marine et al.   Microbiome

Assessment of five soil DNA extraction methods and a rapid laboratory-developed method for quality soil DNA extraction for 16S rDNA-based amplification and library construction

(2013) Kalpana Sagar et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery

(2013) Richard J. Hall et al.   JOURNAL OF VIROLOGICAL METHODS

New Insights into the Evolution of Entomopoxvirinae from the Complete Genome Sequences of Four Entomopoxviruses Infecting Adoxophyes honmai, Choristoneura biennis, Choristoneura rosaceana, and Mythimna separata

(2013) J. Theze et al.   JOURNAL OF VIROLOGY

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

Bacteriophage adhering to mucus provide a non-host-derived immunity

(2013) J. J. Barr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The major role of viruses in cellular evolution: facts and hypotheses

(2013) Patrick Forterre et al.   Current Opinion in Virology

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

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

(2012) Limin Fu et al.   BIOINFORMATICS

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Using Tablet for visual exploration of second-generation sequencing data

(2012) I. Milne et al.   BRIEFINGS IN BIOINFORMATICS

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

(2012) D. M. Kristensen et al.   JOURNAL OF BACTERIOLOGY

Decoy cells in urine cytology: A useful clue to post-transplant polyoma virus infection

(2012) Vidya Monappa et al.   Journal of Cytology

A framework for human microbiome research

(2012)   NATURE

Going viral: next-generation sequencing applied to phage populations in the human gut

(2012) Alejandro Reyes et al.   NATURE REVIEWS MICROBIOLOGY

Hypervariable loci in the human gut virome

(2012) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal Transfer of the OXA-24 Carbapenemase Gene via Outer Membrane Vesicles: a New Mechanism of Dissemination of Carbapenem Resistance Genes in Acinetobacter baumannii

(2011) Carlos Rumbo et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses

(2011) Kyoung-Ho Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Contribution of bacterial outer membrane vesicles to innate bacterial defense

(2011) Andrew J Manning et al.   BMC MICROBIOLOGY

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

(2011) David A. Rasko et al.   NEW ENGLAND JOURNAL OF MEDICINE

A Sensitive Assay for Virus Discovery in Respiratory Clinical Samples

(2011) Michel de Vries et al.   PLoS One

Viral Etiologies of Acute Respiratory Infections among Hospitalized Vietnamese Children in Ho Chi Minh City, 2004–2008

(2011) Anh Ha Lien Do et al.   PLoS One

A Viral Discovery Methodology for Clinical Biopsy Samples Utilising Massively Parallel Next Generation Sequencing

(2011) Gordon M. Daly et al.   PLoS One

Modernizing Reference Genome Assemblies

(2011) Deanna M. Church et al.   PLOS BIOLOGY

Metagenomic Analysis of the Viral Communities in Fermented Foods

(2010) Eun-Jin Park et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Cryptic prophages help bacteria cope with adverse environments

(2010) Xiaoxue Wang et al.   Nature Communications

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Metagenomic analysis of viruses in reclaimed water

(2009) Karyna Rosario et al.   ENVIRONMENTAL MICROBIOLOGY

Viruses manipulate the marine environment

(2009) Forest Rohwer et al.   NATURE

Explaining microbial population genomics through phage predation

(2009) Francisco Rodriguez-Valera et al.   NATURE REVIEWS MICROBIOLOGY

Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

(2009) Dana Willner et al.   PLoS One

PCR method for detection and identification of Lactobacillus casei/paracasei bacteriophages in dairy products

(2008) A BINETTI et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Discovery of a Novel Single-Stranded DNA Virus from a Sea Turtle Fibropapilloma by Using Viral Metagenomics

(2008) T. F. F. Ng et al.   JOURNAL OF VIROLOGY

Characterization of age-related changes in natural killer cells during primary influenza infection in mice

(2008) Shoko Nogusa et al.   MECHANISMS OF AGEING AND DEVELOPMENT