Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

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

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

Evidence for metaviromic islands in marine phages

(2014) Carolina Megumi Mizuno et al.   Frontiers in Microbiology

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

(2014) Genivaldo Gueiros Z. Silva et al.   PeerJ

Marine viruses, a genetic reservoir revealed by targeted viromics

(2013) Joaquín Martínez Martínez et al.   ISME Journal

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

Expanding the Marine Virosphere Using Metagenomics

(2013) Carolina Megumi Mizuno et al.   PLoS Genetics

Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea

(2013) Jessica M. Labonté et al.   Frontiers in Microbiology

Phylogenomics of T4 cyanophages: lateral gene transfer in the ‘core’ and origins of host genes

(2012) J. Cesar Ignacio-Espinoza et al.   ENVIRONMENTAL MICROBIOLOGY

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

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

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

Metavir: a web server dedicated to virome analysis

(2011) Simon Roux et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Phage Eco-Locator: a web tool for visualization and analysis of phage genomes in metagenomic data sets

(2011) Ramy K Aziz et al.   BMC BIOINFORMATICS

Spatial distribution of microbial communities in the cystic fibrosis lung

(2011) Dana Willner et al.   ISME Journal

Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition

(2011) J. Gregory Caporaso et al.   PLoS One

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

(2010) Robert Schmieder et al.   BMC BIOINFORMATICS

Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice

(2010) Kelly S Swanson et al.   ISME Journal

Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean

(2010) Kimberly P Tucker et al.   ISME Journal

Viral and microbial community dynamics in four aquatic environments

(2010) Beltran Rodriguez-Brito et al.   ISME Journal

Mosaic Graphs and Comparative Genomics in Phage Communities

(2010) Mahdi Belcaid et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Accurate quantification of transcriptome from RNA-Seq data by effective length normalization

(2010) Soohyun Lee et al.   NUCLEIC ACIDS RESEARCH

Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber

(2009) Lejla Pašić et al.   BMC GENOMICS

Current insights into phage biodiversity and biogeography

(2009) Rebecca Vega Thurber   CURRENT OPINION IN MICROBIOLOGY

Metagenomic analysis of stressed coral holobionts

(2009) Rebecca Vega Thurber et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2009) Dana Willner et al.   PLoS One

High Diversity of the Viral Community from an Antarctic Lake

(2009) A. Lopez-Bueno et al.   SCIENCE

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

(2009) Florent E. Angly et al.   PLoS Computational Biology

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

(2008) G. Lima-Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

Biodiversity and biogeography of phages in modern stromatolites and thrombolites

(2008) Christelle Desnues et al.   NATURE