Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland

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

(2015) Manuel Kleiner et al.   BMC GENOMICS

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

(2014) Simon Roux et al.   BMC BIOINFORMATICS

Metagenomic analysis of the viral community in Namib Desert hypoliths

(2014) Evelien M. Adriaenssens et al.   ENVIRONMENTAL MICROBIOLOGY

Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing

(2014) Rohit Ghai et al.   MOLECULAR ECOLOGY

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

Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances

(2013) Ching-Hung Tseng et al.   ISME Journal

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

Viral metagenomics analysis of planktonic viruses in East Lake, Wuhan, China

(2013) Xingyi Ge et al.   VIROLOGICA SINICA

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara

(2012) Laura Fancello et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics

(2012) Simon Roux et al.   PLoS One

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

(2011) David Berry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

Metavir: a web server dedicated to virome analysis

(2011) Simon Roux et al.   BIOINFORMATICS

Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria ‘that rule the waves’ (LD12)

(2011) Michaela M Salcher et al.   ISME Journal

A Guide to the Natural History of Freshwater Lake Bacteria

(2011) R. J. Newton et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

SEAS: A System for SEED-Based Pathway Enrichment Analysis

(2011) Xizeng Mao et al.   PLoS One

Climate change: Links to global expansion of harmful cyanobacteria

(2011) Hans W. Paerl et al.   WATER RESEARCH

Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC

(2011) Rohit Ghai et al.   Environmental Microbiology Reports

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments

(2010) Matthew B. Sullivan et al.   ENVIRONMENTAL MICROBIOLOGY

Viral and microbial community dynamics in four aquatic environments

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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Metagenomic signatures of 86 microbial and viral metagenomes

(2009) Dana Willner et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a mesotrophic lake (Lac du Bourget - France)

(2009) Didier Debroas et al.   ENVIRONMENTAL MICROBIOLOGY

Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing

(2009) Seong Woon Roh et al.   ISME Journal

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Metagenomic Analysis of RNA Viruses in a Fresh Water Lake

(2009) Appolinaire Djikeng 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

Coamplification of Eukaryotic DNA with 16S rRNA Gene-Based PCR Primers: Possible Consequences for Population Fingerprinting of Complex Microbial Communities

(2008) Geert Huys et al.   CURRENT MICROBIOLOGY

Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea

(2008) Craig A Carlson et al.   ISME Journal

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

(2008) John H Paul   ISME Journal

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH