Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

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

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

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

Comparative metagenomics of microbial traits within oceanic viral communities

(2011) Itai Sharon et al.   ISME Journal

Single Virus Genomics: A New Tool for Virus Discovery

(2011) Lisa Zeigler Allen et al.   PLoS One

DNA Extraction Columns Contaminated with Murine Sequences

(2011) Otto Erlwein et al.   PLoS One

Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids

(2011) Takashi Yoshida et al.   Virology Journal

Raw Sewage Harbors Diverse Viral Populations

(2011) P. G. Cantalupo et al.   mBio

Hydroxyapatite-Mediated Separation of Double-Stranded DNA, Single-Stranded DNA, and RNA Genomes from Natural Viral Assemblages

(2010) C. Andrews-Pfannkoch et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

(2010) Beifang Niu et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Multiple displacement amplification compromises quantitative analysis of metagenomes

(2010) Suzan Yilmaz et al.   NATURE METHODS

Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes

(2010) Matthew R. Henn et al.   PLoS One

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

(2010) Jenna L. Morgan et al.   PLoS One

A simple and efficient method for concentration of ocean viruses by chemical flocculation

(2010) Seth G. John et al.   Environmental Microbiology Reports

Carrying photosynthesis genes increases ecological fitness of cyanophagein silico

(2009) Ferdi L. Hellweger   ENVIRONMENTAL MICROBIOLOGY

Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing

(2009) Ben Temperton et al.   ISME Journal

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton

(2008) E. J. Biers et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Amplification of Uncultured Single-Stranded DNA Viruses from Rice Paddy Soil

(2008) K.-H. Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Efficient Phage-Mediated Pigment Biosynthesis in Oceanic Cyanobacteria

(2008) Thorben Dammeyer et al.   CURRENT BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples

(2008) Shannon J. Williamson et al.   PLoS One

Modeling the Fitness Consequences of a Cyanophage-Encoded Photosynthesis Gene

(2008) Jason G. Bragg et al.   PLoS One

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA