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

Sequencing platform and library preparation choices impact viral metagenomes

(2013) Sergei A Solonenko et al.   BMC GENOMICS

Temporal Dynamics and Decay of Putatively Allochthonous and Autochthonous Viral Genotypes in Contrasting Freshwater Lakes

(2012) Ian Hewson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes

(2012) Samuel O Oyola et al.   BMC GENOMICS

Oxygen minimum zones harbour novel viral communities with low diversity

(2012) Noriko Cassman et al.   ENVIRONMENTAL MICROBIOLOGY

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

Artificial Polyploidy Improves Bacterial Single Cell Genome Recovery

(2012) Armand E. K. Dichosa et al.   PLoS One

Microarray-Based Evaluation of Whole-Community Genome DNA Amplification Methods

(2011) Jian Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evaluation of a Transposase Protocol for Rapid Generation of Shotgun High-Throughput Sequencing Libraries from Nanogram Quantities of DNA

(2011) Rachel Marine et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces

(2011) Min-Soo Kim 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

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

(2011) M. Krupovic et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Linear amplification for deep sequencing

(2011) Wieteke A M Hoeijmakers et al.   Nature Protocols

Unraveling the viral tapestry (from inside the capsid out)

(2010) Shawn W Polson et al.   ISME Journal

Multiple displacement amplification compromises quantitative analysis of metagenomes

(2010) Suzan Yilmaz et al.   NATURE METHODS

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

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

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

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Metagenomic analysis of viruses in reclaimed water

(2009) Karyna Rosario et al.   ENVIRONMENTAL MICROBIOLOGY

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

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

(2009) Dana Willner et al.   PLoS One

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

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

Successful amplification of degraded DNA for use with high-throughput SNP genotyping platforms

(2008) Simon Mead et al.   HUMAN MUTATION

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

(2008) Erik K Binga et al.   ISME Journal

A Bioinformatician's Guide to Metagenomics

(2008) V. Kunin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

Microbial Ecology of Four Coral Atolls in the Northern Line Islands

(2008) Elizabeth A. Dinsdale et al.   PLoS One