Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

Benchmarking short sequence mapping tools

(2013) Ayat Hatem et al.   BMC BIOINFORMATICS

Sequencing platform and library preparation choices impact viral metagenomes

(2013) Sergei A Solonenko et al.   BMC GENOMICS

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

The Origin of Biased Sequence Depth in Sequence-Independent Nucleic Acid Amplification and Optimization for Efficient Massive Parallel Sequencing

(2013) Toon Rosseel et al.   PLoS One

Comparison of DNA Extraction Methods in Analysis of Salivary Bacterial Communities

(2013) Vladimir Lazarevic et al.   PLoS One

Random Sampling Process Leads to Overestimation of  -Diversity of Microbial Communities

(2013) J. Zhou et al.   mBio

The evolution of the Escherichia coli phylogeny

(2012) Roy R. Chaudhuri et al.   INFECTION GENETICS AND EVOLUTION

Mapping Reads on a Genomic Sequence: An Algorithmic Overview and a Practical Comparative Analysis

(2012) Sophie Schbath et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Novel Bacterial Taxa in the Human Microbiome

(2012) Kristine M. Wylie et al.   PLoS One

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

(2011) Matthew B. Scholz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

(2011) Nathalie Lombard et al.   FEMS MICROBIOLOGY ECOLOGY

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

Impacts of Inter- and Intralaboratory Variations on the Reproducibility of Microbial Community Analyses

(2010) Y. Pan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome-wide sequencing data reveals virulence factors implicated in banana Xanthomonas wilt

(2010) David J. Studholme et al.   FEMS MICROBIOLOGY LETTERS

Average genome size: a potential source of bias in comparative metagenomics

(2010) Bánk Beszteri et al.   ISME Journal

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Metagenomic Pyrosequencing and Microbial Identification

(2009) J. F. Petrosino et al.   CLINICAL CHEMISTRY

Serratia glossinae sp. nov., isolated from the midgut of the tsetse fly Glossina palpalis gambiensis

(2009) A. Geiger et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY