CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction

Obesity as a Risk Factor for Clostridium difficile Infection

(2013) J. Bishara et al.   CLINICAL INFECTIOUS DISEASES

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

Archaea on Human Skin

(2013) Alexander J. Probst et al.   PLoS One

Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly

(2013) Yen-Chun Chen et al.   PLoS One

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

(2013) Omry Koren et al.   PLoS Computational Biology

Bpipe: a tool for running and managing bioinformatics pipelines

(2012) Simon P. Sadedin et al.   BIOINFORMATICS

Ultrafast clustering algorithms for metagenomic sequence analysis

(2012) W. Li et al.   BRIEFINGS IN BIOINFORMATICS

Fast, accurate error-correction of amplicon pyrosequences using Acacia

(2012) Lauren Bragg et al.   NATURE METHODS

Predicting bacterial community assemblages using an artificial neural network approach

(2012) Peter E Larsen et al.   NATURE METHODS

Grinder: a versatile amplicon and shotgun sequence simulator

(2012) Florent E. Angly et al.   NUCLEIC ACIDS RESEARCH

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

(2012) Sanqing Yuan et al.   PLoS One

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

(2012) Ameet J. Pinto et al.   PLoS One

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

BIO::Phylo-phyloinformatic analysis using perl

(2011) Rutger A Vos et al.   BMC BIOINFORMATICS

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

(2010) Beifang Niu et al.   BMC BIOINFORMATICS

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

Optimizing the analysis of human intestinal microbiota with phylogenetic microarray

(2010) Laura Rigsbee et al.   FEMS MICROBIOLOGY ECOLOGY

An Extreme Thermophile, Thermus thermophilus, Is a Polyploid Bacterium

(2010) N. Ohtani et al.   JOURNAL OF BACTERIOLOGY

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

Multiple displacement amplification compromises quantitative analysis of metagenomes

(2010) Suzan Yilmaz et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults

(2010) Nadja Larsen et al.   PLoS One

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

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

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Visualization of ribosomal RNA operon copy number distribution

(2009) Rajat Rastogi et al.   BMC MICROBIOLOGY

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults

(2009) Mirjana Rajilić-Stojanović et al.   ENVIRONMENTAL MICROBIOLOGY

A changing of the guard

(2009) Philip Hugenholtz et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

Mapping the Tree of Life: Progress and Prospects

(2009) N. R. Pace   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE