phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

The Split-Apply-Combine Strategy for Data Analysis

(2015) Hadley Wickham   Journal of Statistical Software

mcaGUI: microbial community analysis R-Graphical User Interface (GUI)

(2012) Wade K. Copeland et al.   BIOINFORMATICS

The case for open computer programs

(2012) Darrel C. Ince et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Unlocking the potential of metagenomics through replicated experimental design

(2012) Rob Knight et al.   NATURE BIOTECHNOLOGY

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

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

Simultaneous analysis of a sequence of paired ecological tables: A comparison of several methods

(2011) Jean Thioulouse   Annals of Applied Statistics

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

(2011) Samuel V Angiuoli et al.   BMC BIOINFORMATICS

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Reproducible Research in Computational Science

(2011) R. D. Peng   SCIENCE

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data

(2011) Thomas J. Sharpton et al.   PLoS Computational Biology

Picante: R tools for integrating phylogenies and ecology

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

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

An invitation to reproducible computational research

(2010) D. L. Donoho   BIOSTATISTICS

NeatMap - non-clustering heat map alternatives in R

(2010) Satwik Rajaram et al.   BMC BIOINFORMATICS

PANGEA: pipeline for analysis of next generation amplicons

(2010) Adriana Giongo et al.   ISME Journal

Publish your computer code: it is good enough

(2010) Nick Barnes   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reproducible research and Biostatistics

(2009) Roger D. Peng   BIOSTATISTICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

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

(2008) Micah Hamady et al.   NATURE METHODS

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

(2008) Z. Liu et al.   NUCLEIC ACIDS RESEARCH

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH