Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Lateral gene transfer of an ABC transporter complex between major constituents of the human gut microbiome

(2012) Conor J Meehan et al.   BMC MICROBIOLOGY

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

(2012) J Kirk Harris et al.   ISME Journal

Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities

(2012) Donovan H Parks et al.   ISME Journal

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome

(2012) R. Eric Collins et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temporal Dynamics of the Human Vaginal Microbiota

(2012) P. Gajer et al.   Science Translational Medicine

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

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

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

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

(2012) Nicola Segata et al.   GENOME BIOLOGY

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

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

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Toward an Efficient Method of Identifying Core Genes for Evolutionary and Functional Microbial Phylogenies

(2011) Nicola Segata et al.   PLoS One

Macroalgal terpenes function as allelopathic agents against reef corals

(2011) D. B. Rasher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial to reef scale interactions between the reef-building coral Montastraea annularis and benthic algae

(2011) K. L. Barott et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families

(2010) P. V. Patel et al.   GENOME RESEARCH

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community

(2010) Christopher L Hemme et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives

(2010) Jesse R. Zaneveld et al.   NUCLEIC ACIDS RESEARCH

An Insect Herbivore Microbiome with High Plant Biomass-Degrading Capacity

(2010) Garret Suen et al.   PLoS Genetics

Direct sequencing of the human microbiome readily reveals community differences

(2010) Justin Kuczynski et al.   GENOME BIOLOGY

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

(2008) Victor Kunin et al.   Molecular Systems Biology

Shifting Baselines, Local Impacts, and Global Change on Coral Reefs

(2008) Nancy Knowlton et al.   PLOS BIOLOGY