Beyond the genome: community-level analysis of the microbial world

Metagenomics and antibiotics

(2012) L. Garmendia et al.   CLINICAL MICROBIOLOGY AND INFECTION

Structure, fluctuation and magnitude of a natural grassland soil metagenome

(2012) Tom O Delmont et al.   ISME Journal

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Unlocking the potential of metagenomics through replicated experimental design

(2012) Rob Knight et al.   NATURE BIOTECHNOLOGY

Predicting bacterial community assemblages using an artificial neural network approach

(2012) Peter E Larsen et al.   NATURE METHODS

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

(2012) Georgia Giannoukos et al.   GENOME BIOLOGY

Omics for understanding microbial functional dynamics

(2011) Janet K. Jansson et al.   ENVIRONMENTAL MICROBIOLOGY

DNA-, rRNA- and mRNA-based stable isotope probing of aerobic methanotrophs in lake sediment

(2011) Marc G. Dumont et al.   ENVIRONMENTAL MICROBIOLOGY

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

(2011) Priya Narasingarao et al.   ISME Journal

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

(2011) Joshua A Steele et al.   ISME Journal

The Western English Channel contains a persistent microbial seed bank

(2011) J Gregory Caporaso et al.   ISME Journal

Defining seasonal marine microbial community dynamics

(2011) Jack A Gilbert et al.   ISME Journal

Exploration of community traits as ecological markers in microbial metagenomes

(2011) ALBERT BARBERÁN et al.   MOLECULAR ECOLOGY

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

(2011) Rachel Mackelprang et al.   NATURE

Microbial seed banks: the ecological and evolutionary implications of dormancy

(2011) Jay T. Lennon et al.   NATURE REVIEWS MICROBIOLOGY

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Modeling Diverse Communities of Marine Microbes

(2010) Michael J. Follows et al.   Annual Review of Marine Science

Microbial Metagenomics: Beyond the Genome

(2010) Jack A. Gilbert et al.   Annual Review of Marine Science

Metagenomics and the Units of Biological Organization

(2010) W. Ford Doolittle et al.   BIOSCIENCE

Environmental distribution of prokaryotic taxa

(2010) Javier Tamames et al.   BMC MICROBIOLOGY

Environmental proteomics of microbial plankton in a highly productive coastal upwelling system

(2010) Sarah M Sowell et al.   ISME Journal

Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction

(2010) Robert M Morris et al.   ISME Journal

The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses

(2010) Etienne Yergeau et al.   ISME Journal

Transcriptional activity of the dominant gut mucosal microbiota in chronic inflammatory bowel disease patients

(2010) A. Rehman et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics

(2010) Karuna Chourey et al.   JOURNAL OF PROTEOME RESEARCH

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

Transcriptional and Translational Regulatory Responses to Iron Limitation in the Globally Distributed Marine Bacterium Candidatus Pelagibacter ubique

(2010) Daniel P. Smith et al.   PLoS One

One Bacterial Cell, One Complete Genome

(2010) Tanja Woyke et al.   PLoS One

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

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

The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

(2010) Jack A. Gilbert et al.   PLoS One

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

Commensal bacteria play a role in mating preference of Drosophila melanogaster

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

Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5

(2010) M. Vijay-Kumar et al.   SCIENCE

Defining the healthy "core microbiome" of oral microbial communities

(2009) Egija Zaura et al.   BMC MICROBIOLOGY

The seasonal structure of microbial communities in the Western English Channel

(2009) Jack A. Gilbert et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial community structure in the North Pacific ocean

(2009) Mark V Brown et al.   ISME Journal

What is microbial community ecology?

(2009) Allan Konopka   ISME Journal

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Functional analysis of natural microbial consortia using community proteomics

(2009) Nathan C. VerBerkmoes et al.   NATURE REVIEWS MICROBIOLOGY

Assembling the Marine Metagenome, One Cell at a Time

(2009) Tanja Woyke et al.   PLoS One

Ecology of the rare microbial biosphere of the Arctic Ocean

(2009) Pierre E. Galand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying environmental adaptation of metabolic pathways in metagenomics

(2009) T. A. Gianoulis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Seeing the Big Picture on Microbe Distribution

(2009) D. J. Patterson   SCIENCE

Community structure of marine bacterioplankton: patterns, networks, and relationships to function

(2008) JA Fuhrman et al.   AQUATIC MICROBIAL ECOLOGY

High genetic similarity between two geographically distinct strains of the sulfur-oxidizing symbiont ‘Candidatus Thiobios zoothamnicoli’

(2008) Christian Rinke et al.   FEMS MICROBIOLOGY ECOLOGY

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

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

(2008) Micah Hamady et al.   NATURE METHODS

Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

(2008) Tim Urich et al.   PLoS One

Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

(2008) Jack A. Gilbert et al.   PLoS One

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A latitudinal diversity gradient in planktonic marine bacteria

(2008) J. A. Fuhrman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA