Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem

(2014) William Inskeep   Frontiers in Microbiology

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Metagenomic analysis of a stable trichloroethene-degrading microbial community

(2012) Vanessa L Brisson 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

Dynamics of Microbial Community Composition and Function during In Situ Bioremediation of a Uranium-Contaminated Aquifer

(2011) Joy D. Van Nostrand et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Metagenomic comparison of microbial communities inhabiting confined and unconfined aquifer ecosystems

(2011) Renee J. Smith et al.   ENVIRONMENTAL MICROBIOLOGY

Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies

(2011) Yong Kong   GENOMICS

High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton

(2011) Manuel Martinez-Garcia et al.   ISME Journal

IMG: the integrated microbial genomes database and comparative analysis system

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

Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities

(2010) Kristen M. DeAngelis et al.   BioEnergy Research

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

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

(2010) Christopher L Hemme et al.   ISME Journal

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

IMG ER: a system for microbial genome annotation expert review and curation

(2009) Victor M. Markowitz et al.   BIOINFORMATICS

GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer

(2009) Joy D. Van Nostrand et al.   ENVIRONMENTAL MICROBIOLOGY

The integrated microbial genomes system: an expanding comparative analysis resource

(2009) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine

(2009) Marcus J. Claesson et al.   PLoS One

Mineralogical characterization of saprolite at the FRC background site in Oak Ridge, Tennessee

(2009) Young-Jin Kim et al.   Environmental geology.

Microbial Communities in Contaminated Sediments, Associated with Bioremediation of Uranium to Submicromolar Levels

(2008) E. Cardenas et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Microbial community dynamics in uranium contaminated subsurface sediments under biostimulated conditions with high nitrate and nickel pressure

(2008) David Moreels et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

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

(2008) Victor Kunin et al.   Molecular Systems Biology

Short read fragment assembly of bacterial genomes

(2007) M. J. Chaisson et al.   GENOME RESEARCH