Aquifer environment selects for microbial species cohorts in sediment and groundwater

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

(2014) Kelly C Wrighton et al.   ISME Journal

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Functional microbial diversity explains groundwater chemistry in a pristine aquifer

(2013) Theodore M Flynn et al.   BMC MICROBIOLOGY

Using Stable Isotope Probing to Characterize Differences Between Free-Living and Sediment-Associated Microorganisms in the Subsurface

(2013) Krista Longnecker et al.   GEOMICROBIOLOGY JOURNAL

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices

(2013) Jenna Morgan Lang et al.   PLoS One

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

(2013) R. S. Kantor et al.   mBio

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

(2013) Cindy J. Castelle et al.   Nature Communications

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

(2013) Laura A Hug et al.   Microbiome

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Global distribution of microbial abundance and biomass in subseafloor sediment

(2012) J. Kallmeyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

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

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

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation

(2009) M. J. Wilkins et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mineral Transformation and Biomass Accumulation Associated With Uranium Bioremediation at Rifle, Colorado

(2009) Li Li et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Microbial diversity and the genetic nature of microbial species

(2008) Mark Achtman et al.   NATURE REVIEWS MICROBIOLOGY

Attached and suspended microbial communities in a pristine confined aquifer

(2008) Theodore M. Flynn et al.   WATER RESOURCES RESEARCH

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY