Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

(2015) Itai Sharon et al.   GENOME RESEARCH

Aquifer environment selects for microbial species cohorts in sediment and groundwater

(2015) Laura A Hug et al.   ISME Journal

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

The changing landscape of microbial biodiversity exploration and its implications for systematics

(2015) Brian P. Hedlund et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Diverse uncultivated ultra-small bacterial cells in groundwater

(2015) Birgit Luef et al.   Nature Communications

Autotrophic Carbon Dioxide Fixation via the Calvin-Benson-Bassham Cycle by the Denitrifying Methanotroph “Candidatus Methylomirabilis oxyfera”

(2014) Olivia Rasigraf et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The complete genome sequence for putative H2- and S-oxidizerCandidatusSulfuricurvum sp., assembledde novofrom an aquifer-derived metagenome

(2014) Kim M. Handley et al.   ENVIRONMENTAL MICROBIOLOGY

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

Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation

(2014) W. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments

(2013) Jennifer B. Glass et al.   ENVIRONMENTAL MICROBIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

Physiology and Diversity of Ammonia-Oxidizing Archaea

(2012) David A. Stahl et al.   Annual Review of Microbiology

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

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

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

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

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

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

Acetate Availability and its Influence on Sustainable Bioremediation of Uranium-Contaminated Groundwater

(2011) Kenneth H. Williams et al.   GEOMICROBIOLOGY JOURNAL

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

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

Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers

(2011) M. Mussmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Denitrifying Bacteria Isolated from Terrestrial Subsurface Sediments Exposed to Mixed-Waste Contamination

(2010) S. J. Green et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Characterization of an Archaeal Medium-Chain Acyl Coenzyme A Synthetase from Methanosarcina acetivorans

(2010) Y. Meng et al.   JOURNAL OF BACTERIOLOGY

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

(2010) C. B. Walker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enrichment and Molecular Detection of Denitrifying Methanotrophic Bacteria of the NC10 Phylum

(2009) K. F. Ettwig et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering

(2009) Ze-Qiang Ma et al.   JOURNAL OF PROTEOME RESEARCH

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria

(2009) Willm Martens-Habbena et al.   NATURE

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Microarray-Based Characterization of Microbial Community Functional Structure and Heterogeneity in Marine Sediments from the Gulf of Mexico

(2008) L. Wu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH