Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

(2017) Sean P. Jungbluth et al.   PeerJ

Variations in microbial carbon sources and cycling in the deep continental subsurface

(2016) Danielle N. Simkus et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

(2016) Kiley W Seitz et al.   ISME Journal

Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

(2016) Daan R. Speth et al.   Nature Communications

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

(2016) Brett J. Baker et al.   Nature Microbiology

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

(2015) Cindy J. Castelle et al.   CURRENT BIOLOGY

Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes

(2015) Sebastian Kolinko et al.   ENVIRONMENTAL MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust

(2015) Cara Magnabosco et al.   ISME Journal

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

(2015) Marcel Huntemann et al.   Standards in Genomic Sciences

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria

(2015) Brett J Baker et al.   Microbiome

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A novel cohabitation between two diazotrophic cyanobacteria in the oligotrophic ocean

(2014) Lily M Momper et al.   ISME Journal

Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’

(2014) Noha H Youssef et al.   ISME Journal

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships

(2014) Maggie C. Y. Lau et al.   Frontiers in Microbiology

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir

(2013) Yiran Dong et al.   ENVIRONMENTAL MICROBIOLOGY

Weighing the deep continental biosphere

(2013) Sean McMahon et al.   FEMS MICROBIOLOGY ECOLOGY

Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield

(2013) Mari Nyyssönen et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

IMG/M 4 version of the integrated metagenome comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

(2013) J. H. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Desulfotomaculum spp. and related gram-positive sulfate-reducing bacteria in deep subsurface environments

(2013) Thomas Aüllo et al.   Frontiers in Microbiology

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

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

Microbial and functional diversity of a subterrestrial high pH groundwater associated to serpentinization

(2012) Igor Tiago et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank

(2012) Sean P Jungbluth et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

Ecological Aspects of the Distribution of Different Autotrophic CO2Fixation Pathways

(2011) Ivan A. Berg   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site

(2011) Xueju Lin et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

(2011) B. N. Orcutt et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

(2011) Christopher J. Creevey et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Manganese- and Iron-Dependent Marine Methane Oxidation

(2009) E. J. Beal et al.   SCIENCE

Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes

(2008) Alexander Loy et al.   ENVIRONMENTAL MICROBIOLOGY

Characterization and Evolution of Cell Division and Cell Wall Synthesis Genes in the Bacterial Phyla Verrucomicrobia, Lentisphaerae, Chlamydiae, and Planctomycetes and Phylogenetic Comparison with rRNA Genes

(2008) M. Pilhofer et al.   JOURNAL OF BACTERIOLOGY

Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

(2008) D. Chivian et al.   SCIENCE

The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains

(2008) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY