Complete Genome Sequence of an Uncultured Bacterium of the Candidate Phylum Bipolaricaulota

Novel prosthecate bacteria from the candidate phylum Acetothermia

(2018) Liping Hao et al.   ISME Journal

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments

(2017) Alex W Hernsdorf et al.   ISME Journal

Uncultivated microbes in need of their own taxonomy

(2017) Konstantinos T Konstantinidis et al.   ISME Journal

Uncultured bacteria and methanogenic archaea predominate in the microbial community of Western Siberian deep subsurface aquifer

(2017) V. V. Kadnikov et al.   MICROBIOLOGY

Variability of the composition of the microbial community of the deep subsurface thermal aquifer in Western Siberia

(2017) V. V. Kadnikov et al.   MICROBIOLOGY

Scaffolding and completing genome assemblies in real-time with nanopore sequencing

(2017) Minh Duc Cao et al.   Nature Communications

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2concentrations

(2016) Alexander J. Probst et al.   ENVIRONMENTAL MICROBIOLOGY

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

HydDB: A web tool for hydrogenase classification and analysis

(2016) Dan Søndergaard et al.   Scientific Reports

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

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

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor

(2015) Masaru K Nobu et al.   ISME Journal

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

(2015) Cara Magnabosco et al.   ISME Journal

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

(2015) Chris Greening et al.   ISME Journal

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem

(2012) Hideto Takami et al.   PLoS One

Bacterial diversity in five Icelandic geothermal waters: temperature and sinter growth rate effects

(2011) Dominique J. Tobler et al.   EXTREMOPHILES

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Microbial communities in iron-silica-rich microbial mats at deep-sea hydrothermal fields of the Southern Mariana Trough

(2009) Shingo Kato et al.   ENVIRONMENTAL MICROBIOLOGY

Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin

(2009) Kyle C. Costa et al.   EXTREMOPHILES

Culture-independent characterization of a novel microbial community at a hydrothermal vent at Brothers volcano, Kermadec arc, New Zealand

(2008) M. B. Stott et al.   JOURNAL OF GEOPHYSICAL RESEARCH