Genomic and metagenomic insights into the microbial community of a thermal spring

The use of balneotherapy in dermatology

(2018) Amy Huang et al.   CLINICS IN DERMATOLOGY

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment

(2017) Kohei Ino et al.   ISME Journal

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

(2017) Donald Pan et al.   Frontiers in Microbiology

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

(2016) Leighton Pritchard et al.   Analytical Methods

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Salinity Affects the Composition of the Aerobic Methanotroph Community in Alkaline Lake Sediments from the Tibetan Plateau

(2016) Yongcui Deng et al.   MICROBIAL ECOLOGY

Spatial and temporal variability of bacterial communities in high alpine water spring sediments

(2016) Alfonso Esposito et al.   RESEARCH IN MICROBIOLOGY

Capturing One of the Human Gut Microbiome’s Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data

(2016) Patricio Jeraldo et al.   Frontiers in Microbiology

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

(2015) Christopher T. Brown et al.   NATURE

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Ecology and exploration of the rare biosphere

(2015) Michael D. J. Lynch et al.   NATURE REVIEWS MICROBIOLOGY

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Methane production potentials, pathways, and communities of methanogens in vertical sediment profiles of river Sitka

(2015) Václav Mach et al.   Frontiers in Microbiology

Stream microbial diversity in response to environmental changes: review and synthesis of existing research

(2015) Lydia H. Zeglin   Frontiers in Microbiology

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

(2015) A. Murat Eren et al.   PeerJ

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

Origins and bioavailability of dissolved organic matter in groundwater

(2014) Yuan Shen et al.   BIOGEOCHEMISTRY

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Dominance of Methanosarcinales Phylotypes and Depth-Wise Distribution of Methanogenic Community in Fresh Water Sediments of Sitka Stream from Czech Republic

(2014) Prem Prashant Chaudhary et al.   CURRENT MICROBIOLOGY

Current developments in groundwater ecology—from biodiversity to ecosystem function and services

(2014) Christian Griebler et al.   CURRENT OPINION IN BIOTECHNOLOGY

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Functional microbial diversity explains groundwater chemistry in a pristine aquifer

(2013) Theodore M Flynn et al.   BMC MICROBIOLOGY

Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species

(2013) Alexander F Koeppel et al.   ISME Journal

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole 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

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

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

(2012) Limin Fu et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Diurnal fluctuations of electrical conductivity in a pre-alpine river: Effects of photosynthesis and groundwater exchange

(2012) Masaki Hayashi et al.   JOURNAL OF HYDROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Crenic habitats, hotspots for freshwater biodiversity conservation: toward an understanding of their ecology

(2012) Marco Cantonati et al.   Freshwater Science

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Cross-Kingdom Amplification Using Bacteria-Specific Primers: Complications for Studies of Coral Microbial Ecology

(2008) J. P. Galkiewicz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Balneotherapy for chronic plaque psoriasis at Comano spa in Trentino, Italy

(2008) Anna Peroni et al.   Dermatologic Therapy

Microbial biodiversity in groundwater ecosystems

(2008) C. GRIEBLER et al.   FRESHWATER BIOLOGY