Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered lakes

(2018) Patricia Tran et al.   ENVIRONMENTAL MICROBIOLOGY

Novel hydrogenases from deep-sea hydrothermal vent metagenomes identified by a recently developed activity-based screen

(2018) Nicole Adam et al.   ISME Journal

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

(2018) Karthik Anantharaman et al.   ISME Journal

Endosymbiont genomes yield clues of tubeworm success

(2018) Yuanning Li et al.   ISME Journal

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

(2018) Tom O. Delmont et al.   Nature Microbiology

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

A review of microcystin detections in Estuarine and Marine waters: Environmental implications and human health risk

(2017) Ellen P. Preece et al.   HARMFUL ALGAE

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

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

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents

(2017) Rika E. Anderson et al.   Nature Communications

Proteobacteria explain significant functional variability in the human gut microbiome

(2017) Patrick H. Bradley et al.   Microbiome

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

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

Global biogeography of Prochlorococcus genome diversity in the surface ocean

(2016) Alyssa G Kent et al.   ISME Journal

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

IMG/M: integrated genome and metagenome comparative data analysis system

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Karthik Anantharaman et al.   Nature Communications

Quantitative PCR Analysis of Functional Genes in Iron-Rich Microbial Mats at an Active Hydrothermal Vent System (Lō'ihi Seamount, Hawai'i)

(2015) Kelsey J. Jesser et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

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

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

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center

(2015) Karthik Anantharaman et al.   ISME Journal

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors

(2015) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea

(2015) Meng Li et al.   Nature Communications

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

Bacterial diversity in snow on North Pole ice floes

(2014) Aviaja L. Hauptmann et al.   EXTREMOPHILES

A novel hydrogen oxidizer amidst the sulfur-oxidizing Thiomicrospira lineage

(2014) Moritz Hansen et al.   ISME Journal

Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling

(2014) Ian DEA Lidbury et al.   ISME Journal

Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin

(2014) Cody S Sheik et al.   ISME Journal

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

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

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Microbial iron uptake as a mechanism for dispersing iron from deep-sea hydrothermal vents

(2014) Meng Li et al.   Nature Communications

Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume

(2013) Meng Li et al.   ENVIRONMENTAL MICROBIOLOGY

Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts

(2013) J G Sanders et al.   ISME Journal

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

BLAST: a more efficient report with usability improvements

(2013) Grzegorz M. Boratyn et al.   NUCLEIC ACIDS RESEARCH

The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats

(2013) Gregory J. Dick et al.   Frontiers in Microbiology

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

(2012) Ryan A Lesniewski et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Chemoautotrophy at Deep-Sea Vents: Past, Present, and Future

(2012) Stefan Sievert et al.   OCEANOGRAPHY

Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria

(2012) K. Anantharaman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stress responses as determinants of antimicrobial resistance in Gram-negative bacteria

(2012) Keith Poole   TRENDS IN MICROBIOLOGY

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

(2011) Chris L Dupont et al.   ISME Journal

Microbial oceanography of the dark ocean's pelagic realm

(2011) Javier Arístegui et al.   LIMNOLOGY AND OCEANOGRAPHY

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Metagenomic Comparison of Two Thiomicrospira Lineages Inhabiting Contrasting Deep-Sea Hydrothermal Environments

(2010) William J. Brazelton et al.   PLoS One

Diversity and ecophysiological features of thermophilic carboxydotrophic anaerobes

(2009) Tatyana G. Sokolova et al.   FEMS MICROBIOLOGY ECOLOGY

Elevated concentrations of formate, acetate and dissolved organic carbon found at the Lost City hydrothermal field

(2009) Susan Q. Lang et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

The alkaline phosphatase PhoX is more widely distributed in marine bacteria than the classical PhoA

(2009) Marta Sebastian et al.   ISME Journal

Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm

(2009) William J Brazelton et al.   ISME Journal

Abundance, composition, diversity and novelty of soil Proteobacteria

(2009) Anne M Spain et al.   ISME Journal

The prebiotic geochemistry of formaldehyde

(2008) H. James Cleaves II   PRECAMBRIAN RESEARCH