Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities

Global Carbon Cycling on a Heterogeneous Seafloor

(2018) Paul V.R. Snelgrove et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Permeability shapes bacterial communities in sublittoral surface sediments

(2017) D. Probandt et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments

(2017) Marc Mußmann et al.   ISME Journal

lmerTest Package: Tests in Linear Mixed Effects Models

(2017) Alexandra Kuznetsova et al.   Journal of Statistical Software

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

(2017) Neil D Rawlings et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Lateral supply and downward export of particulate matter from upper waters to the seafloor in the deep eastern Fram Strait

(2016) Catherine Lalande et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Woeseia oceani gen. nov., sp. nov., a chemoheterotrophic member of the order Chromatiales, and proposal of Woeseiaceae fam. nov.

(2016) Zong-Jun Du et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments

(2016) Stefan Dyksma et al.   ISME Journal

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Biogeochemical and Microbial Variation across 5500 km of Antarctic Surface Sediment Implicates Organic Matter as a Driver of Benthic Community Structure

(2016) Deric R. Learman et al.   Frontiers in Microbiology

Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria

(2016) Christina Bienhold et al.   PLoS One

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

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

The Transporter Classification Database (TCDB): recent advances

(2015) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

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

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

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum

(2015) Sebastian H. Kopf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global dispersion and local diversification of the methane seep microbiome

(2015) S. Emil Ruff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Brett J Baker et al.   Microbiome

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Povalibacter uvarum gen. nov., sp. nov., a polyvinyl-alcohol-degrading bacterium isolated from grapes

(2014) Y. Nogi et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

(2014) A Murat Eren 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

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells

(2014) David Berry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

(2014) Thomas S. B. Schmidt et al.   PLoS Computational Biology

Quantifying the degradation of organic matter in marine sediments: A review and synthesis

(2013) Sandra Arndt et al.   EARTH-SCIENCE REVIEWS

Predominant archaea in marine sediments degrade detrital proteins

(2013) Karen G. Lloyd et al.   NATURE

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R

(2013) Eric Pante et al.   PLoS One

Biogeography of Deep-Sea Benthic Bacteria at Regional Scale (LTER HAUSGARTEN, Fram Strait, Arctic)

(2013) Marianne Jacob et al.   PLoS One

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

Assessing sub-seafloor microbial activity by combined stable isotope probing with deuterated water and 13C-bicarbonate

(2012) Gunter Wegener et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment

(2012) Bente Aa. Lomstein et al.   NATURE

Beyond biogeographic patterns: processes shaping the microbial landscape

(2012) China A. Hanson et al.   NATURE REVIEWS MICROBIOLOGY

ESTHER, the database of the α/β-hydrolase fold superfamily of proteins: tools to explore diversity of functions

(2012) Nicolas Lenfant et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Bacterial sulfur cycling shapes microbial communities in surface sediments of an ultramafic hydrothermal vent field

(2011) Regina Schauer et al.   ENVIRONMENTAL MICROBIOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Microbial seed banks: the ecological and evolutionary implications of dormancy

(2011) Jay T. Lennon et al.   NATURE REVIEWS MICROBIOLOGY

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Ecological Function of Myroilysin, a Novel Bacterial M12 Metalloprotease with Elastinolytic Activity and a Synergistic Role in Collagen Hydrolysis, in Biodegradation of Deep-Sea High-Molecular-Weight Organic Nitrogen

(2009) X.-L. Chen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Steroidobacter denitrificans gen. nov., sp. nov., a steroidal hormone-degrading gammaproteobacterium

(2008) M. Fahrbach et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY