Complete nitrification by Nitrospira bacteria

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

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

Cyanate as an energy source for nitrifiers

(2015) Marton Palatinszky et al.   NATURE

Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genusNitrospira

(2015) Hanna Koch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of Oxidation Kinetics of Nitrite-Oxidizing Bacteria: Nitrite Availability as a Key Factor in Niche Differentiation

(2014) Boris Nowka et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

poRe: an R package for the visualization and analysis of nanopore sequencing data

(2014) Mick Watson et al.   BIOINFORMATICS

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

Functionally relevant diversity of closely related Nitrospira in activated sludge

(2014) Christiane Gruber-Dorninger et al.   ISME Journal

GenBank

(2014) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation

(2014) H. Koch et al.   SCIENCE

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

NxrBencoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizingNitrospira

(2013) Michael Pester et al.   ENVIRONMENTAL MICROBIOLOGY

Isolation of Nitrospira belonging to Sublineage II from a Wastewater Treatment Plant

(2013) Norisuke Ushiki et al.   MICROBES AND ENVIRONMENTS

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

IMG 4 version of the integrated microbial genomes comparative analysis system

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

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Enrichment and Genome Sequence of the Group I.1a Ammonia-Oxidizing Archaeon “Ca. Nitrosotenuis uzonensis” Representing a Clade Globally Distributed in Thermal Habitats

(2013) Elena V. Lebedeva et al.   PLoS One

Unravelling the reasons for disproportion in the ratio of AOB and NOB in aerobic granular sludge

(2012) Mari K. H. Winkler et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi

(2012) Dimitry Y Sorokin et al.   ISME Journal

The Divergent AmoC3 Subunit of Ammonia Monooxygenase Functions as Part of a Stress Response System in Nitrosomonas europaea

(2012) P. M. Berube et al.   JOURNAL OF BACTERIOLOGY

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

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

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

(2012) David Vallenet et al.   NUCLEIC ACIDS RESEARCH

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation

(2012) James I. Prosser et al.   TRENDS IN MICROBIOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions

(2011) Roey Angel et al.   ISME Journal

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

(2011) Chris L Dupont et al.   ISME Journal

Genome Sequence of Nitrosomonas sp. Strain AL212, an Ammonia-Oxidizing Bacterium Sensitive to High Levels of Ammonia

(2011) Y. Suwa et al.   JOURNAL OF BACTERIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Isolation and characterization of a moderately thermophilic nitrite-oxidizing bacterium from a geothermal spring

(2010) Elena V. Lebedeva et al.   FEMS MICROBIOLOGY ECOLOGY

A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria

(2010) S. Lucker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm

(2009) Bärbel U. Foesel et al.   FEMS MICROBIOLOGY ECOLOGY

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria

(2009) Willm Martens-Habbena et al.   NATURE

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Complete Genome Sequence of Nitrosospira multiformis, an Ammonia-Oxidizing Bacterium from the Soil Environment

(2008) J. M. Norton et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evolution of an octahaem cytochromecprotein family that is key to aerobic and anaerobic ammonia oxidation by bacteria

(2008) Martin G. Klotz et al.   ENVIRONMENTAL MICROBIOLOGY

Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms

(2008) Maria Tourna et al.   ENVIRONMENTAL MICROBIOLOGY

Nitrifier genomics and evolution of the nitrogen cycle

(2007) Martin G. Klotz et al.   FEMS MICROBIOLOGY LETTERS