Complete nitrification by a single microorganism

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

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

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

ExSPAnder: a universal repeat resolver for DNA fragment assembly

(2014) A. D. Prjibelski et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Use of Aliphaticn-Alkynes To Discriminate Soil Nitrification Activities of Ammonia-Oxidizing Thaumarchaea and Bacteria

(2013) Anne E. Taylor et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

(2013) Richard M. Leggett et al.   BIOINFORMATICS

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

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

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

(2012) David Vallenet 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

Role for urea in nitrification by polar marine Archaea

(2012) L. Alonso-Saez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity and enrichment of nitrite-dependent anaerobic methane oxidizing bacteria from wastewater sludge

(2011) Francisca A. Luesken et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Integrative analysis of environmental sequences using MEGAN4

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

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

(2011) Chris L Dupont et al.   ISME Journal

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

In quest of the nitrogen oxidizing prokaryotes of the early Earth

(2010) Siegfried E. Vlaeminck et al.   ENVIRONMENTAL MICROBIOLOGY

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

Role of urea in microbial metabolism in aquatic systems: a biochemical and molecular review

(2009) CM Solomon et al.   AQUATIC MICROBIAL ECOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH

Nitrifier genomics and evolution of the nitrogen cycle

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