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

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

(2018) Benjamin J. Tully et al.   Scientific Data

Environmental drivers of a microbial genomic transition zone in the ocean’s interior

(2017) Daniel R. Mende et al.   Nature Microbiology

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Marine Non-Cyanobacterial Diazotrophs: Moving beyond Molecular Detection

(2016) Deniz Bombar et al.   TRENDS IN MICROBIOLOGY

Rapid annotation ofnifHgene sequences using classification and regression trees facilitates environmental functional gene analysis

(2016) Ildiko E. Frank et al.   Environmental Microbiology Reports

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

(2016) Tom O. Delmont et al.   PeerJ

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

Short-term variability in euphotic zone biogeochemistry and primary productivity at Station ALOHA: A case study of summer 2012

(2015) Samuel T. Wilson et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Genomics and Ecophysiology of Heterotrophic Nitrogen-Fixing Bacteria Isolated from Estuarine Surface Water

(2015) Mikkel Bentzon-Tilia et al.   mBio

ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank

(2014) Philip Heller et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Isolation of heterotrophic diazotrophic bacteria from estuarine surface waters

(2013) Hanna Farnelid et al.   ENVIRONMENTAL MICROBIOLOGY

The paradox of marine heterotrophic nitrogen fixation: abundances of heterotrophic diazotrophs do not account for nitrogen fixation rates in the Eastern Tropical South Pacific

(2013) Kendra A. Turk-Kubo et al.   ENVIRONMENTAL MICROBIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Processes and patterns of oceanic nutrient limitation

(2013) C. M. Moore et al.   Nature Geoscience

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

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

Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes

(2012) Patricia C Dos Santos et al.   BMC GENOMICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Unicellular Cyanobacterium Symbiotic with a Single-Celled Eukaryotic Alga

(2012) A. W. Thompson et al.   SCIENCE

Heterotrophic organisms dominate nitrogen fixation in the South Pacific Gyre

(2011) Hannah Halm et al.   ISME Journal

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

(2011) Chris L Dupont et al.   ISME Journal

ggplot2: Elegant Graphics for Data Analysis

(2011) Cedric Ginestet   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY

Emerging patterns of marine nitrogen fixation

(2011) Jill A. Sohm et al.   NATURE REVIEWS MICROBIOLOGY

Nitrogenase Gene Amplicons from Global Marine Surface Waters Are Dominated by Genes of Non-Cyanobacteria

(2011) Hanna Farnelid et al.   PLoS One

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

(2011) Christopher J. Creevey et al.   PLoS One

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Nitrogenase genes in non-cyanobacterial plankton: prevalence, diversity and regulation in marine waters

(2010) L Riemann et al.   AQUATIC MICROBIAL ECOLOGY

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Regional distributions of nitrogen-fixing bacteria in the Pacific Ocean

(2010) Matthew J. Church et al.   LIMNOLOGY AND OCEANOGRAPHY

Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium

(2010) H. James Tripp et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Nitrogen fixation in an anticyclonic eddy in the oligotrophic North Pacific Ocean

(2008) Allison A Fong et al.   ISME Journal

Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon

(2008) Pia H Moisander et al.   ISME Journal

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501

(2008) Y. Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Globally Distributed Uncultivated Oceanic N2-Fixing Cyanobacteria Lack Oxygenic Photosystem II

(2008) J. P. Zehr et al.   SCIENCE