Rapid annotation ofnifHgene sequences using classification and regression trees facilitates environmental functional gene analysis
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Title
Rapid annotation ofnifHgene sequences using classification and regression trees facilitates environmental functional gene analysis
Authors
Keywords
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Journal
Environmental Microbiology Reports
Volume 8, Issue 5, Pages 905-916
Publisher
Wiley
Online
2016-08-25
DOI
10.1111/1758-2229.12455
References
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Note: Only part of the references are listed.- ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank
- (2014) Philip Heller et al. BIOINFORMATICS
- nifHpyrosequencing reveals the potential for location-specific soil chemistry to influence N2-fixing community dynamics
- (2014) Mónica M. Collavino et al. ENVIRONMENTAL MICROBIOLOGY
- Cultivation and isolation of N2-fixing bacteria from suboxic waters in the Baltic Sea
- (2014) Mikkel Bentzon-Tilia et al. FEMS MICROBIOLOGY ECOLOGY
- A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria
- (2014) John Christian Gaby et al. Database-The Journal of Biological Databases and Curation
- Classification of pmoA amplicon pyrosequences using BLAST and the lowest common ancestor method in MEGAN
- (2014) Marc G. Dumont et al. Frontiers in Microbiology
- Nitrogen fixation in distinct microbial niches within a chemoautotrophy-driven cave ecosystem
- (2013) Mahesh S Desai et al. ISME Journal
- Aphotic N2 Fixation in the Eastern Tropical South Pacific Ocean
- (2013) Sophie Bonnet et al. PLoS One
- Dinitrogen fixation in aphotic oxygenated marine environments
- (2013) Eyal Rahav et al. Frontiers in Microbiology
- Corals Form Characteristic Associations with Symbiotic Nitrogen-Fixing Bacteria
- (2012) Kimberley A. Lema et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- A comparative evaluation of sequence classification programs
- (2012) Adam L Bazinet et al. BMC BIOINFORMATICS
- Phylogenetic Diversity of Nitrogen Fixation Genes in the Intestinal Tract of Reticulitermes chinensis Snyder
- (2012) Xin Du et al. CURRENT MICROBIOLOGY
- Diversity, distribution, and expression of diazotrophnifHgenes in oxygen-deficient waters of the Arabian Sea
- (2012) Amal Jayakumar et al. FEMS MICROBIOLOGY ECOLOGY
- A Comprehensive Evaluation of PCR Primers to Amplify the nifH Gene of Nitrogenase
- (2012) John Christian Gaby et al. PLoS One
- Phylogenetic diversity and spatio-temporal distribution of nitrogenase genes (nifH) in the northern South China Sea
- (2011) L Kong et al. AQUATIC MICROBIAL ECOLOGY
- Nitrogen fixation within the water column associated with two hypoxic basins in the Southern California Bight
- (2011) MR Hamersley et al. AQUATIC MICROBIAL ECOLOGY
- Is dinitrogen fixation significant in the Levantine Basin, East Mediterranean Sea?
- (2011) Tali Yogev et al. ENVIRONMENTAL MICROBIOLOGY
- A global census of nitrogenase diversity
- (2011) John Christian Gaby et al. ENVIRONMENTAL MICROBIOLOGY
- Seasonal variations in the diversity and abundance of diazotrophic communities across soils
- (2011) Michele C. Pereira e Silva et al. FEMS MICROBIOLOGY ECOLOGY
- Heterotrophic organisms dominate nitrogen fixation in the South Pacific Gyre
- (2011) Hannah Halm et al. ISME Journal
- Bacteroidales ectosymbionts of gut flagellates shape the nitrogen-fixing community in dry-wood termites
- (2011) Mahesh S Desai et al. ISME Journal
- Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic
- (2011) Kendra A Turk et al. ISME Journal
- Environmental Constraints Underpin the Distribution and Phylogenetic Diversity of nifH in the Yellowstone Geothermal Complex
- (2011) Trinity L. Hamilton et al. MICROBIAL ECOLOGY
- Nitrogen Fixation in Denitrified Marine Waters
- (2011) Camila Fernandez et al. PLoS One
- Nitrogenase Gene Amplicons from Global Marine Surface Waters Are Dominated by Genes of Non-Cyanobacteria
- (2011) Hanna Farnelid et al. PLoS One
- Nitrogen fixation by marine cyanobacteria
- (2011) Jonathan P. Zehr TRENDS IN MICROBIOLOGY
- Search and clustering orders of magnitude faster than BLAST
- (2010) Robert C. Edgar BIOINFORMATICS
- pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
- (2010) Frederick A Matsen et al. BMC BIOINFORMATICS
- Distribution of diazotrophic microorganisms and nifH gene expression in the Mekong River plume during intermonsoon
- (2010) D Bombar et al. MARINE ECOLOGY PROGRESS SERIES
- Microbial community shifts influence patterns in tropical forest nitrogen fixation
- (2010) Sasha C. Reed et al. OECOLOGIA
- FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
- (2010) Morgan N. Price et al. PLoS One
- 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
- Application of CART in ecological landscape mapping: Two case studies
- (2009) Roland Pesch et al. ECOLOGICAL INDICATORS
- FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
- (2009) M. N. Price et al. MOLECULAR BIOLOGY AND EVOLUTION
- The microbial ocean from genomes to biomes
- (2009) Edward F. DeLong NATURE
- Identity and dynamics of putative N2-fixing picoplankton in the Baltic Sea proper suggest complex patterns of regulation
- (2009) Hanna Farnelid et al. Environmental Microbiology Reports
- Characterization of Diazotrophs Containing Mo-Independent Nitrogenases, Isolated from Diverse Natural Environments
- (2008) D. A. Betancourt et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Diversity and expression of nitrogen fixation genes in bacterial symbionts of marine sponges
- (2008) Naglaa M. Mohamed et al. ENVIRONMENTAL MICROBIOLOGY
- 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
- Evidence for the functional significance of diazotroph community structure in soil
- (2008) Shi-Fang Hsu et al. ISME Journal
- Nitrogen fixation by phyllosphere bacteria associated with higher plants and their colonizing epiphytes of a tropical lowland rainforest of Costa Rica
- (2008) Michael Fürnkranz et al. ISME Journal
- Testing of null hypotheses in exploratory community analyses: similarity profiles and biota-environment linkage
- (2008) K. Robert Clarke et al. JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY
- Analysis of a diverse assemblage of diazotrophic bacteria from Spartina alterniflora using DGGE and clone library screening
- (2008) Charles R. Lovell et al. JOURNAL OF MICROBIOLOGICAL METHODS
- High Diversity of Diazotrophs in the Forefield of a Receding Alpine Glacier
- (2008) Laurence Duc et al. MICROBIAL ECOLOGY
- The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
- (2008) J. R. Cole et al. NUCLEIC ACIDS RESEARCH
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