Published in Proc Natl Acad Sci U S A on August 22, 2011
Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res (2013) 6.36
Defining the core Arabidopsis thaliana root microbiome. Nature (2012) 5.56
Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities. Proc Natl Acad Sci U S A (2012) 1.54
Distribution-based clustering: using ecology to refine the operational taxonomic unit. Appl Environ Microbiol (2013) 1.25
Contemporary environmental variation determines microbial diversity patterns in acid mine drainage. ISME J (2012) 1.22
Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. ISME J (2014) 1.19
Does the gut microbiota have a role in type 1 diabetes? Early evidence from humans and animal models of the disease. Diabetologia (2012) 1.04
Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows. BMC Bioinformatics (2011) 1.02
Effect of sugarcane burning or green harvest methods on the Brazilian Cerrado soil bacterial community structure. PLoS One (2013) 0.99
Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia. ISME J (2015) 0.98
Analytical tools and databases for metagenomics in the next-generation sequencing era. Genomics Inform (2013) 0.98
The role of the intestinal microbiota in type 1 diabetes mellitus. Nat Rev Endocrinol (2016) 0.93
Recently deglaciated high-altitude soils of the Himalaya: diverse environments, heterogenous bacterial communities and long-range dust inputs from the upper troposphere. PLoS One (2013) 0.87
Impact of next generation sequencing techniques in food microbiology. Curr Genomics (2014) 0.85
Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing. Sci Rep (2016) 0.82
A comparative study of the bacterial community in denitrifying and traditional enhanced biological phosphorus removal processes. Microbes Environ (2014) 0.81
Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens - A Review. Asian-Australas J Anim Sci (2015) 0.80
Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass. Appl Environ Microbiol (2014) 0.79
Proposed model for the high rate of rearrangement and rapid migration observed in some IncA/C plasmid lineages. Appl Environ Microbiol (2013) 0.78
Baseline survey of root-associated microbes of Taxus chinensis (Pilger) Rehd. PLoS One (2015) 0.78
Statistical object data analysis of taxonomic trees from human microbiome data. PLoS One (2012) 0.78
Exploring the Influence of Environmental Factors on Bacterial Communities within the Rhizosphere of the Cu-tolerant plant, Elsholtzia splendens. Sci Rep (2016) 0.75
Composition and Interactions among Bacterial, Microeukaryotic, and T4-like Viral Assemblages in Lakes from Both Polar Zones. Front Microbiol (2016) 0.75
Exploring gastric bacterial community in young pigs. PLoS One (2017) 0.75
Regime shift in sandy beach microbial communities following Deepwater Horizon oil spill remediation efforts. PLoS One (2014) 0.75
Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds. Front Microbiol (2016) 0.75
Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow. Front Microbiol (2016) 0.75
Operation performance and microbial community dynamics of phosphorus removal sludge with different electron acceptors. J Ind Microbiol Biotechnol (2014) 0.75
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol (2007) 60.97
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol (2006) 57.72
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res (2008) 52.43
UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol (2005) 49.76
Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A (2006) 42.38
The detection of disease clustering and a generalized regression approach. Cancer Res (1967) 39.90
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res (2007) 35.65
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol (2007) 23.58
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A (2010) 19.48
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol (2008) 16.57
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res (2006) 16.26
Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods (2009) 15.25
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol (2009) 15.15
Microbial population structures in the deep marine biosphere. Science (2007) 14.61
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol (2009) 14.17
Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J (2007) 13.95
Infernal 1.0: inference of RNA alignments. Bioinformatics (2009) 12.98
Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet (2008) 10.72
Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res (2007) 9.15
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res (2009) 7.12
A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol (2008) 6.82
Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads. Appl Environ Microbiol (2011) 6.03
Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One (2009) 4.93
Habitat-Lite: a GSC case study based on free text terms for environmental metadata. OMICS (2008) 4.40
Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A (2009) 4.03
Polyphasic taxonomy of the genus vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol (1970) 3.68
The 'rare biosphere': a reality check. Nat Methods (2009) 3.19
Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science (2009) 2.96
Abundance-based similarity indices and their estimation when there are unseen species in samples. Biometrics (2006) 2.72
Novelty and uniqueness patterns of rare members of the soil biosphere. Appl Environ Microbiol (2008) 1.90
Comprehensive census of bacteria in clean rooms by using DNA microarray and cloning methods. Appl Environ Microbiol (2009) 1.37
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol (2007) 60.97
DNA Probe Method for the Detection of Specific Microorganisms in the Soil Bacterial Community. Appl Environ Microbiol (1988) 13.80
DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol (2007) 12.76
Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A (2005) 9.63
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res (2013) 6.36
Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One (2009) 4.93
The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci (2006) 4.47
Towards environmental systems biology of Shewanella. Nat Rev Microbiol (2008) 4.37
Towards a genome-based taxonomy for prokaryotes. J Bacteriol (2005) 4.18
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res (2010) 4.17
The Genomic Standards Consortium. PLoS Biol (2011) 3.99
Trends between gene content and genome size in prokaryotic species with larger genomes. Proc Natl Acad Sci U S A (2004) 3.89
Dechlorination of Four Commercial Polychlorinated Biphenyl Mixtures (Aroclors) by Anaerobic Microorganisms from Sediments. Appl Environ Microbiol (1990) 3.46
Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci U S A (2009) 3.16
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proc Natl Acad Sci U S A (2012) 3.10
Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci U S A (2006) 3.07
Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol (2002) 2.99
Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution. Microb Ecol (2007) 2.78
Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proc Natl Acad Sci U S A (2007) 2.78
Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci U S A (2014) 2.65
In-feed antibiotic effects on the swine intestinal microbiome. Proc Natl Acad Sci U S A (2012) 2.50
Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proc Natl Acad Sci U S A (2013) 2.48
Facilitation of μ-opioid receptor activity by preventing δ-opioid receptor-mediated codegradation. Neuron (2011) 2.42
Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proc Natl Acad Sci U S A (2011) 2.21
Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress. Appl Environ Microbiol (2002) 2.14
Toward a standards-compliant genomic and metagenomic publication record. OMICS (2008) 2.11
Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Appl Environ Microbiol (2006) 2.07
Superwide-band negative refraction of a symmetrical E-shaped metamaterial with two electromagnetic resonances. Phys Rev E Stat Nonlin Soft Matter Phys (2008) 2.02
Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium. Appl Environ Microbiol (2002) 2.02
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci U S A (2005) 1.93
The Exiguobacterium genus: biodiversity and biogeography. Extremophiles (2009) 1.91
Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol (2007) 1.83
Cryptic lineages of the genus Escherichia. Appl Environ Microbiol (2009) 1.81
FunGene: the functional gene pipeline and repository. Front Microbiol (2013) 1.80
Microbial dehalorespiration with 1,1,1-trichloroethane. Science (2002) 1.75
RNAcentral: A vision for an international database of RNA sequences. RNA (2011) 1.73
Changes in land use alter the structure of bacterial communities in Western Amazon soils. ISME J (2009) 1.72
Identification of NUB1 as a suppressor of mutant Huntington toxicity via enhanced protein clearance. Nat Neurosci (2013) 1.71
Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J (2010) 1.71
Coexpression of delta- and mu-opioid receptors in nociceptive sensory neurons. Proc Natl Acad Sci U S A (2010) 1.70
Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils. Appl Environ Microbiol (2002) 1.68
Human rhinovirus 1B exposure induces phosphatidylinositol 3-kinase-dependent airway inflammation in mice. Am J Respir Crit Care Med (2008) 1.67
Species abundance and diversity of Burkholderia cepacia complex in the environment. Appl Environ Microbiol (2005) 1.62
Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities. Proc Natl Acad Sci U S A (2012) 1.54
Bacterial community in ancient Siberian permafrost as characterized by culture and culture-independent methods. Astrobiology (2006) 1.53
Gene-Z: a device for point of care genetic testing using a smartphone. Lab Chip (2012) 1.52
Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400T and relatives as Burkholderia xenovorans sp. nov. Int J Syst Evol Microbiol (2004) 1.50
Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater. Environ Microbiol (2003) 1.49
Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors. OMICS (2002) 1.48
Comparative systems biology across an evolutionary gradient within the Shewanella genus. Proc Natl Acad Sci U S A (2009) 1.47
Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. MBio (2014) 1.46
The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Appl Environ Microbiol (2010) 1.44
Rhinovirus disrupts the barrier function of polarized airway epithelial cells. Am J Respir Crit Care Med (2008) 1.43
Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach. BMC Genomics (2008) 1.43
Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico. Appl Environ Microbiol (2003) 1.43
Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). ISME J (2007) 1.41
Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog. Int J Syst Evol Microbiol (2002) 1.40
Single-camera microscopic stereo digital image correlation using a diffraction grating. Opt Express (2013) 1.38
Rhinovirus infection of allergen-sensitized and -challenged mice induces eotaxin release from functionally polarized macrophages. J Immunol (2010) 1.37
Characterization of two tetrachloroethene-reducing, acetate-oxidizing anaerobic bacteria and their description as Desulfuromonas michiganensis sp. nov. Appl Environ Microbiol (2003) 1.33
Quantitative detection of microbial genes by using DNA microarrays. Appl Environ Microbiol (2002) 1.32
Shewanella--the environmentally versatile genome. Nat Biotechnol (2002) 1.32
Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov. Extremophiles (2006) 1.31
Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. ISME J (2009) 1.31
Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proc Natl Acad Sci U S A (2014) 1.31
Antidepressant effects of ginseng total saponins in the forced swimming test and chronic mild stress models of depression. Prog Neuropsychopharmacol Biol Psychiatry (2009) 1.30
CXCR2 is required for neutrophilic airway inflammation and hyperresponsiveness in a mouse model of human rhinovirus infection. J Immunol (2009) 1.28
Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. MBio (2013) 1.28
Molecular evidence for the broad distribution of anaerobic ammonium-oxidizing bacteria in freshwater and marine sediments. Appl Environ Microbiol (2006) 1.28
On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes. Nucleic Acids Res (2006) 1.27
Psychrobacter cryohalolentis sp. nov. and Psychrobacter arcticus sp. nov., isolated from Siberian permafrost. Int J Syst Evol Microbiol (2006) 1.27
Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico. Appl Environ Microbiol (2008) 1.25
Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels. Appl Environ Microbiol (2008) 1.24
Extensive intestinal first-pass elimination and predominant hepatic distribution of berberine explain its low plasma levels in rats. Drug Metab Dispos (2010) 1.23
Coping with our cold planet. Appl Environ Microbiol (2008) 1.22
Nitric oxide reductase (norB) genes from pure cultures and environmental samples. Appl Environ Microbiol (2003) 1.21
Affective decision-making deficits, linked to a dysfunctional ventromedial prefrontal cortex, revealed in 10th grade Chinese adolescent binge drinkers. Neuropsychologia (2007) 1.20
Isolation of naturally associated bacteria of necromenic Pristionchus nematodes and fitness consequences. J Exp Biol (2008) 1.19
Acetate versus hydrogen as direct electron donors to stimulate the microbial reductive dechlorination process at chloroethene-contaminated sites. Environ Sci Technol (2002) 1.19
Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. ISME J (2010) 1.19
Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean. Int J Syst Evol Microbiol (2006) 1.18
Elastase- and LPS-exposed mice display altered responses to rhinovirus infection. Am J Physiol Lung Cell Mol Physiol (2009) 1.18
Fibroblast growth factor 13 is a microtubule-stabilizing protein regulating neuronal polarization and migration. Cell (2012) 1.17
A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. Microbiome (2013) 1.17
PKA phosphorylation couples hepatic inositol-requiring enzyme 1alpha to glucagon signaling in glucose metabolism. Proc Natl Acad Sci U S A (2011) 1.17