Published in Stand Genomic Sci on April 15, 2013
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From genus to phylum: large-subunit and internal transcribed spacer rRNA operon regions show similar classification accuracies influenced by database composition. Appl Environ Microbiol (2013) 0.87
Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota). PLoS One (2014) 0.83
Complementary amplicon-based genomic approaches for the study of fungal communities in humans. PLoS One (2015) 0.81
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Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J (2012) 16.84
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J (2011) 13.64
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A higher-level phylogenetic classification of the Fungi. Mycol Res (2007) 7.93
The UNITE database for molecular identification of fungi--recent updates and future perspectives. New Phytol (2010) 3.58
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ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol (2010) 2.95
Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol (2009) 2.53
The ITS2 Database III--sequences and structures for phylogeny. Nucleic Acids Res (2009) 2.04
Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences. Mol Phylogenet Evol (1992) 1.80
Accurate, rapid taxonomic classification of fungal large-subunit rRNA genes. Appl Environ Microbiol (2011) 1.63
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
Safety, activity, and immune correlates of anti-PD-1 antibody in cancer. N Engl J Med (2012) 52.99
A core gut microbiome in obese and lean twins. Nature (2008) 52.30
UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol (2005) 49.76
The generic genome browser: a building block for a model organism system database. Genome Res (2002) 42.64
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods (2008) 32.71
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
UCHIME improves sensitivity and speed of chimera detection. Bioinformatics (2011) 29.22
The human microbiome project. Nature (2007) 28.53
Biological, clinical and population relevance of 95 loci for blood lipids. Nature (2010) 28.21
UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics (2006) 25.13
Bacterial community variation in human body habitats across space and time. Science (2009) 24.84
Evolution of mammals and their gut microbes. Science (2008) 21.40
PyCogent: a toolkit for making sense from sequence. Genome Biol (2007) 20.64
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
Human gut microbiome viewed across age and geography. Nature (2012) 19.31
Linking long-term dietary patterns with gut microbial enterotypes. Science (2011) 17.30
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res (2011) 17.21
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The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med (2009) 16.02
PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics (2009) 15.93
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The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol (2003) 13.32
Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. Nature (2011) 13.25
The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A (2008) 12.99
Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science (2010) 12.54
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol (2009) 12.34
Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol (2008) 12.16
Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol (2007) 11.88
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A (2010) 11.21
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol (2013) 11.05
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A (2012) 10.22
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J (2009) 9.71
Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A (2010) 9.57
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods (2010) 9.18
Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res (2007) 9.15
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res (2008) 9.09
Diversity, stability and resilience of the human gut microbiota. Nature (2012) 9.09
Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature (2006) 8.94
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science (2011) 8.88
Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science (2013) 8.81
Global patterns in bacterial diversity. Proc Natl Acad Sci U S A (2007) 8.00
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res (2009) 7.12
An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22. Genomics (2002) 7.10
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A (2010) 7.09
Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science (2013) 6.98
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol (2002) 6.96
Moving pictures of the human microbiome. Genome Biol (2011) 6.72
Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe (2009) 6.67
UniFrac: an effective distance metric for microbial community comparison. ISME J (2010) 6.43
Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res (2013) 6.36
The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010. Stand Genomic Sci (2010) 6.30
Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides. Nat Genet (2008) 6.06
The impact of the gut microbiota on human health: an integrative view. Cell (2012) 6.01
Common genetic variation near MC4R is associated with waist circumference and insulin resistance. Nat Genet (2008) 5.55
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature (2006) 5.52
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods (2012) 5.41
Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J (2010) 5.37
Genetic Loci associated with C-reactive protein levels and risk of coronary heart disease. JAMA (2009) 5.32
The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog (2008) 5.28
Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc Natl Acad Sci U S A (2006) 5.19
The long-term stability of the human gut microbiota. Science (2013) 5.15
Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak. Nature (2005) 5.11
High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology (2009) 5.08
Species divergence and the measurement of microbial diversity. FEMS Microbiol Rev (2008) 4.97
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol (2010) 4.97
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat Methods (2010) 4.93
Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell (2012) 4.86
Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci (2010) 4.70
Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes. Am J Hum Genet (2008) 4.69
Defining seasonal marine microbial community dynamics. ISME J (2011) 4.61
Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A (2010) 4.56
Habitat-Lite: a GSC case study based on free text terms for environmental metadata. OMICS (2008) 4.40
The long-term health consequences of child physical abuse, emotional abuse, and neglect: a systematic review and meta-analysis. PLoS Med (2012) 4.37
Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol (2007) 4.32
The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med (2011) 4.24