Published in ISME J on April 07, 2011
Major submissions tool developments at the European Nucleotide Archive. Nucleic Acids Res (2011) 1.94
The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res (2015) 1.84
Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. ISME J (2014) 1.60
Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective. Brief Bioinform (2012) 1.50
Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes. ISME J (2013) 1.15
Defining the human microbiome. Nutr Rev (2012) 1.15
FANTOM: Functional and taxonomic analysis of metagenomes. BMC Bioinformatics (2013) 1.01
Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae. ISME J (2013) 0.96
Measures for interoperability of phenotypic data: minimum information requirements and formatting. Plant Methods (2016) 0.86
Under-detection of endospore-forming Firmicutes in metagenomic data. Comput Struct Biotechnol J (2015) 0.85
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. Database (Oxford) (2016) 0.85
Bacterial genomes: habitat specificity and uncharted organisms. Microb Ecol (2012) 0.84
Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012. Stand Genomic Sci (2012) 0.84
CDinFusion--submission-ready, on-line integration of sequence and contextual data. PLoS One (2011) 0.81
Value, but high costs in post-deposition data curation. Database (Oxford) (2016) 0.77
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics (2008) 29.20
Comparative metagenomics of microbial communities. Science (2005) 25.88
Topographical and temporal diversity of the human skin microbiome. Science (2009) 15.96
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol (2009) 12.34
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics (2010) 5.60
Megascience. 'Omics data sharing. Science (2009) 4.36
Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A (2009) 3.11
A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML). OMICS (2008) 2.82
The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation. PLoS One (2010) 2.44
A changing of the guard. Environ Microbiol (2009) 1.66
The future of microbial metagenomics (or is ignorance bliss?). ISME J (2010) 1.20
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
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
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res (2007) 35.65
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol (2007) 35.41
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
GenBank. Nucleic Acids Res (2007) 25.54
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
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 SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res (2012) 19.48
Human gut microbiome viewed across age and geography. Nature (2012) 19.31
GenBank. Nucleic Acids Res (2005) 19.25
Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS (2008) 18.69
Linking long-term dietary patterns with gut microbial enterotypes. Science (2011) 17.30
GenBank. Nucleic Acids Res (2002) 17.24
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res (2011) 17.21
GenBank. Nucleic Acids Res (2007) 16.92
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J (2012) 16.84
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
ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res (2003) 15.48
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J (2011) 13.64
GenBank. Nucleic Acids Res (2008) 13.29
The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A (2008) 12.99
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science (2010) 12.54
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res (2008) 12.45
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol (2009) 12.34
GenBank: update. Nucleic Acids Res (2004) 12.28
GenBank. Nucleic Acids Res (2006) 12.21
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
GenBank. Nucleic Acids Res (2009) 11.11
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol (2013) 11.05
GenBank. Nucleic Acids Res (2012) 10.89
EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Res (2006) 9.72
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J (2009) 9.71
GenBank. Nucleic Acids Res (2003) 9.60
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
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science (2011) 8.88
GenBank. Nucleic Acids Res (2011) 8.85
Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science (2013) 8.81
GenBank. Nucleic Acids Res (2010) 8.63
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2011) 8.62
The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol (2008) 8.21
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
The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics (2006) 7.37
The EMBL Nucleotide Sequence Database. Nucleic Acids Res (2005) 7.18
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res (2009) 7.12
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A (2010) 7.09
Archiving next generation sequencing data. Nucleic Acids Res (2009) 6.98
Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science (2013) 6.98
Moving pictures of the human microbiome. Genome Biol (2011) 6.72
The EMBL Nucleotide Sequence Database. Nucleic Acids Res (2004) 6.72
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Res (2011) 6.69
Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe (2009) 6.67
The European Nucleotide Archive. Nucleic Acids Res (2010) 6.48
UniFrac: an effective distance metric for microbial community comparison. ISME J (2010) 6.43
SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics (2012) 6.40
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
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res (2012) 6.21
The impact of the gut microbiota on human health: an integrative view. Cell (2012) 6.01
DDBJ launches a new archive database with analytical tools for next-generation sequence data. Nucleic Acids Res (2009) 5.89
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics (2010) 5.60
Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Res (2011) 5.60
Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases. Nature (2003) 5.48
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
Modeling biomedical experimental processes with OBI. J Biomed Semantics (2010) 5.36
The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog (2008) 5.28
The long-term stability of the human gut microbiota. Science (2013) 5.15
High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology (2009) 5.08
Improvements to services at the European Nucleotide Archive. Nucleic Acids Res (2009) 5.00
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol (2010) 4.97