Published in Nat Biotechnol on September 24, 2006
Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci U S A (2007) 7.82
IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res (2007) 7.18
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol (2013) 6.40
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics (2010) 5.70
Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res (2008) 5.12
A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev (2008) 4.33
Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat Rev Microbiol (2011) 4.09
Community-wide analysis of microbial genome sequence signatures. Genome Biol (2009) 3.96
Explaining microbial population genomics through phage predation. Nat Rev Microbiol (2009) 3.87
Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl Environ Microbiol (2007) 3.55
Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol (2007) 3.26
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol (2010) 3.19
Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). Appl Environ Microbiol (2011) 2.61
Novel approaches to developing new antibiotics for bacterial infections. Br J Pharmacol (2007) 2.43
An insect herbivore microbiome with high plant biomass-degrading capacity. PLoS Genet (2010) 2.28
Metagenomic analyses: past and future trends. Appl Environ Microbiol (2010) 2.21
A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics (2008) 2.17
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol (2008) 2.12
Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl Environ Microbiol (2011) 2.08
The binning of metagenomic contigs for microbial physiology of mixed cultures. Front Microbiol (2012) 2.07
Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms. Appl Environ Microbiol (2009) 1.86
A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Res (2007) 1.85
Systems biology: Functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol (2009) 1.81
Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol (2008) 1.80
A meta-analysis of changes in bacterial and archaeal communities with time. ISME J (2013) 1.80
Metagenomic analysis of RNA viruses in a fresh water lake. PLoS One (2009) 1.69
Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers. BMC Bioinformatics (2010) 1.65
"Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division. J Bacteriol (2008) 1.60
Binning sequences using very sparse labels within a metagenome. BMC Bioinformatics (2008) 1.60
Classifying short genomic fragments from novel lineages using composition and homology. BMC Bioinformatics (2011) 1.60
Assessment of metagenomic assembly using simulated next generation sequencing data. PLoS One (2012) 1.57
An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS One (2008) 1.53
Bioprospecting metagenomes: glycosyl hydrolases for converting biomass. Biotechnol Biofuels (2009) 1.52
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res (2008) 1.50
Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem. J Math Biol (2012) 1.49
Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proc Natl Acad Sci U S A (2007) 1.47
A computational screen for type I polyketide synthases in metagenomics shotgun data. PLoS One (2008) 1.44
Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature (2009) 1.43
Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat Commun (2013) 1.42
The dynamic genetic repertoire of microbial communities. FEMS Microbiol Rev (2008) 1.42
Microbial community structure and diversity in an integrated system of anaerobic-aerobic reactors and a constructed wetland for the treatment of tannery wastewater in Modjo, Ethiopia. PLoS One (2014) 1.41
Mariprofundus ferrooxydans PV-1 the first genome of a marine Fe(II) oxidizing Zetaproteobacterium. PLoS One (2011) 1.40
Rapid identification of high-confidence taxonomic assignments for metagenomic data. Nucleic Acids Res (2012) 1.39
Genetic exchange across a species boundary in the archaeal genus ferroplasma. Genetics (2007) 1.35
A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal. ISME J (2011) 1.34
Molecular diversity of a North Carolina wastewater treatment plant as revealed by pyrosequencing. Appl Environ Microbiol (2008) 1.32
Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS One (2013) 1.32
Metagenomic mining for microbiologists. ISME J (2011) 1.28
"Candidatus Accumulibacter" population structure in enhanced biological phosphorus removal sludges as revealed by polyphosphate kinase genes. Appl Environ Microbiol (2007) 1.26
Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber. BMC Genomics (2009) 1.22
Linking sequence to function in soil bacteria: sequence-directed isolation of novel bacteria contributing to soilborne plant disease suppression. Appl Environ Microbiol (2008) 1.21
Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'. BMC Genomics (2009) 1.21
Strainer: software for analysis of population variation in community genomic datasets. BMC Bioinformatics (2007) 1.16
Functional assignment of metagenomic data: challenges and applications. Brief Bioinform (2012) 1.13
Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition. Nucleic Acids Res (2011) 1.11
Denitrification capabilities of two biological phosphorus removal sludges dominated by different "Candidatus Accumulibacter" clades. Environ Microbiol Rep (2009) 1.11
Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS One (2008) 1.10
Artificial polyploidy improves bacterial single cell genome recovery. PLoS One (2012) 1.10
Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal. Environ Microbiol (2008) 1.09
The activity level of a microbial community function can be predicted from its metatranscriptome. ISME J (2011) 1.08
Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data. PLoS One (2012) 1.08
Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. ISME J (2010) 1.05
Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis. Microb Ecol (2010) 1.01
Inference of microbial recombination rates from metagenomic data. PLoS Genet (2009) 1.00
Phage encoded H-NS: a potential achilles heel in the bacterial defence system. PLoS One (2011) 0.98
Crass: identification and reconstruction of CRISPR from unassembled metagenomic data. Nucleic Acids Res (2013) 0.98
'Candidatus Competibacter'-lineage genomes retrieved from metagenomes reveal functional metabolic diversity. ISME J (2013) 0.96
Progress toward understanding the distribution of Accumulibacter among full-scale enhanced biological phosphorus removal systems. Microb Ecol (2007) 0.96
Whole-genome sequencing in bacteriology: state of the art. Infect Drug Resist (2013) 0.94
Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours. Mol Syst Biol (2012) 0.94
Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities. Front Microbiol (2014) 0.93
Building on basic metagenomics with complementary technologies. Genome Biol (2007) 0.93
ClaMS: A Classifier for Metagenomic Sequences. Stand Genomic Sci (2011) 0.93
Dynamics of polyphosphate-accumulating bacteria in wastewater treatment plant microbial communities detected via DAPI (4',6'-diamidino-2-phenylindole) and tetracycline labeling. Appl Environ Microbiol (2009) 0.92
Metabolic model for the filamentous 'Candidatus Microthrix parvicella' based on genomic and metagenomic analyses. ISME J (2013) 0.91
Flexible taxonomic assignment of ambiguous sequencing reads. BMC Bioinformatics (2011) 0.91
Convergent bacterial microbiotas in the fungal agricultural systems of insects. MBio (2014) 0.90
Dynamics of microbial community structure of and enhanced biological phosphorus removal by aerobic granules cultivated on propionate or acetate. Appl Environ Microbiol (2011) 0.89
Genome-scale computational biology and bioinformatics in Australia. PLoS Comput Biol (2008) 0.89
Environmental shaping of codon usage and functional adaptation across microbial communities. Nucleic Acids Res (2013) 0.89
Deciphering the genome of polyphosphate accumulating actinobacterium Microlunatus phosphovorus. DNA Res (2012) 0.89
A decade of metaproteomics: Where we stand and what the future holds. Proteomics (2015) 0.89
Introduction of a synthetic CO₂-fixing photorespiratory bypass into a cyanobacterium. J Biol Chem (2014) 0.89
Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics. Front Microbiol (2015) 0.88
Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal. ISME J (2013) 0.88
A new subfamily of polyphosphate kinase 2 (class III PPK2) catalyzes both nucleoside monophosphate phosphorylation and nucleoside diphosphate phosphorylation. Appl Environ Microbiol (2014) 0.88
A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal. ISME J (2012) 0.88
'Candidatus Accumulibacter' gene expression in response to dynamic EBPR conditions. ISME J (2010) 0.88
A nitrile hydratase in the eukaryote Monosiga brevicollis. PLoS One (2008) 0.87
Analysis of the fine-scale population structure of "Candidatus accumulibacter phosphatis" in enhanced biological phosphorus removal sludge, using fluorescence in situ hybridization and flow cytometric sorting. Appl Environ Microbiol (2010) 0.87
Microbiology of 'Candidatus Accumulibacter' in activated sludge. Microb Biotechnol (2011) 0.86
Draft Genome Sequence of an Anaerobic Ammonium-Oxidizing Bacterium, "Candidatus Brocadia sinica". Genome Announc (2015) 0.85
GSTaxClassifier: a genomic signature based taxonomic classifier for metagenomic data analysis. Bioinformation (2009) 0.85
Granule formation mechanisms within an aerobic wastewater system for phosphorus removal. Appl Environ Microbiol (2010) 0.84
Dominant and novel clades of Candidatus Accumulibacter phosphatis in 18 globally distributed full-scale wastewater treatment plants. Sci Rep (2015) 0.84
Substrate type determines metagenomic profiles from diverse chemical habitats. PLoS One (2011) 0.84
Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. Brief Bioinform (2015) 0.83
Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities. Biotechnol Biofuels (2015) 0.83
Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems. Front Microbiol (2016) 0.82
Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes. Front Microbiol (2016) 0.82
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res (2005) 29.61
Comparative metagenomics of microbial communities. Science (2005) 25.88
Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature (2004) 20.20
GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res (2003) 18.88
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics (2004) 18.87
IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics (2009) 17.90
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature (2009) 15.06
A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell (2006) 14.70
The Sorghum bicolor genome and the diversification of grasses. Nature (2009) 14.62
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol (2009) 14.17
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res (2007) 13.81
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J (2011) 13.64
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods (2010) 13.05
Prepublication data sharing. Nature (2009) 12.24
IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res (2012) 12.03
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res (2007) 11.24
The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science (2002) 11.11
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res (2009) 9.98
Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods (2006) 9.93
MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature (2008) 9.83
CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol (2008) 8.91
Insights into the phylogeny and coding potential of microbial dark matter. Nature (2013) 8.55
The amphioxus genome and the evolution of the chordate karyotype. Nature (2008) 8.03
Dynamic changes in the human methylome during differentiation. Genome Res (2010) 7.96
Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci U S A (2007) 7.82
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods (2007) 7.73
Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol (2006) 7.64
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature (2007) 7.42
The integrated microbial genomes (IMG) system. Nucleic Acids Res (2006) 7.34
IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res (2007) 7.18
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res (2005) 7.13
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A (2010) 7.09
Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell (2011) 7.02
A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol (2008) 6.82
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res (2006) 6.79
Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science (2006) 6.74
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol (2013) 6.40
IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res (2013) 6.14
The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res (2009) 6.07
CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics (2007) 5.84
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res (2011) 5.79
Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol (2002) 5.56
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes. Stand Genomic Sci (2009) 5.50
Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol (2007) 5.40
The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc Natl Acad Sci U S A (2001) 5.39
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol (2008) 5.38
Symbiosis insights through metagenomic analysis of a microbial consortium. Nature (2006) 5.04
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet (2011) 4.65
Defining seasonal marine microbial community dynamics. ISME J (2011) 4.61
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J Biotechnol (2003) 4.40
A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev (2008) 4.33
The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol (2005) 4.28
The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1. J Neurosci (2008) 4.28
Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J (2010) 4.15
A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev (2011) 4.06
Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol (2010) 4.01
The ERGO genome analysis and discovery system. Nucleic Acids Res (2003) 3.89
Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia. Appl Environ Microbiol (2004) 3.81
Complete genome sequence of Kytococcus sedentarius type strain (541). Stand Genomic Sci (2009) 3.30
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME J (2011) 3.24
Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586. J Bacteriol (2002) 3.18