Published in Stand Genomic Sci on July 20, 2009
IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res (2012) 12.03
The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res (2009) 6.07
RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep (2015) 5.01
IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res (2011) 2.76
BG7: a new approach for bacterial genome annotation designed for next generation sequencing data. PLoS One (2012) 2.15
Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. Stand Genomic Sci (2013) 1.70
Improving microbial genome annotations in an integrated database context. PLoS One (2013) 1.48
CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol (2013) 1.46
The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium. Environ Microbiol (2012) 1.44
Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium. PLoS One (2010) 1.40
Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS One (2013) 1.24
Complete genome sequence of "Enterobacter lignolyticus" SCF1. Stand Genomic Sci (2011) 1.24
Complete genome sequences of six strains of the genus Methylobacterium. J Bacteriol (2012) 1.23
IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. PLoS One (2012) 1.20
A Genomic Encyclopedia of the Root Nodule Bacteria: assessing genetic diversity through a systematic biogeographic survey. Stand Genomic Sci (2015) 1.12
Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PLoS One (2013) 1.08
Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera. Microb Ecol (2011) 1.07
Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci (2014) 0.99
Draft Genome Sequence of Frankia sp. Strain DC12, an Atypical, Noninfective, Ineffective Isolate from Datisca cannabina. Genome Announc (2015) 0.98
Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Front Microbiol (2013) 0.97
Metagenomic analysis of a stable trichloroethene-degrading microbial community. ISME J (2012) 0.97
Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome. J Bacteriol (2012) 0.92
Mobile elements in a single-filament orange Guaymas Basin Beggiatoa ("Candidatus Maribeggiatoa") sp. draft genome: evidence for genetic exchange with cyanobacteria. Appl Environ Microbiol (2013) 0.92
Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat Commun (2016) 0.92
The state of standards in genomic sciences. Stand Genomic Sci (2011) 0.92
Genome sequence of the Leisingera aquimarina type strain (DSM 24565(T)), a member of the marine Roseobacter clade rich in extrachromosomal elements. Stand Genomic Sci (2013) 0.90
Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade. Stand Genomic Sci (2013) 0.89
Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium. Stand Genomic Sci (2014) 0.88
Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans. Stand Genomic Sci (2014) 0.88
Genome (re-)annotation and open-source annotation pipelines. Microb Biotechnol (2010) 0.87
Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2. Stand Genomic Sci (2014) 0.87
CRISPRDetect: A flexible algorithm to define CRISPR arrays. BMC Genomics (2016) 0.86
Genome Sequence of Halomonas sp. Strain MCTG39a, a Hydrocarbon-Degrading and Exopolymeric Substance-Producing Bacterium. Genome Announc (2015) 0.86
Comparative genomics of nucleotide metabolism: a tour to the past of the three cellular domains of life. BMC Genomics (2014) 0.86
Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336(T)), a representative of the Roseobacter clade. Stand Genomic Sci (2013) 0.86
Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens. Stand Genomic Sci (2013) 0.86
Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. ISME J (2017) 0.85
Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis. Stand Genomic Sci (2013) 0.84
Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566(T.). Stand Genomic Sci (2013) 0.84
Genome Sequence and Analysis of Escherichia coli MRE600, a Colicinogenic, Nonmotile Strain that Lacks RNase I and the Type I Methyltransferase, EcoKI. Genome Biol Evol (2016) 0.83
Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle. BMC Genomics (2014) 0.83
Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk. Proc Natl Acad Sci U S A (2014) 0.82
Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4. Stand Genomic Sci (2014) 0.82
Metagenomic approach for understanding microbial population from petroleum muck. Genome Announc (2014) 0.81
Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4. Stand Genomic Sci (2013) 0.81
Genome sequence of Ensifer sp. TW10; a Tephrosia wallichii (Biyani) microsymbiont native to the Indian Thar Desert. Stand Genomic Sci (2013) 0.81
Genome sequence of Ensifer meliloti strain WSM1022; a highly effective microsymbiont of the model legume Medicago truncatula A17. Stand Genomic Sci (2013) 0.81
Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Stand Genomic Sci (2014) 0.81
Draft Genome Sequence of Anoxybacillus suryakundensis Strain JS1T (DSM 27374T) Isolated from a Hot Spring in Jharkhand, India. Genome Announc (2016) 0.81
High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris. Stand Genomic Sci (2015) 0.80
Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)). Stand Genomic Sci (2013) 0.80
Genome sequence of the Lebeckia ambigua-nodulating "Burkholderia sprentiae" strain WSM5005(T.). Stand Genomic Sci (2013) 0.80
Genome sequence of the reddish-pigmented Rubellimicrobium thermophilum type strain (DSM 16684(T)), a member of the Roseobacter clade. Stand Genomic Sci (2013) 0.80
High quality draft genome sequence of Meganema perideroedes str. Gr1(T) and a proposal for its reclassification to the family Meganemaceae fam. nov. Stand Genomic Sci (2015) 0.80
Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos. Stand Genomic Sci (2015) 0.80
Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain TA1. Stand Genomic Sci (2013) 0.79
High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM 19883(T)) isolated from a Chironomus sp. egg mass. Stand Genomic Sci (2015) 0.79
Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug). Stand Genomic Sci (2013) 0.79
Genome comparison provides molecular insights into the phylogeny of the reassigned new genus Lysinibacillus. BMC Genomics (2015) 0.78
Genome sequence of Ensifer medicae strain WSM1369; an effective microsymbiont of the annual legume Medicago sphaerocarpos. Stand Genomic Sci (2013) 0.78
Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T). Stand Genomic Sci (2015) 0.78
Draft genome sequence of a nitrate-reducing, o-phthalate degrading bacterium, Azoarcus sp. strain PA01(T). Stand Genomic Sci (2015) 0.78
Genome sequence of Microvirga lupini strain LUT6(T), a novel Lupinus alphaproteobacterial microsymbiont from Texas. Stand Genomic Sci (2014) 0.78
Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1(T), an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake. Stand Genomic Sci (2015) 0.78
Genome sequence of the Litoreibacter arenae type strain (DSM 19593(T)), a member of the Roseobacter clade isolated from sea sand. Stand Genomic Sci (2013) 0.78
High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512. Stand Genomic Sci (2015) 0.78
Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210(T) (= DSM 26640(T) = BS107(T)). Stand Genomic Sci (2014) 0.78
The genome and transcriptome of Trichormus sp. NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau. Sci Rep (2016) 0.78
Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion. PLoS One (2012) 0.78
Comparative genomic analysis of multiple strains of two unusual plant pathogens: Pseudomonas corrugata and Pseudomonas mediterranea. Front Microbiol (2015) 0.78
High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy. Stand Genomic Sci (2015) 0.77
Draft Genome Sequence of Pseudomonas azotifigens Strain DSM 17556T (6H33bT), a Nitrogen Fixer Strain Isolated from a Compost Pile. Genome Announc (2013) 0.77
Genome sequence of Ensifer arboris strain LMG 14919(T); a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan. Stand Genomic Sci (2013) 0.77
Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift. Stand Genomic Sci (2013) 0.77
Draft-genome sequence of Shewanella algae strain C6G3. Stand Genomic Sci (2015) 0.77
Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia. Stand Genomic Sci (2013) 0.77
Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment. Stand Genomic Sci (2014) 0.77
High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum. Stand Genomic Sci (2015) 0.77
Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)). Stand Genomic Sci (2013) 0.77
High-quality permanent draft genome sequence of Bradyrhizobium sp. Ai1a-2; a microsymbiont of Andira inermis discovered in Costa Rica. Stand Genomic Sci (2015) 0.76
Complete Genome Sequence of Methanoregula formicica SMSPT, a Mesophilic Hydrogenotrophic Methanogen Isolated from a Methanogenic Upflow Anaerobic Sludge Blanket Reactor. Genome Announc (2014) 0.76
Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557(T.). Stand Genomic Sci (2013) 0.76
Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva. Stand Genomic Sci (2013) 0.76
Complete genome sequence of Novosphingobium pentaromativorans US6-1(T). Stand Genomic Sci (2015) 0.76
Permanent draft genome sequence of sulfoquinovose-degrading Pseudomonas putida strain SQ1. Stand Genomic Sci (2015) 0.76
Draft Genome Sequence of the Cellulolytic and Xylanolytic Thermophile Clostridium clariflavum Strain 4-2a. Genome Announc (2015) 0.76
High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169(T) (DSM 21076(T)) from a sea urchin in southern China. Stand Genomic Sci (2014) 0.76
High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T)). Stand Genomic Sci (2013) 0.76
Genome sequence of Burkholderia mimosarum strain LMG 23256(T), a Mimosa pigra microsymbiont from Anso, Taiwan. Stand Genomic Sci (2013) 0.75
Genome sequence of the South American clover-nodulating Rhizobium leguminosarum bv. trifolii strain WSM597. Stand Genomic Sci (2013) 0.75
Genome sequence of the Trifolium rueppellianum -nodulating Rhizobium leguminosarum bv. trifolii strain WSM2012. Stand Genomic Sci (2013) 0.75
Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471. Stand Genomic Sci (2013) 0.75
Complete Genome Sequence of Methanolinea tarda NOBI-1T, a Hydrogenotrophic Methanogen Isolated from Methanogenic Digester Sludge. Genome Announc (2014) 0.75
Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943. Stand Genomic Sci (2013) 0.75
Draft Genome Sequence of Tepidiphilus thermophilus Strain JHK30T (JCM 19170T) Isolated from a Terrestrial Hot Spring in India. Genome Announc (2016) 0.75
Draft Genome Sequences of Type Strain Sediminibacterium salmoneum NJ-44 and Sediminibacterium sp. Strain C3, a Novel Strain Isolated from Activated Sludge. Genome Announc (2014) 0.75
High-quality draft genome sequence of Gracilimonas tropica CL-CB462(T) (DSM 19535(T)), isolated from a Synechococcus culture. Stand Genomic Sci (2015) 0.75
Genome sequence and overview of Oligoflexus tunisiensis Shr3(T) in the eighth class Oligoflexia of the phylum Proteobacteria. Stand Genomic Sci (2016) 0.75
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res (1997) 142.55
RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res (2007) 85.81
Profile hidden Markov models. Bioinformatics (1998) 56.04
KEGG for linking genomes to life and the environment. Nucleic Acids Res (2007) 49.37
The Pfam protein families database. Nucleic Acids Res (2007) 30.53
Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res (2005) 25.49
GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res (2001) 24.24
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res (2007) 13.81
The TIGRFAMs database of protein families. Nucleic Acids Res (2003) 13.59
Infernal 1.0: inference of RNA alignments. Bioinformatics (2009) 12.98
CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res (2006) 11.41
MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res (2006) 6.64
CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics (2007) 5.84
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
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res (2007) 13.81
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 Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res (2009) 9.98
Insights into the phylogeny and coding potential of microbial dark matter. Nature (2013) 8.55
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
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
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
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res (2006) 6.79
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
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol (2006) 5.71
Symbiosis insights through metagenomic analysis of a microbial consortium. Nature (2006) 5.04
A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev (2008) 4.33
One bacterial cell, one complete genome. PLoS One (2010) 3.69
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol (2009) 3.63
Complete genome sequence of Kytococcus sedentarius type strain (541). Stand Genomic Sci (2009) 3.30
IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res (2013) 2.99
High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol (2008) 2.99
Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc Natl Acad Sci U S A (2005) 2.85
IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res (2011) 2.76
An experimental metagenome data management and analysis system. Bioinformatics (2006) 2.71
The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. PLoS One (2012) 2.25
Complete genome sequence of Meiothermus ruber type strain (21). Stand Genomic Sci (2010) 1.96
Gene context analysis in the Integrated Microbial Genomes (IMG) data management system. PLoS One (2009) 1.93
Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS One (2009) 1.83
Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3). Stand Genomic Sci (2009) 1.82
The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet (2011) 1.75
Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains. Proc Natl Acad Sci U S A (2002) 1.73
Individual genome assembly from complex community short-read metagenomic datasets. ISME J (2011) 1.71
Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. J Bacteriol (2007) 1.67
A changing of the guard. Environ Microbiol (2009) 1.66
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol (2008) 1.60
A call for standardized classification of metagenome projects. Environ Microbiol (2010) 1.58
Draft genome sequence of Frankia sp. strain CN3, an atypical, noninfective (Nod-) ineffective (Fix-) isolate from Coriaria nepalensis. Genome Announc (2013) 1.51
The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist. PLoS One (2011) 1.48
Improving microbial genome annotations in an integrated database context. PLoS One (2013) 1.48