Published in Nucleic Acids Res on April 30, 2010
Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. BMC Bioinformatics (2010) 1.95
Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum. J Bacteriol (2012) 1.77
Genome sequence analyses of Pseudomonas savastanoi pv. glycinea and subtractive hybridization-based comparative genomics with nine pseudomonads. PLoS One (2011) 1.18
Genome sequence of Pseudomonas stutzeri SDM-LAC, a typical strain for studying the molecular mechanism of lactate utilization. J Bacteriol (2012) 1.14
Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core. PLoS One (2013) 1.08
Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt. BMC Genomics (2014) 1.05
CoreGenes3.5: a webserver for the determination of core genes from sets of viral and small bacterial genomes. BMC Res Notes (2013) 0.98
Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18. BMC Genomics (2011) 0.96
Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex. BMC Genomics (2014) 0.91
Genome sequence of Pseudomonas chlororaphis GP72, a root-colonizing biocontrol strain. J Bacteriol (2012) 0.91
Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas. BMC Genomics (2013) 0.89
The draft genome sequence of Corynebacterium diphtheriae bv. mitis NCTC 3529 reveals significant diversity between the primary disease-causing biovars. J Bacteriol (2012) 0.87
Comparative Genomics of Erwinia amylovora and Related Erwinia Species-What do We Learn? Genes (Basel) (2011) 0.87
Draft Genome Sequence of the Bisphenol A-Degrading Bacterium Sphingobium sp. Strain YL23. Genome Announc (2013) 0.86
Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness. BMC Genomics (2014) 0.84
PSP: rapid identification of orthologous coding genes under positive selection across multiple closely related prokaryotic genomes. BMC Genomics (2013) 0.84
Genome sequence of Sphingomonas wittichii DP58, the first reported phenazine-1-carboxylic acid-degrading strain. J Bacteriol (2012) 0.84
Virulence and draft genome sequence overview of multiple strains of the swine pathogen Haemophilus parasuis. PLoS One (2014) 0.82
Draft genome sequence of Corynebacterium diphtheriae biovar intermedius NCTC 5011. J Bacteriol (2012) 0.80
Stability of a Pseudomonas putida KT2440 bacteriophage-carried genomic island and its impact on rhizosphere fitness. Appl Environ Microbiol (2012) 0.80
Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase diversity. BMC Genomics (2015) 0.79
The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands. BMC Genomics (2015) 0.79
Draft Genome Sequence of Klebsiella pneumoniae Strain KP-1. Genome Announc (2013) 0.78
The plant growth-promoting bacteria Azospirillum amazonense: genomic versatility and phytohormone pathway. Biomed Res Int (2015) 0.77
Comparative genomics of oral isolates of Streptococcus mutans by in silico genome subtraction does not reveal accessory DNA associated with severe early childhood caries. Infect Genet Evol (2013) 0.77
Genome sequence of Pseudomonas aeruginosa strain AH16, isolated from a patient with chronic pneumonia in China. J Bacteriol (2012) 0.77
Comparative genomic analysis and phenazine production of Pseudomonas chlororaphis, a plant growth-promoting rhizobacterium. Genom Data (2015) 0.76
Loop-mediated isothermal amplification assay for detection of generic and verocytotoxin-producing Escherichia coli among indigenous individuals in Malaysia. ScientificWorldJournal (2014) 0.75
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
Versatile and open software for comparing large genomes. Genome Biol (2004) 49.45
Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics (2009) 31.84
Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res (2004) 28.63
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature (2002) 19.35
Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res (2007) 13.47
Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol Microbiol (1997) 9.50
Circular genome visualization and exploration using CGView. Bioinformatics (2004) 7.78
The microbial pan-genome. Curr Opin Genet Dev (2005) 5.93
Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol (2005) 5.77
xBASE2: a comprehensive resource for comparative bacterial genomics. Nucleic Acids Res (2007) 3.35
The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res (2008) 3.33
VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics. Nucleic Acids Res (2007) 3.07
DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res (2008) 2.94
Extensive genomic diversity in pathogenic Escherichia coli and Shigella Strains revealed by comparative genomic hybridization microarray. J Bacteriol (2004) 2.28
ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res (2009) 2.07
Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Funct Integr Genomics (2006) 1.86
WebACT--an online companion for the Artemis Comparison Tool. Bioinformatics (2005) 1.78
A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Res (2006) 1.60
YODA: selecting signature oligonucleotides. Bioinformatics (2004) 1.59
MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Res (2007) 1.56
ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes. Nucleic Acids Res (2005) 0.97
Translational genomics to develop a Salmonella enterica serovar Paratyphi A multiplex polymerase chain reaction assay. J Mol Diagn (2007) 0.93
The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature (2011) 6.73
ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res (2003) 5.12
Cytological and transcript analyses reveal fat and lazy persister-like bacilli in tuberculous sputum. PLoS Med (2008) 3.01
Phosphorothioation of DNA in bacteria by dnd genes. Nat Chem Biol (2007) 2.57
DEG: a database of essential genes. Nucleic Acids Res (2004) 2.42
TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea. Nucleic Acids Res (2010) 1.83
A novel DNA modification by sulphur. Mol Microbiol (2005) 1.79
Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum. J Bacteriol (2012) 1.77
DNA phosphorothioation is widespread and quantized in bacterial genomes. Proc Natl Acad Sci U S A (2011) 1.69
A deletion defining a common Asian lineage of Mycobacterium tuberculosis associates with immune subversion. Proc Natl Acad Sci U S A (2006) 1.64
ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Nucleic Acids Res (2011) 1.62
A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Res (2006) 1.60
MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Res (2007) 1.56
A novel DNA modification by sulfur: DndA is a NifS-like cysteine desulfurase capable of assembling DndC as an iron-sulfur cluster protein in Streptomyces lividans. Biochemistry (2007) 1.54
'Streptomyces nanchangensis', a producer of the insecticidal polyether antibiotic nanchangmycin and the antiparasitic macrolide meilingmycin, contains multiple polyketide gene clusters. Microbiology (2002) 1.54
Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related bacteria. Mol Microbiol (2007) 1.53
Mixed Salmonella infection: case report and review of the literature. J Travel Med (2007) 1.45
A novel gene, encoding 6-hydroxy-3-succinoylpyridine hydroxylase, involved in nicotine degradation by Pseudomonas putida strain S16. Appl Environ Microbiol (2008) 1.38
A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella. Nucleic Acids Res (2010) 1.36
A complete gene cluster from Streptomyces nanchangensis NS3226 encoding biosynthesis of the polyether ionophore nanchangmycin. Chem Biol (2003) 1.33
Functional analysis of the validamycin biosynthetic gene cluster and engineered production of validoxylamine A. Chem Biol (2006) 1.33
The Z curve database: a graphic representation of genome sequences. Bioinformatics (2003) 1.31
dndDB: a database focused on phosphorothioation of the DNA backbone. PLoS One (2009) 1.31
Gene cluster responsible for validamycin biosynthesis in Streptomyces hygroscopicus subsp. jinggangensis 5008. Appl Environ Microbiol (2005) 1.31
Role and regulation of fatty acid biosynthesis in the response of Shewanella piezotolerans WP3 to different temperatures and pressures. J Bacteriol (2009) 1.28
Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA. PLoS Genet (2010) 1.27
Insights into polyether biosynthesis from analysis of the nigericin biosynthetic gene cluster in Streptomyces sp. DSM4137. Chem Biol (2007) 1.27
Organizational and mutational analysis of a complete FR-008/candicidin gene cluster encoding a structurally related polyene complex. Chem Biol (2003) 1.27
Functional analysis of spfD gene involved in DNA phosphorothioation in Pseudomonas fluorescens Pf0-1. FEBS Lett (2009) 1.24
DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites. Nucleic Acids Res (2007) 1.23
Characterization of the polyoxin biosynthetic gene cluster from Streptomyces cacaoi and engineered production of polyoxin H. J Biol Chem (2009) 1.17
ATPase genes of diverse multidrug-resistant Acinetobacter baumannii isolates frequently harbour integrated DNA. J Antimicrob Chemother (2008) 1.17
A consensus on fungal polymerase chain reaction diagnosis?: a United Kingdom-Ireland evaluation of polymerase chain reaction methods for detection of systemic fungal infections. J Mol Diagn (2006) 1.16
Carnitine metabolism to trimethylamine by an unusual Rieske-type oxygenase from human microbiota. Proc Natl Acad Sci U S A (2014) 1.13
The bifunctional glyceryl transferase/phosphatase OzmB belonging to the HAD superfamily that diverts 1,3-bisphosphoglycerate into polyketide biosynthesis. J Am Chem Soc (2006) 1.13
A cellulose synthase-like protein involved in hyphal tip growth and morphological differentiation in streptomyces. J Bacteriol (2008) 1.12
The mildiomycin biosynthesis: initial steps for sequential generation of 5-hydroxymethylcytidine 5'-monophosphate and 5-hydroxymethylcytosine in Streptoverticillium rimofaciens ZJU5119. Chembiochem (2008) 1.12
Pathogenicity islands PAPI-1 and PAPI-2 contribute individually and synergistically to the virulence of Pseudomonas aeruginosa strain PA14. Infect Immun (2010) 1.10
Direct evidence that ThiI is an ATP pyrophosphatase for the adenylation of uridine in 4-thiouridine biosynthesis. Chembiochem (2008) 1.09
DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus. BMC Microbiol (2009) 1.09
Biotransformation of isoeugenol to vanillin by a newly isolated Bacillus pumilus strain: identification of major metabolites. J Biotechnol (2007) 1.08
Identification and analysis of the biosynthetic gene cluster encoding the thiopeptide antibiotic cyclothiazomycin in Streptomyces hygroscopicus 10-22. Appl Environ Microbiol (2010) 1.08
Characterization of the tunicamycin gene cluster unveiling unique steps involved in its biosynthesis. Protein Cell (2010) 1.06
A self-ligation method for PCR-sequencing the telomeres of Streptomyces and Mycobacterium linear replicons. J Microbiol Methods (2012) 1.04
ValC, a new type of C7-Cyclitol kinase involved in the biosynthesis of the antifungal agent validamycin A. Chembiochem (2007) 1.04
Phosphorothioate DNA as an antioxidant in bacteria. Nucleic Acids Res (2012) 1.03
A subtype of a Pseudomonas aeruginosa cystic fibrosis epidemic strain exhibits enhanced virulence in a murine model of acute respiratory infection. J Infect Dis (2010) 1.03
Molecular epidemiology of the SRL pathogenicity island. Antimicrob Agents Chemother (2003) 1.03
sRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes. PLoS One (2010) 1.02
A novel target of IscS in Escherichia coli: participating in DNA phosphorothioation. PLoS One (2012) 1.02
Cometabolic degradation of dibenzofuran and dibenzothiophene by a newly isolated carbazole-degrading Sphingomonas sp. strain. Appl Environ Microbiol (2007) 1.02
PolY, a transcriptional regulator with ATPase activity, directly activates transcription of polR in polyoxin biosynthesis in Streptomyces cacaoi. Mol Microbiol (2009) 1.01
The enzymology of polyether biosynthesis. Methods Enzymol (2009) 1.01
Regulated site-specific recombination of the she pathogenicity island of Shigella flexneri. Mol Microbiol (2004) 1.01
SecReT4: a web-based bacterial type IV secretion system resource. Nucleic Acids Res (2012) 1.01
Prediction of proteinase cleavage sites in polyproteins of coronaviruses and its applications in analyzing SARS-CoV genomes. FEBS Lett (2003) 1.01
Identification of the gene cluster involved in muraymycin biosynthesis from Streptomyces sp. NRRL 30471. Mol Biosyst (2010) 1.01
Genomic and transcriptomic insights into the thermo-regulated biosynthesis of validamycin in Streptomyces hygroscopicus 5008. BMC Genomics (2012) 1.00
Genome sequence of the thermophilic strain Bacillus coagulans 2-6, an efficient producer of high-optical-purity L-lactic acid. J Bacteriol (2011) 1.00