Published in Bioinformatics on October 09, 2008
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Evidence for several waves of global transmission in the seventh cholera pandemic. Nature (2011) 5.62
DNAPlotter: circular and linear interactive genome visualization. Bioinformatics (2008) 5.49
ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics (2009) 4.98
CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol Med (2011) 4.91
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics (2010) 4.18
High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res (2011) 4.09
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TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res (2009) 3.79
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A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc (2012) 3.17
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome Biol (2012) 3.02
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet (2009) 2.87
Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet (2012) 2.86
PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res (2011) 2.84
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Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat Genet (2013) 2.63
High-throughput decoding of antitrypanosomal drug efficacy and resistance. Nature (2012) 2.55
Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer. Microb Cell Fact (2011) 2.22
Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Res (2011) 2.21
Global dissemination of a multidrug resistant Escherichia coli clone. Proc Natl Acad Sci U S A (2014) 2.20
A simple method for directional transcriptome sequencing using Illumina technology. Nucleic Acids Res (2009) 2.19
Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol (2010) 2.06
Proteomic and genomic characterization of highly infectious Clostridium difficile 630 spores. J Bacteriol (2009) 1.96
Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses. PLoS Genet (2011) 1.91
The genome of a Bacillus isolate causing anthrax in chimpanzees combines chromosomal properties of B. cereus with B. anthracis virulence plasmids. PLoS One (2010) 1.91
Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Res (2011) 1.90
Derivation of Escherichia coli O157:H7 from its O55:H7 precursor. PLoS One (2010) 1.90
Genomic information infrastructure after the deluge. Genome Biol (2010) 1.89
Intraclonal variations among Streptococcus pneumoniae isolates influence the likelihood of invasive disease in children. J Infect Dis (2013) 1.84
The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis. PLoS Negl Trop Dis (2010) 1.83
GeneDB--an annotation database for pathogens. Nucleic Acids Res (2011) 1.82
Computational analysis and identification of an emergent human adenovirus pathogen implicated in a respiratory fatality. Virology (2010) 1.82
Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biol Evol (2010) 1.81
The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis. Nat Commun (2010) 1.75
Pseudomonas syringae pv. actinidiae (PSA) isolates from recent bacterial canker of kiwifruit outbreaks belong to the same genetic lineage. PLoS One (2012) 1.75
Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2. PLoS One (2012) 1.72
Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. J Bacteriol (2012) 1.71
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nat Genet (2015) 1.70
Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis. Nat Genet (2013) 1.67
Bacteriophages φMR299-2 and φNH-4 can eliminate Pseudomonas aeruginosa in the murine lung and on cystic fibrosis lung airway cells. MBio (2012) 1.59
Terminal olefin (1-alkene) biosynthesis by a novel p450 fatty acid decarboxylase from Jeotgalicoccus species. Appl Environ Microbiol (2011) 1.55
Host imprints on bacterial genomes--rapid, divergent evolution in individual patients. PLoS Pathog (2010) 1.54
A functional genomics approach to establish the complement of carbohydrate transporters in Streptococcus pneumoniae. PLoS One (2012) 1.53
Complete sequencing of the bla(NDM-1)-positive IncA/C plasmid from Escherichia coli ST38 isolate suggests a possible origin from plant pathogens. PLoS One (2011) 1.53
ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes. Genome Biol (2011) 1.49
Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathog (2012) 1.44
Diversification of bacterial genome content through distinct mechanisms over different timescales. Nat Commun (2014) 1.40
Characterization of the integration and modular excision of the integrative conjugative element PAISt in Streptomyces turgidiscabies Car8. PLoS One (2014) 1.40
Analysis of the mitochondrial maxicircle of Trypanosoma lewisi, a neglected human pathogen. Parasit Vectors (2015) 1.39
Mechanisms and evolution of oxidative sulfur metabolism in green sulfur bacteria. Front Microbiol (2011) 1.38
MIPS PlantsDB: a database framework for comparative plant genome research. Nucleic Acids Res (2012) 1.33
A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biol (2014) 1.31
Corynebacterium ulcerans 0102 carries the gene encoding diphtheria toxin on a prophage different from the C. diphtheriae NCTC 13129 prophage. BMC Microbiol (2012) 1.30
Genetic organisation, mobility and predicted functions of genes on integrated, mobile genetic elements in sequenced strains of Clostridium difficile. PLoS One (2011) 1.29
The banana genome hub. Database (Oxford) (2013) 1.29
Molecular evolution of human adenoviruses. Sci Rep (2013) 1.29
Single-nucleotide resolution analysis of the transcriptome structure of Clostridium beijerinckii NCIMB 8052 using RNA-Seq. BMC Genomics (2011) 1.29
Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). Genome Res (2012) 1.28
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol (2016) 1.27
The Salmonella genomic island 1 is specifically mobilized in trans by the IncA/C multidrug resistance plasmid family. PLoS One (2010) 1.25
Variation in tropical reef symbiont metagenomes defined by secondary metabolism. PLoS One (2011) 1.24
Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts. Nat Commun (2014) 1.24
Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5. BMC Genomics (2009) 1.22
Photorhabdus insect-related (Pir) toxin-like genes in a plasmid of Vibrio parahaemolyticus, the causative agent of acute hepatopancreatic necrosis disease (AHPND) of shrimp. Dis Aquat Organ (2015) 1.20
Genomic and proteomic analyses of the terminally redundant genome of the Pseudomonas aeruginosa phage PaP1: establishment of genus PaP1-like phages. PLoS One (2013) 1.20
Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies. BMC Genomics (2010) 1.20
Identification, variation and transcription of pneumococcal repeat sequences. BMC Genomics (2011) 1.19
Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems. Eukaryot Cell (2010) 1.18
Complete genome sequence of Geobacillus thermoglucosidans TNO-09.020, a thermophilic sporeformer associated with a dairy-processing environment. J Bacteriol (2012) 1.18
Genome sequence analyses of Pseudomonas savastanoi pv. glycinea and subtractive hybridization-based comparative genomics with nine pseudomonads. PLoS One (2011) 1.18
Characterization of the ELPhiS prophage from Salmonella enterica serovar Enteritidis strain LK5. Appl Environ Microbiol (2012) 1.17
Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection. PLoS Genet (2013) 1.17
Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence. Nucleic Acids Res (2009) 1.17
Characterization of a ViI-like phage specific to Escherichia coli O157:H7. Virol J (2011) 1.16
Whole-genome analysis of Salmonella enterica serovar Typhimurium T000240 reveals the acquisition of a genomic island involved in multidrug resistance via IS1 derivatives on the chromosome. Antimicrob Agents Chemother (2010) 1.15
Characterization of Salmonella enterica serovar Typhimurium isolates harboring a chromosomally encoded CMY-2 beta-lactamase gene located on a multidrug resistance genomic island. Antimicrob Agents Chemother (2011) 1.14
Gene content and diversity of the loci encoding biosynthesis of capsular polysaccharides of the 15 serovar reference strains of Haemophilus parasuis. J Bacteriol (2013) 1.13
The role of the 5'-3' exoribonuclease XRNA in transcriptome-wide mRNA degradation. RNA (2011) 1.13
Molecular characterization of the 2011 Hong Kong scarlet fever outbreak. J Infect Dis (2012) 1.13
Characterization and comparative genomic analysis of a novel bacteriophage, SFP10, simultaneously inhibiting both Salmonella enterica and Escherichia coli O157:H7. Appl Environ Microbiol (2011) 1.11
Comparative genomics of isolates of a Pseudomonas aeruginosa epidemic strain associated with chronic lung infections of cystic fibrosis patients. PLoS One (2014) 1.09
Overreliance on the hexon gene, leading to misclassification of human adenoviruses. J Virol (2012) 1.09
Horizontal gene transfer converts non-toxigenic Clostridium difficile strains into toxin producers. Nat Commun (2013) 1.08
BamView: visualizing and interpretation of next-generation sequencing read alignments. Brief Bioinform (2012) 1.08
Odorant and gustatory receptors in the tsetse fly Glossina morsitans morsitans. PLoS Negl Trop Dis (2014) 1.06
Chado controller: advanced annotation management with a community annotation system. Bioinformatics (2012) 1.06
Complete Genome Sequence of Anoxybacillus flavithermus TNO-09.006, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment. Genome Announc (2013) 1.06
Methods and strategies for gene structure curation in WormBase. Database (Oxford) (2011) 1.06
Complete sequence of pOZ176, a 500-kilobase IncP-2 plasmid encoding IMP-9-mediated carbapenem resistance, from outbreak isolate Pseudomonas aeruginosa 96. Antimicrob Agents Chemother (2013) 1.05
MicrobeDB: a locally maintainable database of microbial genomic sequences. Bioinformatics (2012) 1.05
A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella. PLoS Genet (2013) 1.05
TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes. Front Plant Sci (2012) 1.04
The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone. PLoS One (2014) 1.03
Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5. BMC Genomics (2015) 1.03
Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone. BMC Biol (2014) 1.03
Analysis of human adenovirus type 19 associated with epidemic keratoconjunctivitis and its reclassification as adenovirus type 64. Invest Ophthalmol Vis Sci (2012) 1.03
A study on the geophylogeny of clinical and environmental Vibrio cholerae in Kenya. PLoS One (2013) 1.03
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
Artemis: sequence visualization and annotation. Bioinformatics (2000) 46.68
The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol (2005) 18.20
ACT: the Artemis Comparison Tool. Bioinformatics (2005) 17.91
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
Viewing and annotating sequence data with Artemis. Brief Bioinform (2003) 4.38
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
Enterotypes of the human gut microbiome. Nature (2011) 24.36
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet (2008) 19.97
ACT: the Artemis Comparison Tool. Bioinformatics (2005) 17.91
Evolution of MRSA during hospital transmission and intercontinental spread. Science (2010) 13.34
Prepublication data sharing. Nature (2009) 12.24
The genome of the African trypanosome Trypanosoma brucei. Science (2005) 11.48
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods (2009) 10.41
Rapid pneumococcal evolution in response to clinical interventions. Science (2011) 9.09
Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A (2004) 8.95
The genome of the kinetoplastid parasite, Leishmania major. Science (2005) 8.64
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature (2005) 8.55
The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet (2006) 8.02
Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol (2007) 7.58
Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Proc Natl Acad Sci U S A (2004) 7.30
Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis (2012) 7.18
The complete genome sequence of Mycobacterium bovis. Proc Natl Acad Sci U S A (2003) 6.79
Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis (2012) 6.64
Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. PLoS Genet (2006) 6.43
Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med (2012) 6.36
GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res (2004) 6.30
Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study. Lancet Infect Dis (2011) 6.08
A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science (2005) 5.99
The genome of the blood fluke Schistosoma mansoni. Nature (2009) 5.94
Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature (2009) 5.90
Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi. J Bacteriol (2007) 5.88
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol (2010) 5.79
Evidence for several waves of global transmission in the seventh cholera pandemic. Nature (2011) 5.62
DNAPlotter: circular and linear interactive genome visualization. Bioinformatics (2008) 5.49
Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J (2010) 5.43
Comparative genomics of trypanosomatid parasitic protozoa. Science (2005) 5.37
Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia. Nat Genet (2013) 5.22
Microevolution and history of the plague bacillus, Yersinia pestis. Proc Natl Acad Sci U S A (2004) 5.04
ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics (2009) 4.98
Microbiology in the post-genomic era. Nat Rev Microbiol (2008) 4.88
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics (2004) 4.76
Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet (2013) 4.75
Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog (2012) 4.69
Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat Genet (2007) 4.58
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol (2014) 4.39
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature (2012) 4.37
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics (2011) 4.31
Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics (2006) 4.27
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics (2010) 4.18
Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res (2009) 4.12
Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat Genet (2012) 4.10
High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res (2011) 4.09
Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res (2009) 3.99
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet (2013) 3.89
WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87
The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants. Genome Biol (2008) 3.85
Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog (2012) 3.81
TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res (2009) 3.79
Genome plasticity of BCG and impact on vaccine efficacy. Proc Natl Acad Sci U S A (2007) 3.73
Genome variation and evolution of the malaria parasite Plasmodium falciparum. Nat Genet (2006) 3.68
Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. Genome Biol (2009) 3.66
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol (2009) 3.63
Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J Bacteriol (2007) 3.62
Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. Genome Res (2008) 3.54
Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res (2007) 3.45
Antibiotic treatment of clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts. Infect Immun (2009) 3.36
Comparative genomic structure of prokaryotes. Annu Rev Genet (2004) 3.34
The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081. PLoS Genet (2006) 3.33
Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei. Lancet (2003) 3.30
RATT: Rapid Annotation Transfer Tool. Nucleic Acids Res (2011) 3.29
Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. Genome Res (2008) 3.26
BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics (2010) 3.24
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet (2012) 3.22
Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc Natl Acad Sci U S A (2010) 3.18
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc (2012) 3.17
High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol (2011) 3.11
Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J Bacteriol (2008) 3.10
Extensive DNA inversions in the B. fragilis genome control variable gene expression. Science (2005) 3.08
An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm. Proc Natl Acad Sci U S A (2005) 3.06
REAPR: a universal tool for genome assembly evaluation. Genome Biol (2013) 3.05
A human-curated annotation of the Candida albicans genome. PLoS Genet (2005) 3.04
Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa. Genome Res (2008) 3.03
Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat Genet (2013) 3.03
The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol (2006) 2.93
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet (2009) 2.87
Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet (2012) 2.86
Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science (2005) 2.86
Genome sequence of a recently emerged, highly transmissible, multi-antibiotic- and antiseptic-resistant variant of methicillin-resistant Staphylococcus aureus, sequence type 239 (TW). J Bacteriol (2009) 2.81
Microevolution of extensively drug-resistant tuberculosis in Russia. Genome Res (2012) 2.81