Published in J Clin Microbiol on February 26, 2014
Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol (2014) 3.75
Update on RefSeq microbial genomes resources. Nucleic Acids Res (2014) 3.20
MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads. PLoS One (2017) 1.39
Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics (2015) 1.27
Whole genome sequencing in clinical and public health microbiology. Pathology (2015) 1.06
Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data. BMC Bioinformatics (2014) 0.90
Comparative evaluation of the genomes of three common Drosophila-associated bacteria. Biol Open (2016) 0.84
Reads2Type: a web application for rapid microbial taxonomy identification. BMC Bioinformatics (2015) 0.82
Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae. J Clin Microbiol (2016) 0.80
HostPhinder: A Phage Host Prediction Tool. Viruses (2016) 0.80
A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance. PLoS One (2016) 0.79
Antibiotic Resistance, Core-Genome and Protein Expression in IncHI1 Plasmids in Salmonella Typhimurium. Genome Biol Evol (2016) 0.77
Sequence-Based Characterization of Tn5801-Like Genomic Islands in Tetracycline-Resistant Staphylococcus pseudintermedius and Other Gram-positive Bacteria from Humans and Animals. Front Microbiol (2016) 0.77
Complete Genome Sequence of Staphylococcus aureus FCFHV36, a Methicillin-Resistant Strain Heterogeneously Resistant to Vancomycin. Genome Announc (2015) 0.77
Analysis of Metagenomics Next Generation Sequence Data for Fungal ITS Barcoding: Do You Need Advance Bioinformatics Experience? Front Microbiol (2016) 0.75
MetaPhinder-Identifying Bacteriophage Sequences in Metagenomic Data Sets. PLoS One (2016) 0.75
Whole-Genome Sequence of Salmonella enterica Serovar Enteritidis Phage Type 4, Isolated from a Brazilian Poultry Farm. Genome Announc (2016) 0.75
Accurate differentiation of Escherichia coli and Shigella serogroups: challenges and strategies. New Microbes New Infect (2017) 0.75
Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clin Microbiol Rev (2017) 0.75
Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease. Eur J Clin Microbiol Infect Dis (2017) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res (2007) 85.81
ARB: a software environment for sequence data. Nucleic Acids Res (2004) 58.27
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol (2006) 57.72
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics (2010) 52.01
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (2006) 43.68
Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics (2010) 42.80
Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A (1998) 39.20
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res (2007) 35.65
The Pfam protein families database. Nucleic Acids Res (2011) 33.46
Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A (2009) 17.13
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol (2001) 15.97
Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci U S A (1997) 15.25
Toward automatic reconstruction of a highly resolved tree of life. Science (2006) 14.96
The TIGRFAMs database of protein families. Nucleic Acids Res (2003) 13.59
DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol (2007) 12.76
Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A (1999) 10.34
List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int J Syst Bacteriol (1997) 9.99
Assembly algorithms for next-generation sequencing data. Genomics (2010) 8.56
The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol (2008) 8.21
Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol (2012) 8.15
Genome phylogeny based on gene content. Nat Genet (1999) 8.12
The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res (2011) 7.93
Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis--one species on the basis of genetic evidence. Appl Environ Microbiol (2000) 7.87
Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol (2005) 7.19
Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol (2009) 5.37
Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog (2012) 4.69
En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol (2010) 4.58
Genomics of the Bacillus cereus group of organisms. FEMS Microbiol Rev (2005) 3.23
Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol (2010) 2.96
Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology (2012) 2.72
Phylogeny determined by protein domain content. Proc Natl Acad Sci U S A (2005) 2.37
Escherichia coli in disguise: molecular origins of Shigella. Microbes Infect (2002) 2.27
Sequence variation in Shigella sonnei (Sonnei), a pathogenic clone of Escherichia coli, over four continents and 41 years. J Clin Microbiol (1994) 2.01
Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol (2013) 1.86
A genomic approach to bacterial taxonomy: an examination and proposed reclassification of species within the genus Neisseria. Microbiology (2012) 1.79
Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing. J Clin Microbiol (2013) 1.42
Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations. Syst Appl Microbiol (2013) 1.29
Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J Mol Evol (2002) 1.29
Highlights on molecular identification of closely related species. Infect Genet Evol (2012) 1.07
Prokaryotic taxonomy in the sequencing era--the polyphasic approach revisited. Environ Microbiol (2011) 1.05
In silico analysis of 16S ribosomal RNA gene sequencing-based methods for identification of medically important anaerobic bacteria. J Clin Pathol (2006) 0.93
Description of an unusual Neisseria meningitidis isolate containing and expressing Neisseria gonorrhoeae-Specific 16S rRNA gene sequences. J Clin Microbiol (2013) 0.83
In silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteria. J Med Microbiol (2011) 0.81
Systematics of prokaryotes: the state of the art. Antonie Van Leeuwenhoek (2011) 0.77
RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res (2007) 85.81
Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother (2012) 13.77
Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol (2012) 8.15
Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics (2004) 7.76
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol (2005) 7.40
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. MBio (2012) 6.50
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci (2003) 5.94
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak. MBio (2011) 4.70
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. Nucleic Acids Res (2008) 4.53
Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics (2004) 4.44
Improved method for predicting linear B-cell epitopes. Immunome Res (2006) 4.32
NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS One (2007) 3.99
The Genomic Standards Consortium. PLoS Biol (2011) 3.99
beta-Lactamases among extended-spectrum beta-lactamase (ESBL)-resistant Salmonella from poultry, poultry products and human patients in The Netherlands. J Antimicrob Chemother (2005) 3.82
Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol (2014) 3.75
A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol (2006) 3.73
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics (2004) 3.72
NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics (2008) 3.59
Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015. Euro Surveill (2015) 3.13
Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci (2006) 3.06
The design and implementation of the immune epitope database and analysis resource. Immunogenetics (2005) 3.00
Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol (2010) 2.96
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics (2007) 2.83
International spread of an epidemic population of Salmonella enterica serotype Kentucky ST198 resistant to ciprofloxacin. J Infect Dis (2011) 2.70
Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. Bioinformatics (2008) 2.69
Global monitoring of Salmonella serovar distribution from the World Health Organization Global Foodborne Infections Network Country Data Bank: results of quality assured laboratories from 2001 to 2007. Foodborne Pathog Dis (2011) 2.56
Origin of replication in circular prokaryotic chromosomes. Environ Microbiol (2006) 2.55
World Health Organization ranking of antimicrobials according to their importance in human medicine: A critical step for developing risk management strategies for the use of antimicrobials in food production animals. Clin Infect Dis (2009) 2.54
Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics (2010) 2.53
Pigs as source of methicillin-resistant Staphylococcus aureus CC398 infections in humans, Denmark. Emerg Infect Dis (2008) 2.52
Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods (2013) 2.51
NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics (2009) 2.50
Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan. PLoS Comput Biol (2008) 2.48
The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics (2005) 2.40
The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci U S A (2012) 2.39
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science (2012) 2.38
Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother (2012) 2.23
An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol (2005) 2.19
Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res (2008) 2.14
Immune epitope database analysis resource. Nucleic Acids Res (2012) 2.09
Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics (2007) 2.05
Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J Mol Recognit (2007) 2.02
Results of use of WHO Global Salm-Surv external quality assurance system for antimicrobial susceptibility testing of Salmonella isolates from 2000 to 2007. J Clin Microbiol (2008) 2.02
Association between antimicrobial resistance in Escherichia coli isolates from food animals and blood stream isolates from humans in Europe: an ecological study. Foodborne Pathog Dis (2011) 1.99
PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data. PLoS One (2013) 1.97
Modeling the adaptive immune system: predictions and simulations. Bioinformatics (2007) 1.95
Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae. Plasmid (2012) 1.94
CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles. Nucleic Acids Res (2010) 1.94
snpTree--a web-server to identify and construct SNP trees from whole genome sequence data. BMC Genomics (2012) 1.88
Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol (2013) 1.86
Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Funct Integr Genomics (2006) 1.86
The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology. Mol Biosyst (2008) 1.79
The complete genome sequence and analysis of the epsilonproteobacterium Arcobacter butzleri. PLoS One (2007) 1.78
NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure. Immunome Res (2010) 1.78
Epitope mapping and topographic analysis of VAR2CSA DBL3X involved in P. falciparum placental sequestration. PLoS Pathog (2006) 1.76
The Salmonella enterica pan-genome. Microb Ecol (2011) 1.76
IS21-558 insertion sequences are involved in the mobility of the multiresistance gene cfr. Antimicrob Agents Chemother (2006) 1.74
MHC class II epitope predictive algorithms. Immunology (2010) 1.72
Analysis of intra-genomic GC content homogeneity within prokaryotes. BMC Genomics (2010) 1.71
LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium. Mol Microbiol (2012) 1.70
CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening. Vaccine (2006) 1.66
Genome Update: proteome comparisons. Microbiology (2005) 1.66
Human deaths and third-generation cephalosporin use in poultry, Europe. Emerg Infect Dis (2013) 1.66
Salmonella serovars from humans and other sources in Thailand, 1993-2002. Emerg Infect Dis (2004) 1.65
tcrB, a gene conferring transferable copper resistance in Enterococcus faecium: occurrence, transferability, and linkage to macrolide and glycopeptide resistance. Antimicrob Agents Chemother (2002) 1.63
Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. Genome Biol (2007) 1.63
Genomic taxonomy of Vibrios. BMC Evol Biol (2009) 1.62
CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics (2004) 1.62
Structural insight into epitopes in the pregnancy-associated malaria protein VAR2CSA. PLoS Pathog (2008) 1.60
NetMHCcons: a consensus method for the major histocompatibility complex class I predictions. Immunogenetics (2011) 1.57
Public health risks of enterobacterial isolates producing extended-spectrum β-lactamases or AmpC β-lactamases in food and food-producing animals: an EU perspective of epidemiology, analytical methods, risk factors, and control options. Clin Infect Dis (2012) 1.56
NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ. Immunogenetics (2013) 1.49
Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes. BMC Genomics (2008) 1.46
Microbial comparative pan-genomics using binomial mixture models. BMC Genomics (2009) 1.46
Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response. Emerg Infect Dis (2012) 1.45
Global regulation of virulence and the stress response by CsrA in the highly adapted human gastric pathogen Helicobacter pylori. Mol Microbiol (2004) 1.45