Published in Sci Rep on December 12, 2014
SNP Discovery Using a Pangenome: Has the Single Reference Approach Become Obsolete? Biology (Basel) (2017) 0.76
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
Clustal W and Clustal X version 2.0. Bioinformatics (2007) 126.47
RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res (2007) 85.81
Improved microbial gene identification with GLIMMER. Nucleic Acids Res (1999) 51.34
OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res (2003) 33.03
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One (2010) 24.31
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet (2008) 19.97
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res (2005) 19.81
PHAST: a fast phage search tool. Nucleic Acids Res (2011) 19.09
Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature (2001) 16.89
Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature (2001) 15.44
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A (2005) 14.59
The global burden of typhoid fever. Bull World Health Organ (2004) 14.14
Massive gene decay in the leprosy bacillus. Nature (2001) 11.98
Tablet--next generation sequence assembly visualization. Bioinformatics (2009) 11.75
SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics (1998) 9.87
ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res (2006) 9.58
Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nat Genet (2004) 8.60
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet (2009) 8.51
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics (2011) 7.27
The microbial pan-genome. Curr Opin Genet Dev (2005) 5.93
IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics (2009) 5.69
When less is more: gene loss as an engine of evolutionary change. Am J Hum Genet (1999) 5.32
"Black holes" and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. Proc Natl Acad Sci U S A (1998) 5.02
Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000 years old. Infect Genet Evol (2002) 4.96
An Ergatis-based prokaryotic genome annotation web server. Bioinformatics (2010) 4.49
Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol (2008) 4.40
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
Salmonella, the host and disease: a brief review. Immunol Cell Biol (2006) 2.95
Gegenees: fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups. PLoS One (2012) 2.25
The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen. Nucleic Acids Res (2005) 2.21
Analysis of Salmonella typhi isolates from Southeast Asia by pulsed-field gel electrophoresis. J Clin Microbiol (1995) 2.04
Are pathogenic bacteria just looking for food? Metabolism and microbial pathogenesis. Trends Microbiol (2011) 2.03
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res (2012) 1.91
PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species. Nucleic Acids Res (2012) 1.91
Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi. BMC Genomics (2009) 1.76
Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever. Proc Natl Acad Sci U S A (2014) 1.73
Drug-resistant Salmonella enterica serotype paratyphi A in India. Emerg Infect Dis (2000) 1.72
Analysis of plasmid and chromosomal DNA of multidrug-resistant Salmonella enterica serovar typhi from Asia. J Clin Microbiol (2000) 1.49
Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona. PLoS Genet (2013) 1.48
Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome. BMC Genomics (2013) 1.43
Comparative analysis of Salmonella genomes identifies a metabolic network for escalating growth in the inflamed gut. MBio (2014) 1.40
Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam. PLoS Negl Trop Dis (2011) 1.29
Salmonella: from pathogenesis to therapeutics. J Bacteriol (2006) 1.22
Integron-associated antibiotic resistance in Salmonella enterica serovar typhi from Asia. Antimicrob Agents Chemother (2003) 1.16
Molecular analysis of isolates of Salmonella typhi obtained from patients with fatal and nonfatal typhoid fever. J Clin Microbiol (1996) 1.13
Salmonella's long-term relationship with its host. FEMS Microbiol Rev (2012) 1.13
Shedding light on Salmonella carriers. Trends Microbiol (2012) 1.01
The effect of heterogeneous infectious period and contagiousness on the dynamics of Salmonella transmission in dairy cattle. Epidemiol Infect (2008) 1.00
Pan-genomic analysis provides insights into the genomic variation and evolution of Salmonella Paratyphi A. PLoS One (2012) 1.00
Host specificity of bacterial pathogens. Cold Spring Harb Perspect Med (2013) 0.97
Genome sequence and comparative pathogenomics analysis of a Salmonella enterica Serovar Typhi strain associated with a typhoid carrier in Malaysia. J Bacteriol (2012) 0.96
Genetic fine structure of a Salmonella enterica serovar Typhi strain associated with the 2005 outbreak of typhoid fever in Kelantan, Malaysia. J Bacteriol (2012) 0.95
Is the pan-genome also a pan-selectome? F1000Res (2012) 0.91
Enteropathogenic Escherichia coli, Samonella, Shigella and Yersinia: cellular aspects of host-bacteria interactions in enteric diseases. Gut Pathog (2010) 0.90
Complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12. J Bacteriol (2012) 0.89
Variations in motility and biofilm formation of Salmonella enterica serovar Typhi. Gut Pathog (2014) 0.89
Insights from the genome sequence of a Salmonella enterica serovar Typhi strain associated with a sporadic case of typhoid fever in Malaysia. J Bacteriol (2012) 0.81
Whole-genome sequences and comparative genomics of Salmonella enterica serovar Typhi isolates from patients with fatal and nonfatal typhoid fever in Papua New Guinea. J Bacteriol (2012) 0.80
Genome sequencing and analysis of Salmonella enterica serovar Typhi strain CR0063 representing a carrier individual during an outbreak of typhoid fever in Kelantan, Malaysia. Gut Pathog (2012) 0.79