Published in BMC Bioinformatics on March 03, 2004
Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. J Bacteriol (2007) 3.43
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics (2006) 3.15
Evidence of a large novel gene pool associated with prokaryotic genomic islands. PLoS Genet (2005) 2.71
Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics (2008) 2.62
From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology (2009) 2.62
The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. J Bacteriol (2006) 2.50
Detecting genomic islands using bioinformatics approaches. Nat Rev Microbiol (2010) 2.22
The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc Natl Acad Sci U S A (2008) 2.12
GenomeViz: visualizing microbial genomes. BMC Bioinformatics (2004) 1.97
The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number. Proc Natl Acad Sci U S A (2005) 1.72
Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes. J Bacteriol (2006) 1.48
A computational approach for identifying pathogenicity islands in prokaryotic genomes. BMC Bioinformatics (2005) 1.31
PIPS: pathogenicity island prediction software. PLoS One (2012) 1.23
Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC Genomics (2012) 1.16
Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. Environ Microbiol (2009) 1.14
A benchmark of parametric methods for horizontal transfers detection. PLoS One (2010) 1.00
Computational archaeology of the Pristionchus pacificus genome reveals evidence of horizontal gene transfers from insects. BMC Evol Biol (2011) 0.97
Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus. BMC Genomics (2010) 0.95
Identifying pathogenicity islands in bacterial pathogenomics using computational approaches. Pathogens (2014) 0.93
Modelling the evolution of the archeal tryptophan synthase. BMC Evol Biol (2007) 0.90
Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility. BMC Microbiol (2008) 0.89
Towards more robust methods of alien gene detection. Nucleic Acids Res (2011) 0.89
Complete genome sequence of producer of the glycopeptide antibiotic Aculeximycin Kutzneria albida DSM 43870T, a representative of minor genus of Pseudonocardiaceae. BMC Genomics (2014) 0.86
Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a broad and characteristic spectrum of protein functions. BMC Genomics (2010) 0.86
On detection and assessment of statistical significance of Genomic Islands. BMC Genomics (2008) 0.86
A comparative categorization of protein function encoded in bacterial or archeal genomic islands. J Mol Evol (2005) 0.84
Characterization and inference of gene gain/loss along burkholderia evolutionary history. Evol Bioinform Online (2011) 0.83
A quantitative account of genomic island acquisitions in prokaryotes. BMC Genomics (2011) 0.83
GO4genome: a prokaryotic phylogeny based on genome organization. J Mol Evol (2009) 0.79
The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract. BMC Genomics (2015) 0.77
Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. Proc Natl Acad Sci U S A (2016) 0.77
Computational methods for predicting genomic islands in microbial genomes. Comput Struct Biotechnol J (2016) 0.76
Bioinformatic detection of horizontally transferred DNA in bacterial genomes. F1000 Biol Rep (2009) 0.76
A Computational Framework for Tracing the Origins of Genomic Islands in Prokaryotes. Int Sch Res Notices (2014) 0.75
P-value based visualization of codon usage data. Algorithms Mol Biol (2006) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
Artemis: sequence visualization and annotation. Bioinformatics (2000) 46.68
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res (1987) 26.51
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci U S A (1990) 24.42
Lateral gene transfer and the nature of bacterial innovation. Nature (2000) 20.98
DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature (2000) 19.93
Phylogenetic classification and the universal tree. Science (1999) 14.28
Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol (2000) 9.51
Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol (1997) 8.53
Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature (2002) 8.42
Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A (1998) 7.40
Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol (1996) 7.18
Genome sequence of the plant pathogen Ralstonia solanacearum. Nature (2002) 6.23
Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease. Proc Natl Acad Sci U S A (2002) 6.19
Operons in Escherichia coli: genomic analyses and predictions. Proc Natl Acad Sci U S A (2000) 5.79
Calibrating bacterial evolution. Proc Natl Acad Sci U S A (1999) 5.78
Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier. Genome Res (2001) 5.16
Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res (2000) 4.94
Recent evidence for evolution of the genetic code. Microbiol Rev (1992) 4.32
Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res (2000) 3.95
Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol (2001) 3.64
Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res (1999) 3.44
Horizontal gene transfer: a critical view. Proc Natl Acad Sci U S A (2003) 3.27
Horizontal gene transfer and the origin of species: lessons from bacteria. Trends Microbiol (2000) 3.24
Base composition bias might result from competition for metabolic resources. Trends Genet (2002) 3.17
Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol (2001) 3.08
Origin and evolution of organisms as deduced from 5S ribosomal RNA sequences. Mol Biol Evol (1987) 2.81
On surrogate methods for detecting lateral gene transfer. FEMS Microbiol Lett (2001) 2.80
Predicted highly expressed genes of diverse prokaryotic genomes. J Bacteriol (2000) 2.60
Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models. Nucleic Acids Res (2002) 2.36
Comparative genomics of closely related salmonellae. Trends Microbiol (2002) 2.21
Detection of lateral gene transfer among microbial genomes. Curr Opin Genet Dev (2001) 1.95
Codon bias and base composition are poor indicators of horizontally transferred genes. Mol Biol Evol (2001) 1.91
The source of laterally transferred genes in bacterial genomes. Genome Biol (2003) 1.87
Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res (2002) 1.86
Salmonella enterica serovar Typhi possesses a unique repertoire of fimbrial gene sequences. Infect Immun (2001) 1.83
Detecting alien genes in bacterial genomes. Ann N Y Acad Sci (1999) 1.80
Phylogenetic analyses of two "archaeal" genes in thermotoga maritima reveal multiple transfers between archaea and bacteria. Mol Biol Evol (2001) 1.77
Soft tissue infection and bacteremia caused by Shewanella putrefaciens. J Clin Microbiol (2003) 1.62
Comparative genomics identifies the genetic islands that distinguish Neisseria meningitidis, the agent of cerebrospinal meningitis, from other Neisseria species. Infect Immun (2002) 1.55
Limitations of compositional approach to identifying horizontally transferred genes. J Mol Evol (2001) 1.47
G+C3 structuring along the genome: a common feature in prokaryotes. Mol Biol Evol (2003) 1.38
Codon usage tabulated from the international DNA sequence databases; its status 1999. Nucleic Acids Res (1999) 1.29
Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content. Gene (2003) 1.22
Detection of genes with atypical nucleotide sequence in microbial genomes. J Mol Evol (2002) 1.16
Horizontal transfer of archaeal genes into the deinococcaceae: detection by molecular and computer-based approaches. J Mol Evol (2000) 0.99
A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency. J Mol Evol (2003) 0.97