Published in Bioinformatics on March 10, 2010
PGAP: pan-genomes analysis pipeline. Bioinformatics (2011) 2.65
Systems solutions by lactic acid bacteria: from paradigms to practice. Microb Cell Fact (2011) 1.34
Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays. Microb Biotechnol (2011) 1.19
A brief review of software tools for pangenomics. Genomics Proteomics Bioinformatics (2015) 0.90
Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods. BMC Microbiol (2013) 0.82
The bacterial pangenome as a new tool for analysing pathogenic bacteria. New Microbes New Infect (2015) 0.81
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
Distinguishing homologous from analogous proteins. Syst Zool (1970) 25.10
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol (2001) 16.47
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
Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. Genome Biol (2007) 1.63
Discovery of stable and variable differences in the Mycobacterium avium subsp. paratuberculosis type I, II, and III genomes by pan-genome microarray analysis. Appl Environ Microbiol (2008) 1.15
PanCGH: a genotype-calling algorithm for pangenome CGH data. Bioinformatics (2009) 1.10
Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci U S A (2003) 8.40
Epochal evolution of GGII.4 norovirus capsid proteins from 1995 to 2006. J Virol (2007) 3.71
Visualization for genomics: the Microbial Genome Viewer. Bioinformatics (2004) 3.52
Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J Biol Chem (2006) 2.17
The Lactococcus lactis CodY regulon: identification of a conserved cis-regulatory element. J Biol Chem (2005) 2.11
In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments. Appl Environ Microbiol (2005) 2.04
Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol (2005) 2.03
Exploring Lactobacillus plantarum genome diversity by using microarrays. J Bacteriol (2005) 2.02
Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data. BMC Infect Dis (2013) 2.01
Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle? Brief Bioinform (2012) 2.00
Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics (2006) 1.97
Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium. J Bacteriol (2010) 1.90
The extracellular biology of the lactobacilli. FEMS Microbiol Rev (2010) 1.84
The relative value of operon predictions. Brief Bioinform (2008) 1.81
The tempo and mode of molecular evolution of Mycobacterium tuberculosis at patient-to-patient scale. Infect Genet Evol (2009) 1.76
Genome-wide detection and analysis of cell wall-bound proteins with LPxTG-like sorting motifs. J Bacteriol (2005) 1.75
Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. J Bacteriol (2012) 1.71
Degenerate target sites mediate rapid primed CRISPR adaptation. Proc Natl Acad Sci U S A (2014) 1.68
FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes. Bioinformatics (2007) 1.65
BAGEL: a web-based bacteriocin genome mining tool. Nucleic Acids Res (2006) 1.64
LocateP: genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinformatics (2008) 1.64
Comparative genomics of Lactobacillus. Microb Biotechnol (2010) 1.60
Genome analysis of Moraxella catarrhalis strain BBH18, [corrected] a human respiratory tract pathogen. J Bacteriol (2010) 1.57
Natural diversity and adaptive responses of Lactococcus lactis. Curr Opin Biotechnol (2006) 1.54
Correlation between sequence conservation and the genomic context after gene duplication. Nucleic Acids Res (2005) 1.54
High-resolution typing by integration of genome sequencing data in a large tuberculosis cluster. J Clin Microbiol (2010) 1.52
Regulation of glutamine and glutamate metabolism by GlnR and GlnA in Streptococcus pneumoniae. J Biol Chem (2006) 1.50
Co-regulation of metabolic genes is better explained by flux coupling than by network distance. PLoS Comput Biol (2008) 1.46
Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria. Microbiology (2006) 1.42
Comparative genomics of enzymes in flavor-forming pathways from amino acids in lactic acid bacteria. Appl Environ Microbiol (2008) 1.37
ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data. PLoS One (2012) 1.35
The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content. Microbiology (2004) 1.31
Multifactorial diversity sustains microbial community stability. ISME J (2013) 1.29
The prophage sequences of Lactobacillus plantarum strain WCFS1. Virology (2003) 1.28
Transcriptome analysis and related databases of Lactococcus lactis. Antonie Van Leeuwenhoek (2002) 1.25
A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1. BMC Genomics (2008) 1.23
Regulation of the metC-cysK operon, involved in sulfur metabolism in Lactococcus lactis. J Bacteriol (2002) 1.21
Transcriptome analysis reveals mechanisms by which Lactococcus lactis acquires nisin resistance. Antimicrob Agents Chemother (2006) 1.19
Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays. Microb Biotechnol (2011) 1.19
Fructose utilization in Lactococcus lactis as a model for low-GC gram-positive bacteria: its regulator, signal, and DNA-binding site. J Bacteriol (2005) 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
Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity. PLoS One (2013) 1.18
Microbiome dynamics of human epidermis following skin barrier disruption. Genome Biol (2012) 1.15
The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment. Microbiology (2006) 1.14
Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res (2006) 1.12
The proteolytic system of lactic acid bacteria revisited: a genomic comparison. BMC Genomics (2010) 1.11
An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters. BMC Genomics (2008) 1.11
PanCGH: a genotype-calling algorithm for pangenome CGH data. Bioinformatics (2009) 1.10
Comparative analyses imply that the enigmatic Sigma factor 54 is a central controller of the bacterial exterior. BMC Genomics (2011) 1.07
Complete Genome Sequence of Anoxybacillus flavithermus TNO-09.006, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment. Genome Announc (2013) 1.06
Comparative and functional genomics of lactococci. FEMS Microbiol Rev (2005) 1.05
Comparative analysis of two-component signal transduction systems of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis. Microbiology (2006) 1.05
Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus. Appl Environ Microbiol (2010) 1.03
SNP/RD typing of Mycobacterium tuberculosis Beijing strains reveals local and worldwide disseminated clonal complexes. PLoS One (2011) 1.03
PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains. BMC Genomics (2012) 1.02
Genetic analysis of the capsid gene of genotype GII.2 noroviruses. J Virol (2008) 1.02
LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria. BMC Genomics (2010) 1.02
The identification of response regulator-specific binding sites reveals new roles of two-component systems in Bacillus cereus and closely related low-GC Gram-positives. Environ Microbiol (2008) 1.01
Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype. Infect Genet Evol (2011) 0.99
Functional analysis of three plasmids from Lactobacillus plantarum. Appl Environ Microbiol (2005) 0.99
Classification of the adenylation and acyl-transferase activity of NRPS and PKS systems using ensembles of substrate specific hidden Markov models. PLoS One (2013) 0.98
Genome sequence of the naturally plasmid-free Lactobacillus plantarum strain NC8 (CCUG 61730). J Bacteriol (2012) 0.98
Defining the structure of the general stress regulon of Bacillus subtilis using targeted microarray analysis and random forest classification. Microbiology (2011) 0.98
Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage. Genome Announc (2013) 0.97
Making sense of quorum sensing in lactobacilli: a special focus on Lactobacillus plantarum WCFS1. Microbiology (2007) 0.97
EXProt--a database for EXPerimentally verified Protein functions. In Silico Biol (2002) 0.94
Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs. Microb Biotechnol (2010) 0.93
Challenges in plant cellular pathway reconstruction based on gene expression profiling. Trends Plant Sci (2007) 0.92
SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks. Bioinformatics (2010) 0.92
MGcV: the microbial genomic context viewer for comparative genome analysis. BMC Genomics (2013) 0.92
In silico prediction of horizontal gene transfer events in Lactobacillus bulgaricus and Streptococcus thermophilus reveals protocooperation in yogurt manufacturing. Appl Environ Microbiol (2009) 0.91
DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites. BMC Bioinformatics (2008) 0.91
Genome update: lactic acid bacteria genome sequencing is booming. Microbiology (2005) 0.90
The highly autoaggregative and adhesive phenotype of the vaginal Lactobacillus plantarum strain CMPG5300 is sortase dependent. Appl Environ Microbiol (2013) 0.89
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context. Bioinformatics (2008) 0.89
EXProt: a database for proteins with an experimentally verified function. Nucleic Acids Res (2002) 0.89
Fractional factorial design for optimization of the SELDI protocol for human adipose tissue culture media. Biotechnol Prog (2007) 0.88
Preferential deletion events in the direct repeat locus of Mycobacterium tuberculosis. J Clin Microbiol (2011) 0.88
Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis. Appl Environ Microbiol (2010) 0.87
FACIL: Fast and Accurate Genetic Code Inference and Logo. Bioinformatics (2011) 0.87
Genome (re-)annotation and open-source annotation pipelines. Microb Biotechnol (2010) 0.87
Comparative and functional analysis of the rRNA-operons and their tRNA gene complement in different lactic acid bacteria. Syst Appl Microbiol (2005) 0.86
Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli. BMC Genomics (2012) 0.86
Explaining microbial phenotypes on a genomic scale: GWAS for microbes. Brief Funct Genomics (2013) 0.85
A novel hybrid kinase is essential for regulating the sigma(B)-mediated stress response of Bacillus cereus. Environ Microbiol (2009) 0.85
Novel sigmaB regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases. Microbiology (2010) 0.85
Transcriptome analysis of the Lactococcus lactis ArgR and AhrC regulons. Appl Environ Microbiol (2008) 0.85
MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data. Bioinformatics (2009) 0.85
Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources. BMC Genomics (2008) 0.85
Genomic tracing of epidemics and disease outbreaks. Microb Biotechnol (2010) 0.85
Diversity in robustness of Lactococcus lactis strains during heat stress, oxidative stress, and spray drying stress. Appl Environ Microbiol (2013) 0.85
Computational analysis of cysteine and methionine metabolism and its regulation in dairy starter and related bacteria. J Bacteriol (2012) 0.84
Safety of the surrogate microorganism Enterococcus faecium NRRL B-2354 for use in thermal process validation. Appl Environ Microbiol (2014) 0.84
Single-cell genomics: unravelling the genomes of unculturable microorganisms. Microb Biotechnol (2011) 0.84
Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction. PLoS One (2013) 0.83
Hydrocarbon-degrading bacteria: the oil-spill clean-up crew. Microb Biotechnol (2009) 0.82
A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis. BMC Genomics (2010) 0.82