Published in Appl Environ Microbiol on November 01, 2005
Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics (2007) 9.45
Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. J Bacteriol (2008) 2.25
Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer. Microb Cell Fact (2011) 2.22
Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev (2008) 1.97
Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics (2006) 1.97
Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. J Bacteriol (2012) 1.71
Identification of Lactobacillus plantarum genes modulating the cytokine response of human peripheral blood mononuclear cells. BMC Microbiol (2010) 1.51
Functional analysis of luxS in the probiotic strain Lactobacillus rhamnosus GG reveals a central metabolic role important for growth and biofilm formation. J Bacteriol (2006) 1.39
Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation. PLoS Comput Biol (2009) 1.37
Spatial and temporal expression of Lactobacillus plantarum genes in the gastrointestinal tracts of mice. Appl Environ Microbiol (2006) 1.31
Unraveling microbial interactions in food fermentations: from classical to genomics approaches. Appl Environ Microbiol (2008) 1.25
Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays. Microb Biotechnol (2011) 1.19
Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1. Microb Cell Fact (2007) 1.17
Core and panmetabolism in Escherichia coli. J Bacteriol (2011) 1.16
Lifestyle of Lactobacillus plantarum in the mouse caecum. Environ Microbiol (2009) 1.15
Genome-scale model of Streptococcus thermophilus LMG18311 for metabolic comparison of lactic acid bacteria. Appl Environ Microbiol (2009) 1.10
Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes. Genome Biol (2007) 1.08
Short- and long-term adaptation to ethanol stress and its cross-protective consequences in Lactobacillus plantarum. Appl Environ Microbiol (2011) 1.04
Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus. Appl Environ Microbiol (2010) 1.03
Characterization of the role of para-aminobenzoic acid biosynthesis in folate production by Lactococcus lactis. Appl Environ Microbiol (2007) 1.01
Lactobacillus plantarum WCFS1 electron transport chains. Appl Environ Microbiol (2009) 0.96
Improvement of Lactobacillus plantarum aerobic growth as directed by comprehensive transcriptome analysis. Appl Environ Microbiol (2008) 0.96
Impact of 4 Lactobacillus plantarum capsular polysaccharide clusters on surface glycan composition and host cell signaling. Microb Cell Fact (2012) 0.96
Modulation of Lactobacillus plantarum gastrointestinal robustness by fermentation conditions enables identification of bacterial robustness markers. PLoS One (2012) 0.94
MEMOSys: Bioinformatics platform for genome-scale metabolic models. BMC Syst Biol (2011) 0.93
High-Level folate production in fermented foods by the B12 producer Lactobacillus reuteri JCM1112. Appl Environ Microbiol (2008) 0.92
Effect of amino acid availability on vitamin B12 production in Lactobacillus reuteri. Appl Environ Microbiol (2009) 0.92
MGcV: the microbial genomic context viewer for comparative genome analysis. BMC Genomics (2013) 0.92
Systems biology of lactic acid bacteria: a critical review. Microb Cell Fact (2011) 0.91
Lactobacillus plantarum possesses the capability for wall teichoic acid backbone alditol switching. Microb Cell Fact (2012) 0.91
Transcriptomes reveal genetic signatures underlying physiological variations imposed by different fermentation conditions in Lactobacillus plantarum. PLoS One (2012) 0.90
Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies. Appl Environ Microbiol (2012) 0.89
Physiological responses to folate overproduction in Lactobacillus plantarum WCFS1. Microb Cell Fact (2010) 0.87
Impact of Lactobacillus plantarum sortase on target protein sorting, gastrointestinal persistence, and host immune response modulation. J Bacteriol (2012) 0.86
Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli. BMC Genomics (2012) 0.86
Indigenous and environmental modulation of frequencies of mutation in Lactobacillus plantarum. Appl Environ Microbiol (2009) 0.85
A general method for selection of riboflavin-overproducing food grade micro-organisms. Microb Cell Fact (2006) 0.85
Computational analysis of cysteine and methionine metabolism and its regulation in dairy starter and related bacteria. J Bacteriol (2012) 0.84
Comparative study of sugar fermentation and protein expression patterns of two Lactobacillus plantarum strains grown in three different media. Appl Environ Microbiol (2008) 0.84
Congruent strain specific intestinal persistence of Lactobacillus plantarum in an intestine-mimicking in vitro system and in human volunteers. PLoS One (2012) 0.83
Adaptation of Lactobacillus plantarum IMDO 130201, a wheat sourdough isolate, to growth in wheat sourdough simulation medium at different pH values through differential gene expression. Appl Environ Microbiol (2011) 0.81
Lactobacillus reuteri 100-23 modulates urea hydrolysis in the murine stomach. Appl Environ Microbiol (2014) 0.80
A genome-scale metabolic reconstruction of Lysinibacillus sphaericus unveils unexploited biotechnological potentials. PLoS One (2017) 0.77
Systems Biology of Microbial Exopolysaccharides Production. Front Bioeng Biotechnol (2015) 0.77
Tyrosine-containing peptides are precursors of tyramine produced by Lactobacillus plantarum strain IR BL0076 isolated from wine. BMC Microbiol (2012) 0.77
Lactobacillus plantarum WCFS1 and its host interaction: a dozen years after the genome. Microb Biotechnol (2016) 0.77
Genome-scale reconstruction of metabolic networks of Lactobacillus casei ATCC 334 and 12A. PLoS One (2014) 0.77
Transcriptome signatures of class I and III stress response deregulation in Lactobacillus plantarum reveal pleiotropic adaptation. Microb Cell Fact (2013) 0.76
Analysis of the Lactobacillus metabolic pathway. Appl Environ Microbiol (2010) 0.76
Metabolism of Fructooligosaccharides in Lactobacillus plantarum ST-III via Differential Gene Transcription and Alteration of Cell Membrane Fluidity. Appl Environ Microbiol (2015) 0.75
Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation. Front Microbiol (2017) 0.75
More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes. Microbiome (2017) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res (1997) 175.36
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (2003) 32.92
The Pathway Tools software. Bioinformatics (2002) 14.89
Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria. Microbiol Rev (1993) 11.25
EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res (2005) 11.01
MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res (2004) 10.71
The EcoCyc Database. Nucleic Acids Res (2002) 10.42
The MetaCyc Database. Nucleic Acids Res (2002) 8.91
Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci U S A (2003) 8.40
BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res (2004) 8.21
Integrating high-throughput and computational data elucidates bacterial networks. Nature (2004) 7.72
Metabolic network structure determines key aspects of functionality and regulation. Nature (2002) 6.64
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics (2004) 5.90
Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol (2003) 4.91
Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci U S A (2005) 4.46
Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J Biol Chem (2002) 4.33
ATP-binding cassette transporters in bacteria. Annu Rev Biochem (2004) 3.88
The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc Natl Acad Sci U S A (2004) 3.88
Relation of growth of Streptococcus lactis and Streptococcus cremoris to amino acid transport. J Bacteriol (1988) 3.69
Visualization for genomics: the Microbial Genome Viewer. Bioinformatics (2004) 3.52
Thiamin biosynthesis in prokaryotes. Arch Microbiol (1999) 2.91
Multiple nutritional requirements of lactobacilli: genetic lesions affecting amino acid biosynthetic pathways. J Bacteriol (1981) 2.62
Thiamin biosynthesis in Escherichia coli. Identification of ThiS thiocarboxylate as the immediate sulfur donor in the thiazole formation. J Biol Chem (1998) 2.21
Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res (2004) 1.94
Discovering lactic acid bacteria by genomics. Antonie Van Leeuwenhoek (2002) 1.90
Biosynthesis of the thiazole moiety of thiamin pyrophosphate (vitamin B1). Biochemistry (2003) 1.70
Probiotics in foods not containing milk or milk constituents, with special reference to Lactobacillus plantarum 299v. Am J Clin Nutr (2001) 1.59
Characterization of the Staphylococcus aureus mprF gene, involved in lysinylation of phosphatidylglycerol. Microbiology (2004) 1.59
Methionine biosynthesis in Enterobacteriaceae: biochemical, regulatory, and evolutionary aspects. CRC Crit Rev Biochem (1988) 1.48
Biosynthesis of riboflavin, folic acid, thiamine, and pantothenic acid. Adv Enzymol Relat Areas Mol Biol (1982) 1.45
Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat Biotechnol (2003) 1.41
The dihydroxyacetone kinase of Escherichia coli utilizes a phosphoprotein instead of ATP as phosphoryl donor. EMBO J (2001) 1.39
Increased production of folate by metabolic engineering of Lactococcus lactis. Appl Environ Microbiol (2003) 1.37
Riboflavin production in Lactococcus lactis: potential for in situ production of vitamin-enriched foods. Appl Environ Microbiol (2004) 1.32
Glutamate dehydrogenase activity: a major criterion for the selection of flavour-producing lactic acid bacteria strains. Antonie Van Leeuwenhoek (2002) 1.20
Genome data mining of lactic acid bacteria: the impact of bioinformatics. Curr Opin Biotechnol (2004) 1.19
A nudix enzyme removes pyrophosphate from dihydroneopterin triphosphate in the folate synthesis pathway of bacteria and plants. J Biol Chem (2004) 1.19
Engineering metabolic highways in Lactococci and other lactic acid bacteria. Trends Biotechnol (2004) 1.16
Structural biology of enzymes involved in NAD and molybdenum cofactor biosynthesis. Curr Opin Struct Biol (2002) 1.13
Lactococcus lactis as a cell factory for high-level diacetyl production. Appl Environ Microbiol (2000) 1.12
Metabolic engineering of lactic acid bacteria for the production of nutraceuticals. Antonie Van Leeuwenhoek (2002) 1.09
Extent of genetic lesions of the arginine and pyrimidine biosynthetic pathways in Lactobacillus plantarum, L. paraplantarum, L. pentosus, and L. casei: prevalence of CO(2)-dependent auxotrophs and characterization of deficient arg genes in L. plantarum. Appl Environ Microbiol (2003) 1.07
Lactic acid bacteria as a cell factory: rerouting of carbon metabolism in Lactococcus lactis by metabolic engineering. Enzyme Microb Technol (2000) 1.03
The biosynthesis of folic acid. XII. Purification and properties of dihydroneopterin triphosphate pyrophosphohydrolase. J Biol Chem (1974) 0.97
Ability of thermophilic lactic acid bacteria to produce aroma compounds from amino acids. Appl Environ Microbiol (2004) 0.96
In silico biotechnology. Era of reconstruction and interrogation. Curr Opin Biotechnol (2004) 0.96
Metabolic engineering of Lactococcus lactis: the impact of genomics and metabolic modelling. J Biotechnol (2002) 0.93
Involvement of the molybdenum cofactor biosynthetic machinery in the maturation of the Escherichia coli nitrate reductase A. J Biol Chem (2004) 0.92
Increased exopolysaccharide production in Lactococcus lactis due to increased levels of expression of the NIZO B40 eps gene cluster. Appl Environ Microbiol (2003) 0.92
Review of the BRENDA Database. Metab Eng (2003) 0.91
Chorismate mutase and 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase of the methylotrophic actinomycete Amycolatopsis methanolica. Appl Environ Microbiol (1995) 0.86
Lactococcus lactis, a tool for the delivery of therapeutic proteins treatment of IBD. ScientificWorldJournal (2001) 0.82
Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci U S A (2003) 8.40
How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev (2006) 6.39
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
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
Complete genome sequence of the probiotic Lactobacillus casei strain BL23. J Bacteriol (2010) 1.98
Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics (2006) 1.97
Modelling strategies for the industrial exploitation of lactic acid bacteria. Nat Rev Microbiol (2006) 1.94
Biodiversity-based identification and functional characterization of the mannose-specific adhesin of Lactobacillus plantarum. J Bacteriol (2005) 1.85
The extracellular biology of the lactobacilli. FEMS Microbiol Rev (2010) 1.84
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
LocateP: genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinformatics (2008) 1.64
Comparative genomics of Lactobacillus. Microb Biotechnol (2010) 1.60
Natural diversity and adaptive responses of Lactococcus lactis. Curr Opin Biotechnol (2006) 1.54
Fermentation characteristics of yeasts isolated from traditionally fermented masau (Ziziphus mauritiana) fruits. Int J Food Microbiol (2013) 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
Co-regulation of metabolic genes is better explained by flux coupling than by network distance. PLoS Comput Biol (2008) 1.46
Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2006) 1.45
Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria. Microbiology (2006) 1.42
Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation. PLoS Comput Biol (2009) 1.37
Comparative genomics of enzymes in flavor-forming pathways from amino acids in lactic acid bacteria. Appl Environ Microbiol (2008) 1.37
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
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
A nudix enzyme removes pyrophosphate from dihydroneopterin triphosphate in the folate synthesis pathway of bacteria and plants. J Biol Chem (2004) 1.19
Genome data mining of lactic acid bacteria: the impact of bioinformatics. Curr Opin Biotechnol (2004) 1.19
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
Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1. Microb Cell Fact (2007) 1.17
Resistance of Gram-positive bacteria to nisin is not determined by lipid II levels. FEMS Microbiol Lett (2004) 1.15
A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. BMC Genomics (2013) 1.15
Comparison of quenching and extraction methodologies for metabolome analysis of Lactobacillus plantarum. Microb Cell Fact (2007) 1.14
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
Industrial-scale production and purification of a heterologous protein in Lactococcus lactis using the nisin-controlled gene expression system NICE: the case of lysostaphin. Microb Cell Fact (2005) 1.12
Diversity of human small intestinal Streptococcus and Veillonella populations. FEMS Microbiol Ecol (2013) 1.12
Optimization of the Lactococcus lactis nisin-controlled gene expression system NICE for industrial applications. Microb Cell Fact (2005) 1.11
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
Metabolic engineering of lactic acid bacteria for the production of nutraceuticals. Antonie Van Leeuwenhoek (2002) 1.09
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 analysis of two-component signal transduction systems of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis. Microbiology (2006) 1.05
Clostridial spore germination versus bacilli: genome mining and current insights. Food Microbiol (2010) 1.04
SNP/RD typing of Mycobacterium tuberculosis Beijing strains reveals local and worldwide disseminated clonal complexes. PLoS One (2011) 1.03
LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria. BMC Genomics (2010) 1.02
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
Characterization of the role of para-aminobenzoic acid biosynthesis in folate production by Lactococcus lactis. Appl Environ Microbiol (2007) 1.01
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
PanCGHweb: a web tool for genotype calling in pangenome CGH data. Bioinformatics (2010) 1.00
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
Making sense of quorum sensing in lactobacilli: a special focus on Lactobacillus plantarum WCFS1. Microbiology (2007) 0.97
Improvement of Lactobacillus plantarum aerobic growth as directed by comprehensive transcriptome analysis. Appl Environ Microbiol (2008) 0.96
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
High-Level folate production in fermented foods by the B12 producer Lactobacillus reuteri JCM1112. Appl Environ Microbiol (2008) 0.92
Increased D-alanylation of lipoteichoic acid and a thickened septum are main determinants in the nisin resistance mechanism of Lactococcus lactis. Microbiology (2008) 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
Bacterial vitamin B2, B11 and B12 overproduction: An overview. Int J Food Microbiol (2009) 0.91
Genome update: lactic acid bacteria genome sequencing is booming. Microbiology (2005) 0.90
Transcriptomes reveal genetic signatures underlying physiological variations imposed by different fermentation conditions in Lactobacillus plantarum. PLoS One (2012) 0.90
Characterization of Rhamnosidases from Lactobacillus plantarum and Lactobacillus acidophilus. Appl Environ Microbiol (2009) 0.89
The highly autoaggregative and adhesive phenotype of the vaginal Lactobacillus plantarum strain CMPG5300 is sortase dependent. Appl Environ Microbiol (2013) 0.89
EXProt: a database for proteins with an experimentally verified function. Nucleic Acids Res (2002) 0.89