Published in BMC Bioinformatics on June 13, 2006
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A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. BMC Syst Biol (2012) 0.86
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Genome-scale metabolic network reconstruction of Saccharopolyspora spinosa for spinosad production improvement. Microb Cell Fact (2014) 0.77
Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism. Appl Environ Microbiol (2014) 0.76
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Functional cartography of complex metabolic networks. Nature (2005) 14.18
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Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol (2005) 9.94
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In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol (2001) 8.88
The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res (2001) 8.63
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Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res (2003) 7.22
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res (2005) 7.13
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Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol (2003) 4.91
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Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci U S A (2005) 4.40
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet (2005) 4.19
Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat Biotechnol (2003) 4.06
Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol (2002) 4.00
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metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella. Nucleic Acids Res (2005) 2.21
Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol (2005) 2.14
Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci U S A (2003) 2.08
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
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Modelling strategies for the industrial exploitation of lactic acid bacteria. Nat Rev Microbiol (2006) 1.94
Expression dynamics of a cellular metabolic network. Mol Syst Biol (2005) 1.85
Pentose fermentation by Lactobacillus plantarum. I. The cleavage of xylulose 5-phosphate by phosphoketolase. J Biol Chem (1958) 1.76
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Correlation between sequence conservation and the genomic context after gene duplication. Nucleic Acids Res (2005) 1.54
PseudoCyc, a pathway-genome database for Pseudomonas aeruginosa. J Mol Microbiol Biotechnol (2003) 1.48
IdentiCS--identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. BMC Bioinformatics (2004) 1.17
A method for classifying metabolites in topological pathway analyses based on minimization of pathway number. Biosystems (2003) 0.91
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
Shifts in growth strategies reflect tradeoffs in cellular economics. Mol Syst Biol (2009) 2.26
Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J Biol Chem (2006) 2.17
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
Complete genome sequence of the probiotic Lactobacillus casei strain BL23. J Bacteriol (2010) 1.98
Lost in transition: start-up of glycolysis yields subpopulations of nongrowing cells. Science (2014) 1.96
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
CD36 deficiency increases insulin sensitivity in muscle, but induces insulin resistance in the liver in mice. J Lipid Res (2003) 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
Increased hepatic insulin sensitivity together with decreased hepatic triglyceride stores in hormone-sensitive lipase-deficient mice. Endocrinology (2003) 1.47
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
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
The prophage sequences of Lactobacillus plantarum strain WCFS1. Virology (2003) 1.28
Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PLoS One (2011) 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
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
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
Apolipoprotein C3 deficiency results in diet-induced obesity and aggravated insulin resistance in mice. Diabetes (2005) 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
Genome-scale model of Streptococcus thermophilus LMG18311 for metabolic comparison of lactic acid bacteria. Appl Environ Microbiol (2009) 1.10
Community flux balance analysis for microbial consortia at balanced growth. PLoS One (2013) 1.08
Intestinal lipid absorption is not affected in CD36 deficient mice. Mol Cell Biochem (2002) 1.07
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
FAME, the Flux Analysis and Modeling Environment. BMC Syst Biol (2012) 1.04
Clostridial spore germination versus bacilli: genome mining and current insights. Food Microbiol (2010) 1.04
Predicting metabolic fluxes using gene expression differences as constraints. IEEE/ACM Trans Comput Biol Bioinform (2010) 1.03
The VLDL receptor plays a major role in chylomicron metabolism by enhancing LPL-mediated triglyceride hydrolysis. J Lipid Res (2004) 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
LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria. BMC Genomics (2010) 1.02
Genetic analysis of the capsid gene of genotype GII.2 noroviruses. J Virol (2008) 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
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
Availability of public goods shapes the evolution of competing metabolic strategies. Proc Natl Acad Sci U S A (2013) 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
A critical view of metabolic network adaptations. HFSP J (2008) 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
Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds. Brief Bioinform (2013) 0.96
Standardized assay medium to measure Lactococcus lactis enzyme activities while mimicking intracellular conditions. Appl Environ Microbiol (2011) 0.95
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The transport of triglycerides through the secretory pathway of hepatocytes is impaired in apolipoprotein E deficient mice. J Hepatol (2004) 0.94
Role of phosphate in the central metabolism of two lactic acid bacteria--a comparative systems biology approach. FEBS J (2012) 0.93
Understanding the physiology of Lactobacillus plantarum at zero growth. Mol Syst Biol (2010) 0.93
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
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
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
Genome update: lactic acid bacteria genome sequencing is booming. Microbiology (2005) 0.90
Characterization of Rhamnosidases from Lactobacillus plantarum and Lactobacillus acidophilus. Appl Environ Microbiol (2009) 0.89
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