Published in Trends Microbiol on September 19, 2005
Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics (2007) 9.45
Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer. Microb Cell Fact (2011) 2.22
A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189. PLoS Comput Biol (2009) 2.02
Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics (2006) 1.97
Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics (2009) 1.73
Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. J Bacteriol (2012) 1.71
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput Biol (2009) 1.63
Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major. Mol Syst Biol (2008) 1.49
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Res (2010) 1.47
Comparative genomics of enzymes in flavor-forming pathways from amino acids in lactic acid bacteria. Appl Environ Microbiol (2008) 1.37
Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis. Biotechnol Bioeng (2008) 1.33
Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics (2015) 1.27
SubMAP: aligning metabolic pathways with subnetwork mappings. J Comput Biol (2011) 1.24
Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043. BMC Syst Biol (2011) 1.12
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
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
Biochemical and statistical network models for systems biology. Curr Opin Biotechnol (2007) 1.07
In silico models of cancer. Wiley Interdiscip Rev Syst Biol Med (2010) 1.01
Characterizing the metabolism of Dehalococcoides with a constraint-based model. PLoS Comput Biol (2010) 1.01
Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks. Sci Rep (2012) 1.01
Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics. Genome Biol (2007) 0.99
A critical view of metabolic network adaptations. HFSP J (2008) 0.98
Quantitative effect of luxS gene inactivation on the fitness of Helicobacter pylori. Appl Environ Microbiol (2006) 0.97
Analysis of ultra low genome conservation in Clostridium difficile. PLoS One (2010) 0.96
A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis. BMC Syst Biol (2009) 0.93
Sparse canonical correlation analysis for identifying, connecting and completing gene-expression networks. BMC Bioinformatics (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
Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum. PLoS Comput Biol (2009) 0.91
Network motifs provide signatures that characterize metabolism. Mol Biosyst (2013) 0.85
Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis. PLoS Comput Biol (2010) 0.85
Semi-automated curation of metabolic models via flux balance analysis: a case study with Mycoplasma gallisepticum. PLoS Comput Biol (2013) 0.84
In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae. BMC Syst Biol (2007) 0.83
Reconstructing genome-scale metabolic models with merlin. Nucleic Acids Res (2015) 0.83
Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure. Front Microbiol (2015) 0.82
Metabolic network alignment in large scale by network compression. BMC Bioinformatics (2012) 0.81
Network-based scoring system for genome-scale metabolic reconstructions. BMC Syst Biol (2011) 0.80
Dynamic Proteomic Characteristics and Network Integration Revealing Key Proteins for Two Kernel Tissue Developments in Popcorn. PLoS One (2015) 0.80
Signal correlations in ecological niches can shape the organization and evolution of bacterial gene regulatory networks. Adv Microb Physiol (2012) 0.78
Indexing a protein-protein interaction network expedites network alignment. BMC Bioinformatics (2015) 0.78
A genome-scale metabolic reconstruction of Lysinibacillus sphaericus unveils unexploited biotechnological potentials. PLoS One (2017) 0.77
RINQ: Reference-based Indexing for Network Queries. Bioinformatics (2011) 0.77
Mass conservation and inference of metabolic networks from high-throughput mass spectrometry data. J Comput Biol (2011) 0.76
In silico description of cobalt and nickel assimilation systems in the genomes of methanogens. Syst Synth Biol (2011) 0.76
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti. BMC Syst Biol (2013) 0.76
ocsESTdb: a database of oil crop seed EST sequences for comparative analysis and investigation of a global metabolic network and oil accumulation metabolism. BMC Plant Biol (2015) 0.76
SSER: Species specific essential reactions database. BMC Syst Biol (2017) 0.75
Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach. PLoS One (2015) 0.75
Metabolic network motifs can provide novel insights into evolution: The evolutionary origin of Eukaryotic organelles as a case study. Comput Biol Chem (2014) 0.75
Metabolic pathway reconstruction of eugenol to vanillin bioconversion in Aspergillus niger. Bioinformation (2010) 0.75
Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches. Syst Synth Biol (2012) 0.75
Graphlet-based Characterization of Directed Networks. Sci Rep (2016) 0.75
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
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
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
Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics (2006) 1.97
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
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
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
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
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
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
Availability of public goods shapes the evolution of competing metabolic strategies. Proc Natl Acad Sci U S A (2013) 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
EXProt--a database for EXPerimentally verified Protein functions. In Silico Biol (2002) 0.94
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
EXProt: a database for proteins with an experimentally verified function. Nucleic Acids Res (2002) 0.89
The highly autoaggregative and adhesive phenotype of the vaginal Lactobacillus plantarum strain CMPG5300 is sortase dependent. Appl Environ Microbiol (2013) 0.89
A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803. Plant Physiol (2014) 0.89
Preferential deletion events in the direct repeat locus of Mycobacterium tuberculosis. J Clin Microbiol (2011) 0.88
A specific mutation in the promoter region of the silent cel cluster accounts for the appearance of lactose-utilizing Lactococcus lactis MG1363. Appl Environ Microbiol (2012) 0.87
Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis. Appl Environ Microbiol (2010) 0.87
Functional identification in Lactobacillus reuteri of a PocR-like transcription factor regulating glycerol utilization and vitamin B12 synthesis. Microb Cell Fact (2011) 0.86
Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli. BMC Genomics (2012) 0.86
Comparative and functional analysis of the rRNA-operons and their tRNA gene complement in different lactic acid bacteria. Syst Appl Microbiol (2005) 0.86
Functional ingredient production: application of global metabolic models. Curr Opin Biotechnol (2005) 0.86
A practical guide to genome-scale metabolic models and their analysis. Methods Enzymol (2011) 0.86
A novel hybrid kinase is essential for regulating the sigma(B)-mediated stress response of Bacillus cereus. Environ Microbiol (2009) 0.85
Towards metagenome-scale models for industrial applications--the case of Lactic Acid Bacteria. Curr Opin Biotechnol (2012) 0.85
Novel sigmaB regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases. Microbiology (2010) 0.85
Genomic tracing of epidemics and disease outbreaks. Microb Biotechnol (2010) 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
MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis. Mol Biosyst (2014) 0.84
Single-cell genomics: unravelling the genomes of unculturable microorganisms. Microb Biotechnol (2011) 0.84
Metabolic shifts: a fitness perspective for microbial cell factories. Biotechnol Lett (2012) 0.83
Metabolic states with maximal specific rate carry flux through an elementary flux mode. FEBS J (2014) 0.83
Hydrocarbon-degrading bacteria: the oil-spill clean-up crew. Microb Biotechnol (2009) 0.82
Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods. BMC Microbiol (2013) 0.82
A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis. BMC Genomics (2010) 0.82
How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism. Genetics (2013) 0.82