Published in J Biol Chem on September 08, 2003
Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence. Nat Med (2005) 6.10
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol (2007) 4.61
Metabolic networks in motion: 13C-based flux analysis. Mol Syst Biol (2006) 4.24
(13)C-based metabolic flux analysis. Nat Protoc (2009) 2.75
Impact of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on glucose catabolism in Escherichia coli. J Bacteriol (2005) 2.70
FiatFlux--a software for metabolic flux analysis from 13C-glucose experiments. BMC Bioinformatics (2005) 2.42
Experimental identification and quantification of glucose metabolism in seven bacterial species. J Bacteriol (2005) 2.24
Structure-guided discovery of phenyl-diketo acids as potent inhibitors of M. tuberculosis malate synthase. Chem Biol (2012) 1.71
Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli. Mol Syst Biol (2011) 1.55
Nonlinear dependency of intracellular fluxes on growth rate in miniaturized continuous cultures of Escherichia coli. Appl Environ Microbiol (2006) 1.50
Virulence of Mycobacterium tuberculosis depends on lipoamide dehydrogenase, a member of three multienzyme complexes. Cell Host Microbe (2011) 1.34
anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data. BMC Bioinformatics (2008) 1.33
¹³C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation. PLoS Pathog (2011) 1.32
Compiling a molecular inventory for Mycobacterium bovis BCG at two growth rates: evidence for growth rate-mediated regulation of ribosome biosynthesis and lipid metabolism. J Bacteriol (2005) 1.28
Pathway thermodynamics highlights kinetic obstacles in central metabolism. PLoS Comput Biol (2014) 1.11
Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium. BMC Microbiol (2007) 1.11
Carbon metabolism of enterobacterial human pathogens growing in epithelial colorectal adenocarcinoma (Caco-2) cells. PLoS One (2010) 1.10
Cyclic AMP-dependent catabolite repression is the dominant control mechanism of metabolic fluxes under glucose limitation in Escherichia coli. J Bacteriol (2008) 1.09
Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase. Nat Chem Biol (2012) 1.04
The TB Structural Genomics Consortium: a decade of progress. Tuberculosis (Edinb) (2011) 1.03
The normalcy of dormancy: common themes in microbial quiescence. Cell Host Microbe (2013) 1.03
Effect of iclR and arcA knockouts on biomass formation and metabolic fluxes in Escherichia coli K12 and its implications on understanding the metabolism of Escherichia coli BL21 (DE3). BMC Microbiol (2011) 1.03
An insight into the role of phosphotransacetylase (pta) and the acetate/acetyl-CoA node in Escherichia coli. Microb Cell Fact (2009) 0.97
Protein acetylation affects acetate metabolism, motility and acid stress response in Escherichia coli. Mol Syst Biol (2014) 0.97
Fluxomics: mass spectrometry versus quantitative imaging. Curr Opin Plant Biol (2007) 0.96
Global transcription and metabolic flux analysis of Escherichia coli in glucose-limited fed-batch cultivations. Appl Environ Microbiol (2008) 0.95
Slow growth of Mycobacterium tuberculosis at acidic pH is regulated by phoPR and host-associated carbon sources. Mol Microbiol (2014) 0.94
Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds. Bioinformatics (2011) 0.91
Brucella abortus depends on pyruvate phosphate dikinase and malic enzyme but not on Fbp and GlpX fructose-1,6-bisphosphatases for full virulence in laboratory models. J Bacteriol (2014) 0.91
Recent advances in mapping environmental microbial metabolisms through 13C isotopic fingerprints. J R Soc Interface (2012) 0.89
Non-growing Rhodopseudomonas palustris increases the hydrogen gas yield from acetate by shifting from the glyoxylate shunt to the tricarboxylic acid cycle. J Biol Chem (2013) 0.88
Model-independent fluxome profiling from 2H and 13C experiments for metabolic variant discrimination. Genome Biol (2004) 0.87
NADPH-generating systems in bacteria and archaea. Front Microbiol (2015) 0.86
Phosphoketolase pathway for xylose catabolism in Clostridium acetobutylicum revealed by 13C metabolic flux analysis. J Bacteriol (2012) 0.86
Biochemical characterization of malate synthase G of P. aeruginosa. BMC Biochem (2009) 0.86
On functional module detection in metabolic networks. Metabolites (2013) 0.86
Transcription, translation, and the evolution of specialists and generalists. Mol Biol Evol (2009) 0.84
Metabolic shift of Escherichia coli under salt stress in the presence of glycine betaine. Appl Environ Microbiol (2014) 0.83
Influence of the RelA Activity on E. coli Metabolism by Metabolite Profiling of Glucose-Limited Chemostat Cultures. Metabolites (2012) 0.81
Simple phenotypic sweeps hide complex genetic changes in populations. Genome Biol Evol (2015) 0.81
Network identification and flux quantification of glucose metabolism in Rhodobacter sphaeroides under photoheterotrophic H(2)-producing conditions. J Bacteriol (2011) 0.81
Transcriptional control of metabolic fluxes. Mol Syst Biol (2011) 0.81
The infectious intracellular lifestyle of Salmonella enterica relies on the adaptation to nutritional conditions within the Salmonella-containing vacuole. Virulence (2016) 0.81
Effect of growth phase feeding strategies on succinate production by metabolically engineered Escherichia coli. Appl Environ Microbiol (2009) 0.80
Analysis of fluorescent reporters indicates heterogeneity in glucose uptake and utilization in clonal bacterial populations. BMC Microbiol (2013) 0.80
Sub-optimal phenotypes of double-knockout mutants of Escherichia coli depend on the order of gene deletions. Integr Biol (Camb) (2015) 0.80
Physiological and proteomic analysis of Escherichia coli iron-limited chemostat growth. J Bacteriol (2014) 0.79
Ensemble modeling of hepatic fatty acid metabolism with a synthetic glyoxylate shunt. Biophys J (2010) 0.78
System-level strategies for studying the metabolism of Mycobacterium tuberculosis. Mol Biosyst (2010) 0.78
Photoheterotrophic fluxome in Synechocystis sp. strain PCC 6803 and its implications for cyanobacterial bioenergetics. J Bacteriol (2014) 0.77
Physiological, biomass elemental composition and proteomic analyses of Escherichia coli ammonium-limited chemostat growth, and comparison with iron- and glucose-limited chemostat growth. Microbiology (2015) 0.75
Functional genomics analysis of free fatty acid production under continuous phosphate limiting conditions. J Ind Microbiol Biotechnol (2016) 0.75
A Network Biology Approach to Decipher Stress Response in Bacteria Using Escherichia coli As a Model. OMICS (2016) 0.75
Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli. PLoS Comput Biol (2017) 0.75
Metabolic evolution and the self-organization of ecosystems. Proc Natl Acad Sci U S A (2017) 0.75
Genome scale modeling in systems biology: algorithms and resources. Curr Genomics (2014) 0.75
Derepression of Mineral Phosphate Solubilization Phenotype by Insertional Inactivation of iclR in Klebsiella pneumoniae. PLoS One (2015) 0.75
Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism. PLoS One (2015) 0.75
The BvgAS Regulon of Bordetella pertussis. MBio (2017) 0.75
A novel endogenous induction of ColE7 expression in a csrA mutant of Escherichia coli. Curr Microbiol (2012) 0.75
Robustness of cellular functions. Cell (2004) 6.65
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol (2007) 4.61
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol (2008) 4.55
Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur J Biochem (2003) 3.51
Multidimensional optimality of microbial metabolism. Science (2012) 3.09
Metabolic flux responses to pyruvate kinase knockout in Escherichia coli. J Bacteriol (2002) 3.06
Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism. Nat Genet (2005) 2.82
(13)C-based metabolic flux analysis. Nat Protoc (2009) 2.75
High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints. Anal Biochem (2004) 2.73
Impact of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on glucose catabolism in Escherichia coli. J Bacteriol (2005) 2.70
Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol (2005) 2.68
Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res (2005) 2.68
Quantitative phosphoproteomics reveal mTORC1 activates de novo pyrimidine synthesis. Science (2013) 2.44
FiatFlux--a software for metabolic flux analysis from 13C-glucose experiments. BMC Bioinformatics (2005) 2.42
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science (2012) 2.38
Experimental identification and quantification of glucose metabolism in seven bacterial species. J Bacteriol (2005) 2.24
Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes. J Biol Chem (2005) 2.10
Ultrahigh performance liquid chromatography-tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites. Anal Chem (2010) 2.05
Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli. Am Nat (2006) 1.99
Identification of furfural as a key toxin in lignocellulosic hydrolysates and evolution of a tolerant yeast strain. Microb Biotechnol (2008) 1.88
Ensemble modeling for analysis of cell signaling dynamics. Nat Biotechnol (2007) 1.84
Cross-platform comparison of methods for quantitative metabolomics of primary metabolism. Anal Chem (2009) 1.83
Determination of metabolic flux ratios from 13C-experiments and gas chromatography-mass spectrometry data: protocol and principles. Methods Mol Biol (2007) 1.76
Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts. FEMS Yeast Res (2005) 1.65
Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis. J Bacteriol (2007) 1.57
Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli. Mol Syst Biol (2011) 1.55
Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol Biol Evol (2003) 1.55
Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity. Mol Syst Biol (2010) 1.50
Nonlinear dependency of intracellular fluxes on growth rate in miniaturized continuous cultures of Escherichia coli. Appl Environ Microbiol (2006) 1.50
PhoR autokinase activity is controlled by an intermediate in wall teichoic acid metabolism that is sensed by the intracellular PAS domain during the PhoPR-mediated phosphate limitation response of Bacillus subtilis. Mol Microbiol (2014) 1.47
Evolutionary engineering of Saccharomyces cerevisiae for anaerobic growth on xylose. Appl Environ Microbiol (2003) 1.45
Fumarate reductase activity maintains an energized membrane in anaerobic Mycobacterium tuberculosis. PLoS Pathog (2011) 1.45
TCA cycle activity in Saccharomyces cerevisiae is a function of the environmentally determined specific growth and glucose uptake rates. Microbiology (2004) 1.44
Fermentation performance of engineered and evolved xylose-fermenting Saccharomyces cerevisiae strains. Biotechnol Bioeng (2004) 1.38
Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo. Nat Biotechnol (2013) 1.36
Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. Mol Syst Biol (2011) 1.35
Metabolic-flux profiling of the yeasts Saccharomyces cerevisiae and Pichia stipitis. Eukaryot Cell (2003) 1.33
Systems biology of microbial metabolism. Curr Opin Microbiol (2010) 1.33
Automatic policing of biochemical annotations using genomic correlations. Nat Chem Biol (2009) 1.31
Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism. J Bacteriol (2009) 1.30
Regulation and control of metabolic fluxes in microbes. Curr Opin Biotechnol (2011) 1.25
Novel biological insights through metabolomics and 13C-flux analysis. Curr Opin Microbiol (2009) 1.23
Molecular basis for anaerobic growth of Saccharomyces cerevisiae on xylose, investigated by global gene expression and metabolic flux analysis. Appl Environ Microbiol (2004) 1.20
A prototrophic deletion mutant collection for yeast metabolomics and systems biology. Nat Biotechnol (2012) 1.19
Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains. Nat Commun (2010) 1.18
Dissecting specific and global transcriptional regulation of bacterial gene expression. Mol Syst Biol (2013) 1.17
Aneuploid yeast strains exhibit defects in cell growth and passage through START. Mol Biol Cell (2013) 1.16
Global probabilistic annotation of metabolic networks enables enzyme discovery. Nat Chem Biol (2012) 1.15
Regulation of yeast central metabolism by enzyme phosphorylation. Mol Syst Biol (2012) 1.15
Resistance of Saccharomyces cerevisiae to high concentrations of furfural is based on NADPH-dependent reduction by at least two oxireductases. Appl Environ Microbiol (2009) 1.14
Evolutionary engineering of multiple-stress resistant Saccharomyces cerevisiae. FEMS Yeast Res (2005) 1.13
Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli. J Bacteriol (2007) 1.13
Intracellular carbon fluxes in riboflavin-producing Bacillus subtilis during growth on two-carbon substrate mixtures. Appl Environ Microbiol (2002) 1.11
Metabolic fluxes during strong carbon catabolite repression by malate in Bacillus subtilis. J Biol Chem (2009) 1.11
Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis. Mol Syst Biol (2013) 1.11
Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates. BMC Syst Biol (2010) 1.10
Cyclic AMP-dependent catabolite repression is the dominant control mechanism of metabolic fluxes under glucose limitation in Escherichia coli. J Bacteriol (2008) 1.09
Metabolic engineering of a phosphoketolase pathway for pentose catabolism in Saccharomyces cerevisiae. Appl Environ Microbiol (2004) 1.09
Collisional fragmentation of central carbon metabolites in LC-MS/MS increases precision of ¹³C metabolic flux analysis. Biotechnol Bioeng (2011) 1.09
D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii. J Biol Chem (2009) 1.08
Regulation of CodY activity through modulation of intracellular branched-chain amino acid pools. J Bacteriol (2010) 1.07
Multiple and interconnected pathways for L-lysine catabolism in Pseudomonas putida KT2440. J Bacteriol (2005) 1.07
Efficient classification of complete parameter regions based on semidefinite programming. BMC Bioinformatics (2007) 1.06
Limitations in xylose-fermenting Saccharomyces cerevisiae, made evident through comprehensive metabolite profiling and thermodynamic analysis. Appl Environ Microbiol (2010) 1.05
Oxygen- and glucose-dependent regulation of central carbon metabolism in Pichia anomala. Appl Environ Microbiol (2004) 1.05
Knockout of the high-coupling cytochrome aa3 oxidase reduces TCA cycle fluxes in Bacillus subtilis. FEMS Microbiol Lett (2003) 1.04
Intracellular characterization of aerobic glucose metabolism in seven yeast species by 13C flux analysis and metabolomics. FEMS Yeast Res (2011) 1.02
Transient expression and flux changes during a shift from high to low riboflavin production in continuous cultures of Bacillus subtilis. Biotechnol Bioeng (2005) 1.02
YtsJ has the major physiological role of the four paralogous malic enzyme isoforms in Bacillus subtilis. J Bacteriol (2006) 1.02
The Bacillus subtilis yqjI gene encodes the NADP+-dependent 6-P-gluconate dehydrogenase in the pentose phosphate pathway. J Bacteriol (2004) 0.98
Regulatory tasks of the phosphoenolpyruvate-phosphotransferase system of Pseudomonas putida in central carbon metabolism. MBio (2012) 0.98
Somewhat in control--the role of transcription in regulating microbial metabolic fluxes. Curr Opin Biotechnol (2013) 0.98
13C-flux analysis reveals NADPH-balancing transhydrogenation cycles in stationary phase of nitrogen-starving Bacillus subtilis. J Biol Chem (2012) 0.98
Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast. Mol Syst Biol (2013) 0.97
Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast. Mol Syst Biol (2010) 0.97
A global investigation of the Bacillus subtilis iron-sparing response identifies major changes in metabolism. J Bacteriol (2012) 0.96
Acetate scavenging activity in Escherichia coli: interplay of acetyl-CoA synthetase and the PEP-glyoxylate cycle in chemostat cultures. Appl Microbiol Biotechnol (2011) 0.94
The importance of post-translational modifications in regulating Saccharomyces cerevisiae metabolism. FEMS Yeast Res (2011) 0.94
Maintenance metabolism and carbon fluxes in Bacillus species. Microb Cell Fact (2008) 0.93
Dynamic metabolomics differentiates between carbon and energy starvation in recombinant Saccharomyces cerevisiae fermenting xylose. Biotechnol Biofuels (2012) 0.91
CcpN controls central carbon fluxes in Bacillus subtilis. J Bacteriol (2008) 0.91
Metabolism of pentose sugars in the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius. J Biol Chem (2010) 0.90
The phosphoenolpyruvate carboxykinase also catalyzes C3 carboxylation at the interface of glycolysis and the TCA cycle of Bacillus subtilis. Metab Eng (2004) 0.90
Differential glucose repression in common yeast strains in response to HXK2 deletion. FEMS Yeast Res (2010) 0.90
Nontargeted profiling of coenzyme A thioesters in biological samples by tandem mass spectrometry. Anal Chem (2013) 0.89
Functional expression of arginine kinase improves recovery from pH stress of Escherichia coli. Biotechnol Lett (2003) 0.88
Dynamic flux responses in riboflavin overproducing Bacillus subtilis to increasing glucose limitation in fed-batch culture. Biotechnol Bioeng (2010) 0.88
Non-growing Rhodopseudomonas palustris increases the hydrogen gas yield from acetate by shifting from the glyoxylate shunt to the tricarboxylic acid cycle. J Biol Chem (2013) 0.88
Identification of common traits in improved xylose-growing Saccharomyces cerevisiae for inverse metabolic engineering. Yeast (2008) 0.87
Model-independent fluxome profiling from 2H and 13C experiments for metabolic variant discrimination. Genome Biol (2004) 0.87
Selection of quiescent Escherichia coli with high metabolic activity. Metab Eng (2005) 0.87
Functional expression of phosphagen kinase systems confers resistance to transient stresses in Saccharomyces cerevisiae by buffering the ATP pool. J Biol Chem (2002) 0.86
Screening of Bacillus subtilis transposon mutants with altered riboflavin production. Metab Eng (2008) 0.86
Non-stationary (13)C-metabolic flux ratio analysis. Biotechnol Bioeng (2013) 0.86
Reducing maintenance metabolism by metabolic engineering of respiration improves riboflavin production by Bacillus subtilis. Metab Eng (2003) 0.86
Topological augmentation to infer hidden processes in biological systems. Bioinformatics (2013) 0.85
Quantification and mass isotopomer profiling of α-keto acids in central carbon metabolism. Anal Chem (2014) 0.85
Long-term continuous evolution of acetate resistant Acetobacter aceti. Biotechnol Bioeng (2003) 0.83