Published in Biotechnol Bioeng on October 20, 1998
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol (2007) 11.03
High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol (2010) 6.08
Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol (2008) 5.36
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol (2008) 5.26
Thirteen years of building constraint-based in silico models of Escherichia coli. J Bacteriol (2003) 3.52
(13)C-based metabolic flux analysis. Nat Protoc (2009) 2.75
Metabolic modeling of a mutualistic microbial community. Mol Syst Biol (2007) 2.40
Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Appl Environ Microbiol (2006) 2.09
Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput Biol (2008) 1.79
Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation. PLoS Comput Biol (2010) 1.48
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Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms. Microb Cell Fact (2012) 1.19
Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism. Microb Cell Fact (2006) 1.12
Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes. Genome Biol (2007) 1.08
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
Evidence of selection for low cognate amino acid bias in amino acid biosynthetic enzymes. Mol Microbiol (2005) 1.00
Selective utilization of exogenous amino acids by Dehalococcoides ethenogenes strain 195 and its effects on growth and dechlorination activity. Appl Environ Microbiol (2011) 0.98
Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example. Front Microbiol (2014) 0.95
Metabolic modeling of Chlamydomonas reinhardtii: energy requirements for photoautotrophic growth and maintenance. J Appl Phycol (2011) 0.93
A Method to Constrain Genome-Scale Models with 13C Labeling Data. PLoS Comput Biol (2015) 0.90
Expanding a dynamic flux balance model of yeast fermentation to genome-scale. BMC Syst Biol (2011) 0.90
Reconciling in vivo and in silico key biological parameters of Pseudomonas putida KT2440 during growth on glucose under carbon-limited condition. BMC Biotechnol (2013) 0.88
Predictive modeling of biomass component tradeoffs in Brassica napus developing oilseeds based on in silico manipulation of storage metabolism. Plant Physiol (2012) 0.85
Decrease of energy spilling in Escherichia coli continuous cultures with rising specific growth rate and carbon wasting. BMC Syst Biol (2011) 0.85
Flux balance analysis accounting for metabolite dilution. Genome Biol (2010) 0.83
Relative amino acid composition signatures of organisms and environments. PLoS One (2013) 0.83
Flux balance analysis of ammonia assimilation network in E. coli predicts preferred regulation point. PLoS One (2011) 0.80
Flux Balance Analysis of Plant Metabolism: The Effect of Biomass Composition and Model Structure on Model Predictions. Front Plant Sci (2016) 0.78
Constrained Allocation Flux Balance Analysis. PLoS Comput Biol (2016) 0.78
Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes. Metab Eng (2016) 0.75
Mapping the landscape of metabolic goals of a cell. Genome Biol (2016) 0.75
Improving Escherichia coli membrane integrity and fatty acid production by expression tuning of FadL and OmpF. Microb Cell Fact (2017) 0.75
Population FBA predicts metabolic phenotypes in yeast. PLoS Comput Biol (2017) 0.75
High-level semi-synthetic production of the potent antimalarial artemisinin. Nature (2013) 3.80
Homogeneous expression of the P(BAD) promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter. Microbiology (2001) 3.12
Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. Biotechnol Bioeng (1997) 2.71
Mathematical model of the lac operon: inducer exclusion, catabolite repression, and diauxic growth on glucose and lactose. Biotechnol Prog (1997) 1.92
Metabolic engineering of the nonmevalonate isopentenyl diphosphate synthesis pathway in Escherichia coli enhances lycopene production. Biotechnol Bioeng (2001) 1.82
Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria. Metab Eng (2000) 1.75
Investigating autocatalytic gene expression systems through mechanistic modeling. J Theor Biol (1999) 1.70
Regulatable arabinose-inducible gene expression system with consistent control in all cells of a culture. J Bacteriol (2000) 1.56
Library of synthetic 5' secondary structures to manipulate mRNA stability in Escherichia coli. Biotechnol Prog (1999) 1.35
Controlling messenger RNA stability in bacteria: strategies for engineering gene expression. Biotechnol Prog (1998) 1.25
Kinetics of toluene degradation by a nitrate-reducing bacterium isolated from a groundwater aquifer. Biotechnol Bioeng (1997) 1.17
Coordinated, differential expression of two genes through directed mRNA cleavage and stabilization by secondary structures. Appl Environ Microbiol (2000) 1.15
Cadmium removal by a new strain of Pseudomonas aeruginosa in aerobic culture. Appl Environ Microbiol (1997) 1.09
Dual labeling with green fluorescent proteins for confocal microscopy. Appl Environ Microbiol (2000) 1.09
Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome. Appl Environ Microbiol (2011) 1.02
Commensal interactions in a dual-species biofilm exposed to mixed organic compounds. Appl Environ Microbiol (2000) 1.02
A constructed microbial consortium for biodegradation of the organophosphorus insecticide parathion. Appl Microbiol Biotechnol (2003) 0.99
The in vivo synthesis of plant sesquiterpenes by Escherichia coli. Biotechnol Bioeng (2001) 0.98
A dynamic model of the Escherichia coli phosphate-starvation response. J Theor Biol (1998) 0.92
Aerobic sulfide production and cadmium precipitation by Escherichia coli expressing the Treponema denticola cysteine desulfhydrase gene. Appl Microbiol Biotechnol (2001) 0.91
mRNA stability and plasmid copy number effects on gene expression from an inducible promoter system. Biotechnol Bioeng (1998) 0.90
Polyphosphate binding and chain length recognition of Escherichia coli exopolyphosphatase. J Biol Chem (2000) 0.89
Polyphosphate metabolism in Escherichia coli. Ann N Y Acad Sci (1994) 0.89
Mechanistic modeling of prokaryotic mRNA decay. J Theor Biol (1997) 0.88
Manipulation of independent synthesis and degradation of polyphosphate in Escherichia coli for investigation of phosphate secretion from the cell. Appl Environ Microbiol (1997) 0.87
Metabolic engineering of an aerobic sulfate reduction pathway and its application to precipitation of cadmium on the cell surface. Appl Environ Microbiol (2000) 0.87
Construction and characterization of F plasmid-based expression vectors. Biotechnol Bioeng (1998) 0.85
Controlling the metabolic flux through the carotenoid pathway using directed mRNA processing and stabilization. Metab Eng (2001) 0.85
Engineering hydrogen sulfide production and cadmium removal by expression of the thiosulfate reductase gene (phsABC) from Salmonella enterica serovar typhimurium in Escherichia coli. Appl Environ Microbiol (2000) 0.85
Engineering mRNA stability in E. coli by the addition of synthetic hairpins using a 5' cassette system. Biotechnol Bioeng (1997) 0.84
The recA gene and cadmium toxicity in Escherichia coli K12. Microbios (1996) 0.83
Metabolic engineering of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) composition in recombinant Salmonella enterica serovar typhimurium. Biotechnol Bioeng (2001) 0.83
Polyphosphate kinase of Acinetobacter sp. strain ADP1: purification and characterization of the enzyme and its role during changes in extracellular phosphate levels. Appl Environ Microbiol (1999) 0.83
Uranyl precipitation by biomass from an enhanced biological phosphorus removal reactor. Biodegradation (2001) 0.82
Reductive dechlorination of chlorinated ethene DNAPLs by a culture enriched from contaminated groundwater. Biotechnol Bioeng (1999) 0.82
Analysis of an engineered sulfate reduction pathway and cadmium precipitation on the cell surface. Biotechnol Bioeng (2001) 0.82
Modulation of the phosphate-starvation response in Escherichia coli by genetic manipulation of the polyphosphate pathways. Biotechnol Bioeng (1996) 0.81
Complete reductive dechlorination of trichloroethene by a groundwater microbial consortium. Ann N Y Acad Sci (1997) 0.81
A Monte Carlo simulation of plasmid replication during the bacterial division cycle. Biotechnol Bioeng (1996) 0.81
The regulatory mechanisms of human immunodeficiency virus replication predict multiple expression rates. Proc Natl Acad Sci U S A (1990) 0.80
Cycle-specific replication of chromosomal and F-plasmid origins. FEMS Microbiol Lett (1998) 0.80
Effects of transcription induction homogeneity and transcript stability on expression of two genes in a constructed operon. Appl Microbiol Biotechnol (2001) 0.80
Ultrasonic flexural-plate-wave sensor for detecting the concentration of settling E. coli W3110 cells. Anal Chem (1999) 0.79
Synthesis of DnaK protein during the division cycle of Escherichia coli. Res Microbiol (1994) 0.78
Nickel accumulation and nickel oxalate precipitation by Aspergillus niger. Appl Microbiol Biotechnol (2002) 0.78
Polyphosphate kinase genes from activated sludge carrying out enhanced biological phosphorus removal. Water Sci Technol (2002) 0.78
Biodesulfurization of dibenzothiophene in Escherichia coli is enhanced by expression of a Vibrio harveyi oxidoreductase gene. Biotechnol Bioeng (2000) 0.78
Effect of polyphosphate metabolism on the Escherichia coli phosphate-starvation response. Biotechnol Prog (1999) 0.78
Analysis of biofilm structure and gene expression using fluorescence dual labeling. Biotechnol Prog (2001) 0.77
The effect of monovalent ions on polyphosphate binding to Escherichia coli exopolyphosphatase. Biochem Biophys Res Commun (2000) 0.77
Kinetics of BTEX degradation by a nitrate-reducing mixed culture. Ann N Y Acad Sci (1997) 0.75