Published in Mol Syst Biol on June 26, 2007
What is flux balance analysis? Nat Biotechnol (2010) 9.01
A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc (2010) 6.64
High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol (2010) 6.08
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc (2011) 5.71
Link communities reveal multiscale complexity in networks. Nature (2010) 5.48
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform (2009) 5.44
Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol (2008) 5.36
EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res (2012) 5.30
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol (2008) 5.26
A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. Mol Syst Biol (2011) 4.03
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics (2010) 3.87
Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res (2007) 3.34
Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell (2014) 3.15
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol (2009) 3.03
Global phenotypic characterization of bacteria. FEMS Microbiol Rev (2008) 2.97
Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol (2008) 2.90
Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J (2008) 2.89
Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst Biol (2009) 2.80
CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Anal Chem (2011) 2.76
(13)C-based metabolic flux analysis. Nat Protoc (2009) 2.75
Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol Syst Biol (2011) 2.44
GrowMatch: an automated method for reconciling in silico/in vivo growth predictions. PLoS Comput Biol (2009) 2.41
Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol (2010) 2.41
Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science (2009) 2.33
The biomass objective function. Curr Opin Microbiol (2010) 2.32
Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput Biol (2009) 2.14
Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat Rev Mol Cell Biol (2009) 2.09
Environments that induce synthetic microbial ecosystems. PLoS Comput Biol (2010) 2.04
A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189. PLoS Comput Biol (2009) 2.02
Bacterial adaptation through loss of function. PLoS Genet (2013) 1.99
Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev (2008) 1.97
Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng (2009) 1.96
Machine learning methods for metabolic pathway prediction. BMC Bioinformatics (2010) 1.90
Emergent cooperation in microbial metabolism. Mol Syst Biol (2010) 1.87
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol Syst Biol (2010) 1.86
Systematizing the generation of missing metabolic knowledge. Biotechnol Bioeng (2010) 1.85
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol (2008) 1.81
AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis. Plant Physiol (2009) 1.81
Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol Syst Biol (2013) 1.80
Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis. Proc Natl Acad Sci U S A (2012) 1.75
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. BMC Syst Biol (2008) 1.73
eQuilibrator--the biochemical thermodynamics calculator. Nucleic Acids Res (2011) 1.73
Genome-scale gene/reaction essentiality and synthetic lethality analysis. Mol Syst Biol (2009) 1.69
Computationally efficient flux variability analysis. BMC Bioinformatics (2010) 1.66
Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect. PLoS Comput Biol (2011) 1.66
Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model. Bioinformatics (2010) 1.65
Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys J (2011) 1.64
Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. Biophys Chem (2009) 1.64
Formulating genome-scale kinetic models in the post-genome era. Mol Syst Biol (2008) 1.64
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. ISME J (2010) 1.63
The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli. BMC Genomics (2011) 1.63
Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC Syst Biol (2009) 1.62
Impact of the solvent capacity constraint on E. coli metabolism. BMC Syst Biol (2008) 1.61
Network context and selection in the evolution to enzyme specificity. Science (2012) 1.59
Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production. Nat Biotechnol (2013) 1.59
The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways. Genome Biol Evol (2010) 1.57
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. BMC Bioinformatics (2012) 1.56
Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain. J Biol Chem (2009) 1.55
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biol (2009) 1.53
Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism. Mol Syst Biol (2009) 1.52
Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets. J Bacteriol (2009) 1.51
OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Comput Biol (2010) 1.51
The causes of epistasis. Proc Biol Sci (2011) 1.50
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst Biol (2011) 1.50
Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major. Mol Syst Biol (2008) 1.49
Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation. PLoS Comput Biol (2010) 1.48
OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. BMC Syst Biol (2010) 1.47
Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Mol Syst Biol (2011) 1.45
Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biol (2009) 1.44
Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets. PLoS Comput Biol (2016) 1.43
Construction and completion of flux balance models from pathway databases. Bioinformatics (2012) 1.42
Blueprint for antimicrobial hit discovery targeting metabolic networks. Proc Natl Acad Sci U S A (2010) 1.42
Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol Syst Biol (2012) 1.41
lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites. PLoS Comput Biol (2017) 1.41
Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism. PLoS Comput Biol (2014) 1.41
Metabolic systems biology. FEBS Lett (2009) 1.40
Towards genome-scale signalling network reconstructions. Nat Rev Genet (2010) 1.39
Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci U S A (2013) 1.39
A latent capacity for evolutionary innovation through exaptation in metabolic systems. Nature (2013) 1.38
ECMDB: the E. coli Metabolome Database. Nucleic Acids Res (2012) 1.38
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst Biol (2011) 1.37
Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. Mol Syst Biol (2010) 1.37
Comparative multi-omics systems analysis of Escherichia coli strains B and K-12. Genome Biol (2012) 1.37
Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns. Genome Res (2009) 1.36
Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data. BMC Syst Biol (2008) 1.35
In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling. Nat Rev Microbiol (2010) 1.34
anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data. BMC Bioinformatics (2008) 1.33
The evolution of metabolic networks of E. coli. BMC Syst Biol (2011) 1.32
Large-scale identification of genetic design strategies using local search. Mol Syst Biol (2009) 1.31
Cascading failure and robustness in metabolic networks. Proc Natl Acad Sci U S A (2008) 1.30
Reconstruction annotation jamborees: a community approach to systems biology. Mol Syst Biol (2010) 1.30
Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PLoS One (2012) 1.29
Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli. PLoS Biol (2014) 1.29
Engineering Escherichia coli to synthesize free fatty acids. Trends Biotechnol (2012) 1.28
Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene. PLoS Genet (2010) 1.27
Metabolic engineering for production of biorenewable fuels and chemicals: contributions of synthetic biology. J Biomed Biotechnol (2010) 1.27
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinformatics (2012) 1.26
Metabolic network model of a human oral pathogen. J Bacteriol (2008) 1.26
An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. J Bacteriol (2011) 1.24
Parallel exploitation of diverse host nutrients enhances Salmonella virulence. PLoS Pathog (2013) 1.24
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol (2006) 40.15
Energy conservation in chemotrophic anaerobic bacteria. Bacteriol Rev (1977) 30.41
EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res (2005) 11.01
Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet (2003) 10.52
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol (2003) 10.46
Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol (2004) 9.61
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol (2001) 8.88
The maintenance energy of bacteria in growing cultures. Proc R Soc Lond B Biol Sci (1965) 7.94
Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res (2006) 7.93
Integrating high-throughput and computational data elucidates bacterial networks. Nature (2004) 7.72
The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci U S A (2000) 7.70
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature (2002) 7.38
Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature (2004) 7.18
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng (2003) 6.81
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc (2007) 6.24
MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res (2006) 5.79
Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet (2006) 4.44
Towards multidimensional genome annotation. Nat Rev Genet (2006) 4.44
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet (2005) 4.19
The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol (2006) 3.69
Systems approach to refining genome annotation. Proc Natl Acad Sci U S A (2006) 3.58
Thirteen years of building constraint-based in silico models of Escherichia coli. J Bacteriol (2003) 3.52
Energy balance for analysis of complex metabolic networks. Biophys J (2002) 3.46
Thermodynamics-based metabolic flux analysis. Biophys J (2006) 3.35
Cellular concentrations of enzymes and their substrates. J Theor Biol (1990) 3.12
Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol Syst Biol (2006) 3.04
Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nat Biotechnol (2005) 2.95
Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol (2006) 2.93
Improved chemical synthesis and enzymatic assay of delta-1-pyrroline-5-carboxylic acid. Anal Biochem (1975) 2.84
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol (2006) 2.80
Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem (2002) 2.74
High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints. Anal Biochem (2004) 2.73
Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. Biotechnol Bioeng (1997) 2.71
Genome-scale thermodynamic analysis of Escherichia coli metabolism. Biophys J (2005) 2.70
Bacterial resistances to toxic metal ions--a review. Gene (1996) 2.65
In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng (2005) 2.63
Chance and necessity in the evolution of minimal metabolic networks. Nature (2006) 2.48
Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors. J Theor Biol (1993) 2.39
Systematic assignment of thermodynamic constraints in metabolic network models. BMC Bioinformatics (2006) 2.26
Structural genes for thiamine biosynthetic enzymes (thiCEFGH) in Escherichia coli K-12. J Bacteriol (1993) 2.18
FieF (YiiP) from Escherichia coli mediates decreased cellular accumulation of iron and relieves iron stress. Arch Microbiol (2004) 2.06
Two-dimensional annotation of genomes. Nat Biotechnol (2004) 1.91
Mathematical models in microbial systems biology. Curr Opin Microbiol (2004) 1.90
Energetic efficiency of Escherichia coli: effects of mutations in components of the aerobic respiratory chain. J Bacteriol (1993) 1.90
Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model. Biotechnol Bioeng (1998) 1.67
Simple constrained-optimization view of acetate overflow in E. coli. Biotechnol Bioeng (1990) 1.65
The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states. Proc Natl Acad Sci U S A (2005) 1.63
Biochemical production capabilities of Escherichia coli. Biotechnol Bioeng (1993) 1.54
Viability of an Escherichia coli pgsA null mutant lacking detectable phosphatidylglycerol and cardiolipin. J Bacteriol (2000) 1.50
Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions. Biophys J (2004) 1.42
Lethality and synthetic lethality in the genome-wide metabolic network of Escherichia coli. J Theor Biol (2005) 1.26
Genome coverage, literally speaking. The challenge of annotating 200 genomes with 4 million publications. EMBO Rep (2005) 1.25
Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities. Bioinformatics (2005) 1.24
Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism. Biotechnol Bioeng (1995) 1.20
Speed versus efficiency in microbial growth and the role of parallel pathways. J Bacteriol (2002) 1.17
Alternative hydroxylases for the aerobic and anaerobic biosynthesis of ubiquinone in Escherichia coli. Biochemistry (1978) 1.10
The energetic conversion competence of Escherichia coli during aerobic respiration studied by 31P NMR using a circulating fermentation system. J Biochem (2004) 1.10
Hydrogenase 3 but not hydrogenase 4 is major in hydrogen gas production by Escherichia coli formate hydrogenlyase at acidic pH and in the presence of external formate. Cell Biochem Biophys (2004) 1.07
Proton translocation coupled to formate oxidation in anaerobically grown fermenting Escherichia coli. Biophys Chem (2005) 1.06
Biotin synthase mechanism: an overview. Biochem Soc Trans (2005) 1.05
Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A (2007) 11.46
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 MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res (2007) 10.62
Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol (2005) 9.94
Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol (2004) 9.61
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
What is flux balance analysis? Nat Biotechnol (2010) 9.01
Integrating high-throughput and computational data elucidates bacterial networks. Nature (2004) 7.72
Computational prediction of human metabolic pathways from the complete human genome. Genome Biol (2004) 7.52
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res (2009) 7.33
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res (2003) 7.22
EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res (2008) 7.05
A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc (2010) 6.64
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc (2007) 6.24
The complete genome sequence of Francisella tularensis, the causative agent of tularemia. Nat Genet (2005) 6.22
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res (2004) 6.21
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics (2004) 5.90
MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res (2006) 5.79
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc (2011) 5.71
Applications of genome-scale metabolic reconstructions. Mol Syst Biol (2009) 5.54
Mast cells are essential intermediaries in regulatory T-cell tolerance. Nature (2006) 5.49
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform (2009) 5.44
Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol (2008) 5.36
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res (2011) 5.34
EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res (2012) 5.30
Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. Bioinformatics (2002) 5.29
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol (2008) 5.26
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res (2013) 5.13
EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res (2010) 4.68
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol (2008) 4.55
Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet (2006) 4.44
Network-based prediction of human tissue-specific metabolism. Nat Biotechnol (2008) 4.39
Towards environmental systems biology of Shewanella. Nat Rev Microbiol (2008) 4.37
A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. Mol Syst Biol (2011) 4.03
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics (2003) 3.97
A community-driven global reconstruction of human metabolism. Nat Biotechnol (2013) 3.89
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics (2010) 3.87
The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol (2006) 3.69
Severe human lower respiratory tract illness caused by respiratory syncytial virus and influenza virus is characterized by the absence of pulmonary cytotoxic lymphocyte responses. J Infect Dis (2007) 3.62
Systems approach to refining genome annotation. Proc Natl Acad Sci U S A (2006) 3.58
Querying and computing with BioCyc databases. Bioinformatics (2005) 3.55
Thirteen years of building constraint-based in silico models of Escherichia coli. J Bacteriol (2003) 3.52
Thermodynamics-based metabolic flux analysis. Biophys J (2006) 3.35
Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res (2007) 3.34
Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends Biochem Sci (2004) 3.31
Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet (2004) 3.31
MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol (2005) 3.00
Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol (2006) 2.93
Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res (2005) 2.91
Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J (2008) 2.89
The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol (2009) 2.85
Rapid antigen testing compares favorably with transcription-mediated amplification assay for the detection of Trichomonas vaginalis in young women. Clin Infect Dis (2007) 2.85
Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. J Bacteriol (2005) 2.82
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol (2006) 2.80
The past, present and future of genome-wide re-annotation. Genome Biol (2002) 2.77
Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem (2002) 2.74
Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. Genome Res (2004) 2.71
Genome-scale thermodynamic analysis of Escherichia coli metabolism. Biophys J (2005) 2.70
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Syst Biol (2007) 2.51
Reconstruction of microbial transcriptional regulatory networks. Curr Opin Biotechnol (2004) 2.47
Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol Syst Biol (2011) 2.44
Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol (2010) 2.41
BioWarehouse: a bioinformatics database warehouse toolkit. BMC Bioinformatics (2006) 2.40
Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. J Biol Chem (2004) 2.26
Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space. J Theor Biol (2004) 2.24
Model polymer nanocomposites provide an understanding of confinement effects in real nanocomposites. Nat Mater (2007) 2.16
Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput Biol (2009) 2.14
MS/MS networking guided analysis of molecule and gene cluster families. Proc Natl Acad Sci U S A (2013) 2.12
Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Res (2006) 2.12
The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res (2006) 2.11
Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets. J Bacteriol (2003) 2.10
Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J Bacteriol (2005) 2.06
Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol (2009) 2.06
Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. Genome Res (2008) 2.00
Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli. Proc Natl Acad Sci U S A (2008) 1.99
Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model. J Bacteriol (2003) 1.98
Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput Biol (2010) 1.97
Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng (2009) 1.96
Extreme pathways and Kirchhoff's second law. Biophys J (2002) 1.95
Exploring the diversity of complex metabolic networks. Bioinformatics (2004) 1.93