Published in Curr Opin Biotechnol on November 04, 2011
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Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. J Bacteriol (2014) 0.97
Genome-scale metabolic network guided engineering of Streptomyces tsukubaensis for FK506 production improvement. Microb Cell Fact (2013) 0.92
Integrated network analysis and effective tools in plant systems biology. Front Plant Sci (2014) 0.90
The widespread role of non-enzymatic reactions in cellular metabolism. Curr Opin Biotechnol (2015) 0.89
Genome-scale metabolic network validation of Shewanella oneidensis using transposon insertion frequency analysis. PLoS Comput Biol (2014) 0.86
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Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. PLoS One (2016) 0.84
Long-term phenotypic evolution of bacteria. Nature (2014) 0.84
Flux variability scanning based on enforced objective flux for identifying gene amplification targets. BMC Syst Biol (2012) 0.84
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Unraveling the Light-Specific Metabolic and Regulatory Signatures of Rice through Combined in Silico Modeling and Multiomics Analysis. Plant Physiol (2015) 0.83
Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation. Front Bioeng Biotechnol (2014) 0.83
Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems. Front Microbiol (2016) 0.82
Integrating transcriptomics with metabolic modeling predicts biomarkers and drug targets for Alzheimer's disease. PLoS One (2014) 0.81
Bridging the gap between omics and earth system science to better understand how environmental change impacts marine microbes. Glob Chang Biol (2015) 0.80
Computational approaches for microalgal biofuel optimization: a review. Biomed Res Int (2014) 0.79
Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant. FEMS Microbiol Lett (2013) 0.79
In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories. Microbiol Mol Biol Rev (2015) 0.79
Fumaric acid production in Saccharomyces cerevisiae by in silico aided metabolic engineering. PLoS One (2012) 0.79
redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models. PLoS Comput Biol (2017) 0.79
Swimming in light: a large-scale computational analysis of the metabolism of Dinoroseobacter shibae. PLoS Comput Biol (2013) 0.78
Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network. Plant Physiol (2015) 0.78
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. Brief Bioinform (2015) 0.78
A metabolite-centric view on flux distributions in genome-scale metabolic models. BMC Syst Biol (2013) 0.78
Predictive sulfur metabolism - a field in flux. Front Plant Sci (2014) 0.78
Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism. PLoS One (2016) 0.78
Flux-sum analysis identifies metabolite targets for strain improvement. BMC Syst Biol (2015) 0.77
Fostering synergy between cell biology and systems biology. Trends Cell Biol (2015) 0.77
Genome-scale metabolic network reconstruction of Saccharopolyspora spinosa for spinosad production improvement. Microb Cell Fact (2014) 0.77
Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. BMC Syst Biol (2012) 0.77
Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability. Sci Rep (2015) 0.77
Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data. Biomed Res Int (2016) 0.76
Reporter pathway analysis from transcriptome data: Metabolite-centric versus Reaction-centric approach. Sci Rep (2015) 0.75
EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model. Sci Rep (2017) 0.75
A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems. PLoS One (2017) 0.75
Tools for metabolic engineering in Streptomyces. Bioengineered (2014) 0.75
Modeling Rice Metabolism: From Elucidating Environmental Effects on Cellular Phenotype to Guiding Crop Improvement. Front Plant Sci (2016) 0.75
Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes. Metab Eng (2016) 0.75
Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions. Plant Physiol (2016) 0.75
Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis. Proc Natl Acad Sci U S A (2016) 0.75
PathwayBooster: a tool to support the curation of metabolic pathways. BMC Bioinformatics (2015) 0.75
Reconstructed Metabolic Network Models Predict Flux-Level Metabolic Reprogramming in Glioblastoma. Front Neurosci (2016) 0.75
Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels. mSystems (2017) 0.75
Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis. Biophys Physicobiol (2016) 0.75
Shikimic Acid Production in Escherichia coli: From Classical Metabolic Engineering Strategies to Omics Applied to Improve Its Production. Front Bioeng Biotechnol (2015) 0.75
Discovering missing reactions of metabolic networks by using gene co-expression data. Sci Rep (2017) 0.75
A kidney-specific genome-scale metabolic network model for analyzing focal segmental glomerulosclerosis. Mamm Genome (2016) 0.75
Comprehensive reconstruction and evaluation of Pichia pastoris genome-scale metabolic model that accounts for 1243 ORFs. Bioresour Bioprocess (2017) 0.75
Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol (2011) 3.55
Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation. Proc Natl Acad Sci U S A (2007) 2.43
Systems metabolic engineering of Escherichia coli for L-threonine production. Mol Syst Biol (2007) 2.18
Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat Chem Biol (2012) 2.17
Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation. Appl Environ Microbiol (2005) 2.13
Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat Biotechnol (2013) 1.76
The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens. Nat Biotechnol (2004) 1.64
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
Microbial production of short-chain alkanes. Nature (2013) 1.61
Constraints-based genome-scale metabolic simulation for systems metabolic engineering. Biotechnol Adv (2009) 1.60
Native-sized recombinant spider silk protein produced in metabolically engineered Escherichia coli results in a strong fiber. Proc Natl Acad Sci U S A (2010) 1.51
Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery. Mol Syst Biol (2011) 1.50
Sexual dysfunctions induced by stress of timed intercourse and medical treatment. BJU Int (2012) 1.41
Detection of the most common corneal dystrophies caused by BIGH3 gene point mutations using a multispot gold-capped nanoparticle array chip. Anal Chem (2010) 1.41
MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics (2003) 1.40
Comparative multi-omics systems analysis of Escherichia coli strains B and K-12. Genome Biol (2012) 1.37
Metabolic engineering of Escherichia coli for the production of polylactic acid and its copolymers. Biotechnol Bioeng (2010) 1.36
Identification and characterization of a new enoyl coenzyme A hydratase involved in biosynthesis of medium-chain-length polyhydroxyalkanoates in recombinant Escherichia coli. J Bacteriol (2003) 1.35
Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Appl Microbiol Biotechnol (2008) 1.34
Systems biology as a foundation for genome-scale synthetic biology. Curr Opin Biotechnol (2006) 1.31
Application of systems biology for bioprocess development. Trends Biotechnol (2008) 1.30
Complete genome sequence of the metabolically versatile plant growth-promoting endophyte Variovorax paradoxus S110. J Bacteriol (2010) 1.29
Genome-scale analysis of Mannheimia succiniciproducens metabolism. Biotechnol Bioeng (2007) 1.28
Organizational and mutational analysis of a complete FR-008/candicidin gene cluster encoding a structurally related polyene complex. Chem Biol (2003) 1.27
Metabolite essentiality elucidates robustness of Escherichia coli metabolism. Proc Natl Acad Sci U S A (2007) 1.26
Bio-based production of C2-C6 platform chemicals. Biotechnol Bioeng (2012) 1.25
Combined transcriptome and proteome analysis of Escherichia coli during high cell density culture. Biotechnol Bioeng (2003) 1.24
Enhanced butanol production obtained by reinforcing the direct butanol-forming route in Clostridium acetobutylicum. MBio (2012) 1.24
The Escherichia coli proteome: past, present, and future prospects. Microbiol Mol Biol Rev (2006) 1.23
Metabolic engineering of Escherichia coli for the production of cadaverine: a five carbon diamine. Biotechnol Bioeng (2011) 1.21
Genome-based metabolic engineering of Mannheimia succiniciproducens for succinic acid production. Appl Environ Microbiol (2006) 1.21
In silico identification of gene amplification targets for improvement of lycopene production. Appl Environ Microbiol (2010) 1.18
Systems metabolic engineering for chemicals and materials. Trends Biotechnol (2011) 1.17
Proteome-based identification of fusion partner for high-level extracellular production of recombinant proteins in Escherichia coli. Biotechnol Bioeng (2008) 1.16
Patterned multiplex pathogen DNA detection by Au particle-on-wire SERS sensor. Nano Lett (2010) 1.15
Biosynthesis of polylactic acid and its copolymers using evolved propionate CoA transferase and PHA synthase. Biotechnol Bioeng (2010) 1.14
Novel gene members in the Pho regulon of Escherichia coli. FEMS Microbiol Lett (2006) 1.13
Activation of peroxisome proliferator-activated receptor gamma by rosiglitazone increases sirt6 expression and ameliorates hepatic steatosis in rats. PLoS One (2011) 1.13
BioSilico: an integrated metabolic database system. Bioinformatics (2004) 1.12
Continuous butanol production with reduced byproducts formation from glycerol by a hyper producing mutant of Clostridium pasteurianum. Appl Microbiol Biotechnol (2011) 1.08
Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks. Metab Eng (2009) 1.07
Applications of DNA microarray in disease diagnostics. J Microbiol Biotechnol (2009) 1.07
Towards systems metabolic engineering of microorganisms for amino acid production. Curr Opin Biotechnol (2008) 1.07
Genome-scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production. Biotechnol J (2010) 1.07
Fermentative production of branched chain amino acids: a focus on metabolic engineering. Appl Microbiol Biotechnol (2010) 1.06
Microbial production of building block chemicals and polymers. Curr Opin Biotechnol (2011) 1.06
Prediction of novel synthetic pathways for the production of desired chemicals. BMC Syst Biol (2010) 1.05
Metabolic engineering of Clostridium acetobutylicum ATCC 824 for isopropanol-butanol-ethanol fermentation. Appl Environ Microbiol (2011) 1.05
Metabolic engineering of Escherichia coli for the production of putrescine: a four carbon diamine. Biotechnol Bioeng (2009) 1.05
DNA microarray-based identification of bacterial and fungal pathogens in bloodstream infections. Mol Cell Probes (2009) 1.04
Enhanced production of insulin-like growth factor I fusion protein in Escherichia coli by coexpression of the down-regulated genes identified by transcriptome profiling. Appl Environ Microbiol (2003) 1.03
Comparison of the extracellular proteomes of Escherichia coli B and K-12 strains during high cell density cultivation. Proteomics (2008) 1.02
Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE. Mol Biosyst (2009) 1.02
Metabolic engineering of Escherichia coli for the production of 1-propanol. Metab Eng (2012) 1.00
Butanol production from renewable biomass: rediscovery of metabolic pathways and metabolic engineering. Biotechnol J (2011) 1.00
Construction and optimization of synthetic pathways in metabolic engineering. Curr Opin Microbiol (2010) 0.99
Metabolic engineering of Escherichia coli for the production of 5-aminovalerate and glutarate as C5 platform chemicals. Metab Eng (2012) 0.99
Engineering of microorganisms for the production of biofuels and perspectives based on systems metabolic engineering approaches. Biotechnol Adv (2011) 0.98
Development of a markerless gene knock-out system for Mannheimia succiniciproducens using a temperature-sensitive plasmid. FEMS Microbiol Lett (2007) 0.97
Excretion of human beta-endorphin into culture medium by using outer membrane protein F as a fusion partner in recombinant Escherichia coli. Appl Environ Microbiol (2002) 0.97
Metabolic engineering of Clostridium acetobutylicum M5 for highly selective butanol production. Biotechnol J (2009) 0.96
A well-ordered flower-like gold nanostructure for integrated sensors via surface-enhanced Raman scattering. Nanotechnology (2009) 0.96
WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks. Bioinformatics (2006) 0.95
The proteome of Mannheimia succiniciproducens, a capnophilic rumen bacterium. Proteomics (2006) 0.95
The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies. Microb Cell Fact (2010) 0.95
Display of bacterial lipase on the Escherichia coli cell surface by using FadL as an anchoring motif and use of the enzyme in enantioselective biocatalysis. Appl Environ Microbiol (2004) 0.94
High cell density fed-batch cultivation of Escherichia coli using exponential feeding combined with pH-stat. Bioprocess Biosyst Eng (2004) 0.94
Butanol production from renewable biomass by clostridia. Bioresour Technol (2012) 0.94
Protein nanopatterns and biosensors using gold binding polypeptide as a fusion partner. Anal Chem (2006) 0.94
Prediction of metabolic fluxes by incorporating genomic context and flux-converging pattern analyses. Proc Natl Acad Sci U S A (2010) 0.94
Biosynthesis of polyhydroxyalkanoates containing 2-hydroxybutyrate from unrelated carbon source by metabolically engineered Escherichia coli. Appl Microbiol Biotechnol (2011) 0.93
Metabolic flux analysis and metabolic engineering of microorganisms. Mol Biosyst (2007) 0.93
Isolation and genetic manipulation of the antibiotic down-regulatory gene, wblA ortholog for doxorubicin-producing Streptomyces strain improvement. Appl Microbiol Biotechnol (2009) 0.93
Metabolic engineering of Escherichia coli for the production of medium-chain-length polyhydroxyalkanoates rich in specific monomers. FEMS Microbiol Lett (2002) 0.92
Development of chemically defined medium for Mannheimia succiniciproducens based on its genome sequence. Appl Microbiol Biotechnol (2008) 0.91
Colored Petri net modeling and simulation of signal transduction pathways. Metab Eng (2005) 0.91
Display of lipase on the cell surface of Escherichia coli using OprF as an anchor and its application to enantioselective resolution in organic solvent. Biotechnol Bioeng (2005) 0.91
Metabolic network modeling and simulation for drug targeting and discovery. Biotechnol J (2011) 0.91
In silico prediction and validation of the importance of the Entner-Doudoroff pathway in poly(3-hydroxybutyrate) production by metabolically engineered Escherichia coli. Biotechnol Bioeng (2003) 0.91
High urinary ACE2 concentrations are associated with severity of glucose intolerance and microalbuminuria. Eur J Endocrinol (2013) 0.91
In silico genome-scale metabolic analysis of Pseudomonas putida KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival. Biotechnol J (2010) 0.91
In vivo synthesis of diverse metal nanoparticles by recombinant Escherichia coli. Angew Chem Int Ed Engl (2010) 0.90
Prevalence of and risk factors for diabetic retinopathy in Koreans with type II diabetes: baseline characteristics of Seoul Metropolitan City-Diabetes Prevention Program (SMC-DPP) participants. Br J Ophthalmol (2011) 0.90
Systems metabolic engineering, industrial biotechnology and microbial cell factories. Microb Cell Fact (2012) 0.90
Advanced bacterial polyhydroxyalkanoates: towards a versatile and sustainable platform for unnatural tailor-made polyesters. Biotechnol Adv (2011) 0.90
Metabolic engineering of Escherichia coli for the production of fumaric acid. Biotechnol Bioeng (2013) 0.89
Strategies for systems-level metabolic engineering. Biotechnol J (2008) 0.89
Engineering Escherichia coli for increased productivity of serine-rich proteins based on proteome profiling. Appl Environ Microbiol (2003) 0.89
Nanogap field-effect transistor biosensors for electrical detection of avian influenza. Small (2009) 0.89
DNA microarray-based detection of nosocomial pathogenic Pseudomonas aeruginosa and Acinetobacter baumannii. Mol Cell Probes (2005) 0.89
Applications of genome-scale metabolic network model in metabolic engineering. J Ind Microbiol Biotechnol (2014) 0.89
Transcriptome analysis of phosphate starvation response in Escherichia coli. J Microbiol Biotechnol (2007) 0.88
Production of bulk chemicals via novel metabolic pathways in microorganisms. Biotechnol Adv (2012) 0.88
Extracellular proteome of Aspergillus terreus grown on different carbon sources. Curr Genet (2010) 0.88
Covalent attachment and hybridization of DNA oligonucleotides on patterned single-walled carbon nanotube films. Langmuir (2004) 0.88
High-level conversion of L-lysine into 5-aminovalerate that can be used for nylon 6,5 synthesis. Biotechnol J (2014) 0.87
Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production. BMC Syst Biol (2011) 0.87