Published in Microb Cell Fact on May 01, 2009
13CFLUX2--high-performance software suite for (13)C-metabolic flux analysis. Bioinformatics (2012) 1.60
INCA: a computational platform for isotopically non-stationary metabolic flux analysis. Bioinformatics (2014) 1.46
The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. BMC Bioinformatics (2017) 1.40
Fluxomers: a new approach for 13C metabolic flux analysis. BMC Syst Biol (2011) 1.16
Model based engineering of Pichia pastoris central metabolism enhances recombinant protein production. Metab Eng (2014) 1.05
Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria. Front Genet (2014) 0.96
Stable isotope-labeling studies in metabolomics: new insights into structure and dynamics of metabolic networks. Bioanalysis (2014) 0.96
Methods and advances in metabolic flux analysis: a mini-review. J Ind Microbiol Biotechnol (2015) 0.95
Computational tools for metabolic engineering. Metab Eng (2012) 0.94
OpenMebius: an open source software for isotopically nonstationary 13C-based metabolic flux analysis. Biomed Res Int (2014) 0.93
The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis. J Biol Chem (2014) 0.93
Integrated, Step-Wise, Mass-Isotopomeric Flux Analysis of the TCA Cycle. Cell Metab (2015) 0.93
MicrobesFlux: a web platform for drafting metabolic models from the KEGG database. BMC Syst Biol (2012) 0.90
A Method to Constrain Genome-Scale Models with 13C Labeling Data. PLoS Comput Biol (2015) 0.90
Recent advances in mapping environmental microbial metabolisms through 13C isotopic fingerprints. J R Soc Interface (2012) 0.89
Systems-level organization of yeast methylotrophic lifestyle. BMC Biol (2015) 0.88
Mapping cancer cell metabolism with(13)C flux analysis: Recent progress and future challenges. J Carcinog (2013) 0.88
iMS2Flux--a high-throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis. BMC Bioinformatics (2012) 0.85
OpenFLUX2: (13)C-MFA modeling software package adjusted for the comprehensive analysis of single and parallel labeling experiments. Microb Cell Fact (2014) 0.84
Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation. Front Bioeng Biotechnol (2014) 0.83
Increasing pentose phosphate pathway flux enhances recombinant protein production in Pichia pastoris. Appl Microbiol Biotechnol (2016) 0.81
Proline availability regulates proline-4-hydroxylase synthesis and substrate uptake in proline-hydroxylating recombinant Escherichia coli. Appl Environ Microbiol (2013) 0.81
Metabolic response of Geobacter sulfurreducens towards electron donor/acceptor variation. Microb Cell Fact (2010) 0.81
Robustness and plasticity of metabolic pathway flux among uropathogenic isolates of Pseudomonas aeruginosa. PLoS One (2014) 0.81
Bridging the gap between fluxomics and industrial biotechnology. J Biomed Biotechnol (2011) 0.80
Techniques to monitor glycolysis. Methods Enzymol (2014) 0.80
Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition. BMC Syst Biol (2015) 0.80
Metabolic modelling in the development of cell factories by synthetic biology. Comput Struct Biotechnol J (2012) 0.79
Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming. PLoS Comput Biol (2016) 0.78
SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis. PLoS Comput Biol (2016) 0.77
Computational estimation of tricarboxylic acid cycle fluxes using noisy NMR data from cardiac biopsies. BMC Syst Biol (2013) 0.77
The key to acetate: metabolic fluxes of acetic acid bacteria under cocoa pulp fermentation-simulating conditions. Appl Environ Microbiol (2014) 0.77
Flux-p: automating metabolic flux analysis. Metabolites (2012) 0.77
Understanding metabolism with flux analysis: From theory to application. Metab Eng (2016) 0.75
FluxFix: automatic isotopologue normalization for metabolic tracer analysis. BMC Bioinformatics (2016) 0.75
The importance of accurately correcting for the natural abundance of stable isotopes. Anal Biochem (2016) 0.75
Modeling framework for isotopic labeling of heteronuclear moieties. J Cheminform (2017) 0.75
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data. BMC Syst Biol (2014) 0.75
Fast exchange fluxes around the pyruvate node: a leaky cell model to explain the gain and loss of unlabelled and labelled metabolites in a tracer experiment. Cancer Metab (2016) 0.75
Quantification of Microbial Phenotypes. Metabolites (2016) 0.75
Epithelial-mesenchymal transition induction is associated with augmented glucose uptake and lactate production in pancreatic ductal adenocarcinoma. Cancer Metab (2016) 0.75
WUFlux: an open-source platform for (13)C metabolic flux analysis of bacterial metabolism. BMC Bioinformatics (2016) 0.75
Metabolic network capacity of Escherichia coli for Krebs cycle-dependent proline hydroxylation. Microb Cell Fact (2015) 0.75
(13)C-Metabolic Flux Analysis: An Accurate Approach to Demystify Microbial Metabolism for Biochemical Production. Bioengineering (Basel) (2015) 0.75
Metabolic networks in motion: 13C-based flux analysis. Mol Syst Biol (2006) 4.24
13C metabolic flux analysis. Metab Eng (2001) 3.76
Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur J Biochem (2003) 3.51
Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab Eng (2006) 3.23
Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements. Metab Eng (2006) 2.79
High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints. Anal Biochem (2004) 2.73
Biosynthetically directed fractional 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism. Eur J Biochem (1995) 2.67
FiatFlux--a software for metabolic flux analysis from 13C-glucose experiments. BMC Bioinformatics (2005) 2.42
A universal framework for 13C metabolic flux analysis. Metab Eng (2001) 2.18
Bidirectional reaction steps in metabolic networks: II. Flux estimation and statistical analysis. Biotechnol Bioeng (1997) 2.11
Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments. Biotechnol Bioeng (1997) 2.03
Systems biotechnology for strain improvement. Trends Biotechnol (2005) 1.98
An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis. Biotechnol Bioeng (2008) 1.98
Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices. Biotechnol Bioeng (1997) 1.91
Correcting mass isotopomer distributions for naturally occurring isotopes. Biotechnol Bioeng (2002) 1.90
Bidirectional reaction steps in metabolic networks: IV. Optimal design of isotopomer labeling experiments. Biotechnol Bioeng (1999) 1.74
GC-MS analysis of amino acids rapidly provides rich information for isotopomer balancing. Biotechnol Prog (2000) 1.65
Genealogy profiling through strain improvement by using metabolic network analysis: metabolic flux genealogy of several generations of lysine-producing corynebacteria. Appl Environ Microbiol (2002) 1.58
Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol. Metab Eng (2007) 1.56
Understanding flux in plant metabolic networks. Curr Opin Plant Biol (2004) 1.45
Amplified expression of fructose 1,6-bisphosphatase in Corynebacterium glutamicum increases in vivo flux through the pentose phosphate pathway and lysine production on different carbon sources. Appl Environ Microbiol (2005) 1.44
Isotopomer analysis using GC-MS. Metab Eng (1999) 1.42
Metabolic flux analysis at ultra short time scale: isotopically non-stationary 13C labeling experiments. J Biotechnol (2006) 1.40
Bioreaction network topology and metabolic flux ratio analysis by biosynthetic fractional 13C labeling and two-dimensional NMR spectroscopy. Metab Eng (1999) 1.39
In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome. J Bacteriol (2004) 1.32
Fluxome analysis using GC-MS. Microb Cell Fact (2007) 1.31
Metabolic flux elucidation for large-scale models using 13C labeled isotopes. Metab Eng (2007) 1.31
Metabolic flux analysis using mass spectrometry. Adv Biochem Eng Biotechnol (2002) 1.15
An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments. BMC Bioinformatics (2008) 1.12
Profiling substrate fluxes in the isolated working mouse heart using 13C-labeled substrates: focusing on the origin and fate of pyruvate and citrate carbons. Am J Physiol Heart Circ Physiol (2003) 1.09
Metabolic isotopomer labeling systems. Part II: structural flux identifiability analysis. Math Biosci (2003) 1.09
Metabolic network analysis of lysine producing Corynebacterium glutamicum at a miniaturized scale. Biotechnol Bioeng (2004) 1.02
Modeling and experimental design for metabolic flux analysis of lysine-producing Corynebacteria by mass spectrometry. Metab Eng (2001) 1.00
Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes. Bioinformatics (2006) 0.96
Identification of optimal measurement sets for complete flux elucidation in metabolic flux analysis experiments. Biotechnol Bioeng (2008) 0.94
Hybrid optimization for 13C metabolic flux analysis using systems parametrized by compactification. BMC Syst Biol (2008) 0.94
A priori analysis of metabolic flux identifiability from (13)C-labeling data. Biotechnol Bioeng (2001) 0.92
Metabolic flux and metabolic network analysis of Penicillium chrysogenum using 2D [13C, 1H] COSY NMR measurements and cumulative bondomer simulation. Biotechnol Bioeng (2003) 0.91
Markov Chain Monte Carlo Algorithm based metabolic flux distribution analysis on Corynebacterium glutamicum. Bioinformatics (2006) 0.87
Method for generation of homogeneous multicellular tumor spheroids applicable to a wide variety of cell types. Biotechnol Bioeng (2003) 3.04
Fermentative butanol production by Clostridia. Biotechnol Bioeng (2008) 2.49
Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Biotechnol (2007) 2.43
Towards quantitative metabolomics of mammalian cells: development of a metabolite extraction protocol. Anal Biochem (2010) 2.17
Correcting mass isotopomer distributions for naturally occurring isotopes. Biotechnol Bioeng (2002) 1.90
Sampling for metabolome analysis of microorganisms. Anal Chem (2007) 1.89
Molecular composition of IMP1 ribonucleoprotein granules. Mol Cell Proteomics (2007) 1.80
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
The yeast Kluyveromyces marxianus and its biotechnological potential. Appl Microbiol Biotechnol (2008) 1.61
Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus. Biotechnol Prog (2005) 1.60
Impact of the cold shock phenomenon on quantification of intracellular metabolites in bacteria. Anal Biochem (2004) 1.55
Comparative metabolic flux analysis of lysine-producing Corynebacterium glutamicum cultured on glucose or fructose. Appl Environ Microbiol (2004) 1.50
Systems metabolic engineering of xylose-utilizing Corynebacterium glutamicum for production of 1,5-diaminopentane. Biotechnol J (2013) 1.50
From zero to hero--design-based systems metabolic engineering of Corynebacterium glutamicum for L-lysine production. Metab Eng (2011) 1.47
Characterization of the metabolic shift between oxidative and fermentative growth in Saccharomyces cerevisiae by comparative 13C flux analysis. Microb Cell Fact (2005) 1.47
Amplified expression of fructose 1,6-bisphosphatase in Corynebacterium glutamicum increases in vivo flux through the pentose phosphate pathway and lysine production on different carbon sources. Appl Environ Microbiol (2005) 1.44
Bio-based production of chemicals, materials and fuels -Corynebacterium glutamicum as versatile cell factory. Curr Opin Biotechnol (2011) 1.43
Microbial hyaluronic acid production. Appl Microbiol Biotechnol (2004) 1.42
Integrated optical sensing of dissolved oxygen in microtiter plates: a novel tool for microbial cultivation. Biotechnol Bioeng (2003) 1.41
DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nat Genet (2013) 1.40
Minibioreactors. Biotechnol Lett (2004) 1.37
In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome. J Bacteriol (2004) 1.32
Generation of multicellular tumor spheroids by the hanging-drop method. Methods Mol Med (2007) 1.26
Metabolic flux analysis in mammalian cell culture. Metab Eng (2009) 1.24
In vivo quantification of intracellular amino acids and intermediates of the methionine pathway in Corynebacterium glutamicum. Anal Biochem (2005) 1.23
Industrial biotechnology of Pseudomonas putida and related species. Appl Microbiol Biotechnol (2012) 1.20
Deep sequencing-based transcriptome analysis of Plutella xylostella larvae parasitized by Diadegma semiclausum. BMC Genomics (2011) 1.18
Systems-wide metabolic pathway engineering in Corynebacterium glutamicum for bio-based production of diaminopentane. Metab Eng (2010) 1.17
AlgaGEM--a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome. BMC Genomics (2011) 1.15
On the reconstruction of the Mus musculus genome-scale metabolic network model. Genome Inform (2008) 1.13
Metabolic flux engineering of L-lysine production in Corynebacterium glutamicum--over expression and modification of G6P dehydrogenase. J Biotechnol (2007) 1.12
Design of artificial myocardial microtissues. Tissue Eng (2004) 1.12
Systems and synthetic metabolic engineering for amino acid production - the heartbeat of industrial strain development. Curr Opin Biotechnol (2012) 1.09
Characterization and control of fungal morphology for improved production performance in biotechnology. J Biotechnol (2012) 1.09
Ultra-high-yield manufacture of red blood cells from hematopoietic stem cells. Tissue Eng Part C Methods (2011) 1.09
Isotopomer profiling of Leishmania mexicana promastigotes reveals important roles for succinate fermentation and aspartate uptake in tricarboxylic acid cycle (TCA) anaplerosis, glutamate synthesis, and growth. J Biol Chem (2011) 1.09
Grand challenge commentary: Chassis cells for industrial biochemical production. Nat Chem Biol (2010) 1.07
IL10 and IL12B polymorphisms each influence IL-12p70 secretion by dendritic cells in response to LPS. Immunol Cell Biol (2006) 1.05
Transcriptional and metabolic responses of Bacillus subtilis to the availability of organic acids: transcription regulation is important but not sufficient to account for metabolic adaptation. Appl Environ Microbiol (2006) 1.05
Blood cell manufacture: current methods and future challenges. Trends Biotechnol (2009) 1.03
Metabolic and practical considerations on microbial electrosynthesis. Curr Opin Biotechnol (2011) 1.03
Evolution of the hyaluronic acid synthesis (has) operon in Streptococcus zooepidemicus and other pathogenic streptococci. J Mol Evol (2008) 1.02
Response of the central metabolism of Escherichia coli to modified expression of the gene encoding the glucose-6-phosphate dehydrogenase. FEBS Lett (2007) 1.01
Consequences of phosphoenolpyruvate:sugar phosphotranferase system and pyruvate kinase isozymes inactivation in central carbon metabolism flux distribution in Escherichia coli. Microb Cell Fact (2012) 1.01
Getting the big beast to work--systems biotechnology of Bacillus megaterium for novel high-value proteins. J Biotechnol (2012) 1.00
Theoretical aspects of 13C metabolic flux analysis with sole quantification of carbon dioxide labeling. Comput Biol Chem (2005) 1.00
Morphology engineering of Aspergillus niger for improved enzyme production. Biotechnol Bioeng (2010) 1.00
Free intracellular amino acid pools during autonomous oscillations in Saccharomyces cerevisiae. Biotechnol Bioeng (2003) 0.99
Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade. BMC Microbiol (2009) 0.99
Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum. Metab Eng (2006) 0.99
Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised loci. Microb Cell Fact (2013) 0.98
Hanging-drop multicellular spheroids as a model of tumour angiogenesis. Angiogenesis (2004) 0.98
Metabolic responses to pyruvate kinase deletion in lysine producing Corynebacterium glutamicum. Microb Cell Fact (2008) 0.98
Systems metabolic engineering of Escherichia coli for production of the antitumor drugs violacein and deoxyviolacein. Metab Eng (2013) 0.97
Improved enzyme production by bio-pellets of Aspergillus niger: targeted morphology engineering using titanate microparticles. Biotechnol Bioeng (2011) 0.97
Stable production of hyaluronic acid in Streptococcus zooepidemicus chemostats operated at high dilution rate. Biotechnol Bioeng (2005) 0.97
Alleviating monoterpene toxicity using a two-phase extractive fermentation for the bioproduction of jet fuel mixtures in Saccharomyces cerevisiae. Biotechnol Bioeng (2012) 0.96
Physiology of the yeast Kluyveromyces marxianus during batch and chemostat cultures with glucose as the sole carbon source. FEMS Yeast Res (2007) 0.95
Metabolic engineering of cellular transport for overproduction of the platform chemical 1,5-diaminopentane in Corynebacterium glutamicum. Metab Eng (2011) 0.95
Debottlenecking recombinant protein production in Bacillus megaterium under large-scale conditions--targeted precursor feeding designed from metabolomics. Biotechnol Bioeng (2012) 0.94
Flux Design: In silico design of cell factories based on correlation of pathway fluxes to desired properties. BMC Syst Biol (2009) 0.93
Microbial production of the drugs violacein and deoxyviolacein: analytical development and strain comparison. Biotechnol Lett (2011) 0.93
Identification and elimination of the competing N-acetyldiaminopentane pathway for improved production of diaminopentane by Corynebacterium glutamicum. Appl Environ Microbiol (2010) 0.93
Microparticle based morphology engineering of filamentous microorganisms for industrial bio-production. Biotechnol Lett (2012) 0.92
Systems biology of recombinant protein production using Bacillus megaterium. Methods Enzymol (2011) 0.92
Integration of in vivo and in silico metabolic fluxes for improvement of recombinant protein production. Metab Eng (2011) 0.92
Fluxomics - connecting 'omics analysis and phenotypes. Environ Microbiol (2013) 0.92
Appropriate sampling for intracellular amino acid analysis in five phylogenetically different yeasts. Biotechnol Lett (2008) 0.92
Development of chemically defined medium for Mannheimia succiniciproducens based on its genome sequence. Appl Microbiol Biotechnol (2008) 0.91
Metabolic network simulation using logical loop algorithm and Jacobian matrix. Metab Eng (2004) 0.91
Reconstruction of the Saccharopolyspora erythraea genome-scale model and its use for enhancing erythromycin production. Antonie Van Leeuwenhoek (2012) 0.91
Advanced biotechnology: metabolically engineered cells for the bio-based production of chemicals and fuels, materials, and health-care products. Angew Chem Int Ed Engl (2015) 0.90
Filamentous fungi in good shape: microparticles for tailor-made fungal morphology and enhanced enzyme production. Bioeng Bugs (2011) 0.90
Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch. BMC Genomics (2013) 0.90
Amplifying the cellular reduction potential of Streptococcus zooepidemicus. J Biotechnol (2003) 0.90
Examining the feasibility of bulk commodity production in Escherichia coli. Biotechnol Lett (2011) 0.90
Comparative study on central metabolic fluxes of Bacillus megaterium strains in continuous culture using 13C labelled substrates. Bioprocess Biosyst Eng (2006) 0.90
Metabolic engineering of industrial platform microorganisms for biorefinery applications--optimization of substrate spectrum and process robustness by rational and evolutive strategies. Bioresour Technol (2012) 0.89
Optimized bioprocess for production of fructofuranosidase by recombinant Aspergillus niger. Appl Microbiol Biotechnol (2010) 0.89
Metabolic fluxes and beyond-systems biology understanding and engineering of microbial metabolism. Appl Microbiol Biotechnol (2010) 0.89
Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach. BMC Genomics (2013) 0.88
Electrifying white biotechnology: engineering and economic potential of electricity-driven bio-production. ChemSusChem (2014) 0.88
In-silico-driven metabolic engineering of Pseudomonas putida for enhanced production of poly-hydroxyalkanoates. Metab Eng (2012) 0.88
Quantitative analysis of intracellular sugar phosphates and sugar nucleotides in encapsulated streptococci using HPAEC-PAD. Biotechnol J (2009) 0.88
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
Metabolic engineering of Corynebacterium glutamicum for production of 1,5-diaminopentane from hemicellulose. Biotechnol J (2011) 0.87
Flux balance analysis of CHO cells before and after a metabolic switch from lactate production to consumption. Biotechnol Bioeng (2012) 0.87
Mammalian cells as biopharmaceutical production hosts in the age of omics. Biotechnol J (2011) 0.87
A transferable sucrose utilization approach for non-sucrose-utilizing Escherichia coli strains. Biotechnol Adv (2011) 0.87
Metabolite profiling of CHO cells with different growth characteristics. Biotechnol Bioeng (2012) 0.87
Bio-based production of the platform chemical 1,5-diaminopentane. Appl Microbiol Biotechnol (2011) 0.87
Enhanced polyhydroxybutyrate production in transgenic sugarcane. Plant Biotechnol J (2012) 0.86
Metabolic engineering of the tricarboxylic acid cycle for improved lysine production by Corynebacterium glutamicum. Appl Environ Microbiol (2009) 0.86
Production of polyhydroxybutyrate in sugarcane. Plant Biotechnol J (2007) 0.86
A multi-omics analysis of recombinant protein production in Hek293 cells. PLoS One (2012) 0.86