| scholarly article | Q13442814 |
| P356 | DOI | 10.1016/J.YMBEN.2012.09.005 |
| P698 | PubMed publication ID | 23026121 |
| P2093 | author name string | Ali R Zomorrodi | |
| Costas D Maranas | |||
| Patrick F Suthers | |||
| Sridhar Ranganathan | |||
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| Metabolic flux analysis of CHO cells at growth and non-growth phases using isotopic tracers and mass spectrometry | Q39494168 | ||
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| Synthetic enhancement in gene interaction: a genetic tool come of age. | Q40796844 | ||
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| Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli | Q42120436 | ||
| Production of beta-carotene in Zymomonas mobilis and Agrobacterium tumefaciens by introduction of the biosynthesis genes from Erwinia uredovora | Q42125536 | ||
| PathFinder: reconstruction and dynamic visualization of metabolic pathways | Q42166021 | ||
| Genome-scale gene/reaction essentiality and synthetic lethality analysis | Q42287542 | ||
| Optimization based automated curation of metabolic reconstructions | Q42431633 | ||
| Complementary identification of multiple flux distributions and multiple metabolic pathways | Q42478048 | ||
| Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol | Q42733691 | ||
| Microbial 1-butanol production: Identification of non-native production routes and in silico engineering interventions | Q42954183 | ||
| Improved computational performance of MFA using elementary metabolite units and flux coupling | Q43259632 | ||
| Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer, Clostridium butyricum, and a methanogenic archeon, Methanosarcina mazei, under anaerobic conditions | Q43292159 | ||
| Metabolic flux analysis with a comprehensive isotopomer model in Bacillus subtilis | Q43707338 | ||
| Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments | Q43757062 | ||
| Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices | Q43804186 | ||
| Functional conservation of PAS-LuxR transcriptional regulators in polyene macrolide biosynthesis | Q43984290 | ||
| Correcting mass isotopomer distributions for naturally occurring isotopes | Q44153792 | ||
| Metabolic flux analysis of Escherichia coli K12 grown on 13C-labeled acetate and glucose using GC-MS and powerful flux calculation method | Q44303486 | ||
| Systematic quantification of complex metabolic flux networks using stable isotopes and mass spectrometry | Q44550058 | ||
| Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock | Q44715791 | ||
| Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements | Q45108799 | ||
| Metabolic network simulation using logical loop algorithm and Jacobian matrix | Q45112862 | ||
| In silico design and adaptive evolution of Escherichia coli for production of lactic acid. | Q46023396 | ||
| Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways | Q46385320 | ||
| Using isotopomer path tracing to quantify metabolic fluxes in pathway models containing reversible reactions | Q46518692 | ||
| Identification of optimal measurement sets for complete flux elucidation in metabolic flux analysis experiments | Q46540660 | ||
| An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems | Q46731656 | ||
| Metabolic engineering of Escherichia coli for 1-butanol production. | Q46785830 | ||
| Expression of galactose permease and pyruvate carboxylase in Escherichia coli ptsG mutant increases the growth rate and succinate yield under anaerobic conditions | Q46862357 | ||
| Metabolic Capabilities of Escherichia coli: I. Synthesis of Biosynthetic Precursors and Cofactors | Q47770730 | ||
| Optimization-based framework for inferring and testing hypothesized metabolic objective functions | Q47995846 | ||
| Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways | Q48238418 | ||
| An optimization model for metabolic pathways | Q48267509 | ||
| Bayesian-based selection of metabolic objective functions | Q48421839 | ||
| Construction of an E. Coli genome-scale atom mapping model for MFA calculations | Q50687745 | ||
| A computational procedure for optimal engineering interventions using kinetic models of metabolism | Q51099309 | ||
| On flux coupling analysis of metabolic subsystems | Q51405491 | ||
| Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli | Q51471154 | ||
| EMILiO: A fast algorithm for genome-scale strain design | Q51590419 | ||
| Thermodynamic constraints for biochemical networks | Q51676908 | ||
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| Algorithm for perturbing thermodynamically infeasible metabolic networks | Q51943669 | ||
| What is flux balance analysis? | Q28275348 | ||
| OptFlux: an open-source software platform for in silico metabolic engineering | Q28280084 | ||
| High-throughput generation, optimization and analysis of genome-scale metabolic models | Q28291992 | ||
| Identification of genome-scale metabolic network models using experimentally measured flux profiles | Q28469016 | ||
| Context-specific metabolic networks are consistent with experiments | Q28472711 | ||
| Directed evolution of Methanococcus jannaschii citramalate synthase for biosynthesis of 1-propanol and 1-butanol by Escherichia coli | Q28756069 | ||
| Biomass in the manufacture of industrial products--the use of proteins and amino acids. | Q28757419 | ||
| Regulatory on/off minimization of metabolic flux changes after genetic perturbations | Q28769658 | ||
| Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth | Q29397612 | ||
| An efficient recombination system for chromosome engineering in Escherichia coli | Q29615038 | ||
| Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox | Q29615372 | ||
| Reconstruction of biochemical networks in microorganisms | Q29616018 | ||
| The effects of alternate optimal solutions in constraint-based genome-scale metabolic models | Q29616019 | ||
| Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization | Q29616020 | ||
| In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data | Q29618471 | ||
| Fat synthesis in adipose tissue. An examination of stoichiometric constraints | Q30051073 | ||
| Predicting biological system objectives de novo from internal state measurements | Q30443523 | ||
| Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli | Q30479887 | ||
| Metabolic engineering from a cybernetic perspective. 1. Theoretical preliminaries | Q30707254 | ||
| Integrating high-throughput and computational data elucidates bacterial networks | Q30928624 | ||
| Genealogy profiling through strain improvement by using metabolic network analysis: metabolic flux genealogy of several generations of lysine-producing corynebacteria | Q31119249 | ||
| Exploring the diversity of complex metabolic networks. | Q33210262 | ||
| GrowMatch: an automated method for reconciling in silico/in vivo growth predictions | Q33417622 | ||
| Connecting extracellular metabolomic measurements to intracellular flux states in yeast | Q33422147 | ||
| The elucidation of metabolic pathways and their improvements using stable optimization of large-scale kinetic models of cellular systems | Q33500446 | ||
| In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene. | Q33528295 | ||
| High-throughput metabolic engineering: advances in small-molecule screening and selection | Q33549481 | ||
| Metabolic network topology reveals transcriptional regulatory signatures of type 2 diabetes | Q33549712 | ||
| OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains | Q33567324 | ||
| Genetic Engineering of Escherichia coli for Biofuel Production | Q33686378 | ||
| Computationally efficient flux variability analysis | Q33709846 | ||
| An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models | Q33742075 | ||
| Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data | Q33781701 | ||
| In silico identification of gene amplification targets for improvement of lycopene production | Q33847768 | ||
| Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery | Q33859130 | ||
| FFCA: a feasibility-based method for flux coupling analysis of metabolic networks | Q33933759 | ||
| Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism | Q33960308 | ||
| Fluxomers: a new approach for 13C metabolic flux analysis | Q33994080 | ||
| Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. | Q33994087 | ||
| Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models | Q34002893 | ||
| Large-Scale Bi-Level Strain Design Approaches and Mixed-Integer Programming Solution Techniques | Q34031273 | ||
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| Regulation of Gene Expression in Flux Balance Models of Metabolism | Q34101809 | ||
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| MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases | Q34122951 | ||
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| Energy balance for analysis of complex metabolic networks | Q34178210 | ||
| Dynamic flux balance analysis of diauxic growth in Escherichia coli | Q34178626 | ||
| Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. | Q34200286 | ||
| Genome-scale promoter engineering by coselection MAGE | Q34224602 | ||
| F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks | Q34242017 | ||
| Rational design of 13C-labeling experiments for metabolic flux analysis in mammalian cells | Q34271662 | ||
| MicrobesFlux: a web platform for drafting metabolic models from the KEGG database | Q34362833 | ||
| Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation | Q34490423 | ||
| Elimination of thermodynamically infeasible loops in steady-state metabolic models | Q34536141 | ||
| Stoichiometric network theory for nonequilibrium biochemical systems | Q35050976 | ||
| Systematizing the generation of missing metabolic knowledge | Q35058632 | ||
| Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli | Q35073789 | ||
| Large-scale in silico modeling of metabolic interactions between cell types in the human brain | Q35117087 | ||
| Metabolic engineering for the microbial production of 1,3-propanediol | Q35568895 | ||
| Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model | Q35574107 | ||
| Metabolic modeling of a mutualistic microbial community. | Q35742362 | ||
| Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation | Q35762068 | ||
| Systems approach to refining genome annotation | Q35768707 | ||
| Plasticity of genetic interactions in metabolic networks of yeast | Q35844612 | ||
| Primary hyperoxaluria type 1: AGT mistargeting highlights the fundamental differences between the peroxisomal and mitochondrial protein import pathways | Q36616875 | ||
| Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol | Q37052168 | ||
| Microbial production of organic acids: expanding the markets. | Q37055579 | ||
| Metabolic flux analysis as a tool in metabolic engineering of plants | Q37124077 | ||
| Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction | Q37210160 | ||
| P433 | issue | 6 | |
| P921 | main subject | metabolic network | Q2263094 |
| P304 | page(s) | 672-686 | |
| P577 | publication date | 2012-09-28 | |
| P1433 | published in | Metabolic Engineering | Q6822334 |
| P1476 | title | Mathematical optimization applications in metabolic networks | |
| P478 | volume | 14 |
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