| 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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| 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 | ||
| Path finding methods accounting for stoichiometry in metabolic networks. | Q39221698 | ||
| Metabolic flux analysis of CHO cells at growth and non-growth phases using isotopic tracers and mass spectrometry | Q39494168 | ||
| Can single knockouts accurately single out gene functions? | Q39667259 | ||
| Gratuitous overexpression of genes in Escherichia coli leads to growth inhibition and ribosome destruction | Q39836003 | ||
| Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. | Q39916365 | ||
| OptStrain: a computational framework for redesign of microbial production systems. | Q40299930 | ||
| Flux coupling analysis of genome-scale metabolic network reconstructions. | Q40497938 | ||
| Synthetic enhancement in gene interaction: a genetic tool come of age. | Q40796844 | ||
| Large-scale identification of genetic design strategies using local search | Q41764897 | ||
| MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization | Q41778262 | ||
| Thermodynamics-based metabolic flux analysis | Q41874839 | ||
| Metabolic flux elucidation for large-scale models using 13C labeled isotopes | Q41918100 | ||
| 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 | ||
| Recovering metabolic pathways via optimization. | Q51930134 | ||
| Algorithm for perturbing thermodynamically infeasible metabolic networks. | Q51943669 | ||
| Metabolic engineering for advanced biofuels production from Escherichia coli | Q37257503 | ||
| PathMiner: predicting metabolic pathways by heuristic search | Q37258960 | ||
| iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations | Q37282896 | ||
| Automated design of synthetic ribosome binding sites to control protein expression | Q37436696 | ||
| The biomass objective function | Q37739662 | ||
| Engineering a beta-carotene ketolase for astaxanthin production | Q38310870 | ||
| Quantitative analysis of metabolic fluxes in Escherichia coli, using two-dimensional NMR spectroscopy and complete isotopomer models. | Q52204983 | ||
| Metabolic engineering from a cybernetic perspective. 2. Qualitative investigation of nodal architechtures and their response to genetic perturbation | Q52212915 | ||
| Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments. | Q52259732 | ||
| Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism | Q52425486 | ||
| An integrated computational and experimental study for overproducing fatty acids in Escherichia coli. | Q53358437 | ||
| Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. | Q54356981 | ||
| Heterologous pyc gene expression under various natural and engineered promoters in Escherichia coli for improved succinate production. | Q54358186 | ||
| Flux coupling analysis of metabolic networks is sensitive to missing reactions | Q54378287 | ||
| Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis. | Q54409190 | ||
| Analysis of structural robustness of metabolic networks. | Q54453384 | ||
| A Spatial Branch-and-Bound Framework for the Global Optimization of Kinetic Models of Metabolic Networks | Q57701893 | ||
| A universal framework for 13C metabolic flux analysis | Q74227987 | ||
| Structural robustness of metabolic networks with respect to multiple knockouts | Q79905722 | ||
| Multiple knockout analysis of genetic robustness in the yeast metabolic network | Q80186518 | ||
| Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry | Q81157263 | ||
| Selection of tracers for 13C-metabolic flux analysis using elementary metabolite units (EMU) basis vector methodology | Q83158699 | ||
| 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 | ||
| A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology | Q34063123 | ||
| Regulation of gene expression in flux balance models of metabolism | Q34101809 | ||
| Metabolic flux responses to pyruvate kinase knockout in Escherichia coli | Q34104879 | ||
| MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases | Q34122951 | ||
| OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities | Q34154442 | ||
| 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 |
| Q40551121 | 13C metabolic flux analysis at a genome-scale |
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| Q39800208 | A computational analysis of stoichiometric constraints and trade-offs in cyanobacterial biofuel production. |
| Q35037998 | A vector library for silencing central carbon metabolism genes with antisense RNAs in Escherichia coli. |
| Q26782197 | Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations |
| Q38726899 | Advances and perspectives in computational prediction of microbial gene essentiality |
| Q59052001 | An Improved Geometric Programming Approach for Optimization of Biochemical Systems |
| Q35006722 | An objective function exploiting suboptimal solutions in metabolic networks |
| Q35121927 | Analyzing clonal variation of monoclonal antibody-producing CHO cell lines using an in silico metabolomic platform |
| Q56886814 | Application of a curated genome-scale metabolic model of CHO DG44 to an industrial fed-batch process |
| Q56913561 | BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits |
| Q38092646 | Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models |
| Q35031820 | Comparison and improvement of algorithms for computing minimal cut sets |
| Q47318384 | Computational Approaches on Stoichiometric and Kinetic Modeling for Efficient Strain Design |
| Q44391077 | Construction of robust dynamic genome-scale metabolic model structures of Saccharomyces cerevisiae through iterative re-parameterization |
| Q30885879 | Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data |
| Q31145555 | Degradation Network Reconstruction Guided by Metagenomic Data. |
| Q42609940 | Designing overall stoichiometric conversions and intervening metabolic reactions |
| Q41841619 | Double and multiple knockout simulations for genome-scale metabolic network reconstructions |
| Q51556877 | Elucidation of photoautotrophic carbon flux topology in Synechocystis PCC 6803 using genome-scale carbon mapping models. |
| Q48892018 | Engineering central metabolism - a grand challenge for plant biologists |
| Q34731071 | Enhancing microbial metabolite and enzyme production: current strategies and challenges |
| Q28538235 | Enumeration of smallest intervention strategies in genome-scale metabolic networks |
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| Q38534049 | FastPros: screening of reaction knockout strategies for metabolic engineering |
| Q46236534 | Finding elementary flux modes in metabolic networks based on flux balance analysis and flux coupling analysis: application to the analysis of Escherichia coli metabolism. |
| Q26800805 | From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems |
| Q92923730 | Genome-Scale Metabolic Network Models of Bacillus Species Suggest that Model Improvement is Necessary for Biotechnological Applications |
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| Q34508966 | Genome-scale reconstruction of metabolic networks of Lactobacillus casei ATCC 334 and 12A. |
| Q40612591 | Genome-scale reconstruction of the metabolic network in Pseudomonas stutzeri A1501. |
| Q41013183 | Genome-scale strain designs based on regulatory minimal cut sets |
| Q41010127 | Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms. |
| Q38771023 | Identification of metabolic pathways using pathfinding approaches: a systematic review |
| Q31119097 | Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets. |
| Q28083571 | In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories |
| Q41976274 | Incorporation of flexible objectives and time-linked simulation with flux balance analysis |
| Q92540504 | Kinetic model optimization and its application to mitigating the Warburg effect through multiple enzyme alterations |
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| Q51533799 | Metabolic assessment of E. coli as a Biofactory for commercial products. |
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