| scholarly article | Q13442814 |
| P6179 | Dimensions Publication ID | 1053723065 |
| P356 | DOI | 10.1038/NRMICRO2737 |
| P932 | PMC publication ID | 3536058 |
| P698 | PubMed publication ID | 22367118 |
| P50 | author | Bernhard Palsson | Q4894212 |
| Nathan E. Lewis | Q30506338 | ||
| P2093 | author name string | Harish Nagarajan | |
| P2860 | cites work | Environments that induce synthetic microbial ecosystems | Q21563487 |
| A protocol for generating a high-quality genome-scale metabolic reconstruction | Q24603373 | ||
| The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities | Q24655269 | ||
| Evolutionary programming as a platform for in silico metabolic engineering | Q25257616 | ||
| Systems-level engineering of nonfermentative metabolism in yeast | Q27934748 | ||
| Analysis of optimality in natural and perturbed metabolic networks | Q28213254 | ||
| Metabolic network structure determines key aspects of functionality and regulation | Q28214885 | ||
| Organization of intracellular reactions with rationally designed RNA assemblies | Q28241565 | ||
| Global organization of metabolic fluxes in the bacterium Escherichia coli | Q28247038 | ||
| Improving NADPH availability for natural product biosynthesis in Escherichia coli by metabolic engineering. | Q45921821 | ||
| In silico design and adaptive evolution of Escherichia coli for production of lactic acid. | Q46023396 | ||
| Correction: Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks. | Q46263073 | ||
| Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast | Q47363112 | ||
| Optimization-based framework for inferring and testing hypothesized metabolic objective functions | Q47995846 | ||
| Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks | Q48129351 | ||
| Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways | Q48238418 | ||
| DESHARKY: automatic design of metabolic pathways for optimal cell growth | Q48322620 | ||
| Bayesian-based selection of metabolic objective functions | Q48421839 | ||
| Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli | Q51471154 | ||
| Probabilistic pathway construction | Q51606814 | ||
| Predicting metabolic fluxes using gene expression differences as constraints | Q51638335 | ||
| Capturing the essence of a metabolic network: a flux balance analysis approach | Q51818962 | ||
| The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks | Q51995141 | ||
| Combinatorial complexity of pathway analysis in metabolic networks | Q52032425 | ||
| Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. | Q54356981 | ||
| Is maximization of molar yield in metabolic networks favoured by evolution? | Q57320470 | ||
| Exploring metabolic pathways in genome-scale networks via generating flux modes | Q57988535 | ||
| Multiple knockout analysis of genetic robustness in the yeast metabolic network | Q80186518 | ||
| Network-based prediction of human tissue-specific metabolism | Q81798711 | ||
| Systems-biology approaches for predicting genomic evolution | Q37909892 | ||
| Flux-balance modeling of plant metabolism. | Q38014422 | ||
| Economics of membrane occupancy and respiro‐fermentation | Q38253806 | ||
| Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. | Q38253830 | ||
| Exploiting the pathway structure of metabolism to reveal high-order epistasis | Q38565870 | ||
| 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 balance analysis accounting for metabolite dilution | Q41018622 | ||
| Systems properties of the Haemophilus influenzae Rd metabolic genotype | Q41671443 | ||
| Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis | Q41724916 | ||
| Large-scale identification of genetic design strategies using local search | Q41764897 | ||
| Computational reconstruction of tissue‐specific metabolic models: application to human liver metabolism | Q41846171 | ||
| Thermodynamics-based metabolic flux analysis | Q41874839 | ||
| Genome-scale thermodynamic analysis of Escherichia coli metabolism | Q42155867 | ||
| Genome-scale gene/reaction essentiality and synthetic lethality analysis | Q42287542 | ||
| Emergent cooperation in microbial metabolism | Q42397954 | ||
| Optimization based automated curation of metabolic reconstructions | Q42431633 | ||
| Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns | Q42588973 | ||
| Metabolic modeling of endosymbiont genome reduction on a temporal scale | Q42733463 | ||
| Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol | Q42733691 | ||
| Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments | Q42743118 | ||
| A genome-scale computational study of the interplay between transcriptional regulation and metabolism | Q42801030 | ||
| Network-based prediction of metabolic enzymes' subcellular localization | Q43121052 | ||
| A strategy to calculate the patterns of nutrient consumption by microorganisms applying a two-level optimisation principle to reconstructed metabolic networks | Q43247347 | ||
| Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. | Q43575020 | ||
| Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments | Q43757062 | ||
| Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. | Q45168694 | ||
| Comparison of network-based pathway analysis methods | Q28274818 | ||
| What is flux balance analysis? | Q28275348 | ||
| High-throughput generation, optimization and analysis of genome-scale metabolic models | Q28291992 | ||
| Context-specific metabolic networks are consistent with experiments | Q28472711 | ||
| Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes | Q28474850 | ||
| Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization | Q28474930 | ||
| Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model | Q28475693 | ||
| Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production | Q28475985 | ||
| Computational Design of Auxotrophy-Dependent Microbial Biosensors for Combinatorial Metabolic Engineering Experiments | Q28476801 | ||
| Differential producibility analysis (DPA) of transcriptomic data with metabolic networks: deconstructing the metabolic response of M. tuberculosis | Q28478889 | ||
| Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism | Q28752237 | ||
| Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses | Q28757815 | ||
| Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data | Q28766251 | ||
| Regulatory on/off minimization of metabolic flux changes after genetic perturbations | Q28769658 | ||
| Applications of genome-scale metabolic reconstructions | Q29031028 | ||
| Reconstruction of biochemical networks in microorganisms | Q29616018 | ||
| 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 | ||
| Understanding the physiology of Lactobacillus plantarum at zero growth | Q30226958 | ||
| Dynamic analysis of integrated signaling, metabolic, and regulatory networks | Q30441717 | ||
| Predicting biological system objectives de novo from internal state measurements | Q30443523 | ||
| Functional integration of a metabolic network model and expression data without arbitrary thresholding. | Q30452532 | ||
| Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli | Q30479887 | ||
| An integrated approach to characterize genetic interaction networks in yeast metabolism | Q30501688 | ||
| Integrating high-throughput and computational data elucidates bacterial networks | Q30928624 | ||
| Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks | Q33286434 | ||
| Estimation of the number of extreme pathways for metabolic networks | Q33300475 | ||
| Estimating the size of the solution space of metabolic networks. | Q33335945 | ||
| Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation | Q33415709 | ||
| GrowMatch: an automated method for reconciling in silico/in vivo growth predictions | Q33417622 | ||
| Connecting extracellular metabolomic measurements to intracellular flux states in yeast | Q33422147 | ||
| Impact of gene expression noise on organismal fitness and the efficacy of natural selection | Q34835690 | ||
| 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 | ||
| Predicting selective drug targets in cancer through metabolic networks. | Q35176392 | ||
| Metabolic networks in motion: 13C-based flux analysis | Q35194034 | ||
| Metabolic modeling of a mutualistic microbial community. | Q35742362 | ||
| Systems approach to refining genome annotation | Q35768707 | ||
| Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity. | Q35921620 | ||
| Metabolite essentiality elucidates robustness of Escherichia coli metabolism | Q35939983 | ||
| Systems metabolic engineering of Escherichia coli for L-threonine production | Q36327201 | ||
| Towards multidimensional genome annotation | Q36371202 | ||
| Group contribution method for thermodynamic analysis of complex metabolic networks | Q36783787 | ||
| Use of randomized sampling for analysis of metabolic networks | Q37305068 | ||
| Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism | Q37328003 | ||
| The biomass objective function | Q37739662 | ||
| Which metabolic pathways generate and characterize the flux space? A comparison among elementary modes, extreme pathways and minimal generators. | Q37751917 | ||
| In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling | Q37816217 | ||
| Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation | Q33466794 | ||
| In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study. | Q33517877 | ||
| Characterization of proton production and consumption associated with microbial metabolism | Q33525406 | ||
| Data integration and analysis of biological networks | Q33529995 | ||
| OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains | Q33567324 | ||
| Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli | Q33574191 | ||
| Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models | Q33642720 | ||
| Blueprint for antimicrobial hit discovery targeting metabolic networks | Q33667030 | ||
| Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis | Q33679330 | ||
| Three-dimensional structural view of the central metabolic network of Thermotoga maritima | Q33707860 | ||
| Computationally efficient flux variability analysis | Q33709846 | ||
| A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. | Q33722800 | ||
| 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 | ||
| Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery | Q33859130 | ||
| The role of cellular objectives and selective pressures in metabolic pathway evolution. | Q33868449 | ||
| Analysis of complex metabolic behavior through pathway decomposition | Q33922321 | ||
| Design and analysis of synthetic carbon fixation pathways | Q33928433 | ||
| Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. | Q33994087 | ||
| Chance and necessity in the evolution of minimal metabolic networks | Q33994506 | ||
| A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology | Q34063123 | ||
| Serine Biosynthesis with One Carbon Catabolism and the Glycine Cleavage System Represents a Novel Pathway for ATP Generation | Q34071505 | ||
| Automatic policing of biochemical annotations using genomic correlations | Q34110870 | ||
| Energy balance for analysis of complex metabolic networks | Q34178210 | ||
| Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. | Q34187246 | ||
| Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. | Q34200286 | ||
| Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase | Q34208791 | ||
| HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology | Q34240836 | ||
| Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions | Q34344292 | ||
| Elimination of thermodynamically infeasible loops in steady-state metabolic models | Q34536141 | ||
| Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae | Q34591168 | ||
| Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. | Q34601005 | ||
| Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery | Q34627247 | ||
| The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli | Q34785166 | ||
| P433 | issue | 4 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | phenotype | Q104053 |
| phylogenetics | Q171184 | ||
| in silico | Q192572 | ||
| P304 | page(s) | 291-305 | |
| P577 | publication date | 2012-02-27 | |
| P1433 | published in | Nature Reviews Microbiology | Q1071797 |
| P1476 | title | Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods | |
| P478 | volume | 10 |
| Q39459193 | A Bayesian Framework for the Classification of Microbial Gene Activity States. |
| Q38729154 | A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. |
| Q41144980 | A Markov chain model for N-linked protein glycosylation--towards a low-parameter tool for model-driven glycoengineering |
| Q85892601 | A Method of Accounting for Enzyme Costs in Flux Balance Analysis Reveals Alternative Pathways and Metabolite Stores in an Illuminated Arabidopsis Leaf |
| Q30994004 | A Method to Constrain Genome-Scale Models with 13C Labeling Data |
| Q38715815 | A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models |
| Q33863113 | A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database |
| Q64060916 | A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber |
| Q101407409 | A guide to metabolic flux analysis in metabolic engineering: Methods, tools and applications |
| Q55345065 | A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data. |
| Q50087089 | A mathematical framework for yield (versus rate) optimization in constraint-based modeling and applications in metabolic engineering. |
| Q34669495 | A metabolite-centric view on flux distributions in genome-scale metabolic models |
| Q36238793 | A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks |
| Q36277163 | A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems |
| Q34475028 | A proof for loop-law constraints in stoichiometric metabolic networks. |
| Q94570016 | A reconciliation of genome-scale metabolic network model of Zymomonas mobilis ZM4 |
| Q30994133 | A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data |
| Q38625636 | A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines |
| Q36041661 | A systems biology approach to reconcile metabolic network models with application to Synechocystis sp. PCC 6803 for biofuel production. |
| Q35037998 | A vector library for silencing central carbon metabolism genes with antisense RNAs in Escherichia coli. |
| Q92164086 | A workflow for generating multi-strain genome-scale metabolic models of prokaryotes |
| Q57492086 | Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future |
| Q41211496 | Advances and challenges in logical modeling of cell cycle regulation: perspective for multi-scale, integrative yeast cell models. |
| Q57809307 | Advances in metabolic flux analysis toward genome-scale profiling of higher organisms |
| Q38094406 | Advances in metabolic pathway and strain engineering paving the way for sustainable production of chemical building blocks |
| Q30777076 | Advances in network-based metabolic pathway analysis and gene expression data integration. |
| Q36041733 | Advancing microbial sciences by individual-based modelling |
| Q35723074 | An Economic Framework of Microbial Trade |
| Q35749805 | An algorithm for the reduction of genome-scale metabolic network models to meaningful core models. |
| Q90117746 | An analytical theory of balanced cellular growth |
| Q97643842 | An upper limit on Gibbs energy dissipation governs cellular metabolism |
| Q47565635 | Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing. |
| Q28083054 | Analysis of genetic variation and potential applications in genome-scale metabolic modeling |
| Q96136256 | Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN |
| Q38201031 | Analyzing the genomic variation of microbial cell factories in the era of "New Biotechnology". |
| Q38281289 | Applications of genome-scale metabolic network model in metabolic engineering |
| Q38121257 | Applying systems biology methods to the study of human physiology in extreme environments |
| Q41511932 | Assessing and Resolving Model Misspecifications in Metabolic Flux Analysis |
| Q64974597 | Augmenting Biogas Process Modeling by Resolving Intracellular Metabolic Activity. |
| Q92639589 | Automatic construction of metabolic models with enzyme constraints |
| Q36377654 | BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities |
| Q38103147 | Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli |
| Q24698676 | BiGG Models: A platform for integrating, standardizing and sharing genome-scale models |
| Q26800999 | Big Data Analytics in Healthcare |
| Q27002569 | Bioinformatic approaches for functional annotation and pathway inference in metagenomics data |
| Q46896512 | Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production. |
| Q36828953 | Bridging the gap between non-targeted stable isotope labeling and metabolic flux analysis |
| Q33735418 | CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models. |
| Q50195462 | COBRA methods and metabolic drug targets in cancer. |
| Q89430395 | COBRAme: A computational framework for genome-scale models of metabolism and gene expression |
| Q34911268 | COBRApy: COnstraints-Based Reconstruction and Analysis for Python |
| Q35065247 | Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells |
| Q36124640 | Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods |
| Q61810621 | Cellular determinants of metabolite concentration ranges |
| Q44156854 | Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association |
| Q34465603 | Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii |
| Q57292186 | Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow |
| Q47117353 | Characterizing steady states of genome-scale metabolic networks in continuous cell cultures |
| Q44784575 | Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks |
| Q34405226 | Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma |
| Q46095372 | Combinatorial optimization of cyanobacterial 2,3-butanediol production. |
| Q99727510 | Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism |
| Q37065104 | Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity |
| Q112286897 | Comparison of metabolic states using genome-scale metabolic models |
| Q87889323 | Computational analysis of the productivity potential of CAM |
| Q26859964 | Computational approaches for understanding energy metabolism |
| Q37340891 | Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious |
| Q34785750 | Computational strategies for a system-level understanding of metabolism |
| Q28551270 | Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach |
| Q26767203 | Constraint Based Modeling Going Multicellular |
| Q46323402 | Constraint and Contingency Pervade the Emergence of Novel Phenotypes in Complex Metabolic Systems |
| Q52626796 | Constraint-based modeling in microbial food biotechnology. |
| Q38178893 | Constraint-based models predict metabolic and associated cellular functions. |
| Q35687124 | Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization |
| Q37076979 | Control of fluxes in metabolic networks |
| Q91763183 | Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. |
| Q38415568 | Critical assessment of genome-scale metabolic networks: the need for a unified standard. |
| Q66679640 | Current status and applications of genome-scale metabolic models |
| Q38222613 | Current understanding of the formation and adaptation of metabolic systems based on network theory |
| Q47674753 | CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions |
| Q53243374 | Design of homo-organic acid producing strains using multi-objective optimization |
| Q35131370 | Design of optimally constructed metabolic networks of minimal functionality |
| Q47266589 | Designing Optimized Production Hosts by Metabolic Modeling |
| Q99408279 | Designing and interpreting 'multi-omic' experiments that may change our understanding of biology |
| Q37619116 | Detecting differential growth of microbial populations with Gaussian process regression. |
| Q34625923 | Determining microbial products and identifying molecular targets in the human microbiome |
| Q31158939 | Discovering missing reactions of metabolic networks by using gene co-expression data |
| Q41841619 | Double and multiple knockout simulations for genome-scale metabolic network reconstructions |
| Q60913181 | DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression |
| Q39043466 | EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model |
| Q38053353 | Elementary Mode Analysis: A Useful Metabolic Pathway Analysis Tool for Reprograming Microbial Metabolic Pathways |
| Q37741329 | Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics. |
| Q39157646 | Elucidating rice cell metabolism under flooding and drought stresses using flux-based modeling and analysis |
| Q34313206 | Engineering ecosystems and synthetic ecologies |
| Q28538235 | Enumeration of smallest intervention strategies in genome-scale metabolic networks |
| Q103027935 | Environmental flexibility does not explain metabolic robustness |
| Q58694872 | Escher-FBA: a web application for interactive flux balance analysis |
| Q41013223 | Ethanol production improvement driven by genome-scale metabolic modeling and sensitivity analysis in Scheffersomyces stipitis. |
| Q35740048 | Exhaustive Analysis of a Genotype Space Comprising 10(15 )Central Carbon Metabolisms Reveals an Organization Conducive to Metabolic Innovation. |
| Q42939055 | Experimental evidence suggests the existence of evolutionary conserved global operation principles governing microbial metabolism |
| Q41891063 | Exploration and comparison of inborn capacity of aerobic and anaerobic metabolisms of Saccharomyces cerevisiae for microbial electrical current production. |
| Q37233565 | Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome |
| Q38614404 | Extracellular Microbial Metabolomics: The State of the Art. |
| Q61799466 | Extreme pathway analysis reveals the organizing rules of metabolic regulation |
| Q40666119 | FOCAL: an experimental design tool for systematizing metabolic discoveries and model development |
| Q39331953 | Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models |
| Q34044149 | Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism |
| Q28536139 | Flux imbalance analysis and the sensitivity of cellular growth to changes in metabolite pools |
| Q33723661 | Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism |
| Q35824927 | Flux-sum analysis identifies metabolite targets for strain improvement |
| Q52337391 | From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota |
| Q26800805 | From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems |
| Q36345811 | From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. |
| Q38065538 | From measurement to implementation of metabolic fluxes |
| Q37094845 | Functional genomics of Plasmodium falciparum using metabolic modelling and analysis |
| Q47200755 | Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting |
| Q35063872 | Gas chromatography-mass spectrometry based metabolomic approach for optimization and toxicity evaluation of earthworm sub-lethal responses to carbofuran |
| Q38256965 | Generalized framework for context-specific metabolic model extraction methods |
| Q38797329 | Genome scale metabolic modeling of cancer |
| Q98735789 | Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level |
| Q28551884 | Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom |
| Q93052007 | Genome-driven cell engineering review: in vivo and in silico metabolic and genome engineering |
| Q35086708 | Genome-scale NAD(H/(+)) availability patterns as a differentiating feature between Saccharomyces cerevisiae and Scheffersomyces stipitis in relation to fermentative metabolism |
| Q22122302 | Genome-scale engineering for systems and synthetic biology |
| Q38063161 | Genome-scale metabolic model in guiding metabolic engineering of microbial improvement |
| Q91722716 | Genome-scale metabolic model of the rat liver predicts effects of diet restriction |
| Q33612841 | Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27. |
| Q36317224 | Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1). |
| Q34718110 | Genome-scale modeling of the protein secretory machinery in yeast |
| Q34508966 | Genome-scale reconstruction of metabolic networks of Lactobacillus casei ATCC 334 and 12A. |
| Q92380845 | Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion |
| Q47678723 | Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach. |
| Q33834503 | Genomes by design |
| Q30278439 | Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains |
| Q39230899 | Gut microbiota functions: metabolism of nutrients and other food components |
| Q37117908 | Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population. |
| Q28069401 | Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine |
| Q37520927 | IDENTIFYING CANCER SPECIFIC METABOLIC SIGNATURES USING CONSTRAINT-BASED MODELS. |
| Q58122460 | Identification of growth-coupled production strains considering protein costs and kinetic variability |
| Q38910940 | Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models. |
| Q36943998 | Identifying essential genes/reactions of the rice photorespiration by in silico model-based analysis |
| Q27304727 | Identifying model error in metabolic flux analysis - a generalized least squares approach |
| Q31119097 | Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets. |
| Q50196257 | Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae. |
| Q38639782 | Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints |
| Q28083571 | In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories |
| Q51817220 | In silico model-driven cofactor engineering strategies for improving the overall NADP(H) turnover in microbial cell factories. |
| Q37416202 | In silico profiling of cell growth and succinate production in Escherichia coli NZN111. |
| Q38961555 | Inference and Prediction of Metabolic Network Fluxes |
| Q49270277 | Insights into metabolic osmoadaptation of the ectoines-producer bacterium Chromohalobacter salexigens through a high-quality genome scale metabolic model. |
| Q45984806 | Integrated Host-Pathogen Metabolic Reconstructions. |
| Q36285217 | Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels |
| Q28652732 | Integrated network analysis and effective tools in plant systems biology. |
| Q47249180 | Integrating Extracellular Flux Measurements and Genome-Scale Modeling Reveals Differences between Brown and White Adipocytes |
| Q94948429 | Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth |
| Q47158582 | Integration of Genome Scale Metabolic Networks and Gene Regulation of Metabolic Enzymes With Physiologically Based Pharmacokinetics |
| Q34741381 | Integration of a constraint-based metabolic model of Brassica napus developing seeds with (13)C-metabolic flux analysis |
| Q30425389 | Integration of expression data in genome-scale metabolic network reconstructions |
| Q46813615 | Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis |
| Q28080759 | Integration of metabolomics data into metabolic networks |
| Q30618093 | Integrative analysis of metabolic models - from structure to dynamics |
| Q26824897 | Integrative approaches for finding modular structure in biological networks |
| Q30540108 | Invariance and optimality in the regulation of an enzyme |
| Q30316452 | JSBML 1.0: providing a smorgasbord of options to encode systems biology models |
| Q39315101 | Large-scale computational models of liver metabolism: How far from the clinics? |
| Q88226573 | Light-optimized growth of cyanobacterial cultures: Growth phases and productivity of biomass and secreted molecules in light-limited batch growth |
| Q34350839 | Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models |
| Q38763272 | Limitations of a metabolic network-based reverse ecology method for inferring host-pathogen interactions |
| Q39093715 | Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion |
| Q55192876 | LiverSex Computational Model: Sexual Aspects in Hepatic Metabolism and Abnormalities. |
| Q26798065 | Longitudinal omics modeling and integration in clinical metabonomics research: challenges in childhood metabolic health research |
| Q47215369 | Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular Polymers and Destabilize Bacterial Biofilms |
| Q108126729 | MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics |
| Q34464555 | MC3: a steady-state model and constraint consistency checker for biochemical networks |
| Q90065008 | MCS2: minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks |
| Q38671211 | MUFINS: multi-formalism interaction network simulator. |
| Q91796642 | Machine and deep learning meet genome-scale metabolic modeling |
| Q41859031 | MapMaker and PathTracer for tracking carbon in genome-scale metabolic models. |
| Q30405425 | MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data |
| Q37148097 | MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models |
| Q90376452 | Metabolic Modeling of Microbial Community Interactions for Health, Environmental and Biotechnological Applications |
| Q26744686 | Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems |
| Q33830281 | Metabolic and transcriptional regulatory mechanisms underlying the anoxic adaptation of rice coleoptile. |
| Q51533799 | Metabolic assessment of E. coli as a Biofactory for commercial products. |
| Q28536645 | Metabolic constraint-based refinement of transcriptional regulatory networks |
| Q49790316 | Metabolic division of labor in microbial systems |
| Q52431940 | Metabolic engineering of Pichia pastoris |
| Q40480159 | Metabolic flux analyses of Pseudomonas aeruginosa cystic fibrosis isolates. |
| Q92477417 | Metabolic flux responses to deletion of 20 core enzymes reveal flexibility and limits of E. coli metabolism |
| Q35778015 | Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis |
| Q38292789 | Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation |
| Q83231503 | Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome |
| Q39388483 | Metabolite profiling and integrative modeling reveal metabolic constraints for carbon partitioning under nitrogen starvation in the green algae Haematococcus pluvialis. |
| Q35574156 | Metabolomics integrated elementary flux mode analysis in large metabolic networks. |
| Q30868340 | Methods for integration of transcriptomic data in genome-scale metabolic models |
| Q34471421 | Microbial cultivation and the role of microbial resource centers in the omics era |
| Q34986572 | Minimal metabolic pathway structure is consistent with associated biomolecular interactions |
| Q28076100 | Modeling Rice Metabolism: From Elucidating Environmental Effects on Cellular Phenotype to Guiding Crop Improvement |
| Q58801759 | Modeling the Metabolic State of Upon Infection |
| Q92134921 | Modelling approaches for studying the microbiome |
| Q39433303 | More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes |
| Q28484385 | MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models |
| Q34429661 | Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage |
| Q38092066 | Multi‐scale modeling for sustainable chemical production |
| Q90296845 | NIHBA: A Network Interdiction Approach for Metabolic Engineering Design |
| Q49983962 | Network Analyses in Plant Pathogens |
| Q34296873 | Network context and selection in the evolution to enzyme specificity. |
| Q37526602 | Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance |
| Q38090655 | New Advances in Separation Science for Metabolomics: Resolving Chemical Diversity in a Post-Genomic Era |
| Q64094791 | New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering |
| Q63952409 | OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques |
| Q36384863 | On the effects of alternative optima in context-specific metabolic model predictions |
| Q58699982 | OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli |
| Q37409447 | Optimal control of gene expression for fast proteome adaptation to environmental change |
| Q46774634 | Optimizing genome-scale network reconstructions |
| Q36248806 | Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models |
| Q35855189 | Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires |
| Q55061666 | Phenotypic innovation through recombination in genome-scale metabolic networks. |
| Q39931095 | Photorespiratory Bypasses Lead to Increased Growth in Arabidopsis thaliana: Are Predictions Consistent with Experimental Evidence? |
| Q26786126 | Physiologically Shrinking the Solution Space of a Saccharomyces cerevisiae Genome-Scale Model Suggests the Role of the Metabolic Network in Shaping Gene Expression Noise |
| Q37542238 | Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory. |
| Q46877274 | Predicting dynamic metabolic demands in the photosynthetic eukaryote Chlorella vulgaris. |
| Q33767074 | Predicting growth of the healthy infant using a genome scale metabolic model |
| Q35609075 | Predicting internal cell fluxes at sub-optimal growth |
| Q55279133 | Predicting the accumulation of storage compounds by Rhodococcus jostii RHA1 in the feast-famine growth cycles using genome-scale flux balance analysis. |
| Q30951388 | Prediction of intracellular metabolic states from extracellular metabolomic data |
| Q38283539 | Predictive sulfur metabolism - a field in flux |
| Q34502550 | Principles of genetic circuit design |
| Q31142835 | Principles of proteome allocation are revealed using proteomic data and genome-scale models |
| Q38607654 | Probing the genome-scale metabolic landscape of Bordetella pertussis, the causative agent of whooping cough. |
| Q28727811 | Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering |
| Q99411738 | Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling |
| Q42862600 | QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells |
| Q37023365 | Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models |
| Q40397149 | Rational design of efficient modular cells |
| Q99594982 | Reconstructing organisms in silico: genome-scale models and their emerging applications |
| Q43540202 | Reconstruction and analysis of the industrial strain Bacillus megaterium WSH002 genome-scale in silico metabolic model |
| Q40778167 | Reconstruction and validation of a constraint-based metabolic network model for bone marrow-derived mesenchymal stem cells |
| Q28535020 | Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM |
| Q28388815 | Reconstruction of Tissue-Specific Metabolic Networks Using CORDA |
| Q41367777 | Reconstruction of a Genome-scale Metabolic Network of Komagataeibacter nataicola RZS01 for Cellulose Production |
| Q38757688 | Redesigning metabolism based on orthogonality principles |
| Q52355517 | Review and perspective on mathematical modeling of microbial ecosystems |
| Q127060165 | Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities |
| Q38888646 | Robust Analysis of Fluxes in Genome-Scale Metabolic Pathways |
| Q51597005 | SMET: Systematic multiple enzyme targeting – a method to rationally design optimal strains for target chemical overproduction |
| Q28483028 | Shrinking the Metabolic Solution Space Using Experimental Datasets |
| Q26824185 | Software applications for flux balance analysis |
| Q35029546 | Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti. |
| Q36154863 | Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction |
| Q113308502 | Strain design optimization using reinforcement learning |
| Q92890937 | Stress-tolerant non-conventional microbes enable next-generation chemical biosynthesis |
| Q91614466 | Studying metabolic flux adaptations in cancer through integrated experimental-computational approaches |
| Q88412415 | Systematic metabolic engineering of Methylomicrobium alcaliphilum 20Z for 2,3-butanediol production from methane |
| Q47798093 | Systems Biology Approach to Bioremediation of Nitroaromatics: Constraint-Based Analysis of 2,4,6-Trinitrotoluene Biotransformation by Escherichia coli. |
| Q63351951 | Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community. |
| Q36372378 | Systems analysis of host-parasite interactions |
| Q37604410 | Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism |
| Q55322453 | Systems biology as an emerging paradigm in transfusion medicine. |
| Q35619563 | Systems biology of host-microbe metabolomics |
| Q38006097 | Systems biotechnology of animal cells: the road to prediction |
| Q26750901 | Systems psychopharmacology: A network approach to developing novel therapies |
| Q38602367 | Systems strategies for developing industrial microbial strains |
| Q34499316 | Temporal expression-based analysis of metabolism |
| Q46130601 | The Emerging Facets of Non-Cancerous Warburg Effect. |
| Q36336979 | The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism |
| Q38689208 | The Utility of Fisher's Geometric Model in Evolutionary Genetics |
| Q21129241 | The evolution of genome-scale models of cancer metabolism |
| Q36171483 | The potential for non-adaptive origins of evolutionary innovations in central carbon metabolism. |
| Q34628885 | The value of mechanistic biophysical information for systems-level understanding of complex biological processes such as cytokinesis |
| Q38632109 | Thermodynamic Constraints Improve Metabolic Networks |
| Q35683444 | Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community |
| Q38151877 | Thermophilic lignocellulose deconstruction |
| Q48364480 | Topological and kinetic determinants of the modal matrices of dynamic models of metabolism |
| Q34508185 | Topology of molecular interaction networks |
| Q37524872 | Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity. |
| Q48015386 | Ultra sound assisted one step rapid derivatization and dispersive liquid–liquid microextraction followed by gas chromatography–mass spectrometric determination of amino acids in complex matrices |
| Q34975280 | Understanding the interactions between bacteria in the human gut through metabolic modeling |
| Q34546511 | Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis |
| Q40446923 | Unraveling the Light-Specific Metabolic and Regulatory Signatures of Rice through Combined in Silico Modeling and Multiomics Analysis. |
| Q28085366 | Using Genome-scale Models to Predict Biological Capabilities |
| Q28539829 | Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses |
| Q38947322 | What can mathematical modelling say about CHO metabolism and protein glycosylation? |
| Q36688311 | Whole Cell Modeling: From Single Cells to Colonies |
| Q47110056 | WormJam: A consensus C. elegans Metabolic Reconstruction and Metabolomics Community and Workshop Series |
| Q35810231 | antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters |
| Q91727380 | iMet: A graphical user interface software tool to merge metabolic networks |
| Q39788095 | ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks |
| Q36141892 | solveME: fast and reliable solution of nonlinear ME models |
| Q42023667 | toyLIFE: a computational framework to study the multi-level organisation of the genotype-phenotype map. |
Search more.