Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks - sprookjes - yvandenbroek - TriplyDB

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

http://www.wikidata.org/entity/Q33286434

about

Quantification of Microbial Phenotypes Integration of metabolomics data into metabolic networks A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks System-level insights into yeast metabolism by thermodynamic analysis of elementary flux modes Redirector: designing cell factories by reconstructing the metabolic objective Variability of metabolite levels is linked to differential metabolic pathways in Arabidopsis's responses to abiotic stresses Simulating metabolism with statistical thermodynamics Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli Evaluation of control mechanisms for Saccharomyces cerevisiae central metabolic reactions using metabolome data of eight single-gene deletion mutants.Metabolic Consequences of TGFb Stimulation in CulturedPrimary Mouse Hepatocytes Screened from Transcript Data with ModeScore A procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficient.An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis FASIMU: flexible software for flux-balance computation series in large metabolic networks.IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods Topology of molecular interaction networks.Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models.The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.An objective function exploiting suboptimal solutions in metabolic networks Metabolomics integrated elementary flux mode analysis in large metabolic networks.Predicting internal cell fluxes at sub-optimal growth Obstructions to Sampling Qualitative Properties.Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.How important is thermodynamics for identifying elementary flux modes?Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal Metabolic flux analysis of heterotrophic growth in Chlamydomonas reinhardtii.Metabolite concentrations, fluxes and free energies imply efficient enzyme usage.Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models.Which sets of elementary flux modes form thermodynamically feasible flux distributions?Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment.Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathways.Elementary flux modes in a nutshell: properties, calculation and applications.

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P2860

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

http://www.wikidata.org/entity/Q33286434

description

2007 nî lūn-bûn

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2007 թուականի Յունիսին հրատարակուած գիտական յօդուած

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2007 թվականի հունիսին հրատարակված գիտական հոդված

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2007年の論文

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2007年論文

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2007年論文

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Including metabolite concentra ...... ibutions in metabolic networks

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P1433

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BMC Systems Biology

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Including metabolite concentra ...... ibutions in metabolic networks

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P2093

Andreas Hoppe

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Sabrina Hoffmann

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P2860

An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)

The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities

Analysis of optimality in natural and perturbed metabolic networks

Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data

In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data

Systematic assignment of thermodynamic constraints in metabolic network models.

Metabolic flux responses to pyruvate kinase knockout in Escherichia coli

Energy balance for analysis of complex metabolic networks

Kinetics of electron transfer through the respiratory chain.

Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.

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23

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scholarly article

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10.1186/1752-0509-1-23

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1

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Hermann-Georg Holzhütter

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2007-06-01T00:00:00Z

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6293458

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1032522590

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17543097

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1903363

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