ArticleBiophysical journal2012
Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- The Gibbs free energy landscape based on liver metabolome revealed thermodynamic robustness against fasting and obesity.iScience · 2026Article
- Article
- XomicsToModel: omics data integration and generation of thermodynamically consistent metabolic models.Nature protocols · 2026Article
- Energetic constraints of metal-reducing bacteria as biocatalysts for microbial electrosynthesis.Biotechnology for biofuels and bioproducts · 2025Article
- A mathematically rigorous algorithm to define, compute and assess relevance of the probable dissociation constants in characterizing a biochemical network.Scientific reports · 2024Article
- Inferring mitochondrial and cytosolic metabolism by coupling isotope tracing and deconvolution.Nature communications · 2023Article
- Personalised modelling of clinical heterogeneity between medium-chain acyl-CoA dehydrogenase patients.BMC biology · 2023Article
- ReDirection: an R-package to compute the probable dissociation constant for every reaction of a user-defined biochemical network.Frontiers in molecular biosciences · 2023Article
- eQuilibrator 3.0: a database solution for thermodynamic constant estimation.Nucleic acids research · 2022Article
- Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors.Cell systems · 2021Article
- Thermal and Acidic Treatments of Gluten Epitopes Affect Their Recognition by HLA-DQ2Frontiers in nutrition · 2021Article
- A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks.PLoS computational biology · 2020Article
- Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.Nature protocols · 2019Article
- Automated generation of genome-scale metabolic draft reconstructions based on KEGG.BMC bioinformatics · 2018Article
- Quantum chemistry reveals thermodynamic principles of redox biochemistry.PLoS computational biology · 2018Article
- Quantification of Microbial Phenotypes.Metabolites · 2016Review
- Metabolite concentrations, fluxes and free energies imply efficient enzyme usage.Nature chemical biology · 2016Article
- Integration of metabolomics data into metabolic networks.Frontiers in plant science · 2015Review
- Network thermodynamic curation of human and yeast genome-scale metabolic models.Biophysical journal · 2014Article
- Promise and reality in the expanding field of network interaction analysis: metabolic networks.Bioinformatics and biology insights · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reaction directionality is a key constraint in the modeling of genome-scale metabolic networks. We thermodynamically constrained reaction directionality in a multicompartmental genome-scale model of human metabolism, Recon 1, by calculating, in vivo, standard transformed reaction Gibbs energy as a function of compartment-specific pH, electrical potential, and ionic strength. We show that compartmental pH is an important determinant of thermodynamically determined reaction directionality. The effects of pH on transport reaction thermodynamics are only seen to their full extent when metabolites are represented as pseudoisomer groups of multiple protonated species. We accurately predict the irreversibility of 387 reactions, with detailed propagation of uncertainty in input data, and manually curate the literature to resolve conflicting directionality assignments. In at least half of all cases, a prediction of a reversible reaction directionality is due to the paucity of compartment-specific quantitative metabolomic data, with remaining cases due to uncertainty in estimation of standard reaction Gibbs energy. This study points to the pressing need for 1), quantitative metabolomic data, and 2), experimental measurement of thermochemical properties for human metabolites.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.