ArticleBMC systems biology2011
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions.
Article in BMC systems biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 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
49 citing papers in PubMed, 76 citations in OpenAlex.
- Modeling Microbiome Modulation of Tumor Metabolic Networks to Predict Synergistic Therapies.bioRxiv : the preprint server for biology · 2026Article
- Dynamic metabolic modelling of ATP allocation during viral infection.Journal of the Royal Society, Interface · 2026Article
- In silico analysis and comparison of the metabolic capabilities of different organisms by reducing metabolic complexity.Microbiome · 2026Article
- Revealing the role of a novelFrontiers in molecular biosciences · 2026Article
- Modelling reliable metabolic phenotypes by analysing the context-specific transcriptomics data.NPJ systems biology and applications · 2025Article
- A structural machine learning approach for rapid prediction of thermodynamically destabilizing tyrosine phosphorylations.Cell reports methods · 2025Article
- Withaferin A decreases glycolytic reprogramming in breast cancer.Scientific reports · 2024Article
- Rapid prediction of thermodynamically destabilizing tyrosine phosphorylations in cancers.bioRxiv : the preprint server for biology · 2024Article
- Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model.PLoS computational biology · 2023Article
- Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook.Briefings in bioinformatics · 2021Article
- Personalized whole-body models integrate metabolism, physiology, and the gut microbiome.Molecular systems biology · 2020Article
- Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine.Frontiers in bioengineering and biotechnology · 2020Review
- Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Quantitative flux coupling analysis.Journal of mathematical biology · 2019Article
- Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.Nature protocols · 2019Article
- Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity.NPJ systems biology and applications · 2019Article
- Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach.Molecular plant pathology · 2018Article
- Confronting the catalytic dark matter encoded by sequenced genomes.Nucleic acids research · 2017Article
- Multi-omics approaches to disease.Genome biology · 2017Review
- Metabolic systems biology: a brief primer.The Journal of physiology · 2017Review
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 at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMetabolic network reconstructions formalize our knowledge of metabolism. Gaps in these networks pinpoint regions of metabolism where biological components and functions are "missing." At the same time, a major challenge in the post genomic era involves characterisation of missing biological components to complete genome annotation.
resultsWe used the human metabolic network reconstruction RECON 1 and established constraint-based modelling tools to uncover novel functions associated with human metabolism. Flux variability analysis identified 175 gaps in RECON 1 in the form of blocked reactions. These gaps were unevenly distributed within metabolic pathways but primarily found in the cytosol and often caused by compounds whose metabolic fate, rather than production, is unknown. Using a published algorithm, we computed gap-filling solutions comprised of non-organism specific metabolic reactions capable of bridging the identified gaps. These candidate solutions were found to be dependent upon the reaction environment of the blocked reaction. Importantly, we showed that automatically generated solutions could produce biologically realistic hypotheses of novel human metabolic reactions such as of the fate of iduronic acid following glycan degradation and of N-acetylglutamate in amino acid metabolism.
conclusionsThe results demonstrate how metabolic models can be utilised to direct hypotheses of novel metabolic functions in human metabolism; a process that we find is heavily reliant upon manual curation and biochemical insight. The effectiveness of a systems approach for novel biochemical pathway discovery in mammals is demonstrated and steps required to tailor future gap filling algorithms to mammalian metabolic networks are proposed.
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.