ArticlePLoS computational biology2016
Efficient Reconstruction of Predictive Consensus Metabolic Network Models.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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.
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Who cites it
11 citing papers in PubMed.
- COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions.PLoS computational biology · 2022Article
- Hierarchical Harmonization of Atom-Resolved Metabolic Reactions across Metabolic Databases.Metabolites · 2021Article
- A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration.BMC microbiology · 2021Article
- In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions.Microbial cell factories · 2019Article
- Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling.Metabolites · 2019Article
- CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design.BMC bioinformatics · 2018Article
- DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems.BMC systems biology · 2018Article
- In silico engineering ofPeerJ · 2018Article
- Studying microbial functionality within the gut ecosystem by systems biology.Genes & nutrition · 2018Review
- Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model OrganismFrontiers in molecular biosciences · 2018Article
- Constraint-based stoichiometric modelling from single organisms to microbial communities.Journal of the Royal Society, Interface · 2016Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding cellular function requires accurate, comprehensive representations of metabolism. Genome-scale, constraint-based metabolic models (GSMs) provide such representations, but their usability is often hampered by inconsistencies at various levels, in particular for concurrent models. COMMGEN, our tool for COnsensus Metabolic Model GENeration, automatically identifies inconsistencies between concurrent models and semi-automatically resolves them, thereby contributing to consolidate knowledge of metabolic function. Tests of COMMGEN for four organisms showed that automatically generated consensus models were predictive and that they substantially increased coherence of knowledge representation. COMMGEN ought to be particularly useful for complex scenarios in which manual curation does not scale, such as for eukaryotic organisms, microbial communities, and host-pathogen interactions.
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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.