ReviewCurrent opinion in biotechnology2015
Transparency in metabolic network reconstruction enables scalable biological discovery.
Review in Current opinion in biotechnology, 2015. 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.
- MACAW: a method for semi-automatic detection of errors in genome-scale metabolic models.Genome biology · 2025Article
- Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case ofFrontiers in microbiology · 2024Article
- MEMOTE for standardized genome-scale metabolic model testing.Nature biotechnology · 2020Article
- A genome-scale metabolic model of potato late blight suggests a photosynthesis suppression mechanism.BMC genomics · 2018Article
- Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models.PLoS computational biology · 2018Article
- Genome-scale modeling of yeast: chronology, applications and critical perspectives.FEMS yeast research · 2017Review
- Discovering missing reactions of metabolic networks by using gene co-expression data.Scientific reports · 2017Article
- EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model.Scientific reports · 2017Article
- Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis.Journal of bacteriology · 2016Article
- MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models.Frontiers in physiology · 2016Article
- Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction.PLoS computational biology · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Reconstructing metabolic pathways has long been a focus of active research. Now, draft models can be generated from genomic annotation and used to simulate metabolic fluxes of mass and energy at the whole-cell scale. This approach has led to an explosion in the number of functional metabolic network models. However, more models have not led to expanded coverage of metabolic reactions known to occur in the biosphere. Thus, there exists opportunity to reconsider the process of reconstruction and model derivation to better support the less-scalable investigative processes of biocuration and experimentation. Realizing this opportunity to improve our knowledge of metabolism requires developing new tools that make reconstructions more useful by highlighting metabolic network knowledge limitations to guide future research.
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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.