ReviewFrontiers in plant science2014
Generalized framework for context-specific metabolic model extraction methods.
Review in Frontiers in plant science, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
- Modelling reliable metabolic phenotypes by analysing the context-specific transcriptomics data.NPJ systems biology and applications · 2025Article
- A constraint-based framework for exploring the impact of multireaction dependencies on metabolic functions.NPJ systems biology and applications · 2025Article
- Genome-scale metabolic modelling identifies reactions mediated by SNP-SNP interactions associated with yeast sporulation.NPJ systems biology and applications · 2025Article
- The Evolution of Systems Biology and Systems Medicine: From Mechanistic Models to Uncertainty Quantification.Annual review of biomedical engineering · 2025Review
- In silico encounters: harnessing metabolic modelling to understand plant-microbe interactions.FEMS microbiology reviews · 2025Review
- Integration of metatranscriptomics data improves the predictive capacity of microbial community metabolic models.The ISME journal · 2025Article
- Article
- A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques.BMC bioinformatics · 2024Article
- Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism.Nature communications · 2023Article
- Analysis of companion cell and phloem metabolism using a transcriptome-guided model of Arabidopsis metabolism.Plant physiology · 2023Article
- Extracting functionally accurate context-specific models of Atlantic salmon metabolism.NPJ systems biology and applications · 2023Article
- Toward mechanistic modeling and rational engineering of plant respiration.Plant physiology · 2023Article
- Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures.Metabolites · 2023Review
- Guidelines for extracting biologically relevant context-specific metabolic models using gene expression data.Metabolic engineering · 2023Article
- Identifying essential genes in genome-scale metabolic models of consensus molecular subtypes of colorectal cancer.PloS one · 2023Article
- Genome-scale models as a vehicle for knowledge transfer from microbial to mammalian cell systems.Computational and structural biotechnology journal · 2023Review
- A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale.PLoS computational biology · 2022Article
- Quantitative metabolic fluxes regulated by trans-omic networks.The Biochemical journal · 2022Review
- A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations.Plant physiology · 2022Article
- Compartmentalization of metabolism between cell types in multicellular organisms: a computational perspective.Current opinion in systems biology · 2022Article
Corrections and comments
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2 authors.
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Abstract
Genome-scale metabolic models (GEMs) are increasingly applied to investigate the physiology not only of simple prokaryotes, but also eukaryotes, such as plants, characterized with compartmentalized cells of multiple types. While genome-scale models aim at including the entirety of known metabolic reactions, mounting evidence has indicated that only a subset of these reactions is active in a given context, including: developmental stage, cell type, or environment. As a result, several methods have been proposed to reconstruct context-specific models from existing genome-scale models by integrating various types of high-throughput data. Here we present a mathematical framework that puts all existing methods under one umbrella and provides the means to better understand their functioning, highlight similarities and differences, and to help users in selecting a most suitable method for an application.
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