ArticlePLoS computational biology2008
Context-specific metabolic networks are consistent with experiments.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 346 papers.
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Who cites it
346 citing papers in PubMed.
- Protocol for thermodynamically optimal construction and analysis of metabolic networks using ThermOptCOBRA.STAR protocols · 2026Article
- An adenylyl cyclase switch reroutes carbon from growth to virulence lipids inbioRxiv : the preprint server for biology · 2026Article
- Glycan reachability analysis: A bottleneck-aware framework for inferring tissue-specific glycan biosynthetic potential from transcriptomics.PLoS computational biology · 2026Article
- Nutrient control enables metabolic reconstruction ofbioRxiv : the preprint server for biology · 2026Article
- XomicsToModel: omics data integration and generation of thermodynamically consistent metabolic models.Nature protocols · 2026Article
- A systems-level view of metabolic impact of copper and methane valorization potential inMetabolic engineering communications · 2026Article
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- Aryl hydrocarbon receptor in the kidney regulates metabolic cross-talk with the liver and gut microbiome.Scientific reports · 2026Article
- Predictive multispecies constraint-based metabolic modeling: case studies and best practices.Briefings in bioinformatics · 2026Review
- Flux sampling and context-specific genome-scale metabolic models for biotechnological applications.Trends in biotechnology · 2026Review
- Spatial FBA reveals heterogeneous Warburg niches in renal tumors and lactate consumption in colorectal cancer.NPJ systems biology and applications · 2026Article
- Improved flux profiling in genome-scale modeling of human cell metabolism.Cell reports methods · 2026Article
- Integrative genome-scale metabolic model of GABAergic neurons reveals metabolic signatures across the mild cognitive impairment - Alzheimer disease continuum.Frontiers in systems biology · 2026Article
- Metabolic modeling unveils potential probiotic roles ofISME communications · 2026Article
- ModellingCurrent research in microbial sciences · 2026Article
- IGM: Integrated Gene-expression Modeling for multi-condition flux-preserving genome-scale metabolic models.PloS one · 2026Article
- From Genome to Function: Metabolism-Wide Models of Lifecycle Stages of Parasites.Methods in molecular biology (Clifton, N.J.) · 2026Article
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- Modelling reliable metabolic phenotypes by analysing the context-specific transcriptomics data.NPJ systems biology and applications · 2025Article
286 more citing papers are in PubMed but not listed here.
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Reconstructions of cellular metabolism are publicly available for a variety of different microorganisms and some mammalian genomes. To date, these reconstructions are "genome-scale" and strive to include all reactions implied by the genome annotation, as well as those with direct experimental evidence. Clearly, many of the reactions in a genome-scale reconstruction will not be active under particular conditions or in a particular cell type. Methods to tailor these comprehensive genome-scale reconstructions into context-specific networks will aid predictive in silico modeling for a particular situation. We present a method called Gene Inactivity Moderated by Metabolism and Expression (GIMME) to achieve this goal. The GIMME algorithm uses quantitative gene expression data and one or more presupposed metabolic objectives to produce the context-specific reconstruction that is most consistent with the available data. Furthermore, the algorithm provides a quantitative inconsistency score indicating how consistent a set of gene expression data is with a particular metabolic objective. We show that this algorithm produces results consistent with biological experiments and intuition for adaptive evolution of bacteria, rational design of metabolic engineering strains, and human skeletal muscle cells. This work represents progress towards producing constraint-based models of metabolism that are specific to the conditions where the expression profiling data is available.
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