ArticlePLoS computational biology2017
Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 47 citations in OpenAlex.
- Metabolic Objectives and Trade-Offs: Inference and Applications.Metabolites · 2025Review
- Integration of metabolism and regulation reveals rapid adaptability to growth on non-native substrates.Cell chemical biology · 2023Article
- Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells.NPJ systems biology and applications · 2023Article
- Machine learning for metabolic pathway optimization: A review.Computational and structural biotechnology journal · 2023Review
- Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges.Biomolecules · 2022Review
- Protocol for condition-dependent metabolite yield prediction using the TRIMER pipeline.STAR protocols · 2022Article
- Modelling of glucose repression signalling in yeast Saccharomyces cerevisiae.FEMS yeast research · 2022Review
- Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME.NPJ systems biology and applications · 2021Article
- Article
- Next-Generation Genome-Scale Metabolic Modeling through Integration of Regulatory Mechanisms.Metabolites · 2021Review
- Modeling the Th17 and Tregs Paradigm: Implications for Cancer Immunotherapy.Frontiers in cell and developmental biology · 2021Review
- History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications.Frontiers in physiology · 2021Review
- Review
- Into the wild: new yeast genomes from natural environments and new tools for their analysis.FEMS yeast research · 2020Review
- Mechanistic Modeling of Gene Regulation and Metabolism Identifies Potential Targets for Hepatocellular Carcinoma.Frontiers in genetics · 2020Article
- Genome-scale metabolic model of the rat liver predicts effects of diet restriction.Scientific reports · 2019Article
- Reconciling high-throughput gene essentiality data with metabolic network reconstructions.PLoS computational biology · 2019Article
- OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling.PLoS computational biology · 2019Article
- Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities.Biochemistry · 2019Review
- Next-Generation Genome-Scale Models Incorporating Multilevel 'Omics Data: From Yeast to Human.Methods in molecular biology (Clifton, N.J.) · 2019Article
Corrections and comments
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Authors and funding
11 authors at 5 institutions in 2 countries.
Funding
Abstract
Gene regulatory and metabolic network models have been used successfully in many organisms, but inherent differences between them make networks difficult to integrate. Probabilistic Regulation Of Metabolism (PROM) provides a partial solution, but it does not incorporate network inference and underperforms in eukaryotes. We present an Integrated Deduced And Metabolism (IDREAM) method that combines statistically inferred Environment and Gene Regulatory Influence Network (EGRIN) models with the PROM framework to create enhanced metabolic-regulatory network models. We used IDREAM to predict phenotypes and genetic interactions between transcription factors and genes encoding metabolic activities in the eukaryote, Saccharomyces cerevisiae. IDREAM models contain many fewer interactions than PROM and yet produce significantly more accurate growth predictions. IDREAM consistently outperformed PROM using any of three popular yeast metabolic models and across three experimental growth conditions. Importantly, IDREAM's enhanced accuracy makes it possible to identify subtle synthetic growth defects. With experimental validation, these novel genetic interactions involving the pyruvate dehydrogenase complex suggested a new role for fatty acid-responsive factor Oaf1 in regulating acetyl-CoA production in glucose grown cells.
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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.