ReviewMetabolites2021
Next-Generation Genome-Scale Metabolic Modeling through Integration of Regulatory Mechanisms.
Review in Metabolites, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed.
- Reprogramming SREBP1-dependent lipogenesis and inflammation in high-risk breast with licochalcone A: A novel path to cancer prevention.International journal of cancer · 2026Article
- Advances in genome-scale metabolic modeling of Bacillus subtilis.Biotechnology letters · 2026Review
- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
- A Metabolism-Informed Neural Network Identifies Pathways Influencing the Potency and Toxicity of Antimicrobial Combinations.npj drug discovery · 2026Article
- Metabolic and post-translational modifications in sepsis-associated immune dysfunction: a conceptual framework.Frontiers in immunology · 2026Review
- Metabolic Engineering of Terpenoid Biosynthesis in Medicinal Plants: From Genomic Insights to Biotechnological Applications.Current issues in molecular biology · 2025Review
- Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.Microbiology and molecular biology reviews : MMBR · 2025Review
- Metabolic Objectives and Trade-Offs: Inference and Applications.Metabolites · 2025Review
- RBI: a novel algorithm for regulatory-metabolic network model in designing the optimal mutant strain.PeerJ. Computer science · 2025Article
- Personalized modeling of gut microbiome metabolism throughout the first year of life.Communications medicine · 2024Article
- Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli.NPJ systems biology and applications · 2024Article
- Control Theory and Systems Biology: Potential Applications in Neurodegeneration and Search for Therapeutic Targets.International journal of molecular sciences · 2023Review
- Metabolic stratification of human breast tumors reveal subtypes of clinical and therapeutic relevance.iScience · 2023Article
- Practical sampling of constraint-based models: Optimized thinning boosts CHRR performance.PLoS computational biology · 2023Article
- SynBioTools: a one-stop facility for searching and selecting synthetic biology tools.BMC bioinformatics · 2023Article
- Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures.Metabolites · 2023Review
- Genome sequencing and metabolic network reconstruction of a novel sulfur-oxidizing bacteriumFrontiers in microbiology · 2023Article
- Protocol for CAROM: A machine learning tool to predict post-translational regulation from metabolic signatures.STAR protocols · 2022Article
- A flux-based machine learning model to simulate the impact of pathogen metabolic heterogeneity on drug interactions.PNAS nexus · 2022Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Genome-scale metabolic models (GEMs) are powerful tools for understanding metabolism from a systems-level perspective. However, GEMs in their most basic form fail to account for cellular regulation. A diverse set of mechanisms regulate cellular metabolism, enabling organisms to respond to a wide range of conditions. This limitation of GEMs has prompted the development of new methods to integrate regulatory mechanisms, thereby enhancing the predictive capabilities and broadening the scope of GEMs. Here, we cover integrative models encompassing six types of regulatory mechanisms: transcriptional regulatory networks (TRNs), post-translational modifications (PTMs), epigenetics, protein-protein interactions and protein stability (PPIs/PS), allostery, and signaling networks. We discuss 22 integrative GEM modeling methods and how these have been used to simulate metabolic regulation during normal and pathological conditions. While these advances have been remarkable, there remains a need for comprehensive and widespread integration of regulatory constraints into GEMs. We conclude by discussing challenges in constructing GEMs with regulation and highlight areas that need to be addressed for the successful modeling of metabolic regulation. Next-generation integrative GEMs that incorporate multiple regulatory mechanisms and their crosstalk will be invaluable for discovering cell-type and disease-specific metabolic control mechanisms.
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What OpenQuestion holds
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.