ReviewFrontiers in plant science2015
Integration of metabolomics data into metabolic networks.
Review in Frontiers in plant science, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Overview of molecular mechanisms underlying stress responses; signaling pathways and secondary metabolite synthesis in plants.Plant molecular biology · 2026Review
- A historical journey of metabolite-protein interaction discovery: from data harmonization to AI-driven prediction.Briefings in bioinformatics · 2026Review
- Metabolite correlation-based network analysis combined with machine learning techniques highlights LOX biosynthesis in Vanilla planifolia and Vanilla pompona source leaves.Scientific reports · 2026Article
- Physiological, metabolic, and transcriptional responses of contrasting sorghum (Sorghum bicolor (L.) Moench) cultivars to drought.Plant cell reports · 2026Article
- COBRA-k: A powerful framework bridging constraint-based and kinetic metabolic modeling.Science advances · 2026Article
- Transcriptome characterization and metabolite accumulation: novel insights into metabolite biosynthesis during Angiopteris fokiensis leaf development.BMC genomic data · 2025Article
- Mitochondrial Metabolomics in Cancer: Mass Spectrometry-Based Approaches for Metabolic Rewiring Analysis and Therapeutic Discovery.Metabolites · 2025Review
- Pan-omics insights into abiotic stress responses: bridging functional genomics and precision crop breeding.Functional & integrative genomics · 2025Review
- Comparative metabolomics of two nettle species unveils distinct high-altitude adaptation mechanisms on the Tibetan Plateau.BMC plant biology · 2025Article
- From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies.Molecular biotechnology · 2025Review
- Transcriptome-Based Screening of Candidate Low-Temperature-Associated Genes and Analysis of theInternational journal of molecular sciences · 2024Article
- Molecular mechanisms regulating glucose metabolism in quinoa (Chenopodium quinoa Willd.) seeds under drought stress.BMC plant biology · 2024Article
- Metabolomic Analysis of the Effect of Freezing on Leaves ofInternational journal of molecular sciences · 2023Article
- Non-targeted metabolomics analysis of metabolite changes in two quinoa genotypes under drought stress.BMC plant biology · 2023Article
- Article
- HS-SPME-GC × GC/MS combined with multivariate statistics analysis to investigate the flavor formation mechanism of tank-fermented broad bean paste.Food chemistry: X · 2023Article
- Metabolomic analysis for disclosing nutritional and therapeutic prospective of traditional rice cultivars of Cauvery deltaic region, India.Frontiers in nutrition · 2023Article
- Metabolomics and modelling approaches for systems metabolic engineering.Metabolic engineering communications · 2022Review
- Tuning a high performing multiplexed-CRISPRiMetabolic engineering communications · 2022Article
- Physiology and metabonomics reveal differences in drought resistance among soybean varieties.Botanical studies · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabolite levels together with their corresponding metabolic fluxes are integrative outcomes of biochemical transformations and regulatory processes and they can be used to characterize the response of biological systems to genetic and/or environmental changes. However, while changes in transcript or to some extent protein levels can usually be traced back to one or several responsible genes, changes in fluxes and particularly changes in metabolite levels do not follow such rationale and are often the outcome of complex interactions of several components. The increasing quality and coverage of metabolomics technologies have fostered the development of computational approaches for integrating metabolic read-outs with large-scale models to predict the physiological state of a system. Constraint-based approaches, relying on the stoichiometry of the considered reactions, provide a modeling framework amenable to analyses of large-scale systems and to the integration of high-throughput data. Here we review the existing approaches that integrate metabolomics data in variants of constrained-based approaches to refine model reconstructions, to constrain flux predictions in metabolic models, and to relate network structural properties to metabolite levels. Finally, we discuss the challenges and perspectives in the developments of constraint-based modeling approaches driven by metabolomics data.
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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.