ArticleScientific reports2018
Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- The Arabidopsis leaf quantitative atlas: a cellular and subcellular mapping through unified data integration.Quantitative plant biology · 2024Article
- Genome-Scale Metabolic Reconstruction, Non-Targeted LC-QTOF-MS Based Metabolomics Data, and Evaluation of Anticancer Activity ofMetabolites · 2023Article
- Analysis of companion cell and phloem metabolism using a transcriptome-guided model of Arabidopsis metabolism.Plant physiology · 2023Article
- Elucidating the impact ofFrontiers in plant science · 2023Article
- A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations.Plant physiology · 2022Article
- Exploring synergies between plant metabolic modelling and machine learning.Computational and structural biotechnology journal · 2022Review
- Characterization of effects of genetic variants via genome-scale metabolic modelling.Cellular and molecular life sciences : CMLS · 2021Review
- Multiscale plant modeling: from genome to phenome and beyond.Emerging topics in life sciences · 2021Review
- Data Management and Modeling in Plant Biology.Frontiers in plant science · 2021Review
- Advances in flux balance analysis by integrating machine learning and mechanism-based models.Computational and structural biotechnology journal · 2021Review
- Multi-tissue to whole plant metabolic modelling.Cellular and molecular life sciences : CMLS · 2020Review
- Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology.Frontiers in plant science · 2020Review
- Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways.Plant physiology · 2019Review
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Authors and funding
3 authors.
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Abstract
Plant organs consist of multiple cell types that do not operate in isolation, but communicate with each other to maintain proper functions. Here, we extract models specific to three developmental stages of eight root cell types or tissue layers in Arabidopsis thaliana based on a state-of-the-art constraint-based modeling approach with all publicly available transcriptomics and metabolomics data from this system to date. We integrate these models into a multi-cell root model which we investigate with respect to network structure, distribution of fluxes, and concordance to transcriptomics and proteomics data. From a methodological point, we show that the coupling of tissue-specific models in a multi-tissue model yields a higher specificity of the interconnected models with respect to network structure and flux distributions. We use the extracted models to predict and investigate the flux of the growth hormone indole-3-actetate and its antagonist, trans-Zeatin, through the root. While some of predictions are in line with experimental evidence, constraints other than those coming from the metabolic level may be necessary to replicate the flow of indole-3-actetate from other simulation studies. Therefore, our work provides the means for data-driven multi-tissue metabolic model extraction of other Arabidopsis organs in the constraint-based modeling framework.
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