ArticlePloS one2012
Reconstruction of Danio rerio metabolic model accounting for subcellular compartmentalisation.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Genome-scale metabolic models applied for human health and biopharmaceutical engineering.Quantitative biology (Beijing, China) · 2023Review
- SALARECON connects the Atlantic salmon genome to growth and feed efficiency.PLoS computational biology · 2022Article
- Genome-scale metabolic network reconstruction of model animals as a platform for translational research.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species.Frontiers in molecular biosciences · 2020Article
- Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model ofZebrafish · 2019Article
- Nano-Sampling and Reporter Tools to Study Metabolic Regulation in Zebrafish.Frontiers in cell and developmental biology · 2019Article
- Taurine Biosynthesis in a Fish Liver Cell Line (ZFL) Adapted to a Serum-Free Medium.Marine drugs · 2017Article
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Abstract
Plant and microbial metabolic engineering is commonly used in the production of functional foods and quality trait improvement. Computational model-based approaches have been used in this important endeavour. However, to date, fish metabolic models have only been scarcely and partially developed, in marked contrast to their prominent success in metabolic engineering. In this study we present the reconstruction of fully compartmentalised models of the Danio rerio (zebrafish) on a global scale. This reconstruction involves extraction of known biochemical reactions in D. rerio for both primary and secondary metabolism and the implementation of methods for determining subcellular localisation and assignment of enzymes. The reconstructed model (ZebraGEM) is amenable for constraint-based modelling analysis, and accounts for 4,988 genes coding for 2,406 gene-associated reactions and only 418 non-gene-associated reactions. A set of computational validations (i.e., simulations of known metabolic functionalities and experimental data) strongly testifies to the predictive ability of the model. Overall, the reconstructed model is expected to lay down the foundations for computational-based rational design of fish metabolic engineering in aquaculture.
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