The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Computational reconstruction of tissue‐specific metabolic models: application to human liver metabolism
Open accessAbstract
The computational study of human metabolism has been advanced with the advent of the first generic (non‐tissue specific) stoichiometric model of human metabolism. In this study, we present a new algorithm for rapid reconstruction of tissue‐specific genome‐scale models of human metabolism. The algorithm generates a tissue‐specific model from the generic human model by integrating a variety of tissue‐specific molecular data sources, including literature‐based knowledge, transcriptomic, proteomic, metabolomic and phenotypic data. Applying the algorithm, we constructed the first genome‐scale stoichiometric model of hepatic metabolism. The model is verified using standard cross‐validation procedures, and through its ability to carry out hepatic metabolic functions. The model's flux predictions correlate with flux measurements across a variety of hormonal and dietary conditions, and improve upon the predictive performance obtained using the original, generic human model (prediction accuracy of 0.67 versus 0.46). Finally, the model better predicts biomarker changes in genetic metabolic disorders than the generic human model (accuracy of 0.67 versus 0.59). The approach presented can be used to construct other human tissue‐specific models, and be applied to other organisms.
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Cites
What is flux balance analysis?
Orth, J. D., Thiele, I., & Palsson, B. Ø. (2010) · Nature Biotechnology · doi:10.1038/nbt.1614 · Cited by 3,903
History, Heterogeneity, Developmental Biology, and Functions of Quiescent Hepatic Stellate Cells
Geerts, A. (2001) · Seminars in Liver Disease · doi:10.1055/s-2001-17550 · Cited by 740
Metabolic zonation of the liver: Regulation and implications for liver function
Gebhardt, R. (1992) · Pharmacology & Therapeutics · doi:10.1016/0163-7258(92)90055-5 · Cited by 607
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
Feist, A. M., & Palsson, B. Ø. (2008) · Nature Biotechnology · doi:10.1038/nbt1401 · Cited by 545 · cited 2×
“metabolic models: application to human liver metabolism”
The Edinburgh human metabolic network reconstruction and its functional analysis
Ma, H., Sorokin, A., Mazein, A., Selkov, A., Selkov, E., Demin, O., & Goryanin, I. (2007) · Molecular Systems Biology · doi:10.1038/msb4100177 · Cited by 435
Cited by
Godoy, P., Hewitt, N. J., Albrecht, U., Andersen, M. E., Ansari, N., Bhattacharya, S., Bode, J. G., Bolleyn, J., Borner, C., Böttger, J., et al. (2013) · Archives of Toxicology · doi:10.1007/s00204-013-1078-5 · Cited by 1,280
A community-driven global reconstruction of human metabolism
Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2488 · Cited by 1,019
Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
Lewis, N. E., Nagarajan, H., & Palsson, B. O. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2737 · Cited by 779
Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase
Frezza, C., Zheng, L., Folger, O., Rajagopalan, K. N., MacKenzie, E. D., Jerby, L., Micaroni, M., Chaneton, B., Adam, J., Hedley, A., et al. (2011) · Nature · doi:10.1038/nature10363 · Cited by 503
Self-citationThe gut microbiota modulates host amino acid and glutathione metabolism in mice
Mardinoglu, A., Shoaie, S., Bergentall, M., Ghaffari, P., Zhang, C., Larsson, E., Bäckhed, F., & Nielsen, J. (2015) · Molecular Systems Biology · doi:10.15252/msb.20156487 · Cited by 383
Metadata
- Authors
- Jerby, L., Shlomi, T., & Ruppin, E.
- Venue
- Molecular Systems Biology
- Published
- 2010-01
- Volume
- 6
- Issue
- 1
- Pages
- 401-401
- ISSN
- 1744-4292 (ISSN-L)
- OpenAlex
- W2103950919
- Cited by
- 368
- References
- 5
- FWCI
- 13.71
- Type
- journal article
- Language
- en
- Open access
- gold
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