Genome-scale models in human metabologenomics

Saklayen, M. G. The global epidemic of the metabolic syndrome. Curr. Hypertens. Rep. 20, 12 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Martínez-Reyes, I. & Chandel, N. S. Cancer metabolism: looking forward. Nat. Rev. Cancer 21, 669–680 (2021).

Article  PubMed  Google Scholar 

Xu, Y. et al. An atlas of genetic scores to predict multi-omic traits. Nature 616, 123–131 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aaltonen, L. A. et al. Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020).

Article  Google Scholar 

Mardinoglu, A. & Nielsen, J. Systems medicine and metabolic modelling. J. Intern. Med. 271, 142–154 (2012). An extensive review of the use of GEMs in systems medicine-based applications.

Article  CAS  PubMed  Google Scholar 

Hyduke, D. R., Lewis, N. E. & Palsson, B. Ø. Analysis of omics data with genome-scale models of metabolism. Mol. Biosyst. 9, 167–174 (2013).

Article  CAS  PubMed  Google Scholar 

Hasin, Y., Seldin, M. & Lusis, A. Multi-omics approaches to disease. Genome Biol. 18, 83 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Palsson, B. & Zengler, K. The challenges of integrating multi-omic data sets. Nat. Chem. Biol. 6, 787–789 (2010).

Article  PubMed  Google Scholar 

Mardinoglu, A., Boren, J., Smith, U., Uhlen, M. & Nielsen, J. Systems biology in hepatology: approaches and applications. Nat. Rev. Gastroenterol. Hepatol. 15, 365–377 (2018). An extensive review of the studies that use biological networks for integration of multiomics data for complex liver diseases.

Article  CAS  PubMed  Google Scholar 

Bajwa, J., Munir, U., Nori, A. & Williams, B. Artificial intelligence in healthcare: transforming the practice of medicine. Future Healthc. J. 8, e188–e194 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Oberhardt, M. A., Palsson, B. Ø. & Papin, J. A. Applications of genome-scale metabolic reconstructions. Mol. Syst. Biol. 5, 320 (2009).

Article  PubMed  PubMed Central  Google Scholar 

Mardinoglu, A., Gatto, F. & Nielsen, J. Genome-scale modeling of human metabolism — a systems biology approach. Biotechnol. J. 8, 985–996 (2013). An extensive review of the algorithms for the reconstruction of cell- and tissue- type specific GEMs.

Article  CAS  PubMed  Google Scholar 

O’Brien, E. J., Monk, J. M. & Palsson, B. O. Using genome-scale models to predict biological capabilities. Cell 161, 971–987 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Nielsen, J. Systems biology of metabolism: a driver for developing personalized and precision medicine. Cell Metab. 25, 572–579 (2017).

Article  CAS  PubMed  Google Scholar 

Wagner, A. et al. Metabolic modeling of single Th17 cells reveals regulators of autoimmunity. Cell 184, 4168–4185.e21 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yizhak, K., Chaneton, B., Gottlieb, E. & Ruppin, E. Modeling cancer metabolism on a genome scale. Mol. Syst. Biol. 11, 817 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Terekhanova, N. V. et al. Epigenetic regulation during cancer transitions across 11 tumour types. Nature 623, 432–441 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Duarte, N. C. et al. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl Acad. Sci. USA 104, 1777–1782 (2007). This study presents the first global human GEM and its use for systems biology-based applications.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ma, H. et al. The Edinburgh Human Metabolic Network reconstruction and its functional analysis. Mol. Syst. Biol. 3, 135 (2007).

Article  PubMed  PubMed Central  Google Scholar 

Hao, T., Ma, H. W., Zhao, X. M. & Goryanin, I. Compartmentalization of the Edinburgh Human Metabolic Network. BMC Bioinformatics 11, 393 (2010).

Article  PubMed  PubMed Central  Google Scholar 

Palsson, B. Ø. Systems Biology: Constraint-Based Reconstruction and Analysis (Cambridge Univ. Press, 2015).

Agren, R. et al. Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT. PLoS Comput. Biol. 8, e1002518 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Thiele, I. et al. A community-driven global reconstruction of human metabolism. Nat. Biotechnol. 31, 419–425 (2013).

Article  CAS  PubMed  Google Scholar 

Mardinoglu, A. et al. Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease. Nat. Commun. 5, 3083 (2014).

Article  PubMed  Google Scholar 

Gille, C. et al. HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol. Syst. Biol. 6, 411 (2010).

Article  PubMed  PubMed Central  Google Scholar 

Mardinoglu, A. et al. Integration of clinical data with a genome-scale metabolic model of the human adipocyte. Mol. Syst. Biol. 9, 649 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kanehisa, M. in ‘In Silico’ Simulation of Biological Processes: Novartis Foundation Symposium 247 (eds. Bock, G. & Goode, J. A.) 91–103 (Wiley, 2002).

Milacic, M. et al. The Reactome Pathway Knowledgebase 2024 Nucleic Acids Res. 52, D672–D678 (2024).

Article  PubMed  Google Scholar 

Quek, L.-E. et al. Reducing Recon 2 for steady-state flux analysis of HEK cell culture. J. Biotechnol. 184, 172–178 (2014).

Article  CAS  PubMed  Google Scholar 

Smallbone, K. Striking a balance with Recon 2.1. Preprint at arXiv https://doi.org/10.48550/arXiv.1311.5696 (2014).

Swainston, N. et al. Recon 2.2: from reconstruction to model of human metabolism. Metabolomics 12, 109 (2016).

Article  PubMed  PubMed Central  Google Scholar 

Brunk, E. et al. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat. Biotechnol. 36, 272–281 (2018). This paper presents the community-based global reconstruction of human metabolism.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Robinson, J. L. et al. An atlas of human metabolism. Sci. Signal. 13, eaaz1482 (2020). This paper presents an extensively curated global human GEM that unifies two parallel model lineages.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dahal, S., Yurkovich, J. T., Xu, H., Palsson, B. O. & Yang, L. Synthesizing systems biology knowledge from omics using genome-scale models. Proteomics 20, 1900282 (2020).

Article  CAS  Google Scholar 

Mardinoglu, A. & Nielsen, J. New paradigms for metabolic modeling of human cells. Curr. Opin. Biotechnol. 34, 91–97 (2015).

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