An atlas of human metabolism

Jonathan L. Robinson; Pınar Kocabaş; Hao Wang; Pierre Etienne Cholley; Daniel Cook; Avlant Nilsson; Mihail Anton; Raphael Ferreira; Iván Domenzain; Virinchi Billa; Angelo Limeta; Alex Hedin; Johan Gustafsson; Eduard J. Kerkhoven; L. Thomas Svensson; Bernhard O. Palsson; Adil Mardinoglu; Lena Hansson; Mathias Uhlén; Jens Nielsen

doi:10.1126/scisignal.aaz1482

An atlas of human metabolism

Jonathan L. Robinson, Pınar Kocabaş, Hao Wang, Pierre Etienne Cholley, Daniel Cook, Avlant Nilsson, Mihail Anton, Raphael Ferreira, Iván Domenzain, Virinchi Billa, Angelo Limeta, Alex Hedin, Johan Gustafsson, Eduard J. Kerkhoven, L. Thomas Svensson, Bernhard O. Palsson, Adil Mardinoglu, Lena Hansson, Mathias Uhlén, Jens Nielsen

Centre for Host Microbiome Interactions

Research output: Contribution to journal › Article › peer-review

192 Citations (Scopus)

Abstract

Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. Researchers have developed increasingly comprehensive human GEMs, but the disconnect among different model sources and versions impedes further progress. We therefore integrated and extensively curated the most recent human metabolic models to construct a consensus GEM, Human1. We demonstrated the versatility of Human1 through the generation and analysis of cell- and tissue-specific models using transcriptomic, proteomic, and kinetic data. We also present an accompanying web portal, Metabolic Atlas (https://www.metabolicatlas.org/), which facilitates further exploration and visualization of Human1 content. Human1 was created using a version-controlled, open-source model development framework to enable community-driven curation and refinement. This framework allows Human1 to be an evolving shared resource for future studies of human health and disease.

Original language	English
Article number	eaaz1482
Journal	Science Signaling
Volume	13
Issue number	624
DOIs	https://doi.org/10.1126/scisignal.aaz1482
Publication status	Published - 24 Mar 2020

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Robinson, J. L., Kocabaş, P., Wang, H., Cholley, P. E., Cook, D., Nilsson, A., Anton, M., Ferreira, R., Domenzain, I., Billa, V., Limeta, A., Hedin, A., Gustafsson, J., Kerkhoven, E. J., Svensson, L. T., Palsson, B. O., Mardinoglu, A., Hansson, L., Uhlén, M., & Nielsen, J. (2020). An atlas of human metabolism. Science Signaling, 13(624), Article eaaz1482. https://doi.org/10.1126/scisignal.aaz1482

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title = "An atlas of human metabolism",

abstract = "Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. Researchers have developed increasingly comprehensive human GEMs, but the disconnect among different model sources and versions impedes further progress. We therefore integrated and extensively curated the most recent human metabolic models to construct a consensus GEM, Human1. We demonstrated the versatility of Human1 through the generation and analysis of cell- and tissue-specific models using transcriptomic, proteomic, and kinetic data. We also present an accompanying web portal, Metabolic Atlas (https://www.metabolicatlas.org/), which facilitates further exploration and visualization of Human1 content. Human1 was created using a version-controlled, open-source model development framework to enable community-driven curation and refinement. This framework allows Human1 to be an evolving shared resource for future studies of human health and disease.",

author = "Robinson, {Jonathan L.} and Pınar Kocaba{\c s} and Hao Wang and Cholley, {Pierre Etienne} and Daniel Cook and Avlant Nilsson and Mihail Anton and Raphael Ferreira and Iv{\'a}n Domenzain and Virinchi Billa and Angelo Limeta and Alex Hedin and Johan Gustafsson and Kerkhoven, {Eduard J.} and Svensson, {L. Thomas} and Palsson, {Bernhard O.} and Adil Mardinoglu and Lena Hansson and Mathias Uhl{\'e}n and Jens Nielsen",

note = "Funding Information: Research reported in this publication was supported by funding from the Knut and Alice Wallenberg Foundation, the National Cancer Institute of the NIH under award number F32CA220848 (J.L.R.), the Novo Nordisk Foundation (grant no. NNF10CC1016517), and the European Union?s Horizon 2020 research and innovation program under grant agreement no. 720824 (I.D.). Publisher Copyright: Copyright {\textcopyright} 2020 The Authors, some rights reserved.",

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Robinson, JL, Kocabaş, P, Wang, H, Cholley, PE, Cook, D, Nilsson, A, Anton, M, Ferreira, R, Domenzain, I, Billa, V, Limeta, A, Hedin, A, Gustafsson, J, Kerkhoven, EJ, Svensson, LT, Palsson, BO, Mardinoglu, A, Hansson, L, Uhlén, M & Nielsen, J 2020, 'An atlas of human metabolism', Science Signaling, vol. 13, no. 624, eaaz1482. https://doi.org/10.1126/scisignal.aaz1482

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AU - Robinson, Jonathan L.

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AU - Anton, Mihail

AU - Ferreira, Raphael

AU - Domenzain, Iván

AU - Billa, Virinchi

AU - Limeta, Angelo

AU - Hedin, Alex

AU - Gustafsson, Johan

AU - Kerkhoven, Eduard J.

AU - Svensson, L. Thomas

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AU - Mardinoglu, Adil

AU - Hansson, Lena

AU - Uhlén, Mathias

AU - Nielsen, Jens

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N2 - Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. Researchers have developed increasingly comprehensive human GEMs, but the disconnect among different model sources and versions impedes further progress. We therefore integrated and extensively curated the most recent human metabolic models to construct a consensus GEM, Human1. We demonstrated the versatility of Human1 through the generation and analysis of cell- and tissue-specific models using transcriptomic, proteomic, and kinetic data. We also present an accompanying web portal, Metabolic Atlas (https://www.metabolicatlas.org/), which facilitates further exploration and visualization of Human1 content. Human1 was created using a version-controlled, open-source model development framework to enable community-driven curation and refinement. This framework allows Human1 to be an evolving shared resource for future studies of human health and disease.

AB - Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. Researchers have developed increasingly comprehensive human GEMs, but the disconnect among different model sources and versions impedes further progress. We therefore integrated and extensively curated the most recent human metabolic models to construct a consensus GEM, Human1. We demonstrated the versatility of Human1 through the generation and analysis of cell- and tissue-specific models using transcriptomic, proteomic, and kinetic data. We also present an accompanying web portal, Metabolic Atlas (https://www.metabolicatlas.org/), which facilitates further exploration and visualization of Human1 content. Human1 was created using a version-controlled, open-source model development framework to enable community-driven curation and refinement. This framework allows Human1 to be an evolving shared resource for future studies of human health and disease.

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SN - 1945-0877

VL - 13

JO - Science Signaling

JF - Science Signaling

IS - 624

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ER -

An atlas of human metabolism

Abstract

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