A community-driven global reconstruction of human metabolism
Ines Thiele,Neil Swainston,Ronan M. T. Fleming,Andreas Hoppe,Swagatika Sahoo,Maike K. Aurich,Hulda S. Haraldsdóttir,Monica L. Mo,Ottar Rolfsson,Miranda D. Stobbe,Miranda D. Stobbe,Stefan Gretar Thorleifsson,Rasmus Agren,Christian Bölling,Sergio Bordel,Arvind K. Chavali,Paul D. Dobson,Warwick B. Dunn,Warwick B. Dunn,Lukas Endler,David Hala,Michael Hucka,Duncan Hull,Daniel Jameson,Neema Jamshidi,Jon J. Jonsson,Nick Juty,Sarah M. Keating,Intawat Nookaew,Nicolas Le Novère,Nicolas Le Novère,Naglis Malys,Naglis Malys,Alexander Mazein,Jason A. Papin,Nathan D. Price,Evgeni Selkov,Martin I. Sigurdsson,Evangelos Simeonidis,Evangelos Simeonidis,Nikolaus Sonnenschein,Kieran Smallbone,Anatoly Sorokin,Anatoly Sorokin,Johannes H. G. M. van Beek,Dieter Weichart,Igor Goryanin,Jens Nielsen,Hans V. Westerhoff,Douglas B. Kell,Pedro Mendes,Pedro Mendes,Bernhard O. Palsson,Bernhard O. Palsson +53 more
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TLDR
Recon 2, a community-driven, consensus 'metabolic reconstruction', is described, which is the most comprehensive representation of human metabolism that is applicable to computational modeling and has improved topological and functional features.Abstract:
Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling. Compared with its predecessors, the reconstruction has improved topological and functional features, including ~2× more reactions and ~1.7× more unique metabolites. Using Recon 2 we predicted changes in metabolite biomarkers for 49 inborn errors of metabolism with 77% accuracy when compared to experimental data. Mapping metabolomic data and drug information onto Recon 2 demonstrates its potential for integrating and analyzing diverse data types. Using protein expression data, we automatically generated a compendium of 65 cell type–specific models, providing a basis for manual curation or investigation of cell-specific metabolic properties. Recon 2 will facilitate many future biomedical studies and is freely available at http://humanmetabolism.org/.read more
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An introduction to systems toxicology
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Rineke Steenbergen,Martin Oti,Rob ter Horst,Wilson Tat,Christopher J. Neufeldt,Alexandr Belovodskiy,Tiing Tiing Chua,Woo Jung Cho,Michael A. Joyce,Bas E. Dutilh,Bas E. Dutilh,D. Lorne Tyrrell +11 more
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