A community-driven global reconstruction of human metabolism

I. Thiele; N. Swainston; R.M. Fleming; A. Hoppe; S.. Sahoo; M.K. Aurich; H. Haraldsdottir; M.L. Mo; O. Rolfsson; M.D. Stobbe; S.G. Thorleifsson; R. Agren; C. Bölling; S. Bordel; A.K. Chavali; P. Dobson; W.B. Dunn; L. Endler; D. Hala; M. Hucka; D Hull; D. Jameson; N. Jamshidi; J.J. Jonsson; N. Juty; S. Keating; I. Nokaew; N. Le Novère; N. Malys; A. Mazein; J.A. Papin; N.D. Price; E. Selkov; M.I. Sigurdsson; E. Simeonidis; N. Sonnenschein; K. Smallbone; A. Sorokin; J.H.G.M. van Beek; D. Weichart; I. Goryanin; J. Nielsen; H.V. Westerhoff; D.B. Kell; P. Mendes; B.O. Palsson

doi:10.1038/nbt.2488

A community-driven global reconstruction of human metabolism

I. Thiele, N. Swainston, R.M. Fleming, A. Hoppe, S.. Sahoo, M.K. Aurich, H. Haraldsdottir, M.L. Mo, O. Rolfsson, M.D. Stobbe, S.G. Thorleifsson, R. Agren, C. Bölling, S. Bordel, A.K. Chavali, P. Dobson, W.B. Dunn, L. Endler, D. Hala, M. HuckaD Hull, D. Jameson, N. Jamshidi, J.J. Jonsson, N. Juty, S. Keating, I. Nokaew, N. Le Novère, N. Malys, A. Mazein, J.A. Papin, N.D. Price, E. Selkov, M.I. Sigurdsson, E. Simeonidis, N. Sonnenschein, K. Smallbone, A. Sorokin, J.H.G.M. van Beek, D. Weichart, I. Goryanin, J. Nielsen, H.V. Westerhoff, D.B. Kell, P. Mendes, B.O. Palsson

Research output: Contribution to Journal › Article › Academic › peer-review

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/. © 2013 Nature America, Inc. All rights reserved.

Original language	English
Pages (from-to)	419-425
Journal	Nature Biotechnology
Volume	31
Issue number	5
DOIs	https://doi.org/10.1038/nbt.2488
Publication status	Published - 2013

Access to Document

10.1038/nbt.2488

Persistent URL (handle)

Persistent link

Cite this

Thiele, I., Swainston, N., Fleming, R. M., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., Thorleifsson, S. G., Agren, R., Bölling, C., Bordel, S., Chavali, A. K., Dobson, P., Dunn, W. B., Endler, L., Hala, D., ... Palsson, B. O. (2013). A community-driven global reconstruction of human metabolism. Nature Biotechnology, 31(5), 419-425. https://doi.org/10.1038/nbt.2488

@article{394b03c1cb2c416889923259ef71d0fd,

title = "A community-driven global reconstruction of human metabolism",

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/. {\textcopyright} 2013 Nature America, Inc. All rights reserved.",

author = "I. Thiele and N. Swainston and R.M. Fleming and A. Hoppe and S.. Sahoo and M.K. Aurich and H. Haraldsdottir and M.L. Mo and O. Rolfsson and M.D. Stobbe and S.G. Thorleifsson and R. Agren and C. B{\"o}lling and S. Bordel and A.K. Chavali and P. Dobson and W.B. Dunn and L. Endler and D. Hala and M. Hucka and D Hull and D. Jameson and N. Jamshidi and J.J. Jonsson and N. Juty and S. Keating and I. Nokaew and {Le Nov{\`e}re}, N. and N. Malys and A. Mazein and J.A. Papin and N.D. Price and E. Selkov and M.I. Sigurdsson and E. Simeonidis and N. Sonnenschein and K. Smallbone and A. Sorokin and {van Beek}, J.H.G.M. and D. Weichart and I. Goryanin and J. Nielsen and H.V. Westerhoff and D.B. Kell and P. Mendes and B.O. Palsson",

year = "2013",

doi = "10.1038/nbt.2488",

language = "English",

volume = "31",

pages = "419--425",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Publishing Group",

number = "5",

}

Thiele, I, Swainston, N, Fleming, RM, Hoppe, A, Sahoo, S, Aurich, MK, Haraldsdottir, H, Mo, ML, Rolfsson, O, Stobbe, MD, Thorleifsson, SG, Agren, R, Bölling, C, Bordel, S, Chavali, AK, Dobson, P, Dunn, WB, Endler, L, Hala, D, Hucka, M, Hull, D, Jameson, D, Jamshidi, N, Jonsson, JJ, Juty, N, Keating, S, Nokaew, I, Le Novère, N, Malys, N, Mazein, A, Papin, JA, Price, ND, Selkov, E, Sigurdsson, MI, Simeonidis, E, Sonnenschein, N, Smallbone, K, Sorokin, A, van Beek, JHGM, Weichart, D, Goryanin, I, Nielsen, J, Westerhoff, HV, Kell, DB, Mendes, P & Palsson, BO 2013, 'A community-driven global reconstruction of human metabolism', Nature Biotechnology, vol. 31, no. 5, pp. 419-425. https://doi.org/10.1038/nbt.2488

TY - JOUR

T1 - A community-driven global reconstruction of human metabolism

AU - Thiele, I.

AU - Swainston, N.

AU - Fleming, R.M.

AU - Hoppe, A.

AU - Sahoo, S..

AU - Aurich, M.K.

AU - Haraldsdottir, H.

AU - Mo, M.L.

AU - Rolfsson, O.

AU - Stobbe, M.D.

AU - Thorleifsson, S.G.

AU - Agren, R.

AU - Bölling, C.

AU - Bordel, S.

AU - Chavali, A.K.

AU - Dobson, P.

AU - Dunn, W.B.

AU - Endler, L.

AU - Hala, D.

AU - Hucka, M.

AU - Hull, D

AU - Jameson, D.

AU - Jamshidi, N.

AU - Jonsson, J.J.

AU - Juty, N.

AU - Keating, S.

AU - Nokaew, I.

AU - Le Novère, N.

AU - Malys, N.

AU - Mazein, A.

AU - Papin, J.A.

AU - Price, N.D.

AU - Selkov, E.

AU - Sigurdsson, M.I.

AU - Simeonidis, E.

AU - Sonnenschein, N.

AU - Smallbone, K.

AU - Sorokin, A.

AU - van Beek, J.H.G.M.

AU - Weichart, D.

AU - Goryanin, I.

AU - Nielsen, J.

AU - Westerhoff, H.V.

AU - Kell, D.B.

AU - Mendes, P.

AU - Palsson, B.O.

PY - 2013

Y1 - 2013

N2 - 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/. © 2013 Nature America, Inc. All rights reserved.

AB - 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/. © 2013 Nature America, Inc. All rights reserved.

U2 - 10.1038/nbt.2488

DO - 10.1038/nbt.2488

M3 - Article

SN - 1087-0156

VL - 31

SP - 419

EP - 425

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 5

ER -

A community-driven global reconstruction of human metabolism

Abstract

Access to Document

Persistent URL (handle)

Fingerprint

Cite this