1. A community-driven global reconstruction of human metabolism
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Hulda S. Haraldsdóttir, Douglas B. Kell, Andreas Hoppe, Duncan Hull, Miranda D. Stobbe, Daniel Jameson, Lukas Endler, Swagatika Sahoo, Warwick B. Dunn, Jens Nielsen, Bernhard O. Palsson, Kieran Smallbone, Neema Jamshidi, Stefan Gretar Thorleifsson, David Hala, Hans V. Westerhoff, Ottar Rolfsson, Nikolaus Sonnenschein, Arvind K. Chavali, Ines Thiele, Alexander Mazein, Dieter Weichart, Evgeni Selkov, Sergio Bordel, Michael Hucka, Intawat Nookaew, Nick Juty, Jason A. Papin, Paul D. Dobson, Ronan M. T. Fleming, Jon J. Jonsson, Neil Swainston, Anatoly Sorokin, Maike K. Aurich, Sarah M. Keating, Rasmus Agren, Monica L. Mo, Igor Goryanin, Nathan D. Price, Christian Bölling, Pedro Mendes, Evangelos Simeonidis, Johannes H. G. M. van Beek, Martin I. Sigurdsson, Naglis Malys, Nicolas Le Novère, Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group) [research center], Luxembourg Centre for Systems Biomedicine (LCSB): Molecular Systems Physiology (Thiele Group) [research center], Synthetic Systems Biology (SILS, FNWI), Faculteit der Geneeskunde, Human genetics, NCA - neurodegeneration, Other departments, Univ Iceland, Ctr Syst Biol, Reykjavik, Iceland, Univ Iceland, Fac Ind Engn Mech Engn & Comp Sci, Reykjavik, Iceland, Univ Manchester, Manchester Inst Biotechnol, Manchester Ctr Integrat Syst Biol, Manchester, Lancs, England, Univ Manchester, Sch Comp Sci, Manchester, Lancs, England, Univ Iceland, Dept Biochem & Mol Biol, Reykjavik, Iceland, Charite, Computat Syst Biochem Grp, D-13353 Berlin, Germany, Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA, Univ Amsterdam, Acad Med Ctr, Dept Clin Epidemiol Biostat & Bioinform, NL-1105 AZ Amsterdam, Netherlands, Netherlands Bioinformat Ctr, Nijmegen, Netherlands, Chalmers, Dept Chem & Biol Engn, S-41296 Gothenburg, Sweden, Univ Virginia, Dept Biomed Engn, Charlottesville, VA USA, Univ Sheffield, Dept Chem & Biol Engn, Sheffield, S Yorkshire, England, Cent Manchester Univ Hosp NHS Fdn Trust, Manchester Acad Hlth Sci Ctr, CADET, Manchester, Lancs, England, Univ Vienna, Inst Theoret Chem, Vienna, Austria, Univ N Texas, Dept Biol, Denton, TX 76203 USA, CALTECH, Comp & Math Sci Dept, Pasadena, CA 91125 USA, European Bioinformat Inst, European Mol Biol Lab, Hinxton, England, Babraham Inst, Cambridge, England, Univ Manchester, Fac Life Sci, Manchester, Lancs, England, Univ Warwick, Sch Life Sci, Coventry CV4 7AL, W Midlands, England, Univ Edinburgh, Sch Informat, Edinburgh, Midlothian, Scotland, Inst Syst Biol, Seattle, WA USA, Genome Designs Inc, Walnut Creek, CA USA, Univ Luxembourg, Luxembourg Ctr Syst Biomed, Esch Sur Alzette, Luxembourg, Univ Bremen, Sch Sci & Engn, D-28359 Bremen, Germany, Univ Manchester, Sch Math, Manchester, Lancs, England, Russian Acad Sci, Inst Cell Biophys, Pushchino 142292, Moscow Region, Russia, Vrije Univ Amsterdam, Dept Mol Cell Physiol, Amsterdam, Netherlands, Vrije Univ Amsterdam, Med Ctr, Dept Clin Genet, Sect Med Gen, Amsterdam, Netherlands, Netherlands Consortium Syst Biol, Amsterdam, Netherlands, Univ Manchester, Sch Dent, Manchester, Lancs, England, Okinawa Inst Sci & Technol, Okinawa, Japan, Univ Manchester, Sch Chem Engn & Analyt Sci, Manchester, Lancs, England, Univ Amsterdam, Fac Sci, Swammerdam Inst Life Sci, Amsterdam, Netherlands, Univ Manchester, Sch Chem, Manchester, Lancs, England, Virginia Tech, Virginia Bioinformat Inst, Blacksburg, VA USA, Molecular Cell Physiology, Neuroscience Campus Amsterdam - Neurodegeneration, AIMMS, and Functional Genomics
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Proteome ,Functional features ,computational modelling ,metabolite ,Biomedical Engineering ,Human metabolism ,Bioengineering ,Computational biology ,Multidisciplinary, general & others [F99] [Life sciences] ,Biology ,Data type ,Models, Biological ,biomedical ,Applied Microbiology and Biotechnology ,Article ,03 medical and health sciences ,Multidisciplinaire, généralités & autres [F99] [Sciences du vivant] ,0302 clinical medicine ,Metabolomics ,Multiple Models ,Manchester Institute of Biotechnology ,Humans ,Computer Simulation ,Databases, Protein ,030304 developmental biology ,0303 health sciences ,Representation (systemics) ,Experimental data ,ResearchInstitutes_Networks_Beacons/manchester_institute_of_biotechnology ,Compendium ,3. Good health ,human metabolism ,Metabolome ,biomarker ,Molecular Medicine ,030217 neurology & neurosurgery ,Biotechnology - Abstract
To access publisher's full text version of this article click on the hyperlink at the bottom of the page 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/. Rannis research grant 100406022 Biotechnology and Biological Sciences Research Council (BBSRC) Engineering and Physical Sciences Research Council BB/C008219/1 European Union 201142 Knut and Alice Wallenberg Foundation BBSRC BB/F005938 BB/F00561X German Federal Ministry for Education and Research within the Virtual Liver Network 0315756 0315741 US National Institutes of Health GM088244 National Science Foundation 0643548 Cystic Fibrosis Research Foundation 1060 National Cancer Institute Science and Technology Facilities Council US National Institute of General Medical Sciences R01GM070923 R01GM080219 BioRange programme of The Netherlands Bioinformatics Centre under a Besluit Subsidies Investeringen Kennisinfrastructuur grant through The Netherlands Genomics Initiative SP1.2.4 info:eu-repo/grantAgreement/EC/FP7/232816 info:eu-repo/grantAgreement/EC/FP7/249261
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- 2013
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