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Al-Majdoub ZM, Carroll KM, Gaskell SJ, Barber J. Quantification of the Proteins of the Bacterial Ribosome Using QconCAT Technology. J Proteome Res 2014; 13:1211-22. [DOI: 10.1021/pr400667h] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Zubida M. Al-Majdoub
- Manchester Institute for Biotechnology, 131 Princess Street, Manchester M1 7DS, United Kingdom
- Manchester
Pharmacy School, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Kathleen M. Carroll
- Manchester Institute for Biotechnology, 131 Princess Street, Manchester M1 7DS, United Kingdom
| | - Simon J. Gaskell
- Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Jill Barber
- Manchester Institute for Biotechnology, 131 Princess Street, Manchester M1 7DS, United Kingdom
- Manchester
Pharmacy School, University of Manchester, Manchester M13 9PT, United Kingdom
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Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N. Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC SYSTEMS BIOLOGY 2013; 7:116. [PMID: 24180668 PMCID: PMC4228421 DOI: 10.1186/1752-0509-7-116] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 10/23/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data. RESULTS To increase the efficiency of model creation, the Path2Models project has automatically generated mathematical models from pathway representations using a suite of freely available software. Data sources include KEGG, BioCarta, MetaCyc and SABIO-RK. Depending on the source data, three types of models are provided: kinetic, logical and constraint-based. Models from over 2 600 organisms are encoded consistently in SBML, and are made freely available through BioModels Database at http://www.ebi.ac.uk/biomodels-main/path2models. Each model contains the list of participants, their interactions, the relevant mathematical constructs, and initial parameter values. Most models are also available as easy-to-understand graphical SBGN maps. CONCLUSIONS To date, the project has resulted in more than 140 000 freely available models. Such a resource can tremendously accelerate the development of mathematical models by providing initial starting models for simulation and analysis, which can be subsequently curated and further parameterized.
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Affiliation(s)
- Finja Büchel
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72076, Germany
| | - Nicolas Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Neil Swainston
- Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Clemens Wrzodek
- Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72076, Germany
| | - Tobias Czauderna
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben D-06466, Germany
| | - Roland Keller
- Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72076, Germany
| | - Florian Mittag
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72076, Germany
| | - Michael Schubert
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Mihai Glont
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Martijn van Iersel
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Sarah Keating
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Matthias Rall
- Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72076, Germany
| | - Michael Wybrow
- Caulfield School of Information Technology, Monash University, Victoria 3800, Australia
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Michael Hucka
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Douglas B Kell
- Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
- School of Chemistry, The University of Manchester, Manchester M13 9PL, UK
| | | | - Pedro Mendes
- Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
- School of Computer Science, The University of Manchester, Manchester M13 9PL, UK
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
| | - Andreas Zell
- Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72076, Germany
| | | | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Falk Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben D-06466, Germany
- Institute of Computer Science, University of Halle-Wittenberg, Halle, Germany
| | - Camille Laibe
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Andreas Dräger
- Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72076, Germany
- Present address: University of California, San Diego, Bioengineering Department, La Jolla, CA 92093-0412, USA
| | - Nicolas Le Novère
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Babraham Institute, Babraham Research Campus, Cambridge, UK
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Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JEG, Paton NW, Westerhoff HV, Kell DB, Mendes P. A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Lett 2013; 587:2832-41. [PMID: 23831062 PMCID: PMC3764422 DOI: 10.1016/j.febslet.2013.06.043] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/24/2013] [Accepted: 06/25/2013] [Indexed: 11/17/2022]
Abstract
We present an experimental and computational pipeline for the generation of kinetic models of metabolism, and demonstrate its application to glycolysis in Saccharomyces cerevisiae. Starting from an approximate mathematical model, we employ a “cycle of knowledge” strategy, identifying the steps with most control over flux. Kinetic parameters of the individual isoenzymes within these steps are measured experimentally under a standardised set of conditions. Experimental strategies are applied to establish a set of in vivo concentrations for isoenzymes and metabolites. The data are integrated into a mathematical model that is used to predict a new set of metabolite concentrations and reevaluate the control properties of the system. This bottom-up modelling study reveals that control over the metabolic network most directly involved in yeast glycolysis is more widely distributed than previously thought.
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Affiliation(s)
- Kieran Smallbone
- Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK
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