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Prof Pedro Mendes - publications

List of publications


  • Oshota O. J., Malys N., Winder C. L., Dunn W. B., Simeonidis E., Mendes P. Reduction of elementary flux mode complexity enables rational metabolic engineering for biotechnological products. P L o S Computational Biology (Online). eScholarID:247698


  • Alejandro F Villaverde, David Henriques, Kieran Smallbone, Sophia Bongard, Joachim Schmid, Damjan Cicin-Sain, Anton Crombach, Julio Saez-Rodriguez, Klaus Mauch, Eva Balsa-Canto, Pedro Mendes, Johannes Jaeger, Julio R Banga. BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. B M C Systems Biology. 2015; 9: eScholarID:289628 | DOI:10.1186/s12918-015-0144-4
  • Janna Hastings, Gareth Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, Christoph Steinbeck. ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Research. 2015 October; eScholarID:289559 | DOI:10.1093/nar/gkv1031
  • Pedro Mendes, Stephen G Oliver, Douglas B Kell. Fitting transporter activities to cellular drug concentrations and fluxes: why the bumblebee can fly. Trends in Pharmacological Sciences. 2015 November; 36(11): 710-723. eScholarID:289828 | DOI:10.1016/
  • Philippe Bastiaens, Marc R Birtwistle, Nils Blüthgen, Frank J Bruggeman, Kwang-Hyun Cho, Carlo Cosentino, Alberto de la Fuente, Jan B Hoek, Anatoly Kiyatkin, Steffen Klamt, Walter Kolch, Stefan Legewie, Pedro Mendes, Takashi Naka, Tapesh Santra, Eduardo Sontag, Hans V Westerhoff, Boris N Kholodenko. Silence on the relevant literature and errors in implementation. Nature Biotechnology. 2015 April; 33: 336-339. eScholarID:289509 | DOI:10.1038/nbt.3185
  • Stress tolerant transgenic plants over-expressing ascorbic acid and cell wall synthesis genes 2015 April 07. eScholarID:289532
  • Pierre Millard. Impact of kinetic isotope effects in isotopic studies of metabolic systems. B M C Systems Biology. 2015 September; 9: eScholarID:274868 | DOI:10.1186/s12918-015-0213-8


  • P Mendes, JO Dada, K Smallbone. Computational Methods in Systems Biology. Heidelberg New York Dordrecht London: Springer:2014. eScholarID:289761
  • H Summersgill, H England, G Lopez-Castejon, C B Lawrence, N M Luheshi, J Pahle, P Mendes, D Brough. Zinc depletion regulates the processing and secretion of IL-1β. Cell Death & Disease. 2014 January; 5: eScholarID:227430 | DOI:10.1038/cddis.2013.547


  • Simon Mitchell, Pedro Mendes. A Computational Model of Liver Iron Metabolism. P L o S Computational Biology (Online). 2013 November; 9(11): eScholarID:227420 | DOI:10.1371/journal.pcbi.1003299
  • Avraam Tapinos, Pedro Mendes. A Method for Comparing Multivariate Time Series with Different Dimensions. PLoS ONE. 2013 February; 8(2): . eScholarID:186948 | DOI:10.1371/journal.pone.0054201
  • Thiele et al. A community-driven global reconstruction of human metabolism. Nature Biotechnology. 2013 May; 31: 419-425. eScholarID:198610 | DOI:10.1038/nbt.2488
  • 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 characterization of all its enzymes. FEBS Letters. 2013; 587: 2832-2841. eScholarID:209167 | DOI:10.1016/j.febslet.2013.06.043
  • Mensonides FIC, Bakker BM, Cremazy F, Messiha HL , Mendes P, Boogerd FC, Westerhoff HV. A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides – illustrated for the glycolytic enzymes of Saccharomyces cerevisiae. FEBS Letters. 2013 September; 587(17): 2860-2867. eScholarID:209154
  • Neil Swainston, Pedro Mendes, Douglas B Kell. An analysis of a ‘community-driven’ reconstruction of the human metabolic network. Metabolomics. 2013 July; 9: 757-764. eScholarID:209160 | DOI:10.1007/s11306-013-0564-3
  • Firczuk H, Kannambath S, Pahle J, Claydon A, Beynon R, Duncan J, Westerhoff H, Mendes P, McCarthy JEG. An in vivo control map for the eukaryotic mRNA translation machinery. Molecular Systems Biology. 2013 January; 9: . eScholarID:186878 | DOI:10.1038/msb.2012.73
  • Katherine A. Lisko, Raquel Torres, Rodney S. Harris, Melinda Belisle, Martha M. Vaughan, Berangère Jullian, Boris I. Chevone, Pedro Mendes, Craig L. Nessler, Argelia Lorence. Elevating vitamin C content via overexpression of myo-inositol oxygenase and L-gulono-1,4-lactone oxidase in Arabidopsis leads to enhanced biomass and tolerance to abiotic stresses. 2013 December; 49(6): 643-655. eScholarID:227418 | DOI:10.1007/s11627-013-9568-y
  • Kieran Smallbone, Pedro Mendes. Large-Scale Metabolic Models: From Reconstruction to Differential Equations. Industrial Biotechnology. 2013 August; 9(4): 179-184. eScholarID:227429 | DOI:10.1089/ind.2013.0003
  • Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère. Path2Models: large-scale generation of computational models from biochemical pathway maps. 2013; 7: eScholarID:227419 | DOI:doi:10.1186/1752-0509-7-116
  • Natalie J. Stanford, Timo Lubitz, Kieran Smallbone, Edda Klipp, Pedro Mendes, Wolfram Liebermeister. Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks. P L o S One. 2013 November; 8(11): eScholarID:227421 | DOI:10.1371/journal.pone.0079195
  • Wei Sha, Ana M Martins, Reinhard Laubenbacher, Pedro Mendes, Vladimir Shulaev. The genome-wide early temporal response of Saccharomyces cerevisiae to oxidative stress induced by cumene hydroperoxide. PLOS One. 2013 September; 8(9): . eScholarID:209163 | DOI:10.1371/journal.pone.007493
  • Edward Kent, Stefan Neumann, Ursula Kummer, Pedro Mendes. What Can We Learn from Global Sensitivity Analysis of Biochemical Systems?. P L o S One. 2013 November; 8(11): eScholarID:227427 | DOI:10.1371/journal.pone.0079244


  • Heavner B, Smallbone K, Barker B, Mendes P, Walker L. Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC systems biology. 2012; 6: 55. eScholarID:172482 | PMID:22663945 | DOI:10.1186/1752-0509-6-55
  • Kent E, Hoops S, Mendes P. Condor-COPASI: high-throughput computing for biochemical networks. BMC systems biology. 2012 July; 6(1): 91. eScholarID:172477 | PMID:22834945 | DOI:10.1186/1752-0509-6-91
  • Lee D, Smallbone K, Dunn W, Murabito E, Winder C, Kell D, Mendes P, Swainston N. Improving metabolic flux predictions using absolute gene expression data. BMC systems biology. 2012 June; 6(1): 73. eScholarID:172481 | PMID:22713172 | DOI:10.1186/1752-0509-6-73
  • Pahle J, Challenger J, Mendes P, McKane A. Biochemical fluctuations, optimisation and the linear noise approximation. BMC systems biology. 2012; 6: 86. eScholarID:172480 | PMID:22805626 | DOI:10.1186/1752-0509-6-86


  • Grigoriy Blekherman, Reinhard Laubenbacher, Diego F. Cortes, Pedro Mendes, Frank M. Torti, Steven Akman, Suzy V. Torti, Vladimir Shulaev. Bioinformatics tools for cancer metabolomics. Metabolomics. 2011; 7: 329-343. eScholarID:154870 | DOI:10.1007/s11306-010-0270-3
  • Mélanie Courtot, Nick Juty, Christian Knüpfer, Dagmar Waltemath, Anna Zhukova, Andreas Dräger, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew Pocock, Nicolas Rodriguez, Alice Villeger, Darren J Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, Nicolas Le Novère. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology. 2011 October; 7: . eScholarID:154866 | DOI:doi:10.1038/msb.2011.77
  • Small B.G., McColl B.W., Allmendinger R., Pahle J., López-Castejón G., Rothwell N.J., Knowles J., Mendes P., Brough D., Kell D.B. Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing. Nature Chemical Biology. 2011 October; 7(12): 902-908. eScholarID:135889 | DOI:10.1038/nchembio.689
  • Nobata C., Dobson P.D., Iqbal S.A., Mendes P., Tsujii J., Kell D.B., Ananiadou S. Mining metabolites: extracting the yeast metabolome from the literature. Metabolomics. 2011; 7(1): 94-101. eScholarID:117354 | DOI:10.1007/s11306-010-0251-6
  • Joel L. Shuman, Diego F. Cortes, Jenny M. Armenta, Revonda M. Pokrzywa, Pedro Mendes P, Vladimir Shulaev. Plant metabolomics by GC-MS and differential analysis. Methods in Molecular Biology. 678. Springer.2011: eScholarID:154872
  • Neil Swainston, Kieran Smallbone, Pedro Mendes, Douglas Kell and Norman Paton. The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks. Journal of Integrative Bioinformatics. 2011 November; 8: . eScholarID:163093 | DOI:doi:10.2390/biecoll-jib-2011-186


  • Swainston, N., Golebiewski,N., Messiha, H.L., Malys, N., Kania, R., Kengne, S., Krebs, O., Mir, S., Sauer-Danzwith, H., Smallbone, K., Weidemann, A., Wittig, U., Kell, D.B., Mendes, P., Müller, W., Paton, N.W., Rojas, I. Enzyme kinetics informatics: from instrument to browser. FEBS Journal. 2010; 277: 3769-3779. eScholarID:117350 | DOI:10.1111/j.1742-4658.2010.07778.x
  • Dobson, PD, Smallbone, K, Jameson, D, Simeonidis, E, Lanthaler, K, Pir, P, Lu, C, Swainston, N, Dunn, WB, Fisher, P, Hull, D, Brown, M, Oshota, O, Stanford, NJ, Kell, DB, King, RD, Oliver, SG, Stevens, RD, Mendes, P. Further developments towards a genome-scale metabolic model of yeast. BMC Systems Biology. 2010; 4: . eScholarID:117351 | DOI:10.1186/1752-0509-4-145
  • Li, P., Dada, J.O., Jameson, D., Spasic, I., Swainston, N., Carroll, K., Dunn, W., Khan, F.,Naglis, M., Messiha, H.L., Simeonidis, E., Weichart, D., Winder, C., Whisart, J., Broomhead, D., Goble, C.A., Gaskell, S.J., Kell, D.B., Westerhoff, H.V., Mendes, P., Paton, N.W. Systematic integration of experimental data and models in systems biology. BMC Bioinformatics. 2010 November; 11: . eScholarID:117353 | DOI:10.1186/1471-2105-11-582
  • Smallbone, K., Simeonidis, E., Swainston, N., Mendes, P. Towards a genome-scale kinetic model of cellular metabolism. BMC Systems Biology. 2010 January; 4(January): . eScholarID:117343 | DOI:10.1186/1752-0509-4-6


  • Reinhard Laubenbacher, Valerie Hower, Abdul Jarrah, Suzy V. Torti, Vladimir Shulaev, Pedro Mendes, Frank M. Torti, Steven Akman. A Systems Biology View of Cancer. Biochimica et Biophysica Acta. 2009 June; 1796(2): 129-139. eScholarID:67032 | DOI:10.1016/j.bbcan.2009.06.001
  • Dada, Joseph O, and Pedro Mendes. Design and Architecture of Web Services for Simulation of Biochemical Systems. DILS. Springer: 2009: 182-195. eScholarID:2h999 | DOI:10.1007/978-3-642-02879-3_15
  • Hower V, Mendes P, Torti F, Laubenbacher R, Akman S, Shulaev V, Torti S. A general map of iron metabolism and tissue-specific subnetworks. Molecular bioSystems. 2009 May; 5(5): 422-43. eScholarID:67048 | PMID:19381358 | DOI:10.1039/b816714c
  • Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U. Computational modeling of biochemical networks using COPASI. Methods in molecular biology (Clifton, N.J.). 2009; 500: 17-59. eScholarID:67047 | PMID:19399433 | DOI:10.1007/978-1-59745-525-1_2
  • Swainston N, Mendes P. libAnnotationSBML: a library for exploiting SBML annotations. Bioinformatics. 2009; 25(17): 2292-2293. eScholarID:1h462 | DOI:10.1093/bioinformatics/btp392


  • Herrgård M, Swainston N, Dobson P, Dunn W, Arga K, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo M, Oliveira A, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasié I, Weichart D, Brent R, Broomhead D, Westerhoff H, Kirdar B, Penttilä M, Klipp E, Palsson B, Sauer U, Oliver S, Mendes P, Nielsen J, Kell D. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature biotechnology. 2008 October; 26(10): 1155-1160. eScholarID:67049 | PMID:18846089 | DOI:10.1038/nbt1492
  • Kell D, Mendes P. The markup is the model: reasoning about systems biology models in the Semantic Web era. Journal of theoretical biology. 2008 June; 252(3): 538-43. eScholarID:67051 | PMID:18054049 | DOI:10.1016/j.jtbi.2007.10.023
  • Sahle S, Mendes P, Hoops S, Kummer U. A new strategy for assessing sensitivities in biochemical models. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences. 2008 October; 366(1880): 3619-31. eScholarID:67050 | PMID:18632455 | DOI:10.1098/rsta.2008.0108


  • , Sansone S, Fan T, Goodacre R, Griffin J, Hardy N, Kaddurah-Daouk R, Kristal B, Lindon J, Mendes P, Morrison N, Nikolau B, Robertson D, Sumner L, Taylor C, van der Werf M, van Ommen B, Fiehn O. The metabolomics standards initiative. Nature biotechnology. 2007 August; 25(8): 846-8. eScholarID:67081 | PMID:17687353 | DOI:10.1038/nbt0807-846b
  • Camacho D, Vera Licona P, Mendes P, Laubenbacher R. Comparison of reverse-engineering methods using an in silico network. Annals of the New York Academy of Sciences. 2007 December; 1115: 73-89. eScholarID:67052 | PMID:17925358 | DOI:10.1196/annals.1407.006
  • Henriques I, Aga D, Mendes P, O'Connor S, Love N. Metabolic footprinting: a new approach to identify physiological changes in complex microbial communities upon exposure to toxic chemicals. Environmental science & technology. 2007 June; 41(11): 3945-51. eScholarID:67053 | PMID:17612173
  • Martins A, Sha W, Evans C, Martino-Catt S, Mendes P, Shulaev V. Comparison of sampling techniques for parallel analysis of transcript and metabolite levels in Saccharomyces cerevisiae. Yeast (Chichester, England). 2007 March; 24(3): 181-8. eScholarID:67080 | PMID:17230580 | DOI:10.1002/yea.1442


  • Baharat Mehrotra, Pedro Mendes. Bioinformatics approaches to integrate metabolomics and other systems biology data. In: Kazuki Saito, Richard A. Dixon, Lothar Willmitzer, ed. Plant Metabolomics. Berlin and Heidelberg, Germany, Springer-Verlag.2006: eScholarID:67084
  • Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U. COPASI - a COmplex PAthway SImulator. Bioinformatics. 2006; 22(24): 3067-3074. eScholarID:1h463 | DOI:10.1093/bioinformatics/btl485
  • Mendes P. Metabolomics and the challenges ahead. Briefings in Bioinformatics. 2006; 7(2): 127. eScholarID:1h464 | DOI:10.1093/bib/bbl010
  • Rodriguez-Fernandez M, Mendes P, Banga J. A hybrid approach for efficient and robust parameter estimation in biochemical pathways. Bio Systems. 2006; 83(2-3): 248-65. eScholarID:67056 | PMID:16236429 | DOI:10.1016/j.biosystems.2005.06.016
  • Sahle, Sven, Ralph Gauges, Jürgen Pahle, Natalia Simus, Ursula Kummer, Stefan Hoops, Christine Lee, Mudita Singhal, Liang Xu, and Pedro Mendes. Simulation of biochemical networks using COPASI: a complex pathway simulator. Winter Simulation Conference. WSC: 2006: 1698-1706. eScholarID:2h1007
  • Sauro, Herbert M, David Harel, Marta Z Kwiatkowska, Clifford A Shaffer, Adelinde M Uhrmacher, Michael Hucka, Pedro Mendes, Lena Strömbäck, and John J Tyson. Challenges for modeling and simulation methods in systems biology. Winter Simulation Conference. WSC: 2006: 1720-1730. eScholarID:2h1008


  • Reinhard Laubenbacher, Pedro Mendes. A discrete approach to top-down modeling of biochemical networks. In: Andres Kriete, Roland Eils, ed. Computational Systems Biology. Burlington, MA, Academic Press.2005: eScholarID:67089
  • Grant R. Cramer, John C. Cushman, David A. Schooley, David Quilici, Delphine Vincent, Marlene C. Bohlman, Karen Schlauch, Pedro Mendes. Progress in bioinformatics - the challenge of integrating transcriptomic, proteomic and metabolomic information. Acta Horticulturae. 2005; 689: 417-425. eScholarID:67093
  • Broeckling C, Huhman D, Farag M, Smith J, May G, Mendes P, Dixon R, Sumner L. Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. Journal of experimental botany. 2005 January; 56(410): 323-36. eScholarID:67059 | PMID:15596476 | DOI:10.1093/jxb/eri058
  • Le Novère N, Finney A, Hucka M, Bhalla U, Campagne F, Collado-Vides J, Crampin E, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep J, Spence H, Wanner B. Minimum information requested in the annotation of biochemical models (MIRIAM). Nature biotechnology. 2005 December; 23(12): 1509-15. eScholarID:67054 | PMID:16333295 | DOI:10.1038/nbt1156
  • Lei Z, Elmer A, Watson B, Dixon R, Mendes P, Sumner L. A two-dimensional electrophoresis proteomic reference map and systematic identification of 1367 proteins from a cell suspension culture of the model legume Medicago truncatula. Molecular & cellular proteomics : MCP. 2005 November; 4(11): 1812-25. eScholarID:67057 | PMID:16048909 | DOI:10.1074/mcp.D500005-MCP200
  • Mendes P, Camacho D, de la Fuente A. Modelling and simulation for metabolomics data analysis. Biochemical Society transactions. 2005 December; 33(Pt 6): 1427-9. eScholarID:67055 | PMID:16246137 | DOI:10.1042/BST20051427
  • Suzuki H, Reddy M, Naoumkina M, Aziz N, May G, Huhman D, Sumner L, Blount J, Mendes P, Dixon R. Methyl jasmonate and yeast elicitor induce differential transcriptional and metabolic re-programming in cell suspension cultures of the model legume Medicago truncatula. Planta. 2005 March; 220(5): 696-707. eScholarID:67058 | PMID:15605242 | DOI:10.1007/s00425-004-1387-2


  • Fuente A, Bing N, Hoeschele I, Mendes P. Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics. 2004; 20(18): 3565-3574. eScholarID:1h465 | DOI:10.1093/bioinformatics/bth445


  • PEDROSA MENDES PJ; MOLES C; BANGA J. Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Research. 2003 October; 13(11): 2467-2474. eScholarID:1a10887 | DOI:10.1101/gr.1262503
  • PEDROSA MENDES PJ; HUCKA M; FINNEY A; SAURO H; . The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003 March; 19(4): 524-531. eScholarID:1a10884 | DOI:10.1093/bioinformatics/btg015
  • Mendes, Pedro, Wei Sha, and Keying Ye. Artificial gene networks for objective comparison of analysis algorithms. ECCB. 2003: 122-129. eScholarID:2h1010


  • Guo, Dianjing, Xingjing Li, Aejaaz Kamal, Olga Brazhnik, and Pedro Mendes. A Reference Database for Medicago Truncatula Genes, Protiens, and Metabolites. CSB. IEEE Computer Society: 2002: 343. eScholarID:2h1012
  • Mendes P. Emerging bioinformatics for the metabolome. Briefings in Bioinformatics. 2002; 3(2): 134-145. eScholarID:1h467 | DOI:10.1093/bib/3.2.134


  • Mendes P, Kell D. MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems. Bioinformatics. 2001; 17(3): 288-289. eScholarID:1h469 | DOI:10.1093/bioinformatics/17.3.288
  • Siepel A, Farmer A, Tolopko A, Zhuang M, Mendes P, Beavis W, Sobral B. ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics. 2001; 17(1): 83-94. eScholarID:1h468 | DOI:10.1093/bioinformatics/17.1.83


  • Mendes P, Kell D. Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics. 1998; 14(10): 869-883. eScholarID:1h470


  • Mendes P. GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Computer Applications in the Biosciences. 1993; 9(5): 563-571. eScholarID:1h471