Publications

• Mendes, P., Messiha, H., Malys, N., Hoops, S. (2009) Enzyme kinetics and computational modeling for systems biology. Methods Enzymol. 467, 583-99. [ abstract ]
• Dada, J.O., Mendes, P. (2009) Design and architecture of web services for simulation of biochemical systems. Lecture Notes in Computer Science DILS 5647, 182-195. [ abstract ]
• Swainston, N., Mendes, P. (2009) libAnnotationSBML: a library for exploiting SBML annotations. Bioinformatics 25, 2292-2293. [ abstract ] [ full text ]
• Laubenbacher, R., Hower, V., Jarrah, A., Torti, S.V., Shulaev, V., Mendes, P., Torti, F.M., Akman, S. (2009) A Systems Biology View of Cancer. Biochimica et Biophysica Acta 1796, 129-139. [ abstract ] [ doi:10.1016/j.bbcan.2009.06.001 ]
• Mendes, P, Hoops, S, Sahle, S, Gauges, R, Dada, J, Kummer, U (2009) Computational Modeling of Biochemical Networks Using COPASI. Methods Mol. Biol. 500, 17-59. [ full text ].
• Hower, V., Mendes, P., Torti, F.M., Laubenbacher, R., Akman, S., Shulaev, V. Torti, S.V. (2009) A General Map of Iron Metabolism and Tissue-Specific Subnetworks, Molecular Biosystems, 5, 422-43. [ abstract ] [ full text ]
• Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology, Nature Biotechnol. 26, 1155-1160. [ abstract ] [ full text ].
• Sahle, S. Mendes, P., Hoops, S., Kummer, U. (2008) A new strategy for assessing sensitivities in biochemical models, Phil. Trans. Roy. Soc. A 366, 3619-3631. [ abstract ] [ full text ].
• Flötmann, M., Schaber, J., Hoops, S., Klipp, E., Mendes, P. (2008) ModelMage: A Tool for Automatic Model Generation, Selection and Management Genome Informatics 20, 52-63 [ abstract ] [ full text ]
• Kell, D.B., Mendes, P. (2007) The markup is the model: Reasoning about systems biology models in the Semantic Web era. J. Theoret. Biol. 252, 538-543. [ abstract ]
• Camacho, D., Vera Licona, P., Mendes, P., Laubenbacher, R.. (2007) Comparison of reverse-engineering methods using an in silico network. Ann. N. Y. Acad. Sci. 1115, 73-89. [ abstract ]
• MSI Board Members, Sansone, S.A., Fan, T., Goodacre, R., Griffin, J.L., Hardy, N.W., Kaddurah-Daouk, R., Kristal, B.S., Lindon, J., Mendes, P., Morrison, N., Nikolau, B., Robertson, D., Sumner, L.W., Taylor, C., van der Werf, M., van Ommen, B., Fiehn, O. (2007) The metabolomics standards initiative. Nat. Biotechnol. 25, 846-848.
• Martins, A.M., Sha, W., Evans, C., Martino-Catt, S., Mendes, P., Shulaev, V. (2007) Comparison of sampling techniques for parallel analysis of transcript and metabolite levels in Saccharomyces cerevisiae. Yeast 24, 181-188. [ abstract ]
• Henriques, I.D., Aga, D.S., Mendes, P., O'Connor, S.K., Love, N.G. (2007) Metabolic footprinting: a new approach to identify physiological changes in complex microbial communities upon exposure to toxic chemicals. Environ. Sci. Technol. 41, 3945-3951. [ abstract ]
• Hoops S., Sahle S., Gauges R., Lee C., Pahle J., Simus N., Singhal M., Xu L., Mendes P., Kummer U. (2006) COPASI - a COmplex PAthway SImulator. Bioinformatics 22, 3067-3074 [ abstract ] [ full text ]
• Mendes P., (2006) Metabolomics and the challenges ahead. Briefings in Bioinformatics 7, 127
• Rodriguez-Fernandez, M., Mendes, P., Banga, J.R. (2006) A hybrid approach for efficient and robust parameter estimation in biochemical pathways. Biosystems 83, 248-265 [ abstract ]
• Mehrotra, B., Mendes, P. (2006) Bioinformatics approaches to integrate metabolomics and other systems biology data. in Plant Metabolomics (Biotechnology in Agriculture and Forestry) (Saito, K., Dixon, R.A. & Willmitzer, L. Eds.) Springer-Verlag, Berlin and Heidelberg, Germany, pp. 105-116.
• Novere, N.L., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado-Vides, J., Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J.L., Spence, H.D., Wanner, B.L. (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nature Biotechnology 23, 1509-1515 [ abstract ]
• Lei, Z., Elmer, A.M., Watson, B.S., Dixon, R.A., Mendes, P., Sumner, L.W. (2005) A two-dimensional electrophoresis proteomic reference map and systematic identification of 1367 proteins from a cell suspension culture of the model legume Medicago truncatula. Mol. Cell. Proteomics 4 1812-1825 [ abstract ] [ full text ]
• Camacho, D., de la Fuente, A. & Mendes, P. (2005) The origin of correlations in metabolomics data. Metabolomics 1, 53-63. [ abstract ] [ full text ]
• Mendes, P., Camacho, D., de la Fuente, A. (2005) Modelling and simulation for metabolomics data analysis. Biochem. Soc. Trans. 33, 1427-1429 [ abstract ]
• Laubenbacher, R. & Mendes, P. (2005) A discrete approach to top-down modeling of biochemical networks in Computational Systems Biology (Kriete, A. & Eils, R. Eds.) Elsevier Academic Press, Burlington, MA, pp. 229-247.
• Suzuki, H., Reddy, M.S., Naoumkina, M., Aziz, N., May, G.D., Huhman, D.V., Sumner, L.W., Blount, J.W., Mendes, P. & Dixon, R.A. (2005) Methyl jasmonate and yeast elicitor induce differential transcriptional and metabolic re-programming in cell suspension cultures of the model legume Medicago truncatula. Planta 220, 696-707 [ abstract ] [ Full text ]
• Cramer, G.R., Cushman, J.C., Schooley, D.A., Quilici, D., Vincent, D., Bohlman, M.C., Ergul, A., Tattersall, E.A.R., Tillett, R., Evans, J., Delacruz, R., Schlauch, K. & Mendes, P. (2005) Progress in bioinformatics - the challenge of integrating transcriptomic, proteomic and metabolomic information. Acta Hort. 689, 417-425 [ abstract ]
• Broeckling, C.D., Huhman, D.V., Farag, M.A., Smith, J.T., May, G.D., Mendes, P., Dixon, R.A. & Sumner, L.W. (2005) Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. Journal of Experimental Botany 56, 323-336. [ abstract ] [ full text ]
• Martins, A.M., Camacho, D., Shuman, J., Sha, W., Mendes, P. & Shulaev, V. (2004) A systems biology study of two distinct growth phases of Saccharomyces cerevisiae. Current Genomics 5, 649-663. [ abstract ]
• de la Fuente, A., Bing, N., Hoeschele, I. & Mendes, P. (2004) Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics 20, 3565-3574. [ abstract ]
• Jenkins, H., Hardy, N., Beckmann, M., Draper, J., Smith, A. R., Taylor, J., Fiehn, O., Goodacre, R., Bino, R. J., Hall, R., Kopka, J., Lane, G. A., Lange, B. M., Liu, J. R., Mendes, P., Nikolau, B. J., Oliver, S. G., Paton, N. W., Rhee, S., Roessner-Tunali, U., Saito, K., Smedsgaard, J., Sumner, L. W., Wang, T., Walsh, S., Wurtele, E. S. & Kell, D. B. (2004) A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotechnology 22, 1601-1606. [ abstract ]
• Bino, R. J., Hall, R. D., Fiehn, O., Kopka, J., Saito, K., Draper, J., Nikolau, B. J., Mendes, P., Roessner-Tunali, U., Beale, M. H., Trethewey, R. N., Lange, B. M., Wurtele, E. S. & Sumner, L. W. (2004) Potential of metabolomics as a functional genomics tool. Trends in Plant Sciences 9, 418-25. [ abstract ]
• Lorence, A., Chevone, B.I., Mendes, P. & Nessler, C.L. (2004) myo-Inositol oxygenase offers a possible entry point into plant ascorbate biosynthesis. Plant Physiology 134, 1200-1205. [ abstract ]
• de la Fuente, A. & Mendes, P. (2004) Book Review: Computational analysis of biochemical systems, by Eberhart O. Voit. Bulletin of Mathematical Biology 66, 195-197. [ full text ]
• de la Fuente, A., Brazhnik, P. & Mendes, P. (2004) Regulatory strength analysis for inferring gene networks. in Metabolic engineering in the post-genomics era (Kholodenko, B.N & Westerhoff, H.V. eds.) Horizon Bioscience, Wymondham, UK, pp. 107-137.
• Moles C.G., Mendes P. & Banga J.R. (2003) Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Research 13, 2467-2474. [ abstract ] [ full text ]
• Mendes, P., Sha, W. & Ye, K. (2003) Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics 19, ii122-ii129. [ abstract ] [ full text ]
• Sumner, L.W., Mendes, P., Dixon, R.A. (2003) Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemistry 62, 817-36. [ abstract ] [ full text ]
• de la Fuente, A. & Mendes, P. (2003) Integrative modeling of gene expression and cell metabolism. Applied Bioinformatics 2, 79-90.
• Hucka, M., Finney, A., Sauro, H.M., Bolouri, H., Doyle, J.C., Kitano, H., Arkin, A.P., Bornstein, B.J., Bray, D., Cornish-Bowden, A., Cuellar, A.A., Dronov, S., Gilles, E.D., Ginkel, M., Gor, V., Goryanin, I.I., Hedley, W.J., Hodgman, T.C., Hofmeyr, J.H., Hunter, P.J., Juty, N.S., Kasberger, J.L., Kremling, A., Kummer, U., Le Novere, N., Loew, L.M., Lucio, D., <u>Mendes, P.</u>, Minch, E., Mjolsness, E.D., Nakayama, Y., Nelson, M.R., Nielsen, P.F., Sakurada, T., Schaff, J.C., Shapiro, B.E., Shimizu, T.S., Spence, H.D., Stelling, J., Takahashi, K., Tomita, M., Wagner, J. & Wang, J. (2003). "The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models" Bioinformatics 19, 524-531. [ abstract ]
• Mendes, P. (2002) Emerging bioinformatics for the metabolome. Briefings in Bioinformatics 3, 134-145. [ abstract ]
• Brazhnik, P., de la Fuente, A. & Mendes, P. (2002) Gene networks: how to put the function in genomics. Trends in Biotechnology 20, 467-472. [ abstract ] [ full text ]
• de la Fuente, A. & Mendes, P. (2002) Quantifying gene networks with regulatory strengths. Molecular Biology Reports 29, 73-77. [ abstract ]
• de la Fuente, A., Brazhnik, P. & Mendes, P. (2002) Linking the genes: inferring quantitative gene networks from microarray data. Trends in Genetics 18, 395-398. [ abstract ] [ supplementary information ]
• Mendes, P., de la Fuente, A. & Hoops, S. (2002) Bioinformatics and computational biology for plant functional genomics. Recent Advances in Phytochemistry 36, 1-13.
• Li, X.J., Brazhnik, O., Kamal, A., Guo, D., Lee, C., Hoops, S. & Mendes, P. (2002) Databases and visualization for metabolomics. In Harrigan, G.G. and Goodacre, R. (eds.), Metabolic profiling: its role in biomarker discovery and gene function analysis Kluwer Academic Publishers, Boston, Dordrecht and London, pp. 293-309.
• de la Fuente, A., Snoep, J.L., Westerhoff, H.V. & Mendes, P. (2002) Metabolic control in integrated biochemical systems. European Journal of Biochemistry 269, 4399-4408. [ abstract ] [ supplementary information ]
• de la Fuente, A., Brazhnik, P. & Mendes, P. (2001). A quantitative method for reverse engineering gene networks from microarray experiments using regulatory strengths. Proceedings of the 2nd International Conference on Systems Biology, California Institute of Technology, Pasadena, CA. [ full text ] [ supplementary information ]
• Mendes, P. (2001) Modeling large scale biological systems from functional genomic data: parameter estimation. in Foundations of Systems Biology (Kitano, H., ed), MIT Press, Cambridge, MA, pp. 163-186.
• Mendes, P. & Kell, D.B. (2001) MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems. Bioinformatics 17, 288-289. [ full text ]
• Martins, A.M., Mendes, P., Cordeiro, C. & Freire, A.P. (2001) In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae. European Journal of Biochemistry 268, 3930-3936. [ full text ]
• Siepel, A., Farmer, A., Tolopko, A., Zhuang, M., Mendes, P., Beavis, W. & Sobral, B. (2001) ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics 17, 83-94. [ full text ]
• Sobral, B. W., Mangalam, H., Siepel, A., Mendes, P., Pecherer, R. & McLaren, G. (2001) Bioinformatics for rice resources. Novartis Foundation Symposia 236, 59-81. [ abstract ]
• de la Fuente van Bentem, A., Mendes, P., Westerhoff, H.V. & Snoep, J.L. (2000) Can metabolic control analysis be applied to hierarchical regulated metabolism? MCA versis HCA. in Animating the cellular map (Hofmeyr, J.-H.S., Rohwer, J.H. and Snoep, J.L., eds), Stellenbosch University Press, Stellenbosch, pp. 191-198. [ full text ]
• Mendes, P., Bulmore, D.L., Farmer, A.D., Steadman, P.A., Waugh, M.E. & Wlodek, S.T. (2000) PathDB: a second generation metabolic database. In Animating the cellular map. (Hofmeyr, J.-H.S., Rohwer, J.M. & Snoep, J.L. eds.), Stellenbosch, Stellenbosch University Press, pp. 207-212. [ full text ]
• Kell, D.B. & Mendes, P. (2000) Snapshots of systems: metabolic control analysis and biotechnology in the post-genomic era. In Technological and Medical Implications of Metabolic Control Analysis ( Cornish-Bowden, A. & Cárdenas, M.L. eds.), Dordrecht, Kluwer Academic Publishers, pp. 3-25.
• Mendes, P. (1999) Metabolic simulation as an aid in understanding gene expression data. In Workshop on Computation of Biochemical Pathways and Genetic Networks (Bornberg-Bauer, E., De Beuckelaer, A., Kummer, U., and Rost, U., eds), Logos-Verlag, Heidelberg, pp. 27-34.
• Snoep, J., Mendes, P. and Westerhoff, H. (1999) Teaching Metabolic Control Analysis and kinetic modelling. Towards a portable teaching module. The Biochemist 21 (February 1999), 25-28. [ full text ] (Mounted on the Internet with kind permission from the Biochemical Society, 1999)
• Mendes, P. & Kell, D. B. (1998) Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 10, 869-883. [ abstract ] [ full text ]
• Mendes, P. & Kell, D. B. (1998) Numerical optimisation and simulation for rational metabolic engineering. in BioThermoKinetics in the post genomic era (eds. C. Larsson, I.-L. Påhlman and L. Gustaffson), pp. 345-349. Chalmers Reproservice, Göteborg. full text
• Mendes, P. (1998) Using computers to learn metabolism. Biochemical Society Transactions 27, A21.
• Mendes, P. (1997) Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends in Biochemical Sciences 22, 361-363.
• Mendes, P. & Kell, D.B. (1997) Making cells work - metabolic engineering for everyone. Trends in Biotechnology 15, 6-7. (meeting report)
• Mendes, P., Marmillot, P., Hervagault, J.-F. & Welch, G. R. (1996) Long-range metabolic signalling in heterogeneous catalytic systems: Computer simulation study. In Computation in cellular and molecular biological systems (Cuthbertson, R., Holcombe, M. & Paton, R. eds), pp. 137-149. World Scientific, Singapore.
• Mendes, P., Kell, D.B. & Westerhoff, H.V. (1996) Why and when channelling can decrease pool size at a constant net flux in a simple dynamic channel. Biochimica et Biophysica Acta 1289, 175-186. [ abstract ]
• Mendes, P. & Kell, D.B. (1996) On the analysis of the inverse problem of metabolic pathways using artificial neural networks. BioSystems 38, 15-28. [ abstract ]
• Mendes, P. & Kell, D. B. (1996). Computer simulation of biochemical kinetics. in BioThermoKinetics of the living cell (ed. H. V. Westerhoff, J. L. Snoep, F. E. Sluse, J. E. Wijker & B. N. Kholodenko), pp. 254-257. BioThermoKinetics? Press, Amsterdam. full text
• Mendes, P., Kell, D.B. & Welch, G.R. (1995) Metabolic channelling in organized enzyme systems: experiments and models. Advances in Molecular Cellular Biology 11, 1-19. abstract
• Mendes, P., Kell, D.B. & Westerhoff, H.V. (1995) A series of cases in which metabolic channelling can decrease the pool size at a constant net flux in a simple dynamic channel. Biochemical Society Transactions 23, 287S.
• Mendes, P. (1994). Computer simulation of the dynamics of biochemical pathways. Ph. D. thesis, University of Wales, Aberystwyth. abstract full text (zipped postscript)
• Mendes, P. & Kell, D.B. (1993) Control analysis of metabolic channelling. In Modern Trends in Biothermokinetics (S. Schuster, M. Rigoulet, R. Ouhabi & J.-P. Mazat eds), pp. 211-216, Plenum Press, New York and London.
• Mendes, P. (1993) GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Computer Applications in the Biosciences 9, 563-571. [ abstract ]
• Mendes, P. (1993) GEPASI: A User Oriented Metabolic Simulator. In Modern Trends in Biothermokinetics (S. Schuster, M. Rigoulet, R. Ouhabi & J.-P. Mazat eds), pp. 463-466, Plenum Press, New York and London.
• Mendes, P. & Kell, D.B. (1993), On the role of enzyme kinetic parameters in determining the effectiveness with which channelling can decrease the size of a metabolite pool. Acta Biotheoretica 41, 63-73. [ abstract ]
• Mendes, P., Kell, D.B., & Westerhoff, H.V. (1992) Channelling can decrease pool size. European Journal of Biochemistry 204, 257-266. [ abstract ]
• Mendes, P., Moniz Barreto, J., Vaz Gomes, A. & Ponces Freire, A. (1990) A methodology for simulation of metabolic pathways and calculation of control coefficients. In Control of metabolic processes ( Cornish-Bowden, A. & Cárdenas, M.L. eds.), pp. 221-224, Plenum Press, New York.