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Prof Pedro Mendes - publications

List of publications

2015

  • Pedrosa Mendes, P., Hastings, J., Owen, G., Dekker, A., Ennis, M., Kale, N., ... Steinbeck, C. (2015). ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Research. DOI:10.1093/nar/gkv1031
    . Publication link: 33458f15-1965-4076-bf12-555b196c7e16
  • Pedrosa Mendes, P., Virginia Tech Intellectual Properties, I., Nessler, C. L., Lorence, A., Chevone, B., & Mendes, P. (2015). Patent No. US9000267 B2.
    . Publication link: 34d7653a-2d36-4192-b684-01f98e6676d7
  • Pedrosa Mendes, P., Millard, P., Portais, J-C., & Mendes, P. (2015). Impact of kinetic isotope effects in isotopic studies of metabolic systems. B M C Systems Biology, 9, [64]. DOI:10.1186/s12918-015-0213-8
    . Publication link: 8936585a-3e74-4163-85fc-3c54cbaefb8d
  • Pedrosa Mendes, P., Villaverde, A. F., Henriques, D., Smallbone, K., Bongard, S., Schmid, J., ... Banga, J. R. (2015). BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. B M C Systems Biology, 9, [8]. DOI:10.1186/s12918-015-0144-4
    . Publication link: 92b25c73-12c9-4565-b831-53a05e3202c0
  • Westerhoff, H. V., Bastiaens, P., Birtwistle, M. R., Bluthgen, N., Bruggeman, F. J., Cho, K. H., ... Kholodenko, B. N. (2015). Silence on the relevant literature and errors in implementation. Nature Biotechnology, 33, 336-339. DOI:10.1038/nbt.3185
    . Publication link: 30f49b8b-29ed-4de1-b54c-bbd86edd2371
  • Kell, D. B., Mendes, P., & Oliver, S. G. (2015). Fitting transporter activities to cellular drug concentrations and fluxes: why the bumblebee can fly. Trends in Pharmacological Sciences, 36(11), 710-723. DOI:10.1016/j.tips.2015.07.006
    . Publication link: cd2b707e-5dad-4374-b710-c7ec64c0e5ae

2014

  • Pedrosa Mendes, P., Mendes, P., Dada, J. O., & Smallbone, K. (2014). Computational Methods in Systems Biology: 12th International Conference, CMSB 2014, Manchester, UK, November 17-19, 2014, Proceedings. (Lecture Notes in Bioinformatics). Heidelberg New York Dordrecht London: Springer.
    . Publication link: 548150d0-390f-46ef-89ab-145466d95a87
  • Pedrosa Mendes, P., Summersgill, H., England, H., Lopez-Castejon, G., Lawrence, C. B., Luheshi, N. M., ... Brough, D. (2014). Zinc depletion regulates the processing and secretion of IL-1β.Cell Death and Disease, 5. DOI:10.1038/cddis.2013.547
    . Publication link: ebae3b64-6295-4638-8163-e0fd782c87e1 | PubMed:24481454

2013

2012

2011

  • Nobata, C., Dobson, P. D., Iqbal, S. A., Mendes, P., Tsujii, J., Kell, D. B., & Ananiadou, S. (2011). Mining metabolites: Extracting the yeast metabolome from the literature. Metabolomics, 7(1), 94-101. DOI:10.1007/s11306-010-0251-6
    . Publication link: 4c0af9ba-5794-461b-a55a-c00bf439892b
  • Courtot, M., Juty, N., Knüpfer, C., Waltemath, D., Zhukova, A., Dräger, A., ... Le Novère, N. (2011). Controlled vocabularies and semantics in systems biology. Molecular Systems Biology, 7, [543]. DOI:10.1038/msb.2011.77
    . Publication link: ad5719ba-5cbb-4c0e-a447-6cda7ca7e058 | PubMed:22027554
  • Small, B. G., McColl, B. W., Allmendinger, R., Pahle, J., Lopez-Casteon, G., Rothwell, N. J., ... Kell, D. B. (2011). Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing. Nature Chemical Biology, 7(12), 902-908. DOI:10.1038/nchembio.689
    . Publication link: a9a386a1-3e7f-4ba8-9fa8-9ed58056e249 | PubMed:22020553
  • Shuman, J. L., Cortes, D. F., Armenta, J. M., Pokrzywa, R. M., Mendes, P., & Shulaev, V. (2011). Plant metabolomics by GC-MS and differential analysis.In Methods in molecular biology (Clifton, N.J.)|Methods Mol. Biol.: Plant Reverse Genetics: Methods and Protocols. (Vol. 678, pp. 229-246). Springer.
    . Publication link: 543b2b29-62ff-42ae-858f-d636fd212d8f
  • Swainston, N., Smallbone, K., Mendes, P., Kell, D., & Paton, N. (2011). The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks.Journal of integrative bioinformatics, 8(2), 186. DOI:doi:10.2390/biecoll-jib-2011-186
    . Publication link: dc406f45-39c5-4188-8ce1-0e63ab2bf48b
  • Blekherman, G., Laubenbacher, R., Cortes, D. F., Mendes, P., Torti, F. M., Akman, S., ... Shulaev, V. (2011). Bioinformatics tools for cancer metabolomics. Metabolomics, 7(3), 329-343. DOI:10.1007/s11306-010-0270-3
    . Publication link: a6c20448-1135-4e59-975d-f8222289c61b

2010

2009

2008

2007

2006

  • Sauro, H. M., Harel, D., Kwiatkowska, M., Shaffer, C. A., Uhrmacher, A. M., Hucka, M., ... Tyson, J. J. (2006). Challenges for modeling and simulation methods in systems biology. In Proceedings - Winter Simulation Conference|Proc. Winter Simul. Conf.. (pp. 1720-1730). WSC. DOI:10.1109/WSC.2006.322948
    . Publication link: 202a7cf8-a1fe-4eae-80b0-2df2391cbf79
  • Mendes, P. (2006). Metabolomics and the challenges ahead. Briefings in Bioinformatics, 7(2), 127. DOI:10.1093/bib/bbl010
    . Publication link: 4a0141fb-4ad1-4a9d-848c-1038c169092b
  • Sahle, S., Gauges, R., Pahle, J., Simus, N., Kummer, U., Hoops, S., ... Mendes, P. (2006). Simulation of biochemical networks using COPASI - A complex pathway simulator. In Proceedings - Winter Simulation Conference|Proc. Winter Simul. Conf.. (pp. 1698-1706). WSC. DOI:10.1109/WSC.2006.322945
    . Publication link: 163ef772-9c5c-4fda-9e62-3718fde0ef2d
  • Hoops, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., ... Kummer, U. (2006). COPASI - A COmplex PAthway SImulator. Bioinformatics, 22(24), 3067-3074. DOI:10.1093/bioinformatics/btl485
    . Publication link: 97e559bc-8219-4cc2-aa38-15180da33fc6
  • Pedrosa Mendes, P., Mehrotra, B., Mendes, P., Saito, K. (Ed.), Dixon, R. A. (Ed.), Willmitzer, L. (Ed.), ... Lorz, H. (Ed.) (2006). Bioinformatics approaches to integrate metabolomics and other systems biology data. In Plant Metabolomics. (pp. 105-116). (Biotechnology in Agriculture and Forestry; Vol. 57). Berlin and Heidelberg, Germany: Springer-Verlag.
    . Publication link: 3cb3282a-1f19-4908-ae87-13ca82bc12cb
  • Rodriguez-Fernandez, M., Mendes, P., & Banga, J. R. (2006). A hybrid approach for efficient and robust parameter estimation in biochemical pathways. BioSystems, 83(2-3), 248-265. DOI:10.1016/j.biosystems.2005.06.016
    . Publication link: 833ebf14-d17e-4cdf-9ac7-d128c07d8658 | PubMed:16236429

2005

  • Mendes, P., Camacho, D., & De La Fuente, A. (2005). Modelling and simulation for metabolomics data analysis. Biochemical Society Transactions, 33(6), 1427-1429. DOI:10.1042/BST20051427
    . Publication link: cec5001d-5682-454f-b6c0-1714012222e3 | PubMed:16246137
  • Lei, Z., Elmer, A. M., Watson, B. S., Dixon, R. A., Mendes, P. J., & 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. Molecular and Cellular Proteomics, 4(11), 1812-1825. DOI:10.1074/mcp.D500005-MCP200
    . Publication link: 3cb8c1b8-9743-4c22-a7e5-9e9bf131c4f6 | PubMed:16048909
  • Suzuki, H., Reddy, M. S. S., Naoumkina, M., Aziz, N., May, G. D., Huhman, D. V., ... 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(5), 696-707. DOI:10.1007/s00425-004-1387-2
    . Publication link: 18703abf-f78d-46bc-9fb9-adb33b6cd318 | PubMed:15605242
  • Broeckling, C. D., Huhman, D. V., Farag, M. A., Smith, J. T., May, G. D., Mendes, P., ... 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(410), 323-336. DOI:10.1093/jxb/eri058
    . Publication link: 9372090f-6f91-44bb-b9de-30ac5a6774d7 | PubMed:15596476
  • Pedrosa Mendes, P., Cramer, G. R., Cushman, J. C., Schooley, D. A., Quilici, D., Vincent, D., ... Mendes, P. (2005). Progress in bioinformatics - The challenge of integrating transcriptomic, proteomic and metabolomic information. Acta Horticulturae, 689, 417-426.
    . Publication link: 9e4e7451-d386-471e-8d7b-625026b3862c
  • Le Novère, N., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., ... Wanner, B. L. (2005). Minimum information requested in the annotation of biochemical models (MIRIAM). Nature Biotechnology, 23(12), 1509-1515. DOI:10.1038/nbt1156
    . Publication link: d65b0b2b-7154-4762-8b4f-9c980b298de2 | PubMed:16333295
  • Pedrosa Mendes, P., Laubenbacher, R., Mendes, P., Kriete, A. (Ed.), & Eils, R. (Ed.) (2005). A discrete approach to top-down modeling of biochemical networks. In Computational Systems Biology. (pp. 229-247). Burlington, MA: Academic Press.
    . Publication link: c7047f50-26d2-4152-a565-09a7180b16b2

2004

2003

2002

2001

1998

1993

  • 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(5), 563-571.
    . Publication link: b01865ee-06b9-4242-a43d-2a9c2a34e923