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Prof Pedro Mendes - publications

List of publications


  • Millard, P., Smallbone, K., Mendes, P., & Pedrosa Mendes, P. (2017). Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli. PLoS Computational Biology, 13(2), [e1005396]. DOI: 10.1371/journal.pcbi.1005396. Publication link: 97ec71ac-e7ad-4f5c-9c43-5b35910cf65d



  • 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
  • Villaverde, A. F., Henriques, D., Smallbone, K., Bongard, S., Schmid, J., Cicin-Sain, D., ... 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
  • Bastiaens, P., Birtwistle, M. R., Bluthgen, N., Bruggeman, F. J., Cho, K. H., Cosentino, C., ... 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
  • Hastings, J., Owen, G., Dekker, A., Ennis, M., Kale, N., Muthukrishnan, V., ... 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
  • Mendes, P., Oliver, S. G., & Kell, D. B. (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/ Publication link: cd2b707e-5dad-4374-b710-c7ec64c0e5ae


  • 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 Verlag.. 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 & Disease, 5. DOI: 10.1038/cddis.2013.547. Publication link: 53942f60-f62f-4432-97fa-531a931304dc | PubMed:24481454




  • 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 Verlag. . Publication link: 543b2b29-62ff-42ae-858f-d636fd212d8f
  • 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
  • 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
  • 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





  • Henriques, I. D. S., 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. Environmental Science and Technology, 41(11), 3945-3951. DOI: 10.1021/es062796t. Publication link: dcffafb8-54e5-4ff9-9e5a-e22a202233f0 | PubMed:17612173
  • Fiehn, O., Robertson, D., Griffin, J., vab der Werf, M., Nikolau, B., Morrison, N., ... Sansone, S. A. (2007). The metabolomics standards initiative (MSI). Metabolomics, 3(3), 175-178. DOI: 10.1007/s11306-007-0070-6. Publication link: eb8f02ee-e659-4552-829f-a51a28387567
  • Camacho, D., Licona, P. V., Mendes, P., & Laubenbacher, R. (2007). Comparison of reverse-engineering methods using an in Silico network. Annals of the New York Academy of Sciences, 1115, 73-89. DOI: 10.1196/annals.1407.006. Publication link: 94a8f2bb-542c-417e-9db8-47041c3aae82 | PubMed:17925358
  • 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(3), 181-188. DOI: 10.1002/yea.1442. Publication link: 10e6a3b4-d140-4c36-b828-140eb0735391 | PubMed:17230580
  • Sansone, S. A., Fan, T., Goodacre, R., Griffin, J. L., Hardy, N. W., Kaddurah-Daouk, R., ... Fiehn, O. (2007). The Metabolomics Standards Initiative [3]. Nature Biotechnology, 25(8), 846-848. DOI: 10.1038/nbt0807-846b. Publication link: 3709799e-d24e-4329-84c0-ad446a236a6d | PubMed:17687353


  • 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
  • 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
  • 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
  • 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
  • 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
  • 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., 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
  • 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
  • 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
  • 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
  • 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
  • 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







  • 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