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
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
2012
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
2011
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: 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
2010
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., Messiha, H.L., Simeonidis, E., Weichart, D., Winder, C., 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; 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; 4: . eScholarID:117343 | DOI:10.1186/1752-0509-4-6
2009
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
2008
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): 1155-60. 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
2007
, 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
2006
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
2005
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
2004
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
2003
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
2002
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
2001
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
1998
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
1993
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
