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Associate Professor, Virginia Bioinformatics Institute
Adjunct Associate Professor, Department of Biochemistry, Virginia Tech
Phone: (540) 231-7411
Email:mendes@vt.edu
Fax: 540-231-2606
Administrative Specialist: Maureen Lawrence-Kuether
Phone: (540) 231-3669
Email: mlawre04@vbi.vt.edu
Fax:540-231-2606
Personal_Page
| Biochemical Networks Modeling Group
| COPASI: biochemical network simulator
Publications:
Courtot M JN Kn. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology. 2011;(7):543.
Small BG MCBW Allmendinger R Pahle J L. Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing. Nature Chem. Biol. 2011;(7):902.
Mendes Pde P. Framework for Comparative Assessment of Parameter Estimation and Inference Methods in Systems Biology. In: Lawrence ND, Girolami M, Rattray M, Sanguinetti G, eds. Learning and Inference in Computational Systems Biology. Cambridge, MA: MIT Press; 2010:pp. 33–58.
Mendes P, Dada JO, Spasic I, Paton NW. SBRML: a markup language for associating systems biology data with models. Bioinformatics. 2010;26:932–938.
Simeonidis E, Smallbone K, Swainston N, Mendes P. Towards a genome-scale kinetic model of cellular metabolism. BMC Syst Biol. 2010;4.
Smallbone K, Dobson PD, Jameson D, et al. Further developments towards a genome-scale metabolic model of yeast. BMC Syst Biol. 2010;4.
Swainston N, Golebiewski M, Messiha HL, et al. Enzyme kinetics informatics: from instrument to browser. Febs Journal. 2010;277:3769–3779.
Swainston N, Jameson D, Li P, Spasic I, Mendes P, Paton N. Integrative Information Management for Systems Biology Data Integration in the Life Sciences. In: Lambrix P, Kemp G, eds. Springer Berlin / Heidelberg; 2010:164–178. Lecture Notes in Computer Science 6254. http://dx.doi.org/10.1007%2F978-3-642-15120-0_13
Dada J, Mendes P. Design and Architecture of Web Services for Simulation of Biochemical Systems Data Integration in the Life Sciences. In: Paton N, Missier P, Hedeler C, eds. Springer Berlin / Heidelberg; 2009:182–195. Lecture Notes in Computer Science 5647. http://dx.doi.org/10.1007%2F978-3-642-02879-3_15
Hower V, Mendes P, Torti FM, et al. A general map of iron metabolism and tissue-specific subnetworks. Molecular Biosystems. 2009;5:422–443.
Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U. Computational modeling of biochemical networks using COPASI. Methods in Molecular Biology. 2009;500:17–59.
Hucka M, Hoops S, Mendes P. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. Nature Precedings. 2008.
Sahle S, Mendes P, Hoops S, Kummer U. A new strategy for assessing sensitivities in biochemical models. Philosophical Transactions of the Royal Society A: Physical, Mathematical and Engineering Sciences. 2008;366:3619–3363.
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;1115:73–89. http://dx.doi.org/10.1196%2Fannals.1407.006
Chen D-J, Lee C-Y, Park C-H, Mendes P. Parallelizing simulated annealing algorithms based on high-performance computer. Journal of Global Optimization. 2007;39:261–289.
Martins AM, 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. 2007;24:181–188. http://dx.doi.org/10.1002%2Fyea.1442
Cameron CJ, Workman RG, Williams B, et al. Monitoring amino acid metabolism in Medicago truncatula using capillary electrophoresis-mass spectrometry.; 2006. Abstracts of Papers of the American Chemical Society 231.
Hill J, Beaubien A, Harrison T, et al. Monitoring carbohydrate metabolism in Medicago truncatula using capillary electrophoresis.; 2006. Abstracts of Papers of the American Chemical Society 231.
Hoops S, Sahle S, Gauges R, et al. COPASI- A COmplex PAthway SImulator. Bioinformatics. 2006;22:3067–3074.
Laubenbacher R, Mendes P. A discrete approach to top-down modeling of biochemical networks. In: R E, L K, eds. Computational Systems Biology. Elsevier, Academic Press; 2006.
Mendes P. Metabolomics and the challenges ahead. Briefings in Bioinformatics. 2006;7:127.
Rodriguez-Fernandez M, Mendes P, Banga JR. A hybrid approach for efficient and robust parameter estimation in biochemical pathways. Biosystems. 2006;83:248–265.
Broeckling CD, Farag M, Huhman D, et al. Metabolomics: A tool for gene validation, gene discovery, hypothesis building, and mechanistic understanding.; 2005:U503–U504. Abstracts of Papers of the American Chemical Society 230.
Broeckling CD, Huhman DV, Farag MA, et al. Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. Journal of Experimental Botany. 2005;56:323–336.
Camacho D, de la Fuente A, Mendes P. The origin of correlations in metabolomics data. Metabolomics. 2005;1:53–63.
Le Novere N, Finney A, Hucka M, et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nature Biotechnology. 2005;23:1509–1515.
Lei Z, Elmer AM, Watson BS, Dixon RA, Mendes PJ, Sumner LW. 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. 2005;4:1812–1825.
Mendes P, Camacho D, de la Fuente A. Modelling and simulation for metabolomics data analysis. Biochemical Society Transactions. 2005;33:1427–1429.
Suzuki H, Reddy MSS, Naoumkina M, et al. Methyl jasmonate and yeast elicitor induce differential transcriptional and metabolic re-programming in cell suspension cultures of the model legume Medicago truncatula. Planta. 2005;220:696–707.
Bino RJ, Hall RD, Fiehn O, et al. Potential of metabolomics as a functional genomics tool. Trends in Plant Science. 2004;9:418–425.
de la Fuente A, Bing N, Hoeschele I, Mendes P. Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics. 2004;20:3565–3574.
Jenkins H, Hardy N, Beckmann M, et al. A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotechnology. 2004;22:1601–1606.
Lorence A, Chevone BI, Mendes P, Nessler CL. Myo-inositol oxygenase offers a possible entry point into plant ascorbate biosynthesis. Plant Physiology. 2004;134:1200–1205.
Martins AM, Camacho D, Shuman J, Sha W, Mendes P, Shulaev V. A systems biology study of two distinct growth phases of Saccharomyces cerevisiae cultures. Current Genomics. 2004;5:649–663.
Hucka M, Finney A, Sauro HM, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003;19:524–531.
Martins AM, Mendes P. The Saccharomyces cerevisiae response to oxidative stress: integrative study on the role of the glyoxalase pathway. Yeast. 2003;20:S177.
Moles CG, Mendes P, Banga JR. Parameter estimation in biochemical pathways: A comparison of global optimization methods. Genome Research. 2003;13:2467–2474.
Sumner LW, Mendes P, Dixon RA. Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemistry. 2003;62:817–836.
Brazhnik P, de la Fuente A, Mendes P. Gene networks: how to put the function in genomics. Trends in Biotechnology. 2002;20:467–472.
de la Fuente A, Brazhnik P, Mendes P. Linking the genes: inferring quantitative gene networks from microarray data. Trends in Genetics. 2002;18:395–398.
de la Fuente A, Mendes P. Quantifying gene networks with regulatory strengths. Molecular Biology Reports. 2002;29:73–77.
de la Fuente A, Snoep JL, Westerhoff HV, Mendes P. Metabolic control in integrated biochemical systems. European Journal of Biochemistry. 2002;269:4399–4408.
Li XJ, Brazhnik O, Kamal A, et al. Databases and visualization for metabolomics. In: Harrigan GRG, ed. Metabolic profiling: Its role in biomarker discovery and gene function analysis. Amsterdam: Kluwer Academic Publishing; 2002.
Martins AM, Mendes P, Cordeiro C, Freire AP. In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae. European Journal of Biochemistry. 2001;268:3930–3936.
Mendes P, Kell DB. MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems. Bioinformatics. 2001;17:288–289.
Sobral BWS, Mangalam H, Siepel A, Mendes P, Pecherer R, McLaren G. Bioinformatics for rice resources. In: Rice Biotechnology: Improving Yield, Stress Tolerance and Grain Quality.; 2001:59–84. Novartis Foundation Symposium 236.
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