Pedro Mendes, Ph.D. - Publications

Affiliations: 
University of Manchester, Manchester, England, United Kingdom 
Area:
metabolic modeling, software development, metabolic control analysis, GEPASI, COPASI

78 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Stanford NJ, Scharm M, Dobson PD, Golebiewski M, Hucka M, Kothamachu VB, Nickerson D, Owen S, Pahle J, Wittig U, Waltemath D, Goble C, Mendes P, Snoep J. Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. Methods in Molecular Biology (Clifton, N.J.). 2049: 285-314. PMID 31602618 DOI: 10.1007/978-1-4939-9736-7_17  0.399
2018 Mendes P. Reproducible Research Using Biomodels. Bulletin of Mathematical Biology. PMID 30191472 DOI: 10.1007/S11538-018-0498-Z  0.314
2018 Parmar JH, Quintana J, Ramírez D, Laubenbacher R, Argüello JM, Mendes P. An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study. Molecular Microbiology. PMID 30047562 DOI: 10.1111/Mmi.14086  0.312
2018 Gupta A, Mendes P. An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems. Computation (Basel, Switzerland). 6. PMID 29938118 DOI: 10.3390/Computation6010009  0.329
2017 Swainston N, Batista-Navarro R, Carbonell P, Dobson PD, Dunstan M, Jervis AJ, Vinaixa M, Williams AR, Ananiadou S, Faulon JL, Mendes P, Kell DB, Scrutton NS, Breitling R. biochem4j: Integrated and extensible biochemical knowledge through graph databases. Plos One. 12: e0179130. PMID 28708831 DOI: 10.1371/Journal.Pone.0179130  0.525
2017 Bergmann FT, Hoops S, Klahn B, Kummer U, Mendes P, Pahle J, Sahle S. COPASI and its Applications in Biotechnology. Journal of Biotechnology. PMID 28655634 DOI: 10.1016/J.Jbiotec.2017.06.1200  0.334
2016 Scharm M, Waltemath D, Mendes P, Wolkenhauer O. COMODI: an ontology to characterise differences in versions of computational models in biology. Journal of Biomedical Semantics. 7: 46. PMID 27401413 DOI: 10.1186/S13326-016-0080-2  0.36
2016 Swainston N, Smallbone K, Hefzi H, Dobson PD, Brewer J, Hanscho M, Zielinski DC, Ang KS, Gardiner NJ, Gutierrez JM, Kyriakopoulos S, Lakshmanan M, Li S, Liu JK, Martínez VS, ... ... Mendes P, et al. Recon 2.2: from reconstruction to model of human metabolism. Metabolomics : Official Journal of the Metabolomic Society. 12: 109. PMID 27358602 DOI: 10.1007/S11306-016-1051-4  0.555
2016 Waltemath D, Karr J, Bergmann F, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers C, Pir P, Alaybeyoglu B, Aranganathan N, Baghalian K, Bittig A, Burke P, et al. Toward community standards and software for whole-cell modeling. Ieee Transactions On Bio-Medical Engineering. PMID 27305665 DOI: 10.1109/Tbme.2016.2560762  0.321
2016 Swainston N, Hastings J, Dekker A, Muthukrishnan V, May J, Steinbeck C, Mendes P. libChEBI: an API for accessing the ChEBI database. Journal of Cheminformatics. 8: 11. PMID 26933452 DOI: 10.1186/S13321-016-0123-9  0.341
2016 Mendes P, Oliver SG, Kell DB. Response to 'The Need for Speed', by Matsson et al. Trends in Pharmacological Sciences. 37: 245-6. PMID 26924017 DOI: 10.1016/J.Tips.2016.02.004  0.483
2015 Mendes P, Oliver SG, Kell DB. Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly. Trends in Pharmacological Sciences. 36: 710-23. PMID 26538313 DOI: 10.1016/J.Tips.2015.07.006  0.474
2015 Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Research. PMID 26467479 DOI: 10.1093/Nar/Gkv1031  0.35
2015 Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR. BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. Bmc Systems Biology. 9: 8. PMID 25880925 DOI: 10.1186/S12918-015-0144-4  0.365
2015 Millard P, Portais JC, Mendes P. Impact of kinetic isotope effects in isotopic studies of metabolic systems Bmc Systems Biology. DOI: 10.1186/S12918-015-0213-8  0.379
2014 Cvijovic M, Almquist J, Hagmar J, Hohmann S, Kaltenbach HM, Klipp E, Krantz M, Mendes P, Nelander S, Nielsen J, Pagnani A, Przulj N, Raue A, Stelling J, Stoma S, et al. Bridging the gaps in systems biology. Molecular Genetics and Genomics : Mgg. 289: 727-34. PMID 24728588 DOI: 10.1007/S00438-014-0843-3  0.384
2014 Messiha HL, Kent E, Malys N, Carroll KM, Swainston N, Mendes P, Smallbone K. Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast Peerj. DOI: 10.7287/Peerj.Preprints.146V4  0.4
2013 Stanford NJ, Lubitz T, Smallbone K, Klipp E, Mendes P, Liebermeister W. Systematic construction of kinetic models from genome-scale metabolic networks. Plos One. 8: e79195. PMID 24324546 DOI: 10.1371/Journal.Pone.0079195  0.439
2013 Kent E, Neumann S, Kummer U, Mendes P. What can we learn from global sensitivity analysis of biochemical systems? Plos One. 8: e79244. PMID 24244458 DOI: 10.1371/Journal.Pone.0079244  0.332
2013 Mitchell S, Mendes P. A computational model of liver iron metabolism. Plos Computational Biology. 9: e1003299. PMID 24244122 DOI: 10.1371/Journal.Pcbi.1003299  0.577
2013 Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, ... ... Mendes P, et al. Path2Models: large-scale generation of computational models from biochemical pathway maps. Bmc Systems Biology. 7: 116. PMID 24180668 DOI: 10.1186/1752-0509-7-116  0.587
2013 Swainston N, Mendes P, Kell DB. An analysis of a 'community-driven' reconstruction of the human metabolic network. Metabolomics : Official Journal of the Metabolomic Society. 9: 757-764. PMID 23888127 DOI: 10.1007/S11306-013-0564-3  0.521
2013 Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, ... ... Mendes P, et al. A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. Febs Letters. 587: 2832-41. PMID 23831062 DOI: 10.1016/J.Febslet.2013.06.043  0.61
2013 Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, ... ... Mendes P, et al. A community-driven global reconstruction of human metabolism. Nature Biotechnology. 31: 419-25. PMID 23455439 DOI: 10.1038/Nbt.2488  0.6
2013 Smallbone K, Mendes P. Large-Scale Metabolic Models: From Reconstruction to Differential Equations Industrial Biotechnology. 9: 179-184. DOI: 10.1089/Ind.2013.0003  0.421
2012 Kent E, Hoops S, Mendes P. Condor-COPASI: high-throughput computing for biochemical networks. Bmc Systems Biology. 6: 91. PMID 22834945 DOI: 10.1186/1752-0509-6-91  0.351
2012 Pahle J, Challenger JD, Mendes P, McKane AJ. Biochemical fluctuations, optimisation and the linear noise approximation. Bmc Systems Biology. 6: 86. PMID 22805626 DOI: 10.1186/1752-0509-6-86  0.321
2012 Lee D, Smallbone K, Dunn WB, Murabito E, Winder CL, Kell DB, Mendes P, Swainston N. Improving metabolic flux predictions using absolute gene expression data. Bmc Systems Biology. 6: 73. PMID 22713172 DOI: 10.1186/1752-0509-6-73  0.564
2012 Heavner BD, Smallbone K, Barker B, Mendes P, Walker LP. Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. Bmc Systems Biology. 6: 55. PMID 22663945 DOI: 10.1186/1752-0509-6-55  0.443
2012 Davies O, Mendes P, Smallbone K, Malys N. Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism. Bmb Reports. 45: 259-64. PMID 22531138 DOI: 10.5483/Bmbrep.2012.45.4.259  0.319
2012 Chifman J, Kniss A, Neupane P, Williams I, Leung B, Deng Z, Mendes P, Hower V, Torti FM, Akman SA, Torti SV, Laubenbacher R. The core control system of intracellular iron homeostasis: a mathematical model. Journal of Theoretical Biology. 300: 91-9. PMID 22286016 DOI: 10.1016/J.Jtbi.2012.01.024  0.35
2011 Swainston N, Smallbone K, Mendes P, Kell D, Paton N. The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks. Journal of Integrative Bioinformatics. 8: 186. PMID 22095399 DOI: 10.2390/Biecoll-Jib-2011-186  0.558
2011 Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, ... ... Mendes P, et al. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology. 7: 543. PMID 22027554 DOI: 10.1038/Msb.2011.77  0.554
2011 Small BG, McColl BW, Allmendinger R, Pahle J, López-Castejón G, Rothwell NJ, Knowles J, Mendes P, Brough D, Kell DB. Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing. Nature Chemical Biology. 7: 902-8. PMID 22020553 DOI: 10.1038/Nchembio.689  0.473
2011 Blekherman G, Laubenbacher R, Cortes DF, Mendes P, Torti FM, Akman S, Torti SV, Shulaev V. Bioinformatics tools for cancer metabolomics. Metabolomics : Official Journal of the Metabolomic Society. 7: 329-343. PMID 21949492 DOI: 10.1007/S11306-010-0270-3  0.319
2011 Nobata C, Dobson PD, Iqbal SA, Mendes P, Tsujii J, Kell DB, Ananiadou S. Mining metabolites: extracting the yeast metabolome from the literature. Metabolomics : Official Journal of the Metabolomic Society. 7: 94-101. PMID 21687783 DOI: 10.1007/S11306-010-0251-6  0.588
2011 Dada JO, Mendes P. Multi-scale modelling and simulation in systems biology. Integrative Biology : Quantitative Biosciences From Nano to Macro. 3: 86-96. PMID 21212881 DOI: 10.1039/C0Ib00075B  0.348
2011 Shuman JL, Cortes DF, Armenta JM, Pokrzywa RM, Mendes P, Shulaev V. Plant metabolomics by GC-MS and differential analysis. Methods in Molecular Biology (Clifton, N.J.). 678: 229-46. PMID 20931384 DOI: 10.1007/978-1-60761-682-5_17  0.341
2010 Li P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, ... ... Mendes P, et al. Systematic integration of experimental data and models in systems biology. Bmc Bioinformatics. 11: 582. PMID 21114840 DOI: 10.1186/1471-2105-11-582  0.626
2010 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, ... ... Mendes P, et al. Further developments towards a genome-scale metabolic model of yeast. Bmc Systems Biology. 4: 145. PMID 21029416 DOI: 10.1186/1752-0509-4-145  0.593
2010 Swainston N, Golebiewski M, Messiha HL, Malys N, Kania R, Kengne S, Krebs O, Mir S, Sauer-Danzwith H, Smallbone K, Weidemann A, Wittig U, Kell DB, Mendes P, Müller W, et al. Enzyme kinetics informatics: from instrument to browser. The Febs Journal. 277: 3769-79. PMID 20738395 DOI: 10.1111/J.1742-4658.2010.07778.X  0.548
2010 Dada JO, Spasić I, Paton NW, Mendes P. SBRML: a markup language for associating systems biology data with models. Bioinformatics. 26: 932-938. PMID 20176582 DOI: 10.1093/Bioinformatics/Btq069  0.401
2010 Smallbone K, Simeonidis E, Swainston N, Mendes P. Towards a genome-scale kinetic model of cellular metabolism Bmc Systems Biology. 4: 6-6. PMID 20109182 DOI: 10.1186/1752-0509-4-6  0.43
2009 Mendes P, Messiha H, Malys N, Hoops S. Enzyme kinetics and computational modeling for systems biology. Methods in Enzymology. 467: 583-599. PMID 19897108 DOI: 10.1016/S0076-6879(09)67022-1  0.356
2009 Swainston N, Mendes P. libAnnotationSBML: a library for exploiting SBML annotations. Bioinformatics. 25: 2292-2293. PMID 19561017 DOI: 10.1093/Bioinformatics/Btp392  0.364
2009 Laubenbacher R, Hower V, Jarrah A, Torti SV, Shulaev V, Mendes P, Torti FM, Akman S. A systems biology view of cancer. Biochimica Et Biophysica Acta. 1796: 129-39. PMID 19505535 DOI: 10.1016/J.Bbcan.2009.06.001  0.352
2009 Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U. Computational modeling of biochemical networks using COPASI. Methods of Molecular Biology. 500: 17-59. PMID 19399433 DOI: 10.1007/978-1-59745-525-1_2  0.42
2009 Hower V, Mendes P, Torti FM, Laubenbacher R, Akman S, Shulaev V, Torti SV. A general map of iron metabolism and tissue-specific subnetworks. Molecular Biosystems. 5: 422-43. PMID 19381358 DOI: 10.1039/B816714C  0.336
2008 HerrgÃ¥rd 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, ... ... Mendes P, et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology. 26: 1155-60. PMID 18846089 DOI: 10.1038/Nbt1492  0.593
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. 366: 3619-3631. PMID 18632455 DOI: 10.1098/Rsta.2008.0108  0.357
2008 Kell DB, Mendes P. The markup is the model: Reasoning about systems biology models in the Semantic Web era Journal of Theoretical Biology. 252: 538-543. PMID 18054049 DOI: 10.1016/J.Jtbi.2007.10.023  0.586
2008 Flöttmann M, Schaber J, Hoops S, Klipp E, Mendes P. ModelMage: a tool for automatic model generation, selection and management. Genome Informatics. 20: 52-63. DOI: 10.11234/Gi1990.20.52  0.37
2007 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. 1115: 73-89. PMID 17925358 DOI: 10.1196/Annals.1407.006  0.313
2007 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 (Chichester, England). 24: 181-8. PMID 17230580 DOI: 10.1002/Yea.1442  0.317
2006 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. 22: 3067-3074. PMID 17032683 DOI: 10.1093/Bioinformatics/Btl485  0.324
2006 Mendes P. Metabolomics and the challenges ahead Briefings in Bioinformatics. 7: 127-127. PMID 16914436 DOI: 10.1093/Bib/Bbl010  0.431
2006 Rodriguez-Fernandez M, Mendes P, Banga JR. A hybrid approach for efficient and robust parameter estimation in biochemical pathways. Biosystems. 83: 248-265. PMID 16236429 DOI: 10.1016/J.Biosystems.2005.06.016  0.366
2005 Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nature Biotechnology. 23: 1509-15. PMID 16333295 DOI: 10.1038/Nbt1156  0.377
2005 Mendes P, Camacho D, De La Fuente A. Modelling and simulation for metabolomics data analysis Biochemical Society Transactions. 33: 1427-1429. PMID 16246137 DOI: 10.1042/Bst20051427  0.394
2005 Broeckling CD, Huhman DV, Farag MA, Smith JT, May GD, Mendes P, Dixon RA, Sumner LW. Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism Journal of Experimental Botany. 56: 323-336. PMID 15596476 DOI: 10.1093/Jxb/Eri058  0.331
2005 Camacho D, Fuente Adl, Mendes P. The origin of correlations in metabolomics data Metabolomics. 1: 53-63. DOI: 10.1007/S11306-005-1107-3  0.372
2004 Jenkins H, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J, Fiehn O, Goodacre R, Bino RJ, Hall R, Kopka J, Lane GA, Lange BM, Liu JR, Mendes P, et al. A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotechnology. 22: 1601-6. PMID 15583675 DOI: 10.1038/Nbt1041  0.56
2004 Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J, Nikolau BJ, Mendes P, Roessner-Tunali U, Beale MH, Trethewey RN, Lange BM, Wurtele ES, Sumner LW. Potential of metabolomics as a functional genomics tool. Trends in Plant Science. 9: 418-25. PMID 15337491 DOI: 10.1016/J.Tplants.2004.07.004  0.364
2004 de la Fuente A, Bing N, Hoeschele I, Mendes P. Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics (Oxford, England). 20: 3565-74. PMID 15284096 DOI: 10.1093/Bioinformatics/Bth445  0.345
2004 Martins A, 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. 5: 649-663. DOI: 10.2174/1389202043348643  0.381
2003 Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, ... ... Mendes P, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (Oxford, England). 19: 524-31. PMID 12611808 DOI: 10.1093/Bioinformatics/Btg015  0.405
2003 Sumner LW, Mendes P, Dixon RA. Plant metabolomics: Large-scale phytochemistry in the functional genomics era Phytochemistry. 62: 817-836. PMID 12590110 DOI: 10.1016/S0031-9422(02)00708-2  0.31
2002 Brazhnik P, Fuente Adl, Mendes P. Gene networks: how to put the function in genomics Trends in Biotechnology. 20: 467-472. PMID 12413821 DOI: 10.1016/S0167-7799(02)02053-X  0.326
2002 De La Fuente A, Snoep JL, Westerhoff HV, Mendes P. Metabolic control in integrated biochemical systems European Journal of Biochemistry. 269: 4399-4408. PMID 12230551 DOI: 10.1046/J.1432-1033.2002.03088.X  0.391
2002 Mendes P. Emerging bioinformatics for the metabolome Briefings in Bioinformatics. 3: 134-145. PMID 12139433 DOI: 10.1093/Bib/3.2.134  0.389
2002 Mendes P, Fuente Adl, Hoops S. Chapter One Bioinformatics and computational biology for plant functional genomics Recent Advances in Phytochemistry. 36: 1-13. DOI: 10.1016/S0079-9920(02)80017-X  0.37
2001 Sobral BW, Mangalam H, Siepel A, Mendes P, Pecherer R, McLaren G. Bioinformatics for rice resources. Novartis Foundation Symposium. 236: 59-81; discussion 81. PMID 11387987 DOI: 10.1002/9780470515778.Ch6  0.352
2001 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 (Oxford, England). 17: 83-94. PMID 11222265 DOI: 10.1093/Bioinformatics/17.1.83  0.312
1998 Mendes P, Kell DB. Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics. 14: 869-883. PMID 9927716 DOI: 10.1093/Bioinformatics/14.10.869  0.38
1996 Mendes P, Kell DB. On the analysis of the inverse problem of metabolic pathways using artificial neural networks Biosystems. 38: 15-28. PMID 8833745 DOI: 10.1016/0303-2647(95)01565-5  0.354
1996 Mendes P, Kell DB, Westerhoff HV. Why and when channelling can decrease pool size at constant net flux in a simple dynamic channel. Biochimica Et Biophysica Acta. 1289: 175-86. PMID 8600971 DOI: 10.1016/0304-4165(95)00152-2  0.305
1995 Mendes P, Kell DB, Welch GR. Metabolic Channeling in Organized Enzyme Systems: Experiments and Models Advances in Molecular and Cell Biology. 11: 1-19. DOI: 10.1016/S1569-2558(08)60246-5  0.348
1993 Mendes P. GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems Bioinformatics. 9: 563-571. PMID 8293329 DOI: 10.1093/Bioinformatics/9.5.563  0.383
Show low-probability matches.