Mendes Research Group - Publications

Publications

Our publications, listed by year and with links to abstract and/or full text. You can also find Pedro's publications on Google Scholar, Orcid, and Pubmed.

2023

Masison J, Mendes P (2023) Modeling the iron storage protein ferritin reveals how residual ferrihydrite iron determines initial ferritin iron sequestration kinetics. PLoS One 18:e0281401 [ full text ]

2022

Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Sheriff RSM, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep J, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk D, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR (2022) BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research 50:W108–W114 [ full text ]

2021

Acón M, Geiß C, Torres-Calvo J, Bravo-Estupiñan D, Oviedo G, Arias-Arias JL, Rojas-Matey LA, Baez E, Vásquez-Vargas G, Oses-Vargas Y, Guevara-Coto J, Segura-Castillo A, Siles-Canales F, Quirós-Barrantes S, Régnier-Vigouroux A, Mendes P, Mora-Rodríguez R (2021) MYC dosage compensation is mediated by miRNA-transcription factor interactions in aneuploid cancer. iScience 24:103407. [ full text ]
Archambault L, Koshy-Chenthittayil S, Thompson A, Dongari-Bagtzoglou A, Laubenbacher R, Mendes P (2021) Understanding Lactobacillus paracasei and Streptococcus oralis biofilm interactions through agent-based modeling. mSphere 6:e0087521 [ full text ]
Gupta A, Mendes P (2021) ShinyCOPASI: a web-based exploratory interface for COPASI models. arXiv:2110.03796 [ preprint ]
Koshy-Chenthittayil S, Archambault L, Senthilkumar D, Laubenbacher R, Mendes P, Dongari-Bagtzoglou A (2021) Agent Based Models of Polymicrobial Biofilms and the Microbiome—A Review. Microorganisms 9:417 [ full text ]
Koshy-Chenthittayil S, Mendes P, Laubenbacher R (2021) Optimization of agent-based models through dimension reduction: a case study in microbial ecology. Letters in Biomathematics 8:167-178 [ abstract ] [ full text ]
Hufsky F, Lamkiewicz K, Almeida A, Aouacheria A, Arighi C, Bateman A, Baumbach J, Beerenwinkel N, Brandt C, Cacciabue M, Chuguransky S, Drechsel O, Finn RD, Fritz A, Fuchs F, Hattab G, Hauschild A-C, Heider D, Hoffmann M, Hölzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, Kühnert D, Lasso G, Libin P, List M, Löchel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki EP, O'Toole AN, Ontiveros-Palacios N, Petrov AI, Rangel-Pineros G, Redaschi N, Reimering S, Reinert K, Reyes A, Richardson L, Robertson DL, Sadegh S, Singer JB, Theys K, Upton C, Welzel M, Williams L, Marz M (2021) Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings in Bioinformatics 22:642–663 [ full text ]

2020

Firczuk H, Teahan J, Mendes P, McCarthy JEG (2020) Multi-site rate control analysis identifies ribosomal scanning as the sole high-capacity/low-flux-control step in mRNA translation. FEBS Journal 287:925-940. [ full text ]
Mendes P, Girardi E, Superti-Furga G, Kell DB (2020) Why most transporter mutations that cause antibiotic resistance are to efflux pumps rather than to import transporters. bioRxiv 2020.01.16.909507 [ full text ]

2019

Parmar JH, Mendes P (2019) A computational model to understand mouse iron physiology and diseases. PLoS Computational Biology 15(1):e1006680 [ full text ] [ preprint ]
Cowan AE, Mendes P, Blinov ML (2019) ModelBricks — Modules for reproducible modeling improving model annotation and provenance. npj Systems Biology and Applications 5:37. [ full text ]
Mercadante CJ, Prajapati M, Parmar JH, Conboy HL, Dash ME, Pettiglio MA, Herrera C, Bu JT, Stopa EG, Mendes P, Bartnikas TB (2018) Gastrointestinal iron excretion and reversal of iron excess in a mouse model of inherited iron excess. Haematologica 104:678–689 [ full text ]
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 (2019) Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. Methods in Molecular Biology 2049:285-314. [ full text ]

2018

Mendes P (2018) Reproducible research using biomodels. Bulletin of Mathematical Biology 80:3081-3087 [ full text ] [ preprint ]
Parmar JH, Quintana J, Ramírez D, Laubenbacher R, Argüello JM, Mendes P (2018) An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study. Molecular Microbiology 110:357-369 [ full text ] [ preprint ]
Gupta A, Mendes P (2018) An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems. Computation 6:9 [ full text ]

2017

Bergmann FT, Hoops S, Klahn B, Kummer U, Mendes P, Pahle J, Sahle S (2017) COPASI and its Applications in Biotechnology. Journal of Biotechnology 261:215-220 [ full text ]
Swainston N, Batista-Navarro R, Carbonell P, Dobson PD, Dunstan M, Jervis AJ, Vinaixa M, Williams AR, Ananiadou S, Faulon J-L, Mendes P, Kell DB, Scrutton NJ, Breitling R (2017) biochem4j: integrated and extensible biochemical knowledge through graph databases. PLoS One 12:e0179130. [ full text ]
Parmar JH, Davis G, Shevchuk H, Mendes P (2017) Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient BMC Systems Biology 11:57 [ full text ] [ preprint ]
Dacheux E, Malys N, Meng X, Ramachandran V, Mendes P, McCarthy JEG (2017) Translation initiation events on structured eukaryotic mRNAs generate gene expression noise Nucleic Acids Research 45:6981-6992. [ full text ]
Millard P, Smallbone K, 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. [ full text ]
Meng X, Firczuk H, Pietroni P, Westbrook R, Dacheaux E, Mendes P, McCarthy JEG (2017) Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis. Nucleic Acids Research 45:1015-1025. [ full text ]

2016

Swainston N, Smallbone K, Hefzi H, Dobson PD, Brewer J, Hanscho M, Zielinski DC, Siong Ang K, Gardiner NJ, Gutierrez JM, Kyriakopoulos S, Lakshmanan M, Li S, Liu JK, Martínez VS, Orellana CA, Quek L-E, Thomas A, Zanghellini J, Borth, N, Lee D-Y, Nielsen LK, Kell DB, Lewis NE, Mendes P (2016) Recon 2.2: from reconstruction to model of human metabolism. Metabolomics 12:109 [full text]
Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PEP, Cantarelli M, Chew YH, Costa RS, Cursons J, Czauderna T, Goldberg AP, Harold F. Gómez, Hahn J, Hameri T, Gardiol DFH, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knüpfer C, König M, Lee D, Lloret-Villas A, Mandrik N, Medley JK, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song J-H, Theile T, Tokic M, Tomar N, Touré V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A, Schreiber F (2016) Toward community standards and software for whole-cell modeling. IEEE Transactions on Biomedical Engineering 63:2007-14. [full text]
Scharm M, Waltemath D, Mendes P, Wolkenhauer O (2016) COMODI: An ontology to characterise differences in versions of computational models in biology. J Biomed. Semantics 7:46 [full text] [preprint]
Mendes P, Oliver SG, Kell DB (2016) Response to 'The Need for Speed, by Matsson et al. Trends in Pharmacol. Sci. 37:245-246 [full text]
Swainston N, Hastings J, Dekker A, Muthukrishnan V, May J, Steinbeck C, Mendes P (2016) libChEBI: an API for accessing the ChEBI database. Journal of Cheminformatics 8:11 [ful text]
Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C (2016) ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Research 44(D1):D1214-9. [ful text]

2015

Mendes P, Oliver SG, Kell DB (2015) Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly. Trends in Pharmacological Sciences 36:710-23. [ful text]
Millard P, Portais J-C, Mendes P (2015) Impact of kinetic isotope effects in isotopic studies of metabolic systems. BMC Systems Biology 9:64. [ful text]
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 (2015) BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Systems Biology 9:8. [ful text]
Bastiaens P, Birtwistle MR, Blüthgen N, Bruggeman FJ, Cho KH, Cosentino C, de la Fuente A, Hoek JB, Kiyatkin A, Klamt S, Kolch W, Legewie S, Mendes P, Naka T, Santra T, Sontag E, Westerhoff HV, Kholodenko BN (2015) Silence on the relevant literature and errors in implementation. Nature Biotechnology 33:336-9. [ful text]

2014

Summersgill H, England H, López-Castejón G, Lawrence CB, Luheshi NM, Pahle J, Mendes P, Brough D (2014) Zinc depletion regulates the processing and secretion of IL-1β. Cell Death and Disease 5:e1040 [ful text]
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, Tobin F, Wodke JA, Zecchina R, Jirstrand M (2014) Bridging the gaps in systems biology. Molecular Genetics & Genomics 289:727-34. [abstract] [ful text]
Mendes P, Dada JO, Smallbone K (eds.) (2014) Computational Methods in Systems Biology, Proceedings of the 12th International Conference, CMSB 2014, Manchester, UK, November 17-19, 2014. Springer.

2013

Messiha HL, Kent E, Malys N, Carroll KM, Mendes P et al. (2013) Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast. PeerJ PrePrints 1:e146v2 [pre-print]
Kent E, Neumann S, Kummer U, Mendes P (2013) What can we learn from global sensitivity analysis of biochemical systems? PLOS One 8:e79244 [full text]
Stanford NJ, Lubitz T, Smallbone K, Klipp E, Mendes P, Liebermeister W (2013) Systematic construction of kinetic models from genome-scale metabolic networks PLoS ONE 8:e79195 [full text]
Mitchell S , Mendes P (2013) A computational model of liver iron metabolism. PLoS Computational Biology 9: e1003299 [full text] [pre-print]
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, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N (2013) Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Systems Biology 7:116 [full text]
Lisko KA, Torres R, Harris RS, Belisle M, Vaughan MM, Jullian B, Chevone BI, Mendes P, Nessler CL, Lorence A (2013) Elevating vitamin C content via over-expression of myo-inositol oxygenase and L-gulono-1,4-lactone oxidase in Arabidopsis leads to enhanced biomass and tolerance to abiotic stresses. In Vitro Cellular and Developmental Biology - Plant 49:643-655. [abstract]
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, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JEG, Paton NW, Westerhoff HV, Kell DB, Mendes P (2013) A model of yeast glycolysis based on a consistent kinetic characterization of all its enzymes. FEBS Letters 587:2832-41 [full text]
Sha W, Martins AM, Laubenbacher R, Mendes P, Shulaev V (2013) The genome-wide early temporal response of Saccharomyces cerevisiae to oxidative stress induced by cumene hydroperoxide. PLOS One 8: e74939. [full text] [supplementary data]
Mensonides FIC, Bakker BM, Cremazy F, Messiha HL , Mendes P, Boogerd FC, Westerhoff HV (2013) A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides illustrated for the glycolytic enzymes of Saccharomyces cerevisiae. FEBS Letters 587: 2860-7. [abstract]
Smallbone K, Mendes P (2013) Large-scale metabolic models: from reconstruction to differential equations. Industrial Biotechnology 9 ,179-184 [full text]
Swainston N, Mendes P, Kell DB (2013) An analysis of a community-driven reconstruction of the human metabolic network. Metabolomics 9 ,757-764 [full text]
Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WD, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov Sr E, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JHGM, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P & Palsson BØ (2013) A community-driven global reconstruction of human metabolism Nature Biotechnology 31:419-425 [full text]
Firczuk H, Kannambath S, Pahle J, Claydon A, Beynon R, Duncan J, Westerhoff H, Mendes P, McCarthy JEG (2013) An in vivo control map for the eukaryotic mRNA translation machinery. Molecular Systems Biology 9:635 [full text]
Tapinos A, Mendes P (2013) A Method for Comparing Multivariate Time Series with Different Dimensions. PLoS ONE 8(2): e54201 [full text]

2012

Pahle J, Challenger JD, Mendes P and McKane AJ (2012) Biochemical Fluctuations, Optimisation and the Linear Noise Approximation. BMC Systems Biology 6:86 [full text]
Kent E, Hoops S, Mendes P (2012) Condor-COPASI: High-Throughput Computing for Biochemical Networks. BMC Systems Biology 6:91 [full text]
Lee D, Smallbone K, Dunn WB, Murabito E, Winder CL, Kell DB, Mendes P, Swainston N (2012) Improving metabolic flux predictions using absolute gene expression data BMC Systems Biology 6:73 [full text]
Heavner BD, Smallbone K, Barker B, Mendes P, Walker LP (2012) Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network BMC Systems Biology 6:55 [full text]
Dada J, Mendes P (2012) ManyCell: A Multiscale Simulator for Cellular Systems. Lecture Notes in Computer Science 7605, 366-369. [abstract]
Chifman J, Kniss A, Neupane P, Williams I, Leung, B, Deng Z, Mendes P, Hower V, Torti FM, Akman SA, Torti SV, Laubenbacher R (2012) The core control system of intracellular iron homeostasis: A mathematical model. J. Theoretical Biology 300, 91-99 [abstract] [full text]
Davies O, Mendes P, Smallbone K, Malys N (2012) Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism BMB Reports 45, 259-264 [abstract] [full text]

2011

Small BG, McColl BW, Allmendinger R, Pahle J, López-Castejón G, Rothwell NJ, Knowles J, Mendes P, Brough D, Kell DB (2011) Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing. Nature Chem. Biol. 7, 902-908 [abstract ] [full text]
Dada, JO, Mendes, P (2011) Multi-scale modelling and simulation in systems biology. Integrative Biology 3, 86-96 [abstract ]
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, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N (2011) Controlled vocabularies and semantics in systems biology Molecular Systems Biology 7:543 [full text]
Swainston N, Smallbone K, Mendes P, Kell DB, Paton NW (2011) The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks J. Integrative Bioinformatics 8, 186 [abstract] [full text]
Blekherman G, Laubenbacher R, Cortes DF, Mendes P, Torti FM, Akman S, Torti SV, Shulaev V. (2011) Bioinformatics tools for cancer metabolomics. Metabolomics 7, 329-343 [abstract] [full text]
Nobata C, Dobson PD, Iqbal SA, Mendes P, Tsujii J, Kell DB, Ananiadou S. (2011) Mining metabolites: extracting the yeast metabolome from the literature Metabolomics 7, 94-101. [abstract] [full text]
Shuman, JL, Cortes, DF, Armenta, JM, Pokrzywa, RM, Mendes, P, Shulaev, V (2011) Plant metabolomics by GC-MS and differential analysis Methods in Molecular Biology 678, 229-246. [abstract]

2010

Li, P, Dada, JO, Jameson, D, Spasic, I, Swainston, N, Carroll, K, Dunn, W, Khan, F, Messiha, HL, Simeonidis, E, Weichart, D, Winder, C, Broomhead, D, Goble, CA, Gaskell, SJ, Kell, DB, Westerhoff, HV, Mendes, P, Paton, NW (2010) Systematic integration of experimental data and models in systems biology BMC Bioinformatics 11, 582 [full text]
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 (2010) Further developments towards a genome-scale metabolic model of yeast BMC Systems Biology 4,145. [full text]
Dada, JO, Spasic, I, Paton, NW, Mendes, P (2010) SBRML: a markup language for associating systems biology data with models. Bioinformatics 26, 932-8 [abstract]
Smallbone, K, Simeonidis, E, Swainston, N, Mendes, P (2010) Towards a genome-scale kinetic model of cellular metabolism. BMC Systems Biology 4, 6 [full text]
Swainston, N, Golebiewski,N, 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, Paton, NW, Rojas, I (2010) Enzyme kinetics informatics: from instrument to browser FEBS Journal 277, 3769-79 [full text]
Swainston N, Jameson D, Li P, Spasik I, Mendes P, Paton NW (2010) Integrative information management for systems biology Lecture Notes in Computer Science (DILS) 6254, 164-178 [abstract]
Mendes (2010) Framework for Comparative Assessment of Parameter Estimation and Inference Methods in Systems Biology. in Learning and Inference in Computational Systems Biology (Lawrence, N.D., Girolami, M., Rattray, M., Sanguinetti, G. eds.) MIT Press, Cambridge, MA, pp. 33-58.

2009

Mendes, P, Messiha, H, Malys, N, Hoops, S (2009) Enzyme kinetics and computational modeling for systems biology. Methods Enzymol. 467, 583-99. [abstract] [ full text]
Dada, JO, Mendes, P (2009) Design and architecture of web services for simulation of biochemical systems. Lecture Notes in Computer Science DILS 5647, 182-195. [abstract]
Swainston, N, Mendes, P (2009) libAnnotationSBML: a library for exploiting SBML annotations. Bioinformatics 25, 2292-2293. [abstract] [full text]
Laubenbacher, R, Hower, V, Jarrah, A, Torti, SV, Shulaev, V, Mendes, P, Torti, FM, Akman, S (2009) A Systems Biology View of Cancer. Biochimica et Biophysica Acta 1796, 129-139. [abstract] [full text]
Mendes, P, Hoops, S, Sahle, S, Gauges, R, Dada, J, Kummer, U (2009) Computational Modeling of Biochemical Networks Using COPASI. Methods Mol. Biol. 500, 17-59. [full text].
Hower, V., Mendes, P., Torti, F.M., Laubenbacher, R., Akman, S., Shulaev, V. Torti, S.V. (2009) A General Map of Iron Metabolism and Tissue-Specific Subnetworks, Molecular Biosystems, 5, 422-43. [abstract] [full text]

2008

Herrgård 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, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology, Nature Biotechnol. 26, 1155-1160. [abstract] [full text].
Sahle, S. Mendes, P., Hoops, S., Kummer, U. (2008) A new strategy for assessing sensitivities in biochemical models, Phil. Trans. Roy. Soc. A 366, 3619-3631. [abstract] [full text].
Flötmann, M., Schaber, J., Hoops, S., Klipp, E., Mendes, P. (2008) ModelMage: A Tool for Automatic Model Generation, Selection and Management Genome Informatics 20, 52-63 [abstract] [full text]

2007

Kell, D.B., Mendes, P. (2007) The markup is the model: Reasoning about systems biology models in the Semantic Web era. J. Theoret. Biol. 252, 538-543. [abstract]
Camacho, D., Vera Licona, P., Mendes, P., Laubenbacher, R.. (2007) Comparison of reverse-engineering methods using an in silico network. Ann. N. Y. Acad. Sci. 1115, 73-89. [abstract]
MSI Board Members, Sansone, S.A., Fan, T., Goodacre, R., Griffin, J.L., Hardy, N.W., Kaddurah-Daouk, R., Kristal, B.S., Lindon, J., Mendes, P., Morrison, N., Nikolau, B., Robertson, D., Sumner, L.W., Taylor, C., van der Werf, M., van Ommen, B., Fiehn, O. (2007) The metabolomics standards initiative. Nat. Biotechnol. 25, 846-848.[full text]
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, 181-188. [abstract]
Henriques, I.D., 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. Environ. Sci. Technol. 41, 3945-3951. [abstract]

2006

Hoops S., Sahle S., Gauges R., Lee C., Pahle J., Simus N., Singhal M., Xu L., Mendes P., Kummer U. (2006) COPASI — a COmplex PAthway SImulator. Bioinformatics 22, 3067-3074 [abstract] [full text]
Mendes P., (2006) Metabolomics and the challenges ahead. Briefings in Bioinformatics 7, 127
Rodriguez-Fernandez, M., Mendes, P., Banga, J.R. (2006) A hybrid approach for efficient and robust parameter estimation in biochemical pathways. Biosystems 83, 248-265 [abstract]
Mehrotra, B., Mendes, P. (2006) Bioinformatics approaches to integrate metabolomics and other systems biology data. in Plant Metabolomics (Biotechnology in Agriculture and Forestry) (Saito, K., Dixon, R.A. & Willmitzer, L. Eds.) Springer-Verlag, Berlin and Heidelberg, Germany, pp. 105-116.

2005

Novère, N.L., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado-Vides, J., Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J.L., Spence, H.D., Wanner, B.L. (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nature Biotechnology 23, 1509-1515 [abstract]
Lei, Z., Elmer, A.M., Watson, B.S., Dixon, R.A., Mendes, P., 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. Mol. Cell. Proteomics 4 1812-1825 [abstract] [full text]
Camacho, D., de la Fuente, A. & Mendes, P. (2005) The origin of correlations in metabolomics data. Metabolomics 1, 53-63. [abstract] [full text]
Mendes, P., Camacho, D., de la Fuente, A. (2005) Modelling and simulation for metabolomics data analysis. Biochem. Soc. Trans. 33, 1427-1429 [abstract]
Laubenbacher, R. & Mendes, P. (2005) A discrete approach to top-down modeling of biochemical networks in Computational Systems Biology (Kriete, A. & Eils, R. Eds.) Elsevier Academic Press, Burlington, MA, pp. 229-247.
Suzuki, H., Reddy, M.S., Naoumkina, M., Aziz, N., May, G.D., Huhman, D.V., Sumner, L.W., Blount, J.W., Mendes, P. & 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, 696-707 [abstract] [full text]
Cramer, G.R., Cushman, J.C., Schooley, D.A., Quilici, D., Vincent, D., Bohlman, M.C., Ergul, A., Tattersall, E.A.R., Tillett, R., Evans, J., Delacruz, R., Schlauch, K. & Mendes, P. (2005) Progress in bioinformatics - the challenge of integrating transcriptomic, proteomic and metabolomic information. Acta Hort. 689, 417-425 [abstract]
Broeckling, C.D., Huhman, D.V., Farag, M.A., Smith, J.T., May, G.D., Mendes, P., Dixon, R.A. & 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, 323-336. [abstract] [full text]

2004

Martins, A.M., Camacho, D., Shuman, J., Sha, W., Mendes, P. & Shulaev, V. (2004) A systems biology study of two distinct growth phases of Saccharomyces cerevisiae. Current Genomics 5, 649-663. [abstract]
de la Fuente, A., Bing, N., Hoeschele, I. & Mendes, P. (2004) Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics 20, 3565-3574. [abstract] [full text]
Jenkins, H., Hardy, N., Beckmann, M., Draper, J., Smith, A. R., Taylor, J., Fiehn, O., Goodacre, R., Bino, R. J., Hall, R., Kopka, J., Lane, G. A., Lange, B. M., Liu, J. R., Mendes, P., Nikolau, B. J., Oliver, S. G., Paton, N. W., Rhee, S., Roessner-Tunali, U., Saito, K., Smedsgaard, J., Sumner, L. W., Wang, T., Walsh, S., Wurtele, E. S. & Kell, D. B. (2004) A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotechnology 22, 1601-1606. [abstract]
Bino, R. J., Hall, R. D., Fiehn, O., Kopka, J., Saito, K., Draper, J., Nikolau, B. J., Mendes, P., Roessner-Tunali, U., Beale, M. H., Trethewey, R. N., Lange, B. M., Wurtele, E. S. & Sumner, L. W. (2004) Potential of metabolomics as a functional genomics tool. Trends in Plant Sciences 9, 418-25. [abstract]
Lorence, A., Chevone, B.I., Mendes, P. & Nessler, C.L. (2004) myo-Inositol oxygenase offers a possible entry point into plant ascorbate biosynthesis. Plant Physiology 134, 1200-1205. [abstract] [full text]
de la Fuente, A. & Mendes, P. (2004) Book Review: Computational analysis of biochemical systems, by Eberhart O. Voit. Bulletin of Mathematical Biology 66, 195-197. [full text]
de la Fuente, A., Brazhnik, P. & Mendes, P. (2004) Regulatory strength analysis for inferring gene networks. in Metabolic engineering in the post-genomics era (Kholodenko, B.N & Westerhoff, H.V. eds.) Horizon Bioscience, Wymondham, UK, pp. 107-137.

2003

Moles C.G., Mendes P. & Banga J.R. (2003) Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Research 13, 2467-2474. [abstract] [full text]
Sumner, L.W., Mendes, P., Dixon, R.A. (2003) Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemistry 62, 817-36. [abstract] [full text]
Hucka, M., Finney, A., Sauro, H.M., Bolouri, H., Doyle, J.C., Kitano, H., Arkin, A.P., Bornstein, B.J., Bray, D., Cornish-Bowden, A., Cuellar, A.A., Dronov, S., Gilles, E.D., Ginkel, M., Gor, V., Goryanin, I.I., Hedley, W.J., Hodgman, T.C., Hofmeyr, J.H., Hunter, P.J., Juty, N.S., Kasberger, J.L., Kremling, A., Kummer, U., Le Novere, N., Loew, L.M., Lucio, D., Mendes, P., Minch, E., Mjolsness, E.D., Nakayama, Y., Nelson, M.R., Nielsen, P.F., Sakurada, T., Schaff, J.C., Shapiro, B.E., Shimizu, T.S., Spence, H.D., Stelling, J., Takahashi, K., Tomita, M., Wagner, J. & Wang, J. (2003). The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models Bioinformatics 19, 524-531. [abstract]
Mendes, P., Sha, W. & Ye, K. (2003) Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics 19, ii122-ii129. [abstract] [full text] [supplementary data]
de la Fuente, A. & Mendes, P. (2003) Integrative modeling of gene expression and cell metabolism. Applied Bioinformatics 2, 79-90. [abstract]

2002

Mendes, P. (2002) Emerging bioinformatics for the metabolome. Briefings in Bioinformatics 3, 134-145. [abstract]
Brazhnik, P., de la Fuente, A. & Mendes, P. (2002) Gene networks: how to put the function in genomics. Trends in Biotechnology 20, 467-472. [abstract] [full text]
de la Fuente, A. & Mendes, P. (2002) Quantifying gene networks with regulatory strengths. Molecular Biology Reports 29, 73-77. [abstract]
de la Fuente, A., Brazhnik, P. & Mendes, P. (2002) Linking the genes: inferring quantitative gene networks from microarray data. Trends in Genetics 18, 395-398. [abstract] [supplementary information]
Mendes, P., de la Fuente, A. & Hoops, S. (2002) Bioinformatics and computational biology for plant functional genomics. Recent Advances in Phytochemistry 36, 1-13.
Li, X.J., Brazhnik, O., Kamal, A., Guo, D., Lee, C., Hoops, S. & Mendes, P. (2002) Databases and visualization for metabolomics. In Harrigan, G.G. and Goodacre, R. (eds.), Metabolic profiling: its role in biomarker discovery and gene function analysis Kluwer Academic Publishers, Boston, Dordrecht and London, pp. 293-309.
de la Fuente, A., Snoep, J.L., Westerhoff, H.V. & Mendes, P. (2002) Metabolic control in integrated biochemical systems. European Journal of Biochemistry 269, 4399-4408. [abstract ] [supplementary information]

2001

de la Fuente, A., Brazhnik, P. & Mendes, P. (2001). A quantitative method for reverse engineering gene networks from microarray experiments using regulatory strengths. Proceedings of the 2nd International Conference on Systems Biology, California Institute of Technology, Pasadena, CA. [full text] [supplementary information]
Mendes, P. (2001) Modeling large scale biological systems from functional genomic data: parameter estimation. in Foundations of Systems Biology (Kitano, H., ed), MIT Press, Cambridge, MA, pp. 163-186.
Mendes, P. & Kell, D.B. (2001) MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems. Bioinformatics 17, 288-289. [full text]
Martins, A.M., Mendes, P., Cordeiro, C. & Freire, A.P. (2001) In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae. European Journal of Biochemistry 268, 3930-3936. [full text]
Siepel, A., Farmer, A., Tolopko, A., Zhuang, M., Mendes, P., Beavis, W. & Sobral, B. (2001) ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics 17, 83-94. [full text]
Sobral, B. W., Mangalam, H., Siepel, A., Mendes, P., Pecherer, R. & McLaren, G. (2001) Bioinformatics for rice resources. Novartis Foundation Symposia 236, 59-81. [abstract]

2000

de la Fuente van Bentem, A., Mendes, P., Westerhoff, H.V. & Snoep, J.L. (2000) Can metabolic control analysis be applied to hierarchical regulated metabolism? MCA versis HCA. in Animating the cellular map (Hofmeyr, J.-H.S., Rohwer, J.H. and Snoep, J.L., eds), Stellenbosch University Press, Stellenbosch, pp. 191-198.
Mendes, P., Bulmore, D.L., Farmer, A.D., Steadman, P.A., Waugh, M.E. & Wlodek, S.T. (2000) PathDB: a second generation metabolic database. In Animating the cellular map. (Hofmeyr, J.-H.S., Rohwer, J.M. & Snoep, J.L. eds.), Stellenbosch, Stellenbosch University Press, pp. 207-212. [full text]
Kell, D.B. & Mendes, P. (2000) Snapshots of systems: metabolic control analysis and biotechnology in the post-genomic era. In Technological and Medical Implications of Metabolic Control Analysis ( Cornish-Bowden, A. & Cárdenas, M.L. eds.), Dordrecht, Kluwer Academic Publishers, pp. 3-25.

1990-1999

Mendes, P. (1999) Metabolic simulation as an aid in understanding gene expression data. In Workshop on Computation of Biochemical Pathways and Genetic Networks (Bornberg-Bauer, E., De Beuckelaer, A., Kummer, U., and Rost, U., eds), Logos-Verlag, Heidelberg, pp. 27-34.
Snoep, J., Mendes, P. and Westerhoff, H. (1999) Teaching Metabolic Control Analysis and kinetic modelling. Towards a portable teaching module. The Biochemist 21 (February 1999), 25-28. [full text] (with kind permission from the Biochemical Society, 1999)
Mendes, P. & Kell, D. B. (1998) Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 10, 869-883. [abstract] [full text]
Mendes, P. & Kell, D. B. (1998) Numerical optimisation and simulation for rational metabolic engineering. in BioThermoKinetics in the post genomic era (eds. C. Larsson, I.-L. Påhlman and L. Gustaffson), pp. 345-349. Chalmers Reproservice, Göteborg. [full text]
Mendes, P. (1998) Using computers to learn metabolism. Biochemical Society Transactions 27, A21.
Mendes, P. (1997) Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends in Biochemical Sciences 22, 361-363.
Mendes, P. & Kell, D.B. (1997) Making cells work - metabolic engineering for everyone. Trends in Biotechnology 15, 6-7. (meeting report)
Mendes, P., Marmillot, P., Hervagault, J.-F. & Welch, G. R. (1996) Long-range metabolic signalling in heterogeneous catalytic systems: Computer simulation study. In Computation in cellular and molecular biological systems (Cuthbertson, R., Holcombe, M. & Paton, R. eds), pp. 137-149. World Scientific, Singapore.
Mendes, P., Kell, D.B. & Westerhoff, H.V. (1996) Why and when channelling can decrease pool size at a constant net flux in a simple dynamic channel. Biochimica et Biophysica Acta 1289, 175-186. [abstract]
Mendes, P. & Kell, D.B. (1996) On the analysis of the inverse problem of metabolic pathways using artificial neural networks. BioSystems 38, 15-28. [abstract]
Mendes, P. & Kell, D. B. (1996). Computer simulation of biochemical kinetics. in BioThermoKinetics of the living cell (ed. H. V. Westerhoff, J. L. Snoep, F. E. Sluse, J. E. Wijker & B. N. Kholodenko), pp. 254-257. BioThermoKinetics Press, Amsterdam. [full text]
Mendes, P., Kell, D.B. & Welch, G.R. (1995) Metabolic channelling in organized enzyme systems: experiments and models. Advances in Molecular Cellular Biology 11, 1-19.
Mendes, P., Kell, D.B. & Westerhoff, H.V. (1995) A series of cases in which metabolic channelling can decrease the pool size at a constant net flux in a simple dynamic channel. Biochemical Society Transactions 23, 287S.
Mendes, P. (1994). Computer simulation of the dynamics of biochemical pathways. Ph. D. thesis, University of Wales, Aberystwyth. [abstract] [full text (zipped postscript)]
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, 563-571. [abstract]
Mendes, P. (1993) GEPASI: A User Oriented Metabolic Simulator. In Modern Trends in Biothermokinetics (S. Schuster, M. Rigoulet, R. Ouhabi & J.-P. Mazat eds), pp. 463-466, Plenum Press, New York and London.
Mendes, P. & Kell, D.B. (1993) Control analysis of metabolic channelling. In Modern Trends in Biothermokinetics (S. Schuster, M. Rigoulet, R. Ouhabi & J.-P. Mazat eds), pp. 211-216, Plenum Press, New York and London.
Mendes, P. & Kell, D.B. (1993), On the role of enzyme kinetic parameters in determining the effectiveness with which channelling can decrease the size of a metabolite pool. Acta Biotheoretica 41, 63-73. [abstract]
Mendes, P., Kell, D.B., & Westerhoff, H.V. (1992) Channelling can decrease pool size. European Journal of Biochemistry 204, 257-266. [abstract] [full text]
Mendes, P., Moniz Barreto, J., Vaz Gomes, A. & Ponces Freire, A. (1990) A methodology for simulation of metabolic pathways and calculation of control coefficients. In Control of metabolic processes ( Cornish-Bowden, A. & Cárdenas, M.L. eds.), pp. 221-224, Plenum Press, New York.