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Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli.Millard, Pierre; Smallbone, Kieran; Mendes, Pedro PLoS computational biology 2017 Feb;13(2):e1005396
Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis.Meng, Xiang; Firczuk, Helena; Pietroni, Paola; Westbrook, Richard; Dacheux, Estelle; Mendes, Pedro; McCarthy, John E G Nucleic acids research 2016 Dec;
COMODI: an ontology to characterise differences in versions of computational models in biology.Scharm, Martin; Waltemath, Dagmar; Mendes, Pedro; Wolkenhauer, Olaf Journal of biomedical semantics 2016 Jan;7(1):46
libChEBI: an API for accessing the ChEBI database.Swainston, Neil; Hastings, Janna; Dekker, Adriano; Muthukrishnan, Venkatesh; May, John; Steinbeck, Christoph; Mendes, Pedro Journal of cheminformatics 2016 Jan;811
Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly.Mendes, Pedro; Oliver, Stephen G; Kell, Douglas B Trends in pharmacological sciences 2015 Nov;36(11):710-23
Silence on the relevant literature and errors in implementation.Bastiaens, Philippe; Birtwistle, Marc R; Blüthgen, Nils; Bruggeman, Frank J; Cho, Kwang-Hyun; Cosentino, Carlo; de la Fuente, Alberto; Hoek, Jan B; Kiyatkin, Anatoly; Klamt, Steffen; Kolch, Walter; Legewie, Stefan; Mendes, Pedro; Naka, Takashi; Santra, Tapesh; Sontag, Eduardo; Westerhoff, Hans V; Kholodenko, Boris N Nature biotechnology 2015 Apr;33(4):336-9
Impact of kinetic isotope effects in isotopic studies of metabolic systems.Millard, Pierre; Portais, Jean-Charles; Mendes, Pedro BMC systems biology 2015 Jan;9(1):64
Zinc depletion regulates the processing and secretion of IL-1β.Summersgill, H; England, H; Lopez-Castejon, G; Lawrence, C B; Luheshi, N M; Pahle, J; Mendes, P; Brough, D Cell death & disease 2014 Jan;5e1040
Elevating vitamin C content via overexpression of myo-inositol oxygenase and l-gulono-1,4-lactone oxidase in Arabidopsis leads to enhanced biomass and tolerance to abiotic stresses.Lisko, Katherine A; Torres, Raquel; Harris, Rodney S; Belisle, Melinda; Vaughan, Martha M; Jullian, Berangère; Chevone, Boris I; Mendes, Pedro; Nessler, Craig L; Lorence, Argelia In vitro cellular & developmental biology. Plant : journal of the Tissue Culture Association 2013 Dec;49(6):643-655
A computational model of liver iron metabolism.Mitchell, Simon; Mendes, Pedro PLoS computational biology 2013 Nov;9(11):e1003299
The genome-wide early temporal response of Saccharomyces cerevisiae to oxidative stress induced by cumene hydroperoxide.Sha, Wei; Martins, Ana M; Laubenbacher, Reinhard; Mendes, Pedro; Shulaev, Vladimir PloS one 2013 Sep;8(9):e74939
A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.Smallbone, Kieran; Messiha, Hanan L; Carroll, Kathleen M; Winder, Catherine L; Malys, Naglis; Dunn, Warwick B; Murabito, Ettore; Swainston, Neil; Dada, Joseph O; Khan, Farid; Pir, Pinar; Simeonidis, Evangelos; Spasic, Irena; Wishart, Jill; Weichart, Dieter; Hayes, Neil W; Jameson, Daniel; Broomhead, David S; Oliver, Stephen G; Gaskell, Simon J; McCarthy, John E G; Paton, Norman W; Westerhoff, Hans V; Kell, Douglas B; Mendes, Pedro FEBS letters 2013 Sep;587(17):2832-41
A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides--illustrated for the glycolytic enzymes of Saccharomyces cerevisiae.Mensonides, Femke I C; Bakker, Barbara M; Cremazy, Frederic; Messiha, Hanan L; Mendes, Pedro; Boogerd, Fred C; Westerhoff, Hans V FEBS letters 2013 Sep;587(17):2860-7
An analysis of a 'community-driven' reconstruction of the human metabolic network.Swainston, Neil; Mendes, Pedro; Kell, Douglas B Metabolomics : Official journal of the Metabolomic Society 2013 Aug;9(4):757-764
A community-driven global reconstruction of human metabolism.Thiele, Ines; Swainston, Neil; Fleming, Ronan M T; Hoppe, Andreas; Sahoo, Swagatika; Aurich, Maike K; Haraldsdottir, Hulda; Mo, Monica L; Rolfsson, Ottar; Stobbe, Miranda D; Thorleifsson, Stefan G; Agren, Rasmus; B?lling, Christian; Bordel, Sergio; Chavali, Arvind K; Dobson, Paul; Dunn, Warwick B; Endler, Lukas; Hala, David; Hucka, Michael; Hull, Duncan; Jameson, Daniel; Jamshidi, Neema; Jonsson, Jon J; Juty, Nick; Keating, Sarah; Nookaew, Intawat; Le Novère, Nicolas; Malys, Naglis; Mazein, Alexander; Papin, Jason A; Price, Nathan D; Selkov, Evgeni; Sigurdsson, Martin I; Simeonidis, Evangelos; Sonnenschein, Nikolaus; Smallbone, Kieran; Sorokin, Anatoly; van Beek, Johannes H G M; Weichart, Dieter; Goryanin, Igor; Nielsen, Jens; Westerhoff, Hans V; Kell, Douglas B; Mendes, Pedro; Palsson, Bernhard ? Nature biotechnology 2013 May;31(5):419-25
A method for comparing multivariate time series with different dimensions.Tapinos, Avraam; Mendes, Pedro PloS one 2013 Jan;8(2):e54201
An in vivo control map for the eukaryotic mRNA translation machinery.Firczuk, Helena; Kannambath, Shichina; Pahle, Jürgen; Claydon, Amy; Beynon, Robert; Duncan, John; Westerhoff, Hans; Mendes, Pedro; McCarthy, John Eg Molecular systems biology 2013 Jan;9635
Path2Models: large-scale generation of computational models from biochemical pathway maps.Büchel, Finja; Rodriguez, Nicolas; Swainston, Neil; Wrzodek, Clemens; Czauderna, Tobias; Keller, Roland; Mittag, Florian; Schubert, Michael; Glont, Mihai; Golebiewski, Martin; van Iersel, Martijn; Keating, Sarah; Rall, Matthias; Wybrow, Michael; Hermjakob, Henning; Hucka, Michael; Kell, Douglas B; Müller, Wolfgang; Mendes, Pedro; Zell, Andreas; Chaouiya, Claudine; Saez-Rodriguez, Julio; Schreiber, Falk; Laibe, Camille; Dr?ger, Andreas; Le Novère, Nicolas BMC systems biology 2013 Jan;7116
Systematic construction of kinetic models from genome-scale metabolic networks.Stanford, Natalie J; Lubitz, Timo; Smallbone, Kieran; Klipp, Edda; Mendes, Pedro; Liebermeister, Wolfram PloS one 2013 Jan;8(11):e79195
What can we learn from global sensitivity analysis of biochemical systems?Kent, Edward; Neumann, Stefan; Kummer, Ursula; Mendes, Pedro PloS one 2013 Jan;8(11):e79244
The core control system of intracellular iron homeostasis: a mathematical model.Chifman, J; Kniss, A; Neupane, P; Williams, I; Leung, B; Deng, Z; Mendes, P; Hower, V; Torti, F M; Akman, S A; Torti, S V; Laubenbacher, R Journal of theoretical biology 2012 May;30091-9
Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism.Davies, Oluwafemi; Mendes, Pedro; Smallbone, Kieran; Malys, Naglis BMB reports 2012 Apr;45(4):259-64
Biochemical fluctuations, optimisation and the linear noise approximation.Pahle, Jürgen; Challenger, Joseph D; Mendes, Pedro; McKane, Alan J BMC systems biology 2012 Jan;686
Condor-COPASI: high-throughput computing for biochemical networks.Kent, Edward; Hoops, Stefan; Mendes, Pedro BMC systems biology 2012 Jan;691
Improving metabolic flux predictions using absolute gene expression data.Lee, Dave; Smallbone, Kieran; Dunn, Warwick B; Murabito, Ettore; Winder, Catherine L; Kell, Douglas B; Mendes, Pedro; Swainston, Neil BMC systems biology 2012 Jan;673
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