Pedro Mendes
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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
M Hucka, A Finney, HM Sauro, H Bolouri, JC Doyle, H Kitano, AP Arkin, ...
Bioinformatics 19 (4), 524-531, 2003
COPASI—a complex pathway simulator
S Hoops, S Sahle, R Gauges, C Lee, J Pahle, N Simus, M Singhal, L Xu, ...
Bioinformatics 22 (24), 3067-3074, 2006
Plant metabolomics: large-scale phytochemistry in the functional genomics era
LW Sumner, P Mendes, RA Dixon
Phytochemistry 62 (6), 817-836, 2003
A community-driven global reconstruction of human metabolism
I Thiele, N Swainston, RMT Fleming, A Hoppe, S Sahoo, MK Aurich, ...
Nature biotechnology 31 (5), 419-425, 2013
Parameter estimation in biochemical pathways: a comparison of global optimization methods
CG Moles, P Mendes, JR Banga
Genome research 13 (11), 2467-2474, 2003
ChEBI in 2016: Improved services and an expanding collection of metabolites
J Hastings, G Owen, A Dekker, M Ennis, N Kale, V Muthukrishnan, ...
Nucleic acids research 44 (D1), D1214-D1219, 2016
Potential of metabolomics as a functional genomics tool
RJ Bino, RD Hall, O Fiehn, J Kopka, K Saito, J Draper, BJ Nikolau, ...
Trends in plant science 9 (9), 418-425, 2004
GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems
P Mendes
Bioinformatics 9 (5), 563-571, 1993
Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation.
P Mendes, D Kell
Bioinformatics (Oxford, England) 14 (10), 869-883, 1998
Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3
P Mendes
Trends in biochemical sciences 22 (9), 361-363, 1997
Minimum information requested in the annotation of biochemical models (MIRIAM)
NL Novère, A Finney, M Hucka, US Bhalla, F Campagne, J Collado-Vides, ...
Nature biotechnology 23 (12), 1509-1515, 2005
Discovery of meaningful associations in genomic data using partial correlation coefficients
A De La Fuente, N Bing, I Hoeschele, P Mendes
Bioinformatics 20 (18), 3565-3574, 2004
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
MJ Herrgård, N Swainston, P Dobson, WB Dunn, KY Arga, M Arvas, ...
Nature biotechnology 26 (10), 1155-1160, 2008
myo-Inositol Oxygenase Offers a Possible Entry Point into Plant Ascorbate Biosynthesis
A Lorence, BI Chevone, P Mendes, CL Nessler
Plant Physiology 134 (3), 1200-1205, 2004
The metabolomics standards initiative (MSI)
O Fiehn, D Robertson, J Griffin, M van der Werf, B Nikolau, N Morrison, ...
Metabolomics 3, 175-178, 2007
Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism
CD Broeckling, DV Huhman, MA Farag, JT Smith, GD May, P Mendes, ...
Journal of experimental botany 56 (410), 323-336, 2005
A hybrid approach for efficient and robust parameter estimation in biochemical pathways
M Rodriguez-Fernandez, P Mendes, JR Banga
Biosystems 83 (2-3), 248-265, 2006
Gene networks: how to put the function in genomics
P Brazhnik, A De La Fuente, P Mendes
TRENDS in Biotechnology 20 (11), 467-472, 2002
Controlled vocabularies and semantics in systems biology
M Courtot, N Juty, C Knüpfer, D Waltemath, A Zhukova, A Dräger, ...
Molecular systems biology 7 (1), 543, 2011
The metabolomics standards initiative
Nature biotechnology 25 (8), 846-848, 2007
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