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List of works by Pedro Mendes

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Recon 2.2: from reconstruction to model of human metabolism

scientific article
A community-driven global reconstruction of human metabolism.

scientific article
COPASI--a COmplex PAthway SImulator

scientific article (publication date: 15 December 2006)
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

scientific article
Minimum information requested in the annotation of biochemical models (MIRIAM)

scientific article
Plant metabolomics: large-scale phytochemistry in the functional genomics era.

scientific article
Parameter estimation in biochemical pathways: a comparison of global optimization methods

scientific article
Potential of metabolomics as a functional genomics tool.

scientific article
Discovery of meaningful associations in genomic data using partial correlation coefficients

scientific article
myo-inositol oxygenase offers a possible entry point into plant ascorbate biosynthesis

scientific article published on 19 February 2004
Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism

scientific article published on 13 December 2004
A proposed framework for the description of plant metabolomics experiments and their results

article
Controlled vocabularies and semantics in systems biology

scientific article (publication date: 25 October 2011)
Path2Models: large-scale generation of computational models from biochemical pathway maps

scientific article
Gene networks: how to put the function in genomics

scientific article
A hybrid approach for efficient and robust parameter estimation in biochemical pathways

scientific article published on 19 October 2005
Improving metabolic flux predictions using absolute gene expression data

scientific article
Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

scientific article (publication date: 4 June 2012)
Methyl jasmonate and yeast elicitor induce differential transcriptional and metabolic re-programming in cell suspension cultures of the model legume Medicago truncatula

scientific article published on 17 December 2004
Towards a genome-scale kinetic model of cellular metabolism

scientific article
Artificial gene networks for objective comparison of analysis algorithms

scientific article
Computational modeling of biochemical networks using COPASI

scientific article (publication date: 2009)
Linking the genes: inferring quantitative gene networks from microarray data

scientific article
An in vivo control map for the eukaryotic mRNA translation machinery

scientific article published on January 2013
Further developments towards a genome-scale metabolic model of yeast

scientific article (publication date: 28 October 2010)
Systematic construction of kinetic models from genome-scale metabolic networks

scientific article
The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks

scientific article
A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes

scientific article published on 04 July 2013
Bioinformatics tools for cancer metabolomics

scientific article
A two-dimensional electrophoresis proteomic reference map and systematic identification of 1367 proteins from a cell suspension culture of the model legume Medicago truncatula

scientific article published on 26 July 2005
A general map of iron metabolism and tissue-specific subnetworks

scientific article published on 06 March 2009
Multi-scale modelling and simulation in systems biology

scientific article published on 06 January 2011
A systems biology view of cancer

scientific article published on 06 June 2009
Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing

scientific article
SBRML: a markup language for associating systems biology data with models

scientific article
Emerging bioinformatics for the metabolome

scientific article
A new strategy for assessing sensitivities in biochemical models

scientific article
An analysis of a 'community-driven' reconstruction of the human metabolic network

scientific article
Zinc depletion regulates the processing and secretion of IL-1β.

scientific article published on 30 January 2014
Toward Community Standards and Software for Whole-Cell Modeling

scientific article
Condor-COPASI: high-throughput computing for biochemical networks

scientific article
Mining metabolites: extracting the yeast metabolome from the literature

scientific article
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology

scientific article
libAnnotationSBML: a library for exploiting SBML annotations

scientific article
Comparison of reverse-engineering methods using an in silico network

scientific article published on 09 October 2007
A Computational Model of Liver Iron Metabolism

scientific article published on November 7, 2013
Bridging the gaps in systems biology

scientific article published on 13 April 2014
Systematic integration of experimental data and models in systems biology

scientific article (publication date: 29 November 2010)
Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli.

scientific article
What can we learn from global sensitivity analysis of biochemical systems?

scientific article (publication date: 2013)

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