Mendes, Pedro

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

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., et al. (2003) · Bioinformatics

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

Cited by 3,060

COPASI—a COmplex PAthway SImulator

Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., & Kummer, U. (2006) · Bioinformatics

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 2,618

ChEBI in 2016: Improved services and an expanding collection of metabolites

Hastings, J., Owen, G., Dekker, A., Ennis, M., Kale, N., Muthukrishnan, V., Turner, S., Swainston, N., Mendes, P., & Steinbeck, C. (2016) · Nucleic Acids Research

Biomedical Text Mining and OntologiesSemantic Web and Ontologies

Cited by 1,083

A community-driven global reconstruction of human metabolism

Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., et al. (2013) · Nature Biotechnology

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 1,019

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

Moles, C. G., Mendes, P., & Banga, J. R. (2003) · Genome Research

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 858

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

Novère, N. L., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P., et al. (2005) · Nature Biotechnology

Gene Regulatory Network AnalysisScientific Computing and Data Management

Cited by 622

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., et al. (2008) · Nature Biotechnology

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 588

The Metabolomics Standards Initiative (MSI)

Fiehn, O., Robertson, D., Griffin, J., van der Werf, M., Nikolau, B., Morrison, N., Sumner, L. W., Goodacre, R., Hardy, N. W., Taylor, C., et al. (2007) · Metabolomics

Metabolomics and Mass Spectrometry StudiesResearch Data Management Practices

Cited by 518

Controlled vocabularies and semantics in systems biology

Courtot, M., Juty, N., Knüpfer, C., Waltemath, D., Zhukova, A., Dräger, A., Dumontier, M., Finney, A., Golebiewski, M., Hastings, J., et al. (2011) · Molecular Systems Biology

Biomedical Text Mining and OntologiesGene Regulatory Network Analysis

Cited by 316

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

Rodriguez-Fernandez, M., Mendes, P., & Banga, J. R. (2006) · Biosystems

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 304

Recon 2.2: from reconstruction to model of human metabolism

Swainston, N., Smallbone, K., Hefzi, H., Dobson, P. D., Brewer, J., Hanscho, M., Zielinski, D. C., Ang, K. S., Gardiner, N. J., Gutierrez, J. M., et al. (2016) · Metabolomics

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 285

Multi-scale modelling and simulation in systems biology

Dada, J. O., & Mendes, P. (2011) · Integrative Biology

Advanced Mathematical Modeling in EngineeringGene Regulatory Network Analysis

Cited by 213

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

Smallbone, K., Messiha, H. L., Carroll, K. M., Winder, C. L., Malys, N., Dunn, W. B., Murabito, E., Swainston, N., Dada, J. O., Khan, F., et al. (2013) · FEBS Letters

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 147

What Can We Learn from Global Sensitivity Analysis of Biochemical Systems?

Kent, E., Neumann, S., Kummer, U., & Mendes, P. (2013) · PLoS ONE

Gene Regulatory Network AnalysisProbabilistic and Robust Engineering Design

Cited by 44

A new strategy for assessing sensitivities in biochemical models

Sahle, S., Mendes, P., Hoops, S., & Kummer, U. (2008) · Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 44

Bridging the gaps in systems biology

Cvijovic, M., Almquist, J., Hagmar, J., Hohmann, S., Kaltenbach, H.-M., Klipp, E., Krantz, M., Mendes, P., Nelander, S., Nielsen, J., et al. (2014) · Molecular Genetics and Genomics

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

Cited by 40

libAnnotationSBML: a library for exploiting SBML annotations

Swainston, N., & Mendes, P. (2009) · Bioinformatics

Biomedical Text Mining and OntologiesGene Regulatory Network Analysis

Cited by 29

On the analysis of the inverse problem of metabolic pathways using artificial neural networks

Mendes, P., & Kell, D. B. (1996) · Biosystems

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 24

Reproducible Research Using Biomodels

Mendes, P. (2018) · Bulletin of Mathematical Biology

Scientific Computing and Data ManagementResearch Data Management Practices

Cited by 20

An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems

Gupta, A., & Mendes, P. (2018) · Computation

Gene Regulatory Network AnalysisSimulation Techniques and Applications

Cited by 17

Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient

Parmar, J. H., Davis, G., Shevchuk, H., & Mendes, P. (2017) · BMC Systems Biology

Iron Metabolism and DisordersTrace Elements in Health

Cited by 12