Pedro Mendes

  • University of Connecticut School of Medicine, Farmington, CT, USA
  • University of Manchester, Institute of Biotechnology / School of Computer Science, UK
  • Virginia Tech, Virginia Bioinformatics Institute, Blacksburg, VA, USA (former)
  • Universityof Wales Aberystwyth, UK (former)
  • University of Maryland, MD, USA (PhD 1986)

According to our database1, Pedro Mendes authored at least 45 papers between 1988 and 2022.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 


Online presence:



BioSimulators: a central registry of simulation engines and services for recommending specific tools.
CoRR, 2022

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.
Briefings Bioinform., 2021

A computational model to understand mouse iron physiology and disease.
PLoS Comput. Biol., 2019

An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems.
Comput., 2018

Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli.
PLoS Comput. Biol., 2017

Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient.
BMC Syst. Biol., 2017

Toward Community Standards and Software for Whole-Cell Modeling.
IEEE Trans. Biomed. Eng., 2016

ChEBI in 2016: Improved services and an expanding collection of metabolites.
Nucleic Acids Res., 2016

libChEBI: an API for accessing the ChEBI database.
J. Cheminformatics, 2016

COMODI: an ontology to characterise differences in versions of computational models in biology.
J. Biomed. Semant., 2016

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.
BMC Syst. Biol., 2015

Impact of kinetic isotope effects in isotopic studies of metabolic systems.
BMC Syst. Biol., 2015

ChEBI for systems biology and metabolic modelling.
Proceedings of the International Conference on Biomedical Ontology, 2015

BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology.
CoRR, 2014

A Computational Model of Liver Iron Metabolism.
PLoS Comput. Biol., 2013

Path2Models: large-scale generation of computational models from biochemical pathway maps.
BMC Syst. Biol., 2013

Biochemical fluctuations, optimisation and the linear noise approximation.
BMC Syst. Biol., 2012

Improving metabolic flux predictions using absolute gene expression data.
BMC Syst. Biol., 2012

Condor-COPASI: high-throughput computing for biochemical networks.
BMC Syst. Biol., 2012

Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network.
BMC Syst. Biol., 2012

ManyCell: A Multiscale Simulator for Cellular Systems.
Proceedings of the Computational Methods in Systems Biology, 2012

The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks.
J. Integr. Bioinform., 2011

Kinetic modelling of large-scale metabolic networks.
Proceedings of the Computational Methods in Systems Biology, 9th International Conference, 2011

Towards a genome-scale kinetic model of cellular metabolism.
BMC Syst. Biol., 2010

Further developments towards a genome-scale metabolic model of yeast.
BMC Syst. Biol., 2010

Systematic integration of experimental data and models in systems biology.
BMC Bioinform., 2010

SBRML: a markup language for associating systems biology data with models.
Bioinform., 2010

Integrative Information Management for Systems Biology.
Proceedings of the Data Integration in the Life Sciences, 7th International Conference, 2010

libAnnotationSBML: a library for exploiting SBML annotations.
Bioinform., 2009

Design and Architecture of Web Services for Simulation of Biochemical Systems.
Proceedings of the Data Integration in the Life Sciences, 6th International Workshop, 2009

Parallelizing simulated annealing algorithms based on high-performance computer.
J. Glob. Optim., 2007

COPASI - a COmplex PAthway SImulator.
Bioinform., 2006

Metabolomics and the challenges ahead.
Briefings Bioinform., 2006

Challenges for modeling and simulation methods in systems biology.
Proceedings of the Winter Simulation Conference WSC 2006, 2006

Simulation of biochemical networks using COPASI: a complex pathway simulator.
Proceedings of the Winter Simulation Conference WSC 2006, 2006

Discovery of meaningful associations in genomic data using partial correlation coefficients.
Bioinform., 2004

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Bioinform., 2003

Artificial gene networks for objective comparison of analysis algorithms.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003

Emerging bioinformatics for the metabolome.
Briefings Bioinform., 2002

A Reference Database for Medicago Truncatula Genes, Protiens, and Metabolites.
Proceedings of the 1st IEEE Computer Society Bioinformatics Conference, 2002

ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources.
Bioinform., 2001

MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems.
Bioinform., 2001

Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation.
Bioinform., 1998

GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems.
Comput. Appl. Biosci., 1993

The Responsive System: A New Challenge for AI.
Proceedings of the First International Conference on Industrial & Engineering Applications of Artificial Intelligence & Expert Systems, IEA/AIE 1988, June 1-3, 1988, Tullahoma, TN, USA. ACM, 1988, 1988