List of works - Pedro Mendes

A Metabolic Reaction Balancing Web Service for Computational Systems Biology

A community-driven global reconstruction of human metabolism. ⬇️

scientific article

A computational model of liver iron metabolism

scientific article (publication date: 2013)

A computational model to understand mouse iron physiology and disease

scientific article published on 04 January 2019

A computational model to understand mouse iron physiology and diseases

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

scientific article

A general map of iron metabolism and tissue-specific subnetworks

scientific article published on 06 March 2009

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

scientific article published on 19 October 2005

A method for comparing multivariate time series with different dimensions

scientific article

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

scientific article published on 04 July 2013

A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides--illustrated for the glycolytic enzymes of Saccharomyces cerevisiae

scientific article published on 12 July 2013

A new strategy for assessing sensitivities in biochemical models

scientific article

A proposed framework for the description of plant metabolomics experiments and their results

article

A systems biology view of cancer

scientific article published on 06 June 2009

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

Agent Based Models of Polymicrobial Biofilms and the Microbiome-A Review

scientific article published on 17 February 2021

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

scientific article

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

scientific article

An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study

scientific article published on 16 September 2018

An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study

scientific article published on 13 April 2018

An in vivo control map for the eukaryotic mRNA translation machinery

scientific article published on January 2013

Artificial gene networks for objective comparison of analysis algorithms

scientific article

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

scientific article

Biochemical fluctuations, optimisation and the linear noise approximation

scientific article

Bioinformatics tools for cancer metabolomics

scientific article

Bridging the gaps in systems biology

scientific article published on 13 April 2014

COMODI: an ontology to characterise differences in versions of computational models in biology

scientific article published on 11 July 2016

COPASI and its applications in biotechnology

scientific article published on 24 June 2017

COPASI--a COmplex PAthway SImulator

scientific article (publication date: 15 December 2006)

Challenges for Modeling and Simulation Methods in Systems Biology

Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism.

scientific article

Comparison of reverse-engineering methods using an in silico network

scientific article published on 09 October 2007

Comparison of sampling techniques for parallel analysis of transcript and metabolite levels in Saccharomyces cerevisiae.

scientific article

Complex networks of miRNA-transcription factors mediate gene dosage compensation in aneuploid cancer

scientific article published in February 2020

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

scientific article published on 23 May 2020

Computational modeling of biochemical networks using COPASI

scientific article (publication date: 2009)

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

scientific article published on 04 November 2020

Condor-COPASI: high-throughput computing for biochemical networks

scientific article

Controlled vocabularies and semantics in systems biology

scientific article (publication date: 25 October 2011)

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices

scientific article published on 01 January 2019

Discovery of meaningful associations in genomic data using partial correlation coefficients

scientific article

Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing

scientific article

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

scientific article

Emerging bioinformatics for the metabolome

scientific article

Enzyme kinetics and computational modeling for systems biology.

scientific article published in January 2009

Enzyme kinetics informatics: from instrument to browser

scientific article

Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly

scientific article

Further developments towards a genome-scale metabolic model of yeast

scientific article (publication date: 28 October 2010)

Gene networks: how to put the function in genomics

scientific article

Impact of kinetic isotope effects in isotopic studies of metabolic systems.

scientific article published on 26 September 2015

Improving metabolic flux predictions using absolute gene expression data

scientific article

Integrative modelling of gene expression and cell metabolism.

scientific article published on January 2003

Large-Scale Metabolic Models: From Reconstruction to Differential Equations

scientific article published in August 2013

Linking the genes: inferring quantitative gene networks from microarray data

scientific article

Metabolic control in integrated biochemical systems

scientific article

Metabolic footprinting: a new approach to identify physiological changes in complex microbial communities upon exposure to toxic chemicals

scientific article published in June 2007

Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism

scientific article published on 13 December 2004

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

scientific article

Metabolomics and the challenges ahead

article

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

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

scientific article

Mining metabolites: extracting the yeast metabolome from the literature

scientific article

ModelBricks-modules for reproducible modeling improving model annotation and provenance

scientific article published on 08 October 2019

ModelMage: a tool for automatic model generation, selection and management

scientific article published in January 2008

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

scientific article

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

article

Modeling the iron storage protein ferritin reveals how residual ferrihydrite iron determines initial ferritin iron sequestration kinetics

scientific article published in 2023

Modeling the iron storage protein ferritin reveals how residual ferrihydrite iron determines initial ferritin iron sequestration kinetics

scientific article published on 4 November 2022

Multi-scale modelling and simulation in systems biology ⬇️

scientific article published on 06 January 2011

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

scientific article

Path2Models: large-scale generation of computational models from biochemical pathway maps

scientific article

Plant metabolomics by GC-MS and differential analysis

scientific article

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

scientific article

Potential of metabolomics as a functional genomics tool.

scientific article

Quantifying gene networks with regulatory strengths

scientific article

Recon 2.2: from reconstruction to model of human metabolism ⬇️

scientific article

Reproducible Research Using Biomodels

scholarly article by Pedro Mendes published 6 September 2018 in Bulletin of Mathematical Biology

Response to 'The Need for Speed', by Matsson et al.

scientific article

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

scientific article

Silence on the relevant literature and errors in implementation

scientific article published in April 2015

Systematic construction of kinetic models from genome-scale metabolic networks

scientific article

Systematic integration of experimental data and models in systems biology ⬇️

scientific article (publication date: 29 November 2010)

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

scientific article

The genome-wide early temporal response of Saccharomyces cerevisiae to oxidative stress induced by cumene hydroperoxide.

scientific article

The markup is the model: reasoning about systems biology models in the Semantic Web era

scientific article

The metabolomics standards initiative (MSI)

scientific article

Toward Community Standards and Software for Whole-Cell Modeling

scientific article

Towards a genome-scale kinetic model of cellular metabolism

scientific article

Translation initiation events on structured eukaryotic mRNAs generate gene expression noise.

scientific article published on 17 May 2017

Understanding Lactobacillus paracasei and Streptococcus oralis Biofilm Interactions through Agent-Based Modeling

scientific article published on 22 December 2021

Understanding Lactobacillus paracasei and Streptococcus oralis biofilm interactions through agent-based modeling

scientific article published on 29 April 2021

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

scientific article (publication date: 2013)

Why most transporter mutations that cause antibiotic resistance are to efflux pumps rather than to import transporters

scientific article published on 17 January 2020

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

scientific article (publication date: 4 June 2012)

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

scientific article published on 30 January 2014

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

scientific article published on 14 July 2017

libAnnotationSBML: a library for exploiting SBML annotations

scientific article

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

scientific article published on 19 February 2004

List of works by Pedro Mendes

A Metabolic Reaction Balancing Web Service for Computational Systems Biology

A community-driven global reconstruction of human metabolism. ⬇️

A computational model of liver iron metabolism

A computational model to understand mouse iron physiology and disease

A computational model to understand mouse iron physiology and diseases

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

A general map of iron metabolism and tissue-specific subnetworks

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

A method for comparing multivariate time series with different dimensions

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

A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides--illustrated for the glycolytic enzymes of Saccharomyces cerevisiae

A new strategy for assessing sensitivities in biochemical models

A proposed framework for the description of plant metabolomics experiments and their results

A systems biology view of cancer

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

Agent Based Models of Polymicrobial Biofilms and the Microbiome-A Review

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

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

An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study

An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study

An in vivo control map for the eukaryotic mRNA translation machinery

Artificial gene networks for objective comparison of analysis algorithms

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

Biochemical fluctuations, optimisation and the linear noise approximation

Bioinformatics tools for cancer metabolomics

Bridging the gaps in systems biology

COMODI: an ontology to characterise differences in versions of computational models in biology

COPASI and its applications in biotechnology

COPASI--a COmplex PAthway SImulator

Challenges for Modeling and Simulation Methods in Systems Biology

Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism.

Comparison of reverse-engineering methods using an in silico network

Comparison of sampling techniques for parallel analysis of transcript and metabolite levels in Saccharomyces cerevisiae.

Complex networks of miRNA-transcription factors mediate gene dosage compensation in aneuploid cancer

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

Computational modeling of biochemical networks using COPASI

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Condor-COPASI: high-throughput computing for biochemical networks

Controlled vocabularies and semantics in systems biology

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices

Discovery of meaningful associations in genomic data using partial correlation coefficients

Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing

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

Emerging bioinformatics for the metabolome

Enzyme kinetics and computational modeling for systems biology.

Enzyme kinetics informatics: from instrument to browser

Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly

Further developments towards a genome-scale metabolic model of yeast

Gene networks: how to put the function in genomics

Impact of kinetic isotope effects in isotopic studies of metabolic systems.

Improving metabolic flux predictions using absolute gene expression data

Integrative modelling of gene expression and cell metabolism.

Large-Scale Metabolic Models: From Reconstruction to Differential Equations

Linking the genes: inferring quantitative gene networks from microarray data

Metabolic control in integrated biochemical systems

Metabolic footprinting: a new approach to identify physiological changes in complex microbial communities upon exposure to toxic chemicals

Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism

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

Metabolomics and the challenges ahead

Methyl jasmonate and yeast elicitor induce differential transcriptional and metabolic re-programming in cell suspension cultures of the model legume Medicago truncatula.

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

Mining metabolites: extracting the yeast metabolome from the literature

ModelBricks-modules for reproducible modeling improving model annotation and provenance

ModelMage: a tool for automatic model generation, selection and management

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

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

Modeling the iron storage protein ferritin reveals how residual ferrihydrite iron determines initial ferritin iron sequestration kinetics

Modeling the iron storage protein ferritin reveals how residual ferrihydrite iron determines initial ferritin iron sequestration kinetics

Multi-scale modelling and simulation in systems biology ⬇️

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

Path2Models: large-scale generation of computational models from biochemical pathway maps

Plant metabolomics by GC-MS and differential analysis

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

Potential of metabolomics as a functional genomics tool.

Quantifying gene networks with regulatory strengths

Recon 2.2: from reconstruction to model of human metabolism ⬇️

Reproducible Research Using Biomodels

Response to 'The Need for Speed', by Matsson et al.

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