Pedro Pedrosa Mendes
#41,089
Most Influential Person Now
Portuguese biochemist and computer scientist
Pedro Pedrosa Mendes's AcademicInfluence.com Rankings
Pedro Pedrosa Mendescomputer-science Degrees
Computer Science
#3682
World Rank
#3871
Historical Rank
Database
#7540
World Rank
#7821
Historical Rank
Pedro Pedrosa Mendesbiology Degrees
Biology
#2867
World Rank
#4476
Historical Rank
Systems Biology
#13
World Rank
#13
Historical Rank
Computational Biology
#331
World Rank
#332
Historical Rank
Biochemistry
#1374
World Rank
#1498
Historical Rank
Download Badge
Computer Science Biology
Pedro Pedrosa Mendes's Degrees
- PhD Biochemistry University of Lisbon
- PhD Computer Science University of Porto
Similar Degrees You Can Earn
Why Is Pedro Pedrosa Mendes Influential?
(Suggest an Edit or Addition)According to Wikipedia, Pedro Pedrosa Mendes is a professor of computational systems biology in the Department of Computer Science at the University of Manchester. He is a member of the Manchester Centre for Integrative Systems Biology , the Machine Learning and Optimization group. He is also a professor at the University of Connecticut Health Center.
Pedro Pedrosa Mendes's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models (2003) (3236)
- COPASI - a COmplex PAthway SImulator (2006) (2283)
- Plant metabolomics: large-scale phytochemistry in the functional genomics era. (2003) (1038)
- A community-driven global reconstruction of human metabolism (2013) (974)
- Parameter estimation in biochemical pathways: a comparison of global optimization methods. (2003) (948)
- Potential of metabolomics as a functional genomics tool. (2004) (738)
- Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation (1998) (705)
- Minimum information requested in the annotation of biochemical models (MIRIAM) (2005) (617)
- ChEBI in 2016: Improved services and an expanding collection of metabolites (2015) (606)
- A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology (2008) (601)
- GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems (1993) (565)
- Discovery of meaningful associations in genomic data using partial correlation coefficients (2004) (564)
- myo-Inositol Oxygenase Offers a Possible Entry Point into Plant Ascorbate Biosynthesis1 (2004) (431)
- The Metabolomics Standards Initiative (2007) (395)
- The metabolomics standards initiative (MSI) (2007) (377)
- Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism. (2005) (365)
- A hybrid approach for efficient and robust parameter estimation in biochemical pathways. (2006) (342)
- Controlled vocabularies and semantics in systems biology (2011) (304)
- Gene networks: how to put the function in genomics. (2002) (296)
- A proposed framework for the description of plant metabolomics experiments and their results (2004) (278)
- The origin of correlations in metabolomics data (2005) (254)
- Recon 2.2: from reconstruction to model of human metabolism (2016) (249)
- Artificial gene networks for objective comparison of analysis algorithms (2003) (240)
- Computational modeling of biochemical networks using COPASI. (2009) (202)
- Methyl jasmonate and yeast elicitor induce differential transcriptional and metabolic re-programming in cell suspension cultures of the model legume Medicago truncatula (2005) (196)
- Multi-scale modelling and simulation in systems biology. (2011) (187)
- Linking the genes: inferring quantitative gene networks from microarray data. (2002) (172)
- Towards a genome-scale kinetic model of cellular metabolism (2010) (172)
- Path2Models: large-scale generation of computational models from biochemical pathway maps (2013) (167)
- Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network (2012) (156)
- Improving metabolic flux predictions using absolute gene expression data (2012) (143)
- A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes (2013) (124)
- Emerging bioinformatics for the metabolome (2002) (120)
- Further developments towards a genome-scale metabolic model of yeast (2010) (116)
- Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks (2013) (112)
- Bioinformatics tools for cancer metabolomics (2011) (103)
- A systems biology view of cancer. (2009) (101)
- Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research (2020) (96)
- An in vivo control map for the eukaryotic mRNA translation machinery (2013) (92)
- The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks (2011) (92)
- A general map of iron metabolism and tissue-specific subnetworks. (2009) (90)
- ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources (2001) (89)
- A Two-dimensional Electrophoresis Proteomic Reference Map and Systematic Identification of 1367 Proteins from a Cell Suspension Culture of the Model Legume Medicago truncatula*S (2005) (86)
- Zinc depletion regulates the processing and secretion of IL-1β (2014) (79)
- Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli (2017) (77)
- BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology (2015) (69)
- SBRML: a markup language for associating systems biology data with models (2010) (69)
- COPASI and its applications in biotechnology. (2017) (68)
- Efficient discovery of anti-inflammatory small molecule combinations using evolutionary computing (2011) (67)
- 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 (2013) (65)
- Large-Scale Metabolic Models: From Reconstruction to Differential Equations (2013) (62)
- Comparison of Reverse‐Engineering Methods Using an in Silico Network (2007) (57)
- Toward community standards and software for whole-cell modeling (2016) (51)
- Systems biology COPASI — a COmplex PAthway SImulator (2006) (49)
- A new strategy for assessing sensitivities in biochemical models (2008) (46)
- Systematic integration of experimental data and models in systems biology (2010) (45)
- Condor-COPASI: high-throughput computing for biochemical networks (2012) (45)
- SNAPSHOTS OF SYSTEMS - METABOLIC CONTROL ANALYSIS AND BIOTECHNOLOGY (1999) (45)
- Mining metabolites: extracting the yeast metabolome from the literature (2010) (44)
- Simulation of Biochemical Networks using Copasi - A Complex Pathway Simulator (2006) (42)
- MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems (2001) (42)
- Bridging the gaps in systems biology (2014) (40)
- A Computational Model of Liver Iron Metabolism (2013) (38)
- A Systems Biology Study of Two Distinct Growth Phases of Saccharomyces cerevisiae Cultures (2004) (38)
- What Can We Learn from Global Sensitivity Analysis of Biochemical Systems? (2013) (38)
- Challenges for Modeling and Simulation Methods in Systems Biology (2006) (37)
- Modelling and simulation for metabolomics data analysis. (2005) (37)
- Metabolic footprinting: a new approach to identify physiological changes in complex microbial communities upon exposure to toxic chemicals. (2007) (34)
- Metabolic control in integrated biochemical systems. (2002) (32)
- Biochemical fluctuations, optimisation and the linear noise approximation (2012) (32)
- An analysis of a ‘community-driven’ reconstruction of the human metabolic network (2013) (32)
- The Genome-Wide Early Temporal Response of Saccharomyces cerevisiae to Oxidative Stress Induced by Cumene Hydroperoxide (2013) (32)
- Snapshots of Systems (2000) (32)
- Enzyme kinetics and computational modeling for systems biology. (2009) (32)
- The core control system of intracellular iron homeostasis: a mathematical model. (2012) (31)
- libAnnotationSBML: a library for exploiting SBML annotations (2009) (31)
- The markup is the model: reasoning about systems biology models in the Semantic Web era. (2008) (31)
- biochem4j: Integrated and extensible biochemical knowledge through graph databases (2017) (30)
- Metabolic Channeling in Organized Enzyme Systems: Experiments and Models (1995) (30)
- On the analysis of the inverse problem of metabolic pathways using artificial neural networks. (1996) (28)
- Bioinformatics Approaches to Integrate Metabolomics and Other Systems Biology Data (2006) (25)
- Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism. (2012) (25)
- Impact of kinetic isotope effects in isotopic studies of metabolic systems (2015) (24)
- Enzyme kinetics informatics: from instrument to browser (2010) (24)
- Plant metabolomics by GC-MS and differential analysis. (2011) (23)
- Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly (2015) (22)
- A Method for Comparing Multivariate Time Series with Different Dimensions (2013) (21)
- libChEBI: an API for accessing the ChEBI database (2016) (20)
- Quantifying Gene Networks with Regulatory Strengths (2004) (18)
- Metabolomics and the challenges ahead (2006) (17)
- Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast (2014) (17)
- Translation initiation events on structured eukaryotic mRNAs generate gene expression noise (2017) (17)
- Silence on the relevant literature and errors in implementation (2015) (16)
- Comparison of sampling techniques for parallel analysis of transcript and metabolite levels in Saccharomyces cerevisiae (2007) (16)
- A new regulatory principle for in vivo biochemistry: Pleiotropic low affinity regulation by the adenine nucleotides – Illustrated for the glycolytic enzymes of Saccharomyces cerevisiae (2013) (16)
- An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems (2018) (15)
- An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study (2018) (15)
- COMODI: an ontology to characterise differences in versions of computational models in biology (2016) (14)
- Design and Architecture of Web Services for Simulation of Biochemical Systems (2009) (12)
- N-Hydroxysuccinimide-activated esters as a functionalization agent for amino cellulose: synthesis and solid-state NMR characterization (2019) (12)
- Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient (2017) (11)
- Reproducible Research Using Biomodels (2018) (11)
- Gastrointestinal iron excretion and reversal of iron excess in a mouse model of inherited iron excess (2018) (11)
- Databases and Visualization for Metabolomics (2003) (10)
- Agent Based Models of Polymicrobial Biofilms and the Microbiome—A Review (2021) (9)
- A Discrete Approach to Top-Down Modeling of Biochemical Networks (2005) (9)
- ModelBricks—modules for reproducible modeling improving model annotation and provenance (2019) (9)
- Integrative modelling of gene expression and cell metabolism. (2003) (8)
- A computational model to understand mouse iron physiology and disease (2019) (8)
- MYC dosage compensation is mediated by miRNA-transcription factor interactions in aneuploid cancer (2021) (7)
- Integrative Information Management for Systems Biology (2010) (7)
- Progress in bioinformatics - the challenge of integrating transcriptomic, proteomic and metabolomic information (2005) (6)
- Progress in bioinformatics - the challenge of integrating transcriptomic, proteomic and metabolomic information (2005) (6)
- Decomposition rate and enzymatic activity of composted municipal waste and poultry manure in the soil in a biofuel crops field. (2017) (4)
- Why most transporter mutations that cause antibiotic resistance are to efflux pumps rather than to import transporters (2020) (4)
- Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis (2016) (4)
- ManyCell: A Multiscale Simulator for Cellular Systems (2012) (4)
- Bioinformatics for rice resources. (2007) (3)
- Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. (2019) (3)
- ModelBricks-modules for reproducible modeling improving model annotation and provenance. (2019) (2)
- Response to 'The Need for Speed', by Matsson et al. (2016) (2)
- BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology (2014) (2)
- A computational model to understand mouse iron physiology and diseases (2018) (2)
- Kinetic modelling of large-scale metabolic networks (2011) (2)
- 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 (2013) (2)
- The further development of metabolomics as a functional genomics tool (2004) (1)
- Chapter One Bioinformatics and computational biology for plant functional genomics (2002) (1)
- Computational Methods in Systems Biology: 12th International Conference, CMSB 2014, Manchester, UK, November 17-19, 2014, Proceedings (2014) (1)
- Understanding Lactobacillus paracasei and Streptococcus oralis Biofilm Interactions through Agent-Based Modeling (2021) (1)
- Computer Simulation of Biochemical Kinetics (2013) (1)
- Methodology for Simulation of Metabolic Pathways and Calculation of Control Coefficients (1990) (1)
- Complex networks of miRNA-transcription factors mediate gene dosage compensation in aneuploid cancer (2020) (1)
- Constraint-based optimisation tools for semi-automated refinement of genome-scale yeast metabolic models (2010) (1)
- INFLUENCE OF WOOD PULPING CONDITIONS AND UNBLEACHED PULP COMPOSITION AND STRUCTURE ON THE ECF BLEACHABILITY OF HARDWOOD KRAFT PULPS (2003) (1)
- A Metabolic Reaction Balancing Web Service for Computational Systems Biology (2017) (1)
- Recon 2.2: from reconstruction to model of human metabolism (2016) (1)
- Numerical optimisation and simulation for rational metabolic engineering (2013) (0)
- Automatic translation of high ‐ level bio ‐ designs into wet ‐ lab protocols through learning and formalizing expert ’ s practices (2015) (0)
- An analysis of a ‘community-driven’ reconstruction of the human metabolic network (2013) (0)
- Reproducibility and FAIR Principles: The Case of a Segment Polarity Network Model (2023) (0)
- A reference database for Medicago truncatula genes, proteins, and metabolites (2002) (0)
- Bridging the gaps in systems biology (2014) (0)
- Multisite rate control analysis identifies ribosomal scanning as the sole high‐capacity/low‐flux‐control step in mRNA translation (2019) (0)
- Global Optimization Methods Parameter Estimation in Biochemical Pathways : A Comparison of References (2003) (0)
- Mathematical Models of Some Signaling Pathways Regulating Cell Survival and Death (2008) (0)
- Foundations of Systems Biology Foundations of Systems Biology Library of Congress Cataloging-in-publication Data (2000) (0)
- Chasing the flux: selecting target pathways through flux analysis of carbon metabolism (2011) (0)
- Toward standards for tomorrow’s whole-cell models (2015) (0)
- GEPASI: A User Oriented Metabolic Simulator (1993) (0)
- ChEBI for systems biology and metabolic modelling (2015) (0)
- Letting the flux define the kinetics: using a single steady state to predict network behaviour under diverse stress conditions (2012) (0)
- Computational Approaches to the Study of Biochemical Pathways and Metabolic Control (2000) (0)
- Mathematical Modeling of Transcription Regulation by Protein Assemblies at Promoters: Regulation of E2F Dependent Genes (2001) (0)
- Comparative Expression Analysis between Proteomic and Transcriptomic Datasets Provides Novel Insights into TOR Signaling Regulation in Yeast Newly Configured Intact Protein-based Analysis System (IPAS) Its Application Plasma Proteomics Handling (2007) (0)
- Constraining flux balance analysis with genome-scale data (2012) (0)
- TABOLIC CHANNELING IN RGANIZED ENZYME SYSTEMS : XPERIMENTS AND MODELS (2014) (0)
- Systems biology libAnnotationSBML : a library for exploiting SBML annotations (2009) (0)
- Computational Methods in Systems Biology (2014) (0)
- Top-Down Dynamical Modeling of Molecular Regulatory Networks (2014) (0)
- COMODI: an ontology to characterise differences in versions of computational models in biology (2016) (0)
- ShinyCOPASI: a web-based exploratory interface for COPASI models (2021) (0)
- Chapter 16 DATABASES AND VISUALIZATION FOR METABOLOMICS (0)
- Reproducible Research Using Biomodels (2018) (0)
- Control Analysis of Metabolic Channeling (1993) (0)
- Corrected and Republished from: “Understanding Lactobacillus paracasei and Streptococcus oralis Biofilm Interactions through Agent-Based Modeling” (2023) (0)
- Modeling the iron storage protein ferritin reveals how residual ferrihydrite iron determines initial ferritin iron sequestration kinetics (2022) (0)
This paper list is powered by the following services:
Other Resources About Pedro Pedrosa Mendes
What Schools Are Affiliated With Pedro Pedrosa Mendes?
Pedro Pedrosa Mendes is affiliated with the following schools:
