World's Best Scientists 2026 revealed!

D-Index & Metrics

Biology and Biochemistry

D-Index
58
Citations
28874
World Ranking
12882
National Ranking
5482

Overview

Pedro Mendes is affiliated with the University of Connecticut in the United States. Their research primarily lies within the field of Biochemistry, Genetics and Molecular Biology, with a focus on Molecular Biology, Periodontics, Information Systems and Management, Biophysics, and Cancer Research.

The scientist's work encompasses diverse topics including Gene Regulatory Network Analysis, Bioinformatics and Genomic Networks, Oral Microbiology and Periodontitis Research, Scientific Computing and Data Management, Cell Image Analysis Techniques, Microbial Metabolic Engineering and Bioproduction, and Gut Microbiota and Health.

Frequent co-authors collaborating with Pedro Mendes include Sherli Koshy-Chenthittayil, Reinhard Laubenbacher, Stefan Hoops, Linda Archambault, and Anna Dongari-Bagtzoglou.

Their recent papers cover a range of subjects and venues:

  • Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research, 2020, Briefings in Bioinformatics
  • BioSimulators: a central registry of simulation engines and services for recommending specific tools, 2022, CU Scholar (University of Colorado Boulder)
  • Agent Based Models of Polymicrobial Biofilms and the Microbiome-A Review, 2021, Microorganisms
  • Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research, 2020, Preprints.org
  • MYC dosage compensation is mediated by miRNA-transcription factor interactions in aneuploid cancer, 2021, iScience

Pedro Mendes has published frequently in venues such as bioRxiv (Cold Spring Harbor Laboratory), mSphere, arXiv (Cornell University), Zenodo (CERN European Organization for Nuclear Research), and Briefings in Bioinformatics.

Best Publications

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

    M. Hucka;A. Finney;H. M. Sauro;H. Bolouri;H. Bolouri

  • COPASI---a COmplex PAthway SImulator

    Stefan Hoops;Sven Sahle;Ralph Gauges;Christine Lee

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

    Lloyd W Sumner;Pedro Mendes;Richard A Dixon

  • A community-driven global reconstruction of human metabolism

    Ines Thiele;Neil Swainston;Ronan M T Fleming;Andreas Hoppe

  • Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods

    Carmen G. Moles;Pedro Mendes;Julio R. Banga

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

    Janna Hastings;Gareth Owen;Adriano Dekker;Marcus Ennis

  • Potential of metabolomics as a functional genomics tool

    Raoul J. Bino;Robert D. Hall;Oliver Fiehn;Joachim Kopka

  • GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems

    Pedro Mendes

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

    Pedro Mendes;Douglas B. Kell

  • Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3

    Pedro Mendes

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

    Nicolas Le Novère;Andrew Finney;Michael Hucka;Upinder S. Bhalla

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

    Markus Herrgard;Neil Swainston;Paul Dobson;Warwick B. Dunn

  • Discovery of meaningful associations in genomic data using partial correlation coefficients

    Alberto De La Fuente;Nan Bing;Ina Hoeschele;Pedro Mendes

  • The metabolomics standards initiative (MSI)

    Oliver Fiehn;Don Robertson;Jules Griffin;Mariet vab der Werf

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

    Argelia Lorence;Boris I. Chevone;Pedro Mendes;Craig L. Nessler

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

    Corey D. Broeckling;David V. Huhman;Mohamed A. Farag;Joel T. Smith

  • The Metabolomics Standards Initiative

    Susanna Assunta Sansone;Teresa Fan;Royston Goodacre;Julian L. Griffin

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

    Maria Rodriguez-Fernandez;Pedro Mendes;Julio R. Banga

  • Gene networks: how to put the function in genomics

    Paul Brazhnik;Alberto de la Fuente;Pedro Mendes

  • Controlled vocabularies and semantics in systems biology

    Mélanie Courtot;Nick Juty;Christian Knüpfer;Dagmar Waltemath

Frequent Co-Authors

Douglas B. Kell
Douglas B. Kell University of Liverpool
Neil Swainston
Neil Swainston Epoch BioDesign
Hans V. Westerhoff
Hans V. Westerhoff Vrije Universiteit Amsterdam
Reinhard Laubenbacher
Reinhard Laubenbacher University of Florida
Michael Hucka
Michael Hucka California Institute of Technology
Warwick B. Dunn
Warwick B. Dunn University of Liverpool
Nicolas Le Novère
Nicolas Le Novère Babraham Institute
Lloyd W. Sumner
Lloyd W. Sumner University of Missouri
Stephen G. Oliver
Stephen G. Oliver University of Cambridge
Julio Saez-Rodriguez
Julio Saez-Rodriguez Heidelberg University

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