World's Best Scientists 2026 revealed!

D-Index & Metrics

Computer Science

D-Index
33
Citations
5689
World Ranking
12531
National Ranking
43

Overview

Miguel Rocha is affiliated with the University of Minho in Portugal and has an extensive research profile in the fields of biochemistry, genetics, and molecular biology. Their work spans multiple subfields including molecular biology, biomedical engineering, computational theory and mathematics, surgery, and materials chemistry.

Their research covers a range of topics, with significant contributions in microbial metabolic engineering and bioproduction, bioinformatics and genomic networks, computational drug discovery methods, gene regulatory network analysis, biofuel production and bioconversion, machine learning in materials science, and plant biochemistry and biosynthesis.

Recent publications by Miguel Rocha include:

  • Generative Deep Learning for Targeted Compound Design, 2021, Journal of Chemical Information and Modeling
  • Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses, 2021, Molecular Systems Biology
  • UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets, 2022, Computational and Structural Biotechnology Journal
  • merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models, 2022, Nucleic Acids Research
  • Evaluating molecular representations in machine learning models for drug response prediction and interpretability, 2022, Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics

Miguel Rocha has frequently collaborated with co-authors including Óscar Dias, Vítor Pereira, João Capela, Fernando Cruz, and Ana Marta Sequeira.

The scientist's work has been published in prominent venues, with multiple publications in:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Zenodo (CERN European Organization for Nuclear Research)
  • PLoS Computational Biology
  • Computational and Structural Biotechnology Journal
  • Molecular Systems Biology

In addition to journal articles, Miguel Rocha has contributed to book publications with Springer International Publishing and Springer Nature. Titles include:

  • Practical Applications of Computational Biology and Bioinformatics, 16th International Conference (PACBB 2022), 2022
  • Practical Applications of Computational Biology and Bioinformatics, 17th International Conference (PACBB 2023), 2023
  • Practical Applications of Computational Biology & Bioinformatics, 14th International Conference (PACBB 2020), 2020

Best Publications

  • OptFlux: an open-source software platform for in silico metabolic engineering

    Isabel Rocha;Paulo Maia;Pedro Evangelista;Paulo Vilaça

  • Particle swarms for feedforward neural network training

    R. Mendes;P. Cortez;M. Rocha;J. Neves

  • Integrating Sustainable Development into Existing Management Systems

    Miguel Rocha;Cory Searcy;Stanislav Karapetrovic

  • Modeling formalisms in Systems Biology

    Daniel Machado;Rafael S Costa;Miguel Rocha;Eugénio C Ferreira

  • Multi-scale Internet traffic forecasting using neural networks and time series methods

    Paulo Cortez;Miguel Rio;Miguel Rocha;Pedro Sousa

  • Deep learning for drug response prediction in cancer

    Delora Baptista;Pedro G Ferreira;Miguel Rocha

  • Generative deep learning for targeted compound design

    Tiago Sousa;João Correia;Vítor Pereira;Miguel Rocha

  • Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data

    Justin Guinney;Tao Wang;Teemu D Laajala;Teemu D Laajala;Kimberly Kanigel Winner

  • Reconstructing genome-scale metabolic models with merlin

    Oscar Dias;Miguel Rocha;Eugénio C. Ferreira;Isabel Rocha

  • Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living

    Sigeru Omatu;Miguel P. Rocha;José Bravo;Florentino Fernández

  • Evolution of neural networks for classification and regression

    Miguel Rocha;Paulo Cortez;José Neves

  • Internet Traffic Forecasting using Neural Networks

    P. Cortez;M. Rio;M. Rocha;P. Sousa

  • Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses.

    Aurelien Dugourd;Christoph Kuppe;Christoph Kuppe;Marco Sciacovelli;Enio Gjerga;Enio Gjerga

  • Preventing premature convergence to local optima in genetic algorithms via random offspring generation

    Miguel Rocha;José Neves

  • Internet Traffic Forecasting using Neural Networks

    Unknown

  • Natural computation meta-heuristics for the in silico optimization of microbial strains

    Miguel Rocha;Paulo Maia;Rui Mendes;José P Pinto

  • Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models.

    Emanuel Gonçalves;Joachim Bucher;Anke Ryll;Jens Niklas

  • Evolving Time Series Forecasting ARMA Models

    Paulo Cortez;Miguel Rocha;José Neves

  • A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering.

    Osvaldo D. Kim;Miguel Rocha;Paulo Maia

  • Optimization of fed-batch fermentation processes with bio-inspired algorithms

    Miguel Rocha;Rui Mendes;Orlando Rocha;Isabel Rocha

  • 13C-based metabolic flux analysis

    Rafael Carreira;S. Carneiro;S. G. Villas-Bôas;I. Rocha

Frequent Co-Authors

Eugénio C. Ferreira
Eugénio C. Ferreira University of Minho
Paulo Cortez
Paulo Cortez University of Minho
Marcelo Maraschin
Marcelo Maraschin Universidade Federal de Santa Catarina
Florentino Fdez-Riverola
Florentino Fdez-Riverola Universidade de Vigo
Julio Saez-Rodriguez
Julio Saez-Rodriguez Heidelberg University
Ross Overbeek
Ross Overbeek Argonne National Laboratory
Nuno Sousa
Nuno Sousa University of Minho
Tero Aittokallio
Tero Aittokallio University of Helsinki
Jens Nielsen
Jens Nielsen Chalmers University of Technology
Juan M. Corchado
Juan M. Corchado University of Salamanca

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