Miguel Rocha
Orcid: 0000-0001-8439-8172Affiliations:
- University of Minho, Center of Biological Engineering, Braga, Portugal
According to our database1,
Miguel Rocha
authored at least 185 papers
between 1995 and 2024.
Collaborative distances:
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Bibliography
2024
Reconstruction of cell-specific models capturing the influence of metabolism on DNA methylation in cancer.
Comput. Biol. Medicine, March, 2024
BioISO: An Objective-Oriented Application for Assisting the Curation of Genome-Scale Metabolic Models.
IEEE ACM Trans. Comput. Biol. Bioinform., 2024
2023
A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer.
PLoS Comput. Biol., March, 2023
The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber.
PLoS Comput. Biol., 2023
Proceedings of the Practical Applications of Computational Biology and Bioinformatics, 2023
Combining Evolutionary Algorithms with Reaction Rules Towards Focused Molecular Design.
Proceedings of the Genetic and Evolutionary Computation Conference, 2023
Proceedings of the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2023
2022
A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale.
PLoS Comput. Biol., 2022
A comparison of multi-objective optimization algorithms for weight setting problems in traffic engineering.
Nat. Comput., 2022
Evaluating molecular representations in machine learning models for drug response prediction and interpretability.
J. Integr. Bioinform., 2022
ProPythia: A Python package for protein classification based on machine and deep learning.
Neurocomputing, 2022
Going virtual and going wide: comparing Team-Based Learning in-class versus online and across disciplines.
Educ. Inf. Technol., 2022
Reconstruction of tissue-specific genome-scale metabolic models for human cancer stem cells.
Comput. Biol. Medicine, 2022
Predicting the number of biochemical transformations needed to synthesize a compound.
Proceedings of the International Joint Conference on Neural Networks, 2022
Development of Deep Learning approaches to predict relationships between chemical structures and sweetness.
Proceedings of the International Joint Conference on Neural Networks, 2022
Variational Autoencoders and Evolutionary Algorithms for Targeted Novel Enzyme Design.
Proceedings of the IEEE Congress on Evolutionary Computation, 2022
2021
Proceedings of the Practical Applications of Computational Biology & Bioinformatics, 2021
Proceedings of the Practical Applications of Computational Biology & Bioinformatics, 2021
Proceedings of the Practical Applications of Computational Biology & Bioinformatics, 2021
Proceedings of the Practical Applications of Computational Biology & Bioinformatics, 2021
Computational Methods for the Identification of Genetic Variants in Complex Diseases.
Proceedings of the Practical Applications of Computational Biology & Bioinformatics, 2021
Proceedings of the Practical Applications of Computational Biology & Bioinformatics, 2021
Proceedings of the International Joint Conference on Neural Networks, 2021
Combining Multi-objective Evolutionary Algorithms with Deep Generative Models Towards Focused Molecular Design.
Proceedings of the Applications of Evolutionary Computation, 2021
2020
IEEE Trans. Netw. Serv. Manag., 2020
ProPythia: A Python Automated Platform for the Classification of Proteins Using Machine Learning.
Proceedings of the Practical Applications of Computational Biology & Bioinformatics, 2020
Reconciliation of Regulatory Data: The Regulatory Networks of Escherichia coli and Bacillus subtilis.
Proceedings of the Practical Applications of Computational Biology & Bioinformatics, 2020
2019
A Model Integration Pipeline for the Improvement of Human Genome-Scale Metabolic Reconstructions.
J. Integr. Bioinform., 2019
Selected Extended Papers of the 12th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB).
J. Integr. Bioinform., 2019
BMC Bioinform., 2019
SamPler - a novel method for selecting parameters for gene functional annotation routines.
BMC Bioinform., 2019
CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models.
Bioinform., 2019
Proceedings of the Practical Applications of Computational Biology and Bioinformatics, 2019
Troppo - A Python Framework for the Reconstruction of Context-Specific Metabolic Models.
Proceedings of the Practical Applications of Computational Biology and Bioinformatics, 2019
Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression.
Proceedings of the Practical Applications of Computational Biology and Bioinformatics, 2019
Proceedings of the Practical Applications of Computational Biology and Bioinformatics, 2019
Triptych: Multi-objective Optimisation of Service Deployment Costs, Application Delay and Bandwidth Usage.
Proceedings of the 2019 IFIP Networking Conference, 2019
Proceedings of the International Joint Conference on Neural Networks, 2019
Proceedings of the 2019 IEEE 8th International Conference on Cloud Networking, 2019
2018
Comput. Methods Programs Biomed., 2018
Proceedings of the Practical Applications of Computational Biology and Bioinformatics, 2018
MOSCA: An Automated Pipeline for Integrated Metagenomics and Metatranscriptomics Data Analysis.
Proceedings of the Practical Applications of Computational Biology and Bioinformatics, 2018
17α-Ethinylestradiol Analysis of Endo- and Exometabolome of Ulva lactuca (Chlorophyta) by 1H-NMR Spectroscopy and Bioinformatics Tools.
Proceedings of the Practical Applications of Computational Biology and Bioinformatics, 2018
Proceedings of the Practical Applications of Computational Biology and Bioinformatics, 2018
In Silico Predictions for Fucoxanthin Production by the Diatom Phaeodactylum Tricornutum.
Proceedings of the Practical Applications of Computational Biology and Bioinformatics, 2018
Proceedings of the Advances in Data Mining. Applications and Theoretical Aspects, 2018
Proceedings of the 15th International Joint Conference on e-Business and Telecommunications, 2018
2017
IEEE ACM Trans. Comput. Biol. Bioinform., 2017
Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.
PLoS Comput. Biol., 2017
Selected Extended Papers of the 11th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB).
J. Integr. Bioinform., 2017
A Chemometrics Approach for Nuclear Magnetic Resonance Data to Characterize the Partial Metabolome Banana Peels from Southern Brazil.
J. Integr. Bioinform., 2017
UV-Vis and CIELAB Based Chemometric Characterization of Manihot esculenta Carotenoid Contents.
J. Integr. Bioinform., 2017
Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017
Influence of Solar Radiation on the Production of Secondary Metabolites in Three Rice (Oryza sativa) Cultivars.
Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017
Classification Tools for Carotenoid Content Estimation in Manihot esculenta via Metabolomics and Machine Learning.
Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017
UV-Vis Spectrophotometry and Chemometrics as Tools for Recognition of the Biochemical Profiles of Organic Banana Peels (Musa sp.) According to the Seasonality in Southern Brazil.
Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017
Characterization of the Chemical Composition of Banana Peels from Southern Brazil Across the Seasons Using Nuclear Magnetic Resonance and Chemometrics.
Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017
Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017
Mixed-Integer Programming Model for Profiling Disease Biomarkers from Gene Expression Studies.
Proceedings of the Bioinformatics and Biomedical Engineering, 2017
Evolutionary computation at work for the optimization of link state routing protocols.
Proceedings of the Genetic and Evolutionary Computation Conference, 2017
Proceedings of the Genetic and Evolutionary Computation Conference, 2017
Proceedings of the 14th International Conference on Mobile Systems and Pervasive Computing (MobiSPC 2017) / 12th International Conference on Future Networks and Communications (FNC 2017) / Affiliated Workshops, 2017
2016
Comput. Methods Programs Biomed., 2016
Development of an Integrated Framework for Minimal Cut Set Enumeration in Constraint-Based Models.
Proceedings of the 10th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2016
Proceedings of the 10th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2016
Proceedings of the 10th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2016
Proceedings of the Intelligent Environments 2016, 2016
2015
J. Integr. Bioinform., 2015
Discrimination of Brazilian propolis according to the seasoning using chemometrics and machine learning based on UV-Vis scanning data.
J. Integr. Bioinform., 2015
UV-visible scanning spectrophotometry and chemometric analysis as tools for carotenoids analysis in cassava genotypes (Manihot esculenta Crantz).
J. Integr. Bioinform., 2015
J. Integr. Bioinform., 2015
Development and application of efficient pathway enumeration algorithms for metabolic engineering applications.
Comput. Methods Programs Biomed., 2015
Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.
Bioinform., 2015
Proceedings of the 30th Annual ACM Symposium on Applied Computing, 2015
Microarray Gene Expression Data Integration: An Application to Brain Tumor Grade Determination.
Proceedings of the 9th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2015
UV-Visible Scanning Spectrophotometry and Chemometric Analysis as Tools to Build Descriptive and Classification Models for Propolis from Southern Brazil.
Proceedings of the 9th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2015
UV-Visible Spectrophotometry-Based Metabolomic Analysis of Cedrela Fissilis Velozzo (Meliaceae) Calluses - A Screening Tool for Culture Medium Composition and Cell Metabolic Profiles.
Proceedings of the 9th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2015
Carotenoid Analysis of Cassava Genotypes Roots (Manihot Esculenta Crantz) Cultivated in Southern Brazil Using Chemometric Tools.
Proceedings of the 9th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2015
Proceedings of the 9th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2015
Proceedings of the 9th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2015
Proceedings of the Intelligent Distributed Computing IX - Proceedings of the 9th International Symposium on Intelligent Distributed Computing, 2015
Proceedings of the Progress in Artificial Intelligence, 2015
Comparison of Single and Multi-objective Evolutionary Algorithms for Robust Link-State Routing.
Proceedings of the Evolutionary Multi-Criterion Optimization, 2015
Reconstructing transcriptional Regulatory Networks using data integration and Text Mining.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015
2014
Expert Syst. Appl., 2014
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data.
BMC Syst. Biol., 2014
An integrated network visualization framework towards metabolic engineering applications.
BMC Bioinform., 2014
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.
Briefings Bioinform., 2014
Discrimination of Brazilian Cassava Genotypes (Manihot esculenta Crantz) According to Their Physicochemical Traits and Functional Properties through Bioinformatics Tools.
Proceedings of the 8th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2014
Proceedings of the 8th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2014
Proceedings of the 8th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2014
Reg4OptFlux: an OptFlux plug-in that comprises meta-heuristics approaches for Metabolic engineering using integrated models.
Proceedings of the 2014 Sixth World Congress on Nature and Biologically Inspired Computing, 2014
2013
J. Integr. Bioinform., 2013
Email Spam Detection: a Symbiotic Feature Selection Approach Fostered by Evolutionary Computation.
Int. J. Inf. Technol. Decis. Mak., 2013
Comput. Methods Programs Biomed., 2013
Proceedings of the 7th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2013
Proceedings of the Adaptive and Natural Computing Algorithms, 2013
Proceedings of the Distributed Computing and Artificial Intelligence, 2013
Proceedings of the IEEE Congress on Evolutionary Computation, 2013
Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies.
Proceedings of the IEEE Congress on Evolutionary Computation, 2013
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013
Proceedings of the Emerging Management Mechanisms for the Future Internet, 2013
2012
J. Integr. Bioinform., 2012
Optimization Approaches for the <i>In Silico</i> Discovery of Optimal Targets for Gene Over/Underexpression.
J. Comput. Biol., 2012
An integrated computational environment for elementary modes analysis of biochemical networks.
Int. J. Data Min. Bioinform., 2012
Multi-scale Internet traffic forecasting using neural networks and time series methods.
Expert Syst. J. Knowl. Eng., 2012
A Machine Learning and Chemometrics Assisted Interpretation of Spectroscopic Data - A NMR-Based Metabolomics Platform for the Assessment of Brazilian Propolis.
Proceedings of the Pattern Recognition in Bioinformatics, 2012
An Algorithm to Assemble Gene-Protein-Reaction Associations for Genome-Scale Metabolic Model Reconstruction.
Proceedings of the Pattern Recognition in Bioinformatics, 2012
Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression.
Proceedings of the 6th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2012
Proceedings of the 6th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2012
Evolutionary Symbiotic Feature Selection for Email Spam Detection.
Proceedings of the ICINCO 2012 - Proceedings of the 9th International Conference on Informatics in Control, Automation and Robotics, Volume 1, Rome, Italy, 28, 2012
2011
J. Integr. Bioinform., 2011
Semantic annotation of biological concepts interplaying microbial cellular responses.
BMC Bioinform., 2011
A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information.
Biosyst., 2011
Briefings Bioinform., 2011
Appl. Soft Comput., 2011
Proceedings of the Wired/Wireless Internet Communications, 2011
Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results.
Proceedings of the Pattern Recognition in Bioinformatics, 2011
Proceedings of the 5th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2011
Proceedings of the 5th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2011
A Software Platform for Evolutionary Computation with Pluggable Parallelism and Quality Assurance.
Proceedings of the Artificial Intelligence Applications and Innovations, 2011
Proceedings of the IEEE Congress on Evolutionary Computation, 2011
2010
Expert Syst. Appl., 2010
AIBench: A rapid application development framework for translational research in biomedicine.
Comput. Methods Programs Biomed., 2010
BMC Syst. Biol., 2010
Pluggable Parallelization of Evolutionary Algorithms Applied to the Optimization of Biological Processes.
Proceedings of the 18th Euromicro Conference on Parallel, 2010
Enhancing Elementary Flux Modes Analysis Using Filtering Techniques in an Integrated Environment.
Proceedings of the Advances in Bioinformatics, 2010
Analysis of the Effect of Reversibility Constraints on the Predictions of Genome-Scale Metabolic Models.
Proceedings of the Advances in Bioinformatics, 2010
Proceedings of the Advances in Data Mining. Applications and Theoretical Aspects, 2010
Metaheuristics for Strain Optimization Using Transcriptional Information Enriched Metabolic Models.
Proceedings of the Evolutionary Computation, 2010
A software tool for network topology analysis under a metabolic engineering perspective.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010
Proceedings of the Workshops of the 31st International Conference on Application and Theory of Petri Nets and Other Models of Concurrency (PETRI NETS 2010) and of the 10th International Conference on Application of Concurrency to System Design (ACSD 2010), 2010
2009
Proceedings of the 2009 IEEE/WIC/ACM International Conference on Web Intelligence, 2009
A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems.
Proceedings of the Distributed Computing, 2009
Proceedings of the Distributed Computing, 2009
Proceedings of the Distributed Computing, 2009
Proceedings of the Ninth International Conference on Intelligent Systems Design and Applications, 2009
Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective.
Proceedings of the Evolutionary Computation, 2009
2008
getALife - An Artificial Life Environment for the Evaluation of Agent-Based Systems and Evolutionary Algorithms for Reinforcement Learning.
Proceedings of the New Challenges in Applied Intelligence Technologies, 2008
Natural computation meta-heuristics for the in silico optimization of microbial strains.
BMC Bioinform., 2008
Proceedings of the Management of Converged Multimedia Networks and Services, 2008
Modelling Fed-Batch Fermentation Processes: An Approach Based on Artificial Neural Networks.
Proceedings of the 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics, 2008
Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis.
Proceedings of the 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics, 2008
A Comparative Impact Study of Attribute Selection Techniques on Naïve Bayes Spam Filters.
Proceedings of the Advances in Data Mining. Medical Applications, 2008
An Evolutionary Algorithm for Unicast/ Multicast Traffic Engineering.
Proceedings of the ICINCO 2008, 2008
Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering, 2008
Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains.
Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering, 2008
Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering, 2008
2007
Proceedings of the Wired/Wireless Internet Communications, 5th International Conference, 2007
Proceedings of the Artificial Neural Networks, 2007
A platform for the selection of genes in DNA microarraydata using evolutionary algorithms.
Proceedings of the Genetic and Evolutionary Computation Conference, 2007
Proceedings of the Applications of Evolutinary Computing, 2007
Evaluating Evolutionary Algorithms and Differential Evolution for the Online Optimization of Fermentation Processes.
Proceedings of the Evolutionary Computation, 2007
Proceedings of the Progress in Artificial Intelligence, 2007
Proceedings of the 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2007
2006
Proceedings of the Autonomic Principles of IP Operations and Management, 2006
Proceedings of the International Joint Conference on Neural Networks, 2006
Proceedings of the IEEE International Conference on Evolutionary Computation, 2006
Proceedings of the IEEE International Conference on Evolutionary Computation, 2006
2005
Simultaneous Evolution of Neural Network Topologies and Weights for Classification and Regression.
Proceedings of the Computational Intelligence and Bioinspired Systems, 2005
A new representation in evolutionary algorithms for the optimization of bioprocesses.
Proceedings of the IEEE Congress on Evolutionary Computation, 2005
2004
Proceedings of the Applications of Evolutionary Computing, 2004
2003
Proceedings of the 11th European Symposium on Artificial Neural Networks, 2003
Proceedings of the Progress in Artificial Intelligence, 2003
2002
2001
A Genetic and Evolutionary Programming Environment with Spatially Structured Populations and Built-In Parallelism.
Proceedings of the Engineering of Intelligent Systems, 2001
Proceedings of the Engineering of Intelligent Systems, 2001
Proceedings of the 9th European Symposium on Artificial Neural Networks, 2001
Sitting guests at a wedding party: experiments on genetic and evolutionary constrained optimization.
Proceedings of the 2001 Congress on Evolutionary Computation, 2001
2000
Proceedings of the Parallel and Distributed Processing, 2000
A Study of Order Based Genetic and Evolutionary Algorithms in Combinatorial Optimization Problems.
Proceedings of the Intelligent Problem Solving, 2000
1999
Proceedings of the Medical Informatics Europe '99, Proceedings, Ljubljana, Slovenia, 1999
Preventing Premature Convergence to Local Optima in Genetic Algorithms via Random Offspring Generation.
Proceedings of the Multiple Approaches to Intelligent Systems, 1999
1995
Proceedings of International Conference on Neural Networks (ICNN'95), Perth, WA, Australia, November 27, 1995