Miguel Rocha

ORCID

Publication Activity (10 Years)

Years Active: 1995-2021
Publications (10 Years): 57

Top Venues

PACBB

J. Integr. Bioinform.

Bioinform.

Comput. Methods Programs Biomed.

Publications

Vitor Pereira, Miguel Rocha
Combinatorial Optimization of Succinate Production in Escherichia coli. PACBB (2021)
Vitor Pereira, Fernando Cruz, Miguel Rocha
MEWpy: a computational strain optimization workbench in Python. Bioinform. 37 (16) (2021)
Delora Baptista, João Correia, Bruno Pereira, Miguel Rocha
A Comparison of Different Compound Representations for Drug Sensitivity Prediction. PACBB (2021)
Tiago Sousa, João Correia, Vitor Pereira, Miguel Rocha
Combining Multi-objective Evolutionary Algorithms with Deep Generative Models Towards Focused Molecular Design. EvoApplications (2021)
Delora Baptista, Pedro G. Ferreira, Miguel Rocha
Deep learning for drug response prediction in cancer. Briefings Bioinform. 22 (1) (2021)
Ana Marta Sequeira, Miguel Rocha
Recurrent Deep Neural Networks for Enzyme Functional Annotation. PACBB (2021)
João Reis, Truong Khoa Phan, Morteza Kheirkhah, Fan Yang, David Griffin, Miguel Rocha, Miguel Rio
R2L: Routing With Reinforcement Learning. IJCNN (2021)
Nuno Alves, Rúben Rodrigues, Miguel Rocha
BioTMPy: A Deep Learning-Based Tool to Classify Biomedical Literature. PACBB (2021)
Débora Antunes, Daniel Martins, Fernanda Correia, Miguel Rocha, Joel P. Arrais
Computational Methods for the Identification of Genetic Variants in Complex Diseases. PACBB (2021)
Anabela Oliveira, André B. Fortunato, Marta Rodrigues, Alberto Azevedo, João Rogeiro, Samuel Bernardo, Laura Lavaud, Xavier Bertin, Alphonse Nahon, Gonçalo de Jesus, Miguel Rocha, Pedro Lopes
Forecasting contrasting coastal and estuarine hydrodynamics with OPENCoastS. Environ. Model. Softw. 143 (2021)
Bruno Pereira, Marcelo Maraschin, Miguel Rocha
Computational Tools for the Analysis of 2D-Nuclear Magnetic Resonance Data. PACBB (2021)
Tiago Sousa, João Correia, Vitor Pereira, Miguel Rocha
Generative Deep Learning for Targeted Compound Design. J. Chem. Inf. Model. 61 (11) (2021)
Diogo Lima, Fernando Cruz, Miguel Rocha, Oscar Días
Reconciliation of Regulatory Data: The Regulatory Networks of Escherichia coli and Bacillus subtilis. PACBB (2020)
Vitor Pereira, Miguel Rocha, Pedro Sousa
Traffic Engineering With Three-Segments Routing. IEEE Trans. Netw. Serv. Manag. 17 (3) (2020)
Ana Marta Sequeira, Diana Lousa, Miguel Rocha
ProPythia: A Python Automated Platform for the Classification of Proteins Using Machine Learning. PACBB (2020)
Fernando Cruz, Diogo Lima, José P. Faria, Miguel Rocha, Oscar Días
Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression. PACBB (2019)
Vitor Pereira, Miguel Rocha, Pedro Sousa
Hybrid IP/SDN Routing for Inter-Data Center Communications. CloudNet (2019)
João Correia, Tiago Resende, Delora Baptista, Miguel Rocha
Artificial Intelligence in Biological Activity Prediction. PACBB (2019)
Vítor Vieira, Paulo Maia, Miguel Rocha, Isabel Rocha
Comparison of pathway analysis and constraint-based methods for cell factory design. BMC Bioinform. 20 (1) (2019)
Marta Sampaio, Miguel Rocha, Hugo Oliveira, Oscar Días
Predicting promoters in phage genomes using PhagePromoter. Bioinform. 35 (24) (2019)
Jorge Ferreira, Vítor Vieira, Jorge Gomes, Sara Correia, Miguel Rocha
Troppo - A Python Framework for the Reconstruction of Context-Specific Metabolic Models. PACBB (2019)
Marta Sampaio, Miguel Rocha, Hugo Oliveira, Oscar Días
Predicting Promoters in Phage Genomes Using Machine Learning Models. PACBB (2019)
Fernando Cruz, Davide Lagoa, João Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha, Oscar Días
SamPler - a novel method for selecting parameters for gene functional annotation routines. BMC Bioinform. 20 (1) (2019)
Vítor Vieira, Miguel Rocha
CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models. Bioinform. 35 (24) (2019)
Vítor Vieira, Jorge Ferreira, Rúben Rodrigues, Filipe Liu, Miguel Rocha
A Model Integration Pipeline for the Improvement of Human Genome-Scale Metabolic Reconstructions. J. Integr. Bioinform. 16 (1) (2019)
Miguel Rocha, Truong Khoa Phan, João Reis, David Griffin, Miguel Rio
Triptych: Multi-objective Optimisation of Service Deployment Costs, Application Delay and Bandwidth Usage. Networking (2019)
Florentino Fdez-Riverola, Miguel Rocha
Selected Extended Papers of the 12th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB). J. Integr. Bioinform. 16 (1) (2019)
João Reis, Miguel Rocha, Truong Khoa Phan, David Griffin, Franck Le, Miguel Rio
Deep Neural Networks for Network Routing. IJCNN (2019)
João Carlos Sequeira, Miguel Rocha, Maria Madalena Alves, Andreia Ferreira Salvador
MOSCA: An Automated Pipeline for Integrated Metagenomics and Metatranscriptomics Data Analysis. PACBB (2018)
Vitor Pereira, Miguel Rocha, Pedro Sousa
Segment Routing Single Link Failure Congestion Optimization. ICETE (1) (2018)
Cláudia M. Bauer, Paulo Vilaça, Fernanda Ramlov, Eva Regina de Oliveira, Débora Cabral Nazário, Caroline Schmitz, Rafaela Gordo Corrêa, Miguel Rocha, Marcelo Maraschin
In Silico Predictions for Fucoxanthin Production by the Diatom Phaeodactylum Tricornutum. PACBB (2018)
Vítor Vieira, Jorge Ferreira, Rúben Rodrigues, Miguel Rocha
Metabolite Integration Pipeline for the Improvement of Human Metabolic Models. PACBB (2018)
Sara Cardoso, Delora Baptista, Rebeca Santos, Miguel Rocha
A Review on Metabolomics Data Analysis for Cancer Applications. PACBB (2018)
Rúben Rodrigues, Hugo Costa, Miguel Rocha
Automating the Extraction of Essential Genes from Literature. ICDM (2018)
Truong Khoa Phan, Miguel Rocha, David Griffin, Miguel Rio
Utilitarian Placement of Composite Services. IEEE Trans. Netw. Serv. Manag. 15 (2) (2018)
Tiago Alves, Rúben Rodrigues, Hugo Costa, Miguel Rocha
Development of an information retrieval tool for biomedical patents. Comput. Methods Programs Biomed. 159 (2018)
Débora Cabral Nazário, Sara Cardoso, Silvana Rocco, Maurício Sforça, Simone Fanan Hengeltraub, Cláudia M. Bauer, Miguel Rocha, Marcelo Maraschin
17α-Ethinylestradiol Analysis of Endo- and Exometabolome of Ulva lactuca (Chlorophyta) by 1H-NMR Spectroscopy and Bioinformatics Tools. PACBB (2018)
Eva Regina Oliveira, Ester Wickert, Fernanda Ramlov, Rodolfo Moresco, Larissa Simão, Bruno Bachiega Navarro, Cláudia M. Bauer, Débora Cabral Nazário, Miguel Rocha, Marcelo Maraschin
Influence of Solar Radiation on the Production of Secondary Metabolites in Three Rice (Oryza sativa) Cultivars. PACBB (2017)
Vitor Pereira, Pedro Sousa, Miguel Rocha
Evolutionary computation at work for the optimization of link state routing protocols. GECCO (Companion) (2017)
Sara Cardoso, Marcelo Maraschin, Luiz Augusto Martins Peruch, Miguel Rocha, Aline Pereira
A Chemometrics Approach for Nuclear Magnetic Resonance Data to Characterize the Partial Metabolome Banana Peels from Southern Brazil. J. Integr. Bioinform. 14 (4) (2017)
André M. Santiago, Miguel Rocha, António Dourado, Joel P. Arrais
Mixed-Integer Programming Model for Profiling Disease Biomarkers from Gene Expression Studies. IWBBIO (2) (2017)
David Henriques, Alejandro Fernández Villaverde, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga
Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. PLoS Comput. Biol. 13 (2) (2017)
Sara Cardoso, Marcelo Maraschin, Luiz Augusto Martins Peruch, Miguel Rocha, Aline Pereira
Characterization of the Chemical Composition of Banana Peels from Southern Brazil Across the Seasons Using Nuclear Magnetic Resonance and Chemometrics. PACBB (2017)
Telma Afonso, Rodolfo Moresco, Virgílio G. Uarrota, Bruno Bachiega Navarro, Eduardo da C. Nunes, Marcelo Maraschin, Miguel Rocha
UV-Vis and CIELAB Based Chemometric Characterization of Manihot esculenta Carotenoid Contents. J. Integr. Bioinform. 14 (4) (2017)
Rodolfo Moresco, Telma Afonso, Virgílio G. Uarrota, Bruno Bachiega Navarro, Eduardo da C. Nunes, Miguel Rocha, Marcelo Maraschin
Classification Tools for Carotenoid Content Estimation in Manihot esculenta via Metabolomics and Machine Learning. PACBB (2017)
Nuno Osório, Paulo Vilaça, Miguel Rocha
A Critical Evaluation of Automatic Atom Mapping Algorithms and Tools. PACBB (2017)
Susane Lopes, Rodolfo Moresco, Luiz Augusto Martins Peruch, Miguel Rocha, Marcelo Maraschin
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. PACBB (2017)
Oscar Días, Daniel Gomes, Paulo Vilaça, João G. R. Cardoso, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha
Genome-Wide Semi-Automated Annotation of Transporter Systems. IEEE ACM Trans. Comput. Biol. Bioinform. 14 (2) (2017)
Florentino Fdez-Riverola, Miguel Rocha
Selected Extended Papers of the 11th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB). J. Integr. Bioinform. 14 (4) (2017)
Paulo Maia, Isabel Rocha, Miguel Rocha
Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction. GECCO (Companion) (2017)
Vitor Pereira, Miguel Rocha, Pedro Sousa
Optimizing Segment Routing using Evolutionary Computation. FNC/MobiSPC (2017)
Tiago Alves, Rúben Rodrigues, Hugo Costa, Miguel Rocha
Development of Text Mining Tools for Information Retrieval from Patents. PACBB (2017)
Christopher Costa, Marcelo Maraschin, Miguel Rocha
An R package for the integrated analysis of metabolomics and spectral data. Comput. Methods Programs Biomed. 129 (2016)
Jorge Ferreira, Sara Correia, Miguel Rocha
Reconstruction of Metabolic Models for Liver Cancer Cells. PACBB (2016)
Vítor Vieira, Paulo Maia, Isabel Rocha, Miguel Rocha
Development of an Integrated Framework for Minimal Cut Set Enumeration in Constraint-Based Models. PACBB (2016)
Vitor Pereira, Miguel Rocha, Pedro Sousa
Optimizing Load Balancing Routing Mechanisms with Evolutionary Computation. Intelligent Environments (Workshops) (2016)
Rúben Rodrigues, Hugo Costa, Miguel Rocha
Development of a Machine Learning Framework for Biomedical Text Mining. PACBB (2016)
Maíra Maciel Tomazzoli, Remi Dal Pai Neto, Rodolfo Moresco, Larissa Westphal, Amélia Regina Somensi-Zeggio, Leandro Specht, Christopher Costa, Miguel Rocha, Marcelo Maraschin
Discrimination of Brazilian propolis according to the seasoning using chemometrics and machine learning based on UV-Vis scanning data. J. Integr. Bioinform. 12 (4) (2015)
David Henriques, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga
Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach. Bioinform. 31 (18) (2015)
Filipe Liu, Paulo Vilaça, Isabel Rocha, Miguel Rocha
Development and application of efficient pathway enumeration algorithms for metabolic engineering applications. Comput. Methods Programs Biomed. 118 (2) (2015)
Vitor Pereira, Miguel Rocha, Pedro Sousa
Automated Network Resilience Optimization Using Computational Intelligence Methods. IDC (2015)
Eduardo Valente, Miguel Rocha
Microarray Gene Expression Data Integration: An Application to Brain Tumor Grade Determination. PACBB (2015)
Fernanda Kokowicz Pilatti, Christopher Costa, Miguel Rocha, Marcelo Maraschin, Ana Maria Viana
UV-Visible Spectrophotometry-Based Metabolomic Analysis of Cedrela Fissilis Velozzo (Meliaceae) Calluses - A Screening Tool for Culture Medium Composition and Cell Metabolic Profiles. PACBB (2015)
Sara Correia, Miguel Rocha
A Critical Evaluation of Methods for the Reconstruction of Tissue-Specific Models. EPIA (2015)
Rodolfo Moresco, Virgílio Gavicho Uarrota, Aline Pereira, Maíra Maciel Tomazzoli, Eduardo da C. Nunes, Luiz Augusto Martins Peruch, Jussara Gazzola, Christopher Costa, Miguel Rocha, Marcelo Maraschin
UV-visible scanning spectrophotometry and chemometric analysis as tools for carotenoids analysis in cassava genotypes (Manihot esculenta Crantz). J. Integr. Bioinform. 12 (4) (2015)
Eduardo Valente, Miguel Rocha
Integrating data from heterogeneous DNA microarray platforms. J. Integr. Bioinform. 12 (4) (2015)
Ana Alão Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha
Extracting kinetic information from literature with KineticRE. J. Integr. Bioinform. 12 (4) (2015)
Eduardo Valente, Miguel Rocha
Transcript-based reannotation for microarray probesets. SAC (2015)
Christopher Costa, Marcelo Maraschin, Miguel Rocha
An Integrated Computational Platform for Metabolomics Data Analysis. PACBB (2015)
Rodolfo Moresco, Virgílio G. Uarrota, Aline Pereira, Maíra M. Tomazzoli, Eduardo da C. Nunes, Luiz Augusto Martins Peruch, Christopher Costa, Miguel Rocha, Marcelo Maraschin
Carotenoid Analysis of Cassava Genotypes Roots (Manihot Esculenta Crantz) Cultivated in Southern Brazil Using Chemometric Tools. PACBB (2015)
Maíra M. Tomazzoli, Remi Dal Pai Neto, Rodolfo Moresco, Larissa Westphal, Amélia Regina Somensi-Zeggio, Leandro Specht, Christopher Costa, Miguel Rocha, Marcelo Maraschin
UV-Visible Scanning Spectrophotometry and Chemometric Analysis as Tools to Build Descriptive and Classification Models for Propolis from Southern Brazil. PACBB (2015)
Rafael T. Pereira, Hugo Costa, Sónia Carneiro, Miguel Rocha, Rui Mendes
Reconstructing transcriptional Regulatory Networks using data integration and Text Mining. BIBM (2015)
Vitor Pereira, Pedro Sousa, Paulo Cortez, Miguel Rio, Miguel Rocha
Comparison of Single and Multi-objective Evolutionary Algorithms for Robust Link-State Routing. EMO (2) (2015)
Ana Alão Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha
A Text Mining Approach for the Extraction of Kinetic Information from Literature. PACBB (2015)
Rafael Carreira, Pedro Evangelista, Paulo Maia, Paulo Vilaça, Marcellinus Pont, Jean-François Tomb, Isabel Rocha, Miguel Rocha
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data. BMC Syst. Biol. 8 (2014)
Orlando Rocha, Paulo Vilaça, Miguel Rocha, Rui Mendes
Reg4OptFlux: an OptFlux plug-in that comprises meta-heuristics approaches for Metabolic engineering using integrated models. NaBIC (2014)
Miguel Rocha, Rui Mendes, Orlando Rocha, Isabel Rocha, Eugénio C. Ferreira
Optimization of fed-batch fermentation processes with bio-inspired algorithms. Expert Syst. Appl. 41 (5) (2014)
Filipe Liu, Paulo Vilaça, Isabel Rocha, Miguel Rocha
Evaluating Pathway Enumeration Algorithms in Metabolic Engineering Case Studies. PACBB (2014)
José P. Faria, Ross A. Overbeek, Fangfang Xia, Miguel Rocha, Isabel Rocha, Christopher S. Henry
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. Briefings Bioinform. 15 (4) (2014)
Pedro Barbosa, Oscar Días, Joel P. Arrais, Miguel Rocha
Metagenomic Analysis of the Saliva Microbiome with Merlin. PACBB (2014)
Alberto Noronha, Paulo Vilaça, Miguel Rocha
An integrated network visualization framework towards metabolic engineering applications. BMC Bioinform. 15 (2014)
Joao C. Guimaraes, Miguel Rocha, Adam P. Arkin, Guillaume Cambray
D-Tailor: automated analysis and design of DNA sequences. Bioinform. 30 (8) (2014)
Miguel Rocha
Large Scale Metabolic Characterization Using Flux Balance Analysis and Data Mining. ICANNGA (2013)
Vitor Pereira, Pedro Sousa, Paulo Cortez, Miguel Rio, Miguel Rocha
Robust Optimization of Intradomain Routing Using Evolutionary Algorithms. DCAI (2013)
Paulo Maia, Isabel Rocha, Miguel Rocha
An integrated framework for strain optimization. IEEE Congress on Evolutionary Computation (2013)
Tiago Resende, Daniela M. Correia, Miguel Rocha, Isabel Rocha
Re-annotation of the genome sequence of Helicobacter pylori 26695. J. Integr. Bioinform. 10 (3) (2013)
Pedro Sousa, Paulo Cortez, Rui Vaz, Miguel Rocha, Miguel Rio
Email Spam Detection: a Symbiotic Feature Selection Approach Fostered by Evolutionary Computation. Int. J. Inf. Technol. Decis. Mak. 12 (4) (2013)
Jorge Henrique Martins de Pinho, João Luís Ferreira Sobral, Miguel Rocha
Parallel evolutionary computation in bioinformatics applications. Comput. Methods Programs Biomed. 110 (2) (2013)
Alberto Noronha, Paulo Vilaça, Miguel Rocha
Network Visualization Tools to Enhance Metabolic Engineering Platforms. PACBB (2013)
Vitor Pereira, Miguel Rocha, Paulo Cortez, Miguel Rio, Pedro Sousa
A Framework for Robust Traffic Engineering Using Evolutionary Computation. AIMS (2013)
Pedro Evangelista, Miguel Rocha, Isabel Rocha
Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies. IEEE Congress on Evolutionary Computation (2013)
Rafael Carreira, Miguel Rocha, Silas Granato Villas-Bôas, Isabel Rocha
Algorithms to infer metabolic flux ratios from fluxomics data. BIBM (2013)
Emanuel J. V. Gonçalves, Isabel Rocha, Miguel Rocha
Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression. PACBB (2012)
Emanuel J. V. Gonçalves, Rui Pereira, Isabel Rocha, Miguel Rocha
Discovery of Optimal Targets for Gene Over/Underexpression. J. Comput. Biol. 19 (2) (2012)
Paulo Maia, Paulo Vilaça, Isabel Rocha, Marcellinus Pont, Jean-François Tomb, Miguel Rocha
An integrated computational environment for elementary modes analysis of biochemical networks. Int. J. Data Min. Bioinform. 6 (4) (2012)
André Zúquete, Pedro Correia, Miguel Rocha
A Framework for Enforcing User-Based Authorization Policies on Packet Filter Firewalls. Communications and Multimedia Security (2012)
Paulo Cortez, Miguel Rio, Miguel Rocha, Pedro Sousa
Multi-scale Internet traffic forecasting using neural networks and time series methods. Expert Syst. J. Knowl. Eng. 29 (2) (2012)
João G. R. Cardoso, Paulo Vilaça, Simão Soares, Miguel Rocha
An Algorithm to Assemble Gene-Protein-Reaction Associations for Genome-Scale Metabolic Model Reconstruction. PRIB (2012)
Sara Correia, Miguel Rocha
In silico strain optimization by adding reactions to metabolic models. J. Integr. Bioinform. 9 (3) (2012)
André Zúquete, Miguel Rocha
Identification of source applications for enhanced traffic analysis and anomaly detection. ICC (2012)

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Publication Activity (10 Years)

Top Topics

Top Venues

Miguel Rocha