Miguel Rocha - RankMe

198 papers A* 3A 3B 18C 10Misc 52Journal 67Unranked 42

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Correction: A diel multi-tissue genome-scale metabolic model of Vitis vinifera. PLoS Comput. Biol. Marta Sampaio, Miguel Rocha, Oscar Dias
2026	J	`jnl`	NeuroScaler: Towards Energy-Optimal Autoscaling for Container-Based Services. CoRR Alisson O. Chaves, Rodrigo Moreira, Larissa F. Rodrigues Moreira, Joao Correia, David Santos, Rui Silva, Tiago Barros, Daniel Corujo, Miguel Rocha, Flávio de Oliveira Silva
2025	J	`jnl`	Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction. BMC Bioinform. João Capela, Maria Zimmermann-Kogadeeva, Aalt D. J. van Dijk, Dick de Ridder, Oscar Dias, Miguel Rocha
2025	A	`conf`	Evolutionary Algorithms for Metabolic Transformation through Multi-gene Knockout Optimization. GECCO Bruno Sá, Alexandre Oliveira, Miguel Rocha
2025	—	`conf`	Leveraging Large Language Models on Assay Descriptions to Improve the Prediction of Inhibitors for Mycobacterium Tuberculosis. IWANN (1) Nuno Alves, Nuno S. Osório, Vítor Pereira, Miguel Rocha
2025	J	`jnl`	Predicting precursors of plant specialized metabolites using DeepMol automated machine learning. J. Integr. Bioinform. João Capela, João Cheixo, Dick de Ridder, Oscar Dias, Miguel Rocha
2024	J	`jnl`	A diel multi-tissue genome-scale metabolic model of Vitis vinifera. PLoS Comput. Biol. Marta Sampaio, Miguel Rocha, Oscar Dias
2024	J	`jnl`	BioISO: An Objective-Oriented Application for Assisting the Curation of Genome-Scale Metabolic Models. IEEE ACM Trans. Comput. Biol. Bioinform. Fernando Cruz, João Capela, Eugénio C. Ferreira, Miguel Rocha, Oscar Dias
2024	J	`jnl`	Deepmol: an automated machine and deep learning framework for computational chemistry. J. Cheminformatics João Correia, João Capela, Miguel Rocha
2024	J	`jnl`	Reconstruction of cell-specific models capturing the influence of metabolism on DNA methylation in cancer. Comput. Biol. Medicine Tânia Barata, Vítor Pereira, Ricardo Pires das Neves, Miguel Rocha
2023	Misc	`conf`	A New GIMME-Based Heuristic for Compartmentalised Transcriptomics Data Integration. PACBB Diego Troitiño-Jordedo, Lucas Carvalho, David Henriques, Vítor Pereira, Miguel Rocha, Eva Balsa-Canto
2023	J	`jnl`	A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer. PLoS Comput. Biol. Delora Baptista, Pedro G. Ferreira, Miguel Rocha
2023	A	`conf`	Combining Evolutionary Algorithms with Reaction Rules Towards Focused Molecular Design. GECCO João Correia, Vitor Pereira, Miguel Rocha
2023	Misc	`ed.`	Practical Applications of Computational Biology and Bioinformatics, 16th International Conference (PACBB 2022), 13-15 July, 2022, L'Aquila, Italy. PACBB Florentino Fdez-Riverola, Miguel Rocha, Mohd Saberi Mohamad, Simona Caraiman, Ana Belén Gil González
2023	Misc	`ed.`	Practical Applications of Computational Biology and Bioinformatics, 17th International Conference (PACBB 2023), 12th-14th July, 2023, Guimarães, Portugal PACBB Miguel Rocha, Florentino Fdez-Riverola, Mohd Saberi Mohamad, Ana Belén Gil González
2023	J	`jnl`	The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber. PLoS Comput. Biol. Emanuel Cunha, Miguel Silva, Inês Chaves, Hüseyin Demirci, Davide Lagoa, Diogo Lima, Miguel Rocha, Isabel Rocha, Oscar Dias
2023	C	`conf`	Word embeddings for protein sequence analysis. CIBCB Ana Marta Sequeira, Ivan Gomes, Miguel Rocha
2022	J	`jnl`	A comparison of multi-objective optimization algorithms for weight setting problems in traffic engineering. Nat. Comput. Vitor Pereira, Pedro Sousa, Miguel Rocha
2022	J	`jnl`	A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale. PLoS Comput. Biol. Vítor Vieira, Jorge Ferreira, Miguel Rocha
2022	B	`conf`	Development of Deep Learning approaches to predict relationships between chemical structures and sweetness. IJCNN João Capela, João Correia, Vitor Pereira, Miguel Rocha
2022	J	`jnl`	Evaluating molecular representations in machine learning models for drug response prediction and interpretability. J. Integr. Bioinform. Delora Baptista, João Correia, Bruno Pereira, Miguel Rocha
2022	J	`jnl`	Going virtual and going wide: comparing Team-Based Learning in-class versus online and across disciplines. Educ. Inf. Technol. Elsa Costa e Silva, Teresa Lino-Neto, Eugénia Ribeiro, Miguel Rocha, Manuel João Costa
2022	Misc	`ed.`	Practical Applications of Computational Biology & Bioinformatics, 15th International Conference (PACBB 2021), Salamanca, Spain, 6-8 October, 2021. PACBB Miguel Rocha, Florentino Fdez-Riverola, Mohd Saberi Mohamad, Roberto Casado-Vara
2022	B	`conf`	Predicting the number of biochemical transformations needed to synthesize a compound. IJCNN João Correia, Rafael Carreira, Vitor Pereira, Miguel Rocha
2022	J	`jnl`	ProPythia: A Python package for protein classification based on machine and deep learning. Neurocomputing Ana Marta Sequeira, Diana Lousa, Miguel Rocha
2022	J	`jnl`	Reconstruction of tissue-specific genome-scale metabolic models for human cancer stem cells. Comput. Biol. Medicine Tânia Barata, Vítor Vieira, Rúben Rodrigues, Ricardo Pires das Neves, Miguel Rocha
2022	B	`conf`	Variational Autoencoders and Evolutionary Algorithms for Targeted Novel Enzyme Design. CEC Miguel Martins, Miguel Rocha, Vitor Pereira
2021	Misc	`conf`	A Comparison of Different Compound Representations for Drug Sensitivity Prediction. PACBB Delora Baptista, João Correia, Bruno Pereira, Miguel Rocha
2021	Misc	`conf`	BioTMPy: A Deep Learning-Based Tool to Classify Biomedical Literature. PACBB Nuno Alves, Rúben Rodrigues, Miguel Rocha
2021	Misc	`conf`	Combinatorial Optimization of Succinate Production in Escherichia coli. PACBB Vitor Pereira, Miguel Rocha
2021	B	`conf`	Combining Multi-objective Evolutionary Algorithms with Deep Generative Models Towards Focused Molecular Design. EvoApplications Tiago Sousa, João Correia, Vitor Pereira, Miguel Rocha
2021	Misc	`conf`	Computational Methods for the Identification of Genetic Variants in Complex Diseases. PACBB Débora Antunes, Daniel Martins, Fernanda Correia, Miguel Rocha, Joel P. Arrais
2021	Misc	`conf`	Computational Tools for the Analysis of 2D-Nuclear Magnetic Resonance Data. PACBB Bruno Pereira, Marcelo Maraschin, Miguel Rocha
2021	J	`jnl`	Deep learning for drug response prediction in cancer. Briefings Bioinform. Delora Baptista, Pedro G. Ferreira, Miguel Rocha
2021	J	`jnl`	Generative Deep Learning for Targeted Compound Design. J. Chem. Inf. Model. Tiago Sousa, João Correia, Vitor Pereira, Miguel Rocha
2021	J	`jnl`	MEWpy: a computational strain optimization workbench in Python. Bioinform. Vitor Pereira, Fernando Cruz, Miguel Rocha
2021	Misc	`ed.`	Practical Applications of Computational Biology & Bioinformatics, 14th International Conference (PACBB 2020), L'Aquila, Italy, 17-19 June, 2020. PACBB Gabriella Panuccio, Miguel Rocha, Florentino Fdez-Riverola, Mohd Saberi Mohamad, Roberto Casado-Vara
2021	B	`conf`	R2L: Routing With Reinforcement Learning. IJCNN João Reis, Truong Khoa Phan, Morteza Kheirkhah, Fan Yang, David Griffin, Miguel Rocha, Miguel Rio
2021	Misc	`conf`	Recurrent Deep Neural Networks for Enzyme Functional Annotation. PACBB Ana Marta Sequeira, Miguel Rocha
2020	Misc	`ed.`	Practical Applications of Computational Biology and Bioinformatics, 13th International Conference, PABCC 2019, Avila, Spain, 26-28 June 2019. PACBB Florentino Fdez-Riverola, Miguel Rocha, Mohd Saberi Mohamad, Nazar Zaki, José A. Castellanos-Garzón
2020	Misc	`conf`	ProPythia: A Python Automated Platform for the Classification of Proteins Using Machine Learning. PACBB Ana Marta Sequeira, Diana Lousa, Miguel Rocha
2020	Misc	`conf`	Reconciliation of Regulatory Data: The Regulatory Networks of Escherichia coli and Bacillus subtilis. PACBB Diogo Lima, Fernando Cruz, Miguel Rocha, Oscar Dias
2020	J	`jnl`	Traffic Engineering With Three-Segments Routing. IEEE Trans. Netw. Serv. Manag. Vitor Pereira, Miguel Rocha, Pedro Sousa
2019	J	`jnl`	A Model Integration Pipeline for the Improvement of Human Genome-Scale Metabolic Reconstructions. J. Integr. Bioinform. Vítor Vieira, Jorge Ferreira, Rúben Rodrigues, Filipe Liu, Miguel Rocha
2019	Misc	`conf`	Artificial Intelligence in Biological Activity Prediction. PACBB João Correia, Tiago Resende, Delora Baptista, Miguel Rocha
2019	J	`jnl`	CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models. Bioinform. Vítor Vieira, Miguel Rocha
2019	J	`jnl`	Comparison of pathway analysis and constraint-based methods for cell factory design. BMC Bioinform. Vítor Vieira, Paulo Maia, Miguel Rocha, Isabel Rocha
2019	B	`conf`	Deep Neural Networks for Network Routing. IJCNN João Reis, Miguel Rocha, Truong Khoa Phan, David Griffin, Franck Le, Miguel Rio
2019	—	`conf`	Hybrid IP/SDN Routing for Inter-Data Center Communications. CloudNet Vitor Pereira, Miguel Rocha, Pedro Sousa
2019	Misc	`ed.`	Practical Applications of Computational Biology and Bioinformatics, 12th International Conference, PACBB 2018, Toledo, Spain, 20-22 May, 2018. PACBB Florentino Fdez-Riverola, Mohd Saberi Mohamad, Miguel Rocha, Juan F. De Paz, Pascual González
2019	Misc	`conf`	Predicting Promoters in Phage Genomes Using Machine Learning Models. PACBB Marta Sampaio, Miguel Rocha, Hugo Oliveira, Oscar Dias
2019	J	`jnl`	Predicting promoters in phage genomes using PhagePromoter. Bioinform. Marta Sampaio, Miguel Rocha, Hugo Oliveira, Oscar Dias
2019	J	`jnl`	SamPler - a novel method for selecting parameters for gene functional annotation routines. BMC Bioinform. Fernando Cruz, Davide Lagoa, João Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha, Oscar Dias
2019	J	`jnl`	Selected Extended Papers of the 12th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB). J. Integr. Bioinform. Florentino Fdez-Riverola, Miguel Rocha
2019	Misc	`conf`	Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression. PACBB Fernando Cruz, Diogo Lima, José P. Faria, Miguel Rocha, Oscar Dias
2019	B	`conf`	Triptych: Multi-objective Optimisation of Service Deployment Costs, Application Delay and Bandwidth Usage. Networking Miguel Rocha, Truong Khoa Phan, João Reis, David Griffin, Miguel Rio
2019	Misc	`conf`	Troppo - A Python Framework for the Reconstruction of Context-Specific Metabolic Models. PACBB Jorge Ferreira, Vítor Vieira, Jorge Gomes, Sara Correia, Miguel Rocha
2018	Misc	`conf`	17α-Ethinylestradiol Analysis of Endo- and Exometabolome of Ulva lactuca (Chlorophyta) by 1H-NMR Spectroscopy and Bioinformatics Tools. PACBB Débora Cabral Nazário, Sara Cardoso, Silvana Rocco, Maurício Sforça, Simone Fanan Hengeltraub, Cláudia M. Bauer, Miguel Rocha, Marcelo Maraschin
2018	Misc	`conf`	A Review on Metabolomics Data Analysis for Cancer Applications. PACBB Sara Cardoso, Delora Baptista, Rebeca Santos, Miguel Rocha
2018	A*	`conf`	Automating the Extraction of Essential Genes from Literature. ICDM Rúben Rodrigues, Hugo Costa, Miguel Rocha
2018	J	`jnl`	Development of an information retrieval tool for biomedical patents. Comput. Methods Programs Biomed. Tiago Alves, Rúben Rodrigues, Hugo Costa, Miguel Rocha
2018	Misc	`conf`	In Silico Predictions for Fucoxanthin Production by the Diatom Phaeodactylum Tricornutum. PACBB Cláudia M. Bauer, Paulo Vilaça, Fernanda Ramlov, Eva Regina de Oliveira, Débora Cabral Nazário, Caroline Schmitz, Rafaela Gordo Corrêa, Miguel Rocha, Marcelo Maraschin
2018	Misc	`conf`	MOSCA: An Automated Pipeline for Integrated Metagenomics and Metatranscriptomics Data Analysis. PACBB João Carlos Sequeira, Miguel Rocha, Maria Madalena Alves, Andreia Ferreira Salvador
2018	Misc	`conf`	Metabolite Integration Pipeline for the Improvement of Human Metabolic Models. PACBB Vítor Vieira, Jorge Ferreira, Rúben Rodrigues, Miguel Rocha
2018	—	`conf`	Segment Routing Single Link Failure Congestion Optimization. ICETE (1) Vitor Pereira, Miguel Rocha, Pedro Sousa
2018	J	`jnl`	Utilitarian Placement of Composite Services. IEEE Trans. Netw. Serv. Manag. Truong Khoa Phan, Miguel Rocha, David Griffin, Miguel Rio
2017	J	`jnl`	A Chemometrics Approach for Nuclear Magnetic Resonance Data to Characterize the Partial Metabolome Banana Peels from Southern Brazil. J. Integr. Bioinform. Sara Cardoso, Marcelo Maraschin, Luiz Augusto Martins Peruch, Miguel Rocha, Aline Pereira
2017	Misc	`conf`	A Critical Evaluation of Automatic Atom Mapping Algorithms and Tools. PACBB Nuno Osório, Paulo Vilaça, Miguel Rocha
2017	Misc	`conf`	Characterization of the Chemical Composition of Banana Peels from Southern Brazil Across the Seasons Using Nuclear Magnetic Resonance and Chemometrics. PACBB Sara Cardoso, Marcelo Maraschin, Luiz Augusto Martins Peruch, Miguel Rocha, Aline Pereira
2017	Misc	`conf`	Classification Tools for Carotenoid Content Estimation in Manihot esculenta via Metabolomics and Machine Learning. PACBB Rodolfo Moresco, Telma Afonso, Virgílio G. Uarrota, Bruno Bachiega Navarro, Eduardo da C. Nunes, Miguel Rocha, Marcelo Maraschin
2017	J	`jnl`	Data-driven reverse engineering of signaling pathways using ensembles of dynamic models. PLoS Comput. Biol. David Henriques, Alejandro Fernández Villaverde, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga
2017	Misc	`conf`	Development of Text Mining Tools for Information Retrieval from Patents. PACBB Tiago Alves, Rúben Rodrigues, Hugo Costa, Miguel Rocha
2017	—	`conf`	Evolutionary computation at work for the optimization of link state routing protocols. GECCO (Companion) Vitor Pereira, Pedro Sousa, Miguel Rocha
2017	J	`jnl`	Genome-Wide Semi-Automated Annotation of Transporter Systems. IEEE ACM Trans. Comput. Biol. Bioinform. Oscar Dias, Daniel Gomes, Paulo Vilaça, João G. R. Cardoso, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha
2017	—	`conf`	Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction. GECCO (Companion) Paulo Maia, Isabel Rocha, Miguel Rocha
2017	Misc	`conf`	Influence of Solar Radiation on the Production of Secondary Metabolites in Three Rice (Oryza sativa) Cultivars. PACBB Eva Regina Oliveira, Ester Wickert, Fernanda Ramlov, Rodolfo Moresco, Larissa Simão, Bruno Bachiega Navarro, Cláudia M. Bauer, Débora Cabral Nazário, Miguel Rocha, Marcelo Maraschin
2017	—	`conf`	Mixed-Integer Programming Model for Profiling Disease Biomarkers from Gene Expression Studies. IWBBIO (2) André M. Santiago, Miguel Rocha, António Dourado, Joel P. Arrais
2017	—	`conf`	Optimizing Segment Routing using Evolutionary Computation. FNC/MobiSPC Vitor Pereira, Miguel Rocha, Pedro Sousa
2017	J	`jnl`	Selected Extended Papers of the 11th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB). J. Integr. Bioinform. Florentino Fdez-Riverola, Miguel Rocha
2017	Misc	`conf`	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 Susane Lopes, Rodolfo Moresco, Luiz Augusto Martins Peruch, Miguel Rocha, Marcelo Maraschin
2017	J	`jnl`	UV-Vis and CIELAB Based Chemometric Characterization of Manihot esculenta Carotenoid Contents. J. Integr. Bioinform. Telma Afonso, Rodolfo Moresco, Virgílio G. Uarrota, Bruno Bachiega Navarro, Eduardo da C. Nunes, Marcelo Maraschin, Miguel Rocha
2016	J	`jnl`	An R package for the integrated analysis of metabolomics and spectral data. Comput. Methods Programs Biomed. Christopher Costa, Marcelo Maraschin, Miguel Rocha
2016	Misc	`conf`	Development of a Machine Learning Framework for Biomedical Text Mining. PACBB Rúben Rodrigues, Hugo Costa, Miguel Rocha
2016	Misc	`conf`	Development of an Integrated Framework for Minimal Cut Set Enumeration in Constraint-Based Models. PACBB Vítor Vieira, Paulo Maia, Isabel Rocha, Miguel Rocha
2016	B	`conf`	Optimizing Load Balancing Routing Mechanisms with Evolutionary Computation. Intelligent Environments (Workshops) Vitor Pereira, Miguel Rocha, Pedro Sousa
2016	Misc	`conf`	Reconstruction of Metabolic Models for Liver Cancer Cells. PACBB Jorge Ferreira, Sara Correia, Miguel Rocha
2015	Misc	`conf`	A Critical Evaluation of Methods for the Reconstruction of Tissue-Specific Models. EPIA Sara Correia, Miguel Rocha
2015	Misc	`conf`	A Text Mining Approach for the Extraction of Kinetic Information from Literature. PACBB Ana Alão Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha
2015	Misc	`conf`	An Integrated Computational Platform for Metabolomics Data Analysis. PACBB Christopher Costa, Marcelo Maraschin, Miguel Rocha
2015	Misc	`conf`	Automated Network Resilience Optimization Using Computational Intelligence Methods. IDC Vitor Pereira, Miguel Rocha, Pedro Sousa
2015	Misc	`conf`	Carotenoid Analysis of Cassava Genotypes Roots (Manihot Esculenta Crantz) Cultivated in Southern Brazil Using Chemometric Tools. PACBB Rodolfo Moresco, Virgílio G. Uarrota, Aline Pereira, Maíra M. Tomazzoli, Eduardo da C. Nunes, Luiz Augusto Martins Peruch, Christopher Costa, Miguel Rocha, Marcelo Maraschin
2015	—	`conf`	Comparison of Single and Multi-objective Evolutionary Algorithms for Robust Link-State Routing. EMO (2) Vitor Pereira, Pedro Sousa, Paulo Cortez, Miguel Rio, Miguel Rocha
2015	J	`jnl`	Development and application of efficient pathway enumeration algorithms for metabolic engineering applications. Comput. Methods Programs Biomed. Filipe Liu, Paulo Vilaça, Isabel Rocha, Miguel Rocha
2015	J	`jnl`	Discrimination of Brazilian propolis according to the seasoning using chemometrics and machine learning based on UV-Vis scanning data. J. Integr. Bioinform. Maíra Maciel Tomazzoli, Remi Dal Pai Neto, Rodolfo Moresco, Larissa Westphal, Amélia Regina Somensi-Zeggio, Leandro Specht, Christopher Costa, Miguel Rocha, Marcelo Maraschin
2015	J	`jnl`	Extracting kinetic information from literature with KineticRE. J. Integr. Bioinform. Ana Alão Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha
2015	J	`jnl`	Integrating data from heterogeneous DNA microarray platforms. J. Integr. Bioinform. Eduardo Valente, Miguel Rocha
2015	Misc	`conf`	Microarray Gene Expression Data Integration: An Application to Brain Tumor Grade Determination. PACBB Eduardo Valente, Miguel Rocha
2015	—	`conf`	Reconstructing transcriptional Regulatory Networks using data integration and Text Mining. BIBM Rafael T. Pereira, Hugo Costa, Sónia Carneiro, Miguel Rocha, Rui Mendes
2015	J	`jnl`	Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach. Bioinform. David Henriques, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga
2015	Misc	`conf`	Transcript-based reannotation for microarray probesets. SAC Eduardo Valente, Miguel Rocha
2015	Misc	`conf`	UV-Visible Scanning Spectrophotometry and Chemometric Analysis as Tools to Build Descriptive and Classification Models for Propolis from Southern Brazil. PACBB Maíra M. Tomazzoli, Remi Dal Pai Neto, Rodolfo Moresco, Larissa Westphal, Amélia Regina Somensi-Zeggio, Leandro Specht, Christopher Costa, Miguel Rocha, Marcelo Maraschin
2015	Misc	`conf`	UV-Visible Spectrophotometry-Based Metabolomic Analysis of Cedrela Fissilis Velozzo (Meliaceae) Calluses - A Screening Tool for Culture Medium Composition and Cell Metabolic Profiles. PACBB Fernanda Kokowicz Pilatti, Christopher Costa, Miguel Rocha, Marcelo Maraschin, Ana Maria Viana
2015	J	`jnl`	UV-visible scanning spectrophotometry and chemometric analysis as tools for carotenoids analysis in cassava genotypes (Manihot esculenta Crantz). J. Integr. Bioinform. 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
2014	J	`jnl`	An integrated network visualization framework towards metabolic engineering applications. BMC Bioinform. Alberto Noronha, Paulo Vilaça, Miguel Rocha
2014	J	`jnl`	CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data. BMC Syst. Biol. Rafael Carreira, Pedro Evangelista, Paulo Maia, Paulo Vilaça, Marcellinus Pont, Jean-François Tomb, Isabel Rocha, Miguel Rocha
2014	J	`jnl`	D-Tailor: automated analysis and design of DNA sequences. Bioinform. Joao C. Guimaraes, Miguel Rocha, Adam P. Arkin, Guillaume Cambray
2014	Misc	`conf`	Evaluating Pathway Enumeration Algorithms in Metabolic Engineering Case Studies. PACBB Filipe Liu, Paulo Vilaça, Isabel Rocha, Miguel Rocha
2014	J	`jnl`	Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. Briefings Bioinform. José P. Faria, Ross A. Overbeek, Fangfang Xia, Miguel Rocha, Isabel Rocha, Christopher S. Henry
2014	Misc	`conf`	Metagenomic Analysis of the Saliva Microbiome with Merlin. PACBB Pedro Barbosa, Oscar Dias, Joel P. Arrais, Miguel Rocha
2014	J	`jnl`	Optimization of fed-batch fermentation processes with bio-inspired algorithms. Expert Syst. Appl. Miguel Rocha, Rui Mendes, Orlando Rocha, Isabel Rocha, Eugénio C. Ferreira
2014	—	`conf`	Reg4OptFlux: an OptFlux plug-in that comprises meta-heuristics approaches for Metabolic engineering using integrated models. NaBIC Orlando Rocha, Paulo Vilaça, Miguel Rocha, Rui Mendes
2013	—	`conf`	A Framework for Robust Traffic Engineering Using Evolutionary Computation. AIMS Vitor Pereira, Miguel Rocha, Paulo Cortez, Miguel Rio, Pedro Sousa
2013	—	`conf`	Algorithms to infer metabolic flux ratios from fluxomics data. BIBM Rafael Carreira, Miguel Rocha, Silas Granato Villas-Bôas, Isabel Rocha
2013	B	`conf`	An integrated framework for strain optimization. IEEE Congress on Evolutionary Computation Paulo Maia, Isabel Rocha, Miguel Rocha
2013	J	`jnl`	Email Spam Detection: a Symbiotic Feature Selection Approach Fostered by Evolutionary Computation. Int. J. Inf. Technol. Decis. Mak. Pedro Sousa, Paulo Cortez, Rui Vaz, Miguel Rocha, Miguel Rio
2013	B	`conf`	Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies. IEEE Congress on Evolutionary Computation Pedro Evangelista, Miguel Rocha, Isabel Rocha
2013	—	`conf`	Large Scale Metabolic Characterization Using Flux Balance Analysis and Data Mining. ICANNGA Miguel Rocha
2013	Misc	`conf`	Network Visualization Tools to Enhance Metabolic Engineering Platforms. PACBB Alberto Noronha, Paulo Vilaça, Miguel Rocha
2013	J	`jnl`	Parallel evolutionary computation in bioinformatics applications. Comput. Methods Programs Biomed. Jorge Henrique Martins de Pinho, João Luís Ferreira Sobral, Miguel Rocha
2013	J	`jnl`	Re-annotation of the genome sequence of Helicobacter pylori 26695. J. Integr. Bioinform. Tiago Resende, Daniela M. Correia, Miguel Rocha, Isabel Rocha
2013	Misc	`conf`	Robust Optimization of Intradomain Routing Using Evolutionary Algorithms. DCAI Vitor Pereira, Pedro Sousa, Paulo Cortez, Miguel Rio, Miguel Rocha
2012	—	`conf`	A Machine Learning and Chemometrics Assisted Interpretation of Spectroscopic Data - A NMR-Based Metabolomics Platform for the Assessment of Brazilian Propolis. PRIB Marcelo Maraschin, Amélia Somensi-Zeggio, Simone K. Oliveira, Shirley Kuhnen, Maíra M. Tomazzoli, Ana C. M. Zeri, Rafael Carreira, Miguel Rocha
2012	—	`conf`	An Algorithm to Assemble Gene-Protein-Reaction Associations for Genome-Scale Metabolic Model Reconstruction. PRIB João G. R. Cardoso, Paulo Vilaça, Simão Soares, Miguel Rocha
2012	J	`jnl`	An integrated computational environment for elementary modes analysis of biochemical networks. Int. J. Data Min. Bioinform. Paulo Maia, Paulo Vilaça, Isabel Rocha, Marcellinus Pont, Jean-François Tomb, Miguel Rocha
2012	Misc	`conf`	Computational Tools for Strain Optimization by Adding Reactions. PACBB Sara Correia, Miguel Rocha
2012	Misc	`conf`	Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression. PACBB Emanuel J. V. Gonçalves, Isabel Rocha, Miguel Rocha
2012	—	`conf`	Evolutionary Symbiotic Feature Selection for Email Spam Detection. ICINCO (1) Paulo Cortez, Rui Vaz, Miguel Rocha, Miguel Rio, Pedro Sousa
2012	J	`jnl`	In silico strain optimization by adding reactions to metabolic models. J. Integr. Bioinform. Sara Correia, Miguel Rocha
2012	J	`jnl`	Multi-scale Internet traffic forecasting using neural networks and time series methods. Expert Syst. J. Knowl. Eng. Paulo Cortez, Miguel Rio, Miguel Rocha, Pedro Sousa
2012	J	`jnl`	Optimization Approaches for the J. Comput. Biol. Emanuel J. V. Gonçalves, Rui Pereira, Isabel Rocha, Miguel Rocha
2011	J	`jnl`	A Study of the Short and Long-term Regulation of E. coli Metabolic Pathways. J. Integr. Bioinform. Anália Lourenço, Sónia Carneiro, José P. Pinto, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha
2011	Misc	`conf`	A Study on the Robustness of Strain Optimization Algorithms. PACBB Paulo Vilaça, Paulo Maia, Miguel Rocha
2011	J	`jnl`	A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information. Biosyst. Paulo Vilaça, Isabel Rocha, Miguel Rocha
2011	J	`jnl`	Challenges in integrating Briefings Bioinform. Anália Lourenço, Sónia Carneiro, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha
2011	—	`conf`	Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results. PRIB José Pedro Pinto, Isabel Rocha, Miguel Rocha
2011	Misc	`conf`	Interpreting the Regulatory Interplay in PACBB Anália Lourenço, Sónia Carneiro, José P. Pinto, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha
2011	B	`conf`	Multiobjective Evolutionary Algorithms for intradomain routing optimization. IEEE Congress on Evolutionary Computation Miguel Rocha, Tiago Sá, Pedro Nuno Miranda de Sousa, Paulo Cortez, Miguel Rio
2011	J	`jnl`	Quality of Service constrained routing optimization using Evolutionary Computation. Appl. Soft Comput. Miguel Rocha, Pedro Nuno Miranda de Sousa, Paulo Cortez, Miguel Rio
2011	J	`jnl`	Semantic annotation of biological concepts interplaying microbial cellular responses. BMC Bioinform. Rafael Carreira, Sónia Carneiro, Rui Pereira, Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira, Anália Lourenço
2011	J	`jnl`	Symbiotic filtering for spam email detection. Expert Syst. Appl. Clotilde Lopes, Paulo Cortez, Pedro Nuno Miranda de Sousa, Miguel Rocha, Miguel Rio
2011	—	`conf`	Traffic Engineering Approaches Using Multicriteria Optimization Techniques. WWIC Pedro Nuno Miranda de Sousa, Paulo Cortez, Miguel Rio, Miguel Rocha
2010	—	`conf`	A software tool for network topology analysis under a metabolic engineering perspective. BCB José P. Pinto, Isabel Rocha, Miguel Rocha
2010	J	`jnl`	AIBench: A rapid application development framework for translational research in biomedicine. Comput. Methods Programs Biomed. Daniel Glez-Peña, Miguel Reboiro-Jato, Paulo Maia, Miguel Rocha, Fernando Díaz, Florentino Fdez-Riverola
2010	—	`conf`	Analysis of the Effect of Reversibility Constraints on the Predictions of Genome-Scale Metabolic Models. IWPACBB José P. Faria, Miguel Rocha, Rick L. Stevens, Christopher S. Henry
2010	J	`jnl`	BioDR: Semantic indexing networks for biomedical document retrieval. Expert Syst. Appl. Anália Lourenço, Rafael Carreira, Daniel Glez-Peña, José Ramón Méndez, Sónia Carneiro, Luis Mateus Rocha, Fernando Díaz, Eugénio C. Ferreira, Isabel Rocha, Florentino Fdez-Riverola, Miguel Rocha
2010	—	`conf`	Enhancing Elementary Flux Modes Analysis Using Filtering Techniques in an Integrated Environment. IWPACBB Paulo Maia, Marcellinus Pont, Jean-François Tomb, Isabel Rocha, Miguel Rocha
2010	—	`conf`	Metaheuristics for Strain Optimization Using Transcriptional Information Enriched Metabolic Models. EvoBIO Paulo Vilaça, Paulo Maia, Isabel Rocha, Miguel Rocha
2010	—	`conf`	Model Transformation of Metabolic Networks using a Petri Net Based Framework. ACSD/Petri Nets Workshops Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira
2010	J	`jnl`	OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst. Biol. Isabel Rocha, Paulo Maia, Pedro Evangelista, Paulo Vilaça, Simão Soares, José P. Pinto, Jens Nielsen, Kiran Raosaheb Patil, Eugénio C. Ferreira, Miguel Rocha
2010	A*	`conf`	Spam Email Filtering Using Network-Level Properties. ICDM Paulo Cortez, André Correia, Pedro Nuno Miranda de Sousa, Miguel Rocha, Miguel Rio
2009	—	`ed.`	2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics, IWPACBB 2008, Salamanca, Spain, 22th-24th October 2008 IWPACBB Juan M. Corchado, Juan Francisco de Paz, Miguel Rocha, Florentino Fernández Riverola
2009	J	`jnl`	@Note: A workbench for Biomedical Text Mining. J. Biomed. Informatics Anália Lourenço, Rafael Carreira, Sónia Carneiro, Paulo Maia, Daniel Glez-Peña, Florentino Fdez-Riverola, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha
2009	—	`conf`	A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems. IWANN (2) Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira
2009	—	`conf`	A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models. IWANN (2) Pedro Evangelista, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha
2009	—	`conf`	Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing. IWANN (2) Anália Lourenço, Sónia Carneiro, Eugénio C. Ferreira, Rafael Carreira, Luis M. Rocha, Daniel Glez-Peña, José Ramón Méndez, Florentino Fdez-Riverola, Fernando Díaz, Isabel Rocha, Miguel Rocha
2009	—	`ed.`	Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living, 10th International Work-Conference on Artificial Neural Networks, IWANN 2009 Workshops, Salamanca, Spain, June 10-12, 2009. Proceedings, Part II IWANN (2) Sigeru Omatu, Miguel Rocha, José Bravo, Florentino Fernández Riverola, Emilio Corchado, Andrés Bustillo, Juan M. Corchado
2009	—	`conf`	Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective. EvoBIO Pedro Evangelista, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha
2009	C	`conf`	Implementing Metaheuristic Optimization Algorithms with JECoLi. ISDA Pedro Evangelista, Paulo Maia, Miguel Rocha
2009	—	`conf`	Symbiotic Data Mining for Personalized Spam Filtering. Web Intelligence Paulo Cortez, Clotilde Lopes, Pedro Nuno Miranda de Sousa, Miguel Rocha, Miguel Rio
2008	A*	`conf`	A Comparative Impact Study of Attribute Selection Techniques on Naïve Bayes Spam Filters. ICDM José Ramón Méndez, I. Cid, Daniel Glez-Peña, Miguel Rocha, Florentino Fdez-Riverola
2008	C	`conf`	A framework for the development of Biomedical Text Mining software tools. BIBE Anália Lourenço, Rafael Carreira, Sónia Carneiro, Paulo Maia, Daniel Glez-Peña, Florentino Fdez-Riverola, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha
2008	C	`conf`	A framework for the integrated analysis of metabolic and regulatory networks. BIBE Rui Mendes, Anália Lourenço, Sónia Carneiro, Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira
2008	—	`conf`	An Evolutionary Algorithm for Unicast/ Multicast Traffic Engineering. ICINCO-ICSO Miguel Rocha, Pedro Nuno Miranda de Sousa, Paulo Cortez, Miguel Rio
2008	—	`conf`	Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis. IWPACBB José P. Pinto, Oscar Dias, Anália Lourenço, Sónia Carneiro, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha
2008	C	`conf`	Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains. BIBE Paulo Maia, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha
2008	—	`conf`	Modelling Fed-Batch Fermentation Processes: An Approach Based on Artificial Neural Networks. IWPACBB Eduardo Valente, Isabel Rocha, Miguel Rocha
2008	—	`conf`	Multiconstrained Optimization of Networks with Multicast and Unicast Traffic. MMNS Pedro Nuno Miranda de Sousa, Miguel Rocha, Paulo Cortez, Miguel Rio
2008	J	`jnl`	Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinform. Miguel Rocha, Paulo Maia, Rui Mendes, José P. Pinto, Eugénio C. Ferreira, Jens Nielsen, Kiran Raosaheb Patil, Isabel Rocha
2008	—	`ch.`	getALife - An Artificial Life Environment for the Evaluation of Agent-Based Systems and Evolutionary Algorithms for Reinforcement Learning. New Challenges in Applied Intelligence Technologies Daniel Machado, Miguel Rocha
2007	A	`conf`	A platform for the selection of genes in DNA microarraydata using evolutionary algorithms. GECCO Miguel Rocha, Rui Mendes, Paulo Maia, Daniel Glez-Peña, Florentino Fdez-Riverola
2007	J	`jnl`	Automatic Provisioning of QoS Aware OSPF Configurations. J. Networks Pedro Nuno Miranda de Sousa, Miguel Rocha, Miguel Rio, Paulo Cortez
2007	—	`conf`	Class-Based OSPF Traffic Engineering Inspired on Evolutionary Computation. WWIC Pedro Nuno Miranda de Sousa, Miguel Rocha, Miguel Rio, Paulo Cortez
2007	—	`conf`	Evaluating Evolutionary Algorithms and Differential Evolution for the Online Optimization of Fermentation Processes. EvoBIO Miguel Rocha, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira
2007	—	`conf`	Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains. EPIA Workshops Miguel Rocha, Rui Mendes, Paulo Maia, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira
2007	J	`jnl`	Evolution of neural networks for classification and regression. Neurocomputing Miguel Rocha, Paulo Cortez, José Neves
2007	—	`conf`	Evolutionary Computation for Quality of Service Internet Routing Optimization. EvoWorkshops Miguel Rocha, Pedro Nuno Miranda de Sousa, Paulo Cortez, Miguel Rio
2007	C	`conf`	Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms. CIBCB Miguel Rocha, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira
2007	—	`conf`	Topology Aware Internet Traffic Forecasting Using Neural Networks. ICANN (2) Paulo Cortez, Miguel Rio, Pedro Nuno Miranda de Sousa, Miguel Rocha
2006	B	`conf`	A Comparison of Algorithms for the Optimization of Fermentation Processes. IEEE Congress on Evolutionary Computation Rui Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha
2006	—	`conf`	Efficient OSPF Weight Allocation for Intra-domain QoS Optimization. IPOM Pedro Nuno Miranda de Sousa, Miguel Rocha, Miguel Rio, Paulo Cortez
2006	B	`conf`	Internet Traffic Forecasting using Neural Networks. IJCNN Paulo Cortez, Miguel Rio, Miguel Rocha, Pedro Nuno Miranda de Sousa
2006	B	`conf`	QoS Constrained Internet Routing with Evolutionary Algorithms. IEEE Congress on Evolutionary Computation Miguel Rocha, Pedro Sousa, Miguel Rio, Paulo Cortez
2005	B	`conf`	A new representation in evolutionary algorithms for the optimization of bioprocesses. Congress on Evolutionary Computation Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira
2005	Misc	`conf`	Simultaneous Evolution of Neural Network Topologies and Weights for Classification and Regression. IWANN Miguel Rocha, Paulo Cortez, José Neves
2004	—	`conf`	Evolutionary Algorithms for Optimal Control in Fed-Batch Fermentation Processes. EvoWorkshops Miguel Rocha, José Neves, Isabel Rocha, Eugénio C. Ferreira
2004	J	`jnl`	Evolving Time Series Forecasting ARMA Models. J. Heuristics Paulo Cortez, Miguel Rocha, José Neves
2003	B	`conf`	Adaptive Learning in Changing Environments. ESANN Miguel Rocha, Paulo Cortez, José Neves
2003	Misc	`conf`	Evolutionary Neural Network Learning. EPIA Miguel Rocha, Paulo Cortez, José Neves
2002	J	`jnl`	A Lamarckian Approach for Neural Network Training. Neural Process. Lett. Paulo Cortez, Miguel Rocha, José Neves
2001	C	`conf`	A Genetic and Evolutionary Programming Environment with Spatially Structured Populations and Built-In Parallelism. IEA/AIE Miguel Rocha, Filipe Pereira, Sónia Afonso, José Neves
2001	C	`conf`	Genetic and Evolutionary Algorithms for Time Series Forecasting. IEA/AIE Paulo Cortez, Miguel Rocha, José Neves
2001	B	`conf`	Lamarckian training of feedforward neural networks. ESANN Paulo Cortez, Miguel Rocha, José Neves
2001	B	`conf`	Sitting guests at a wedding party: experiments on genetic and evolutionary constrained optimization. CEC Miguel Rocha, Rui Mendes, Paulo Cortez, José Neves
2000	C	`conf`	A Study of Order Based Genetic and Evolutionary Algorithms in Combinatorial Optimization Problems. IEA/AIE Miguel Rocha, Carla Vilela, José Neves
2000	—	`conf`	Viewing Scheduling Problems through Genetic and Evolutionary Algorithms. IPDPS Workshops Miguel Rocha, Carla Vilela, Paulo Cortez, José Neves
1999	—	`conf`	A Unified Framework for Data Modeling on Medical Information Systems. MIE José Neves, Paulo Cortez, Miguel Rocha, António Abelha, José Machado, Victor Alves, Sousa Basto, Henrique Botelho, João Neves
1999	C	`conf`	Preventing Premature Convergence to Local Optima in Genetic Algorithms via Random Offspring Generation. IEA/AIE Miguel Rocha, José Neves
1995	—	`conf`	A neural network based time series forecasting system. ICNN Paulo Cortez, Miguel Rocha, José Machado, José Neves