| 2026 | ICCSA | Survival Analysis of HIV Seroconversion Using Interval-Censored Data: Nonparametric and Regression Approaches. | Rui Alves, Filipa Pinto, Aurlio Sidumo, Carla Moreira, Lus Meira-Machado, Paula Meireles, Miguel Rocha, Maria Joo Novais |
| 2025 | GECCO | Evolutionary Algorithms for Metabolic Transformation through Multi-gene Knockout Optimization. | Bruno S, Alexandre Oliveira, Miguel Rocha |
| 2025 | IWANN | Leveraging Large Language Models on Assay Descriptions to Improve the Prediction of Inhibitors for Mycobacterium Tuberculosis. | Nuno Alves, Nuno S. Osrio, Vtor Pereira, Miguel Rocha |
| 2023 | CIBCB | Word embeddings for protein sequence analysis. | Ana Marta Sequeira, Ivan Gomes, Miguel Rocha |
| 2023 | GECCO | Combining Evolutionary Algorithms with Reaction Rules Towards Focused Molecular Design. | Joo Correia, Vitor Pereira, Miguel Rocha |
| 2023 | PACBB | A New GIMME-Based Heuristic for Compartmentalised Transcriptomics Data Integration. | Diego Troitio-Jordedo, Lucas Carvalho, David Henriques, Vtor Pereira, Miguel Rocha, Eva Balsa-Canto |
| 2022 | CEC | Variational Autoencoders and Evolutionary Algorithms for Targeted Novel Enzyme Design. | Miguel Martins, Miguel Rocha, Vitor Pereira |
| 2022 | IJCNN | Development of Deep Learning approaches to predict relationships between chemical structures and sweetness. | Joo Capela, Joo Correia, Vitor Pereira, Miguel Rocha |
| 2022 | IJCNN | Predicting the number of biochemical transformations needed to synthesize a compound. | Joo Correia, Rafael Carreira, Vitor Pereira, Miguel Rocha |
| 2021 | IJCNN | R2L: Routing With Reinforcement Learning. | Joo Reis, Truong Khoa Phan, Morteza Kheirkhah, Fan Yang, David Griffin, Miguel Rocha, Miguel Rio |
| 2021 | PACBB | BioTMPy: A Deep Learning-Based Tool to Classify Biomedical Literature. | Nuno Alves, Rben Rodrigues, Miguel Rocha |
| 2021 | PACBB | Computational Methods for the Identification of Genetic Variants in Complex Diseases. | Dbora Antunes, Daniel Martins, Fernanda Correia, Miguel Rocha, Joel P. Arrais |
| 2021 | PACBB | A Comparison of Different Compound Representations for Drug Sensitivity Prediction. | Delora Baptista, Joo Correia, Bruno Pereira, Miguel Rocha |
| 2021 | PACBB | Computational Tools for the Analysis of 2D-Nuclear Magnetic Resonance Data. | Bruno Pereira, Marcelo Maraschin, Miguel Rocha |
| 2021 | PACBB | Combinatorial Optimization of Succinate Production in Escherichia coli. | Vitor Pereira, Miguel Rocha |
| 2021 | PACBB | Recurrent Deep Neural Networks for Enzyme Functional Annotation. | Ana Marta Sequeira, Miguel Rocha |
| 2020 | PACBB | Reconciliation of Regulatory Data: The Regulatory Networks of Escherichia coli and Bacillus subtilis. | Diogo Lima, Fernando Cruz, Miguel Rocha, Oscar Dias |
| 2020 | PACBB | ProPythia: A Python Automated Platform for the Classification of Proteins Using Machine Learning. | Ana Marta Sequeira, Diana Lousa, Miguel Rocha |
| 2019 | IJCNN | Deep Neural Networks for Network Routing. | Joo Reis, Miguel Rocha, Truong Khoa Phan, David Griffin, Franck Le, Miguel Rio |
| 2019 | Networking | Triptych: Multi-objective Optimisation of Service Deployment Costs, Application Delay and Bandwidth Usage. | Miguel Rocha, Truong Khoa Phan, Joo Reis, David Griffin, Miguel Rio |
| 2019 | PACBB | Artificial Intelligence in Biological Activity Prediction. | Joo Correia, Tiago Resende, Delora Baptista, Miguel Rocha |
| 2019 | PACBB | Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression. | Fernando Cruz, Diogo Lima, Jos P. Faria, Miguel Rocha, Oscar Dias |
| 2019 | PACBB | Troppo - A Python Framework for the Reconstruction of Context-Specific Metabolic Models. | Jorge Ferreira, Vtor Vieira, Jorge Gomes, Sara Correia, Miguel Rocha |
| 2019 | PACBB | Predicting Promoters in Phage Genomes Using Machine Learning Models. | Marta Sampaio, Miguel Rocha, Hugo Oliveira, Oscar Dias |
| 2018 | PACBB | In Silico Predictions for Fucoxanthin Production by the Diatom Phaeodactylum Tricornutum. | Cludia M. Bauer, Paulo Vilaa, Fernanda Ramlov, Eva Regina de Oliveira, Dbora Cabral Nazrio, Caroline Schmitz, Rafaela Gordo Corra, Miguel Rocha, Marcelo Maraschin |
| 2018 | PACBB | A Review on Metabolomics Data Analysis for Cancer Applications. | Sara Cardoso, Delora Baptista, Rebeca Santos, Miguel Rocha |
| 2018 | PACBB | 17α-Ethinylestradiol Analysis of Endo- and Exometabolome of Ulva lactuca (Chlorophyta) by 1H-NMR Spectroscopy and Bioinformatics Tools. | Dbora Cabral Nazrio, Sara Cardoso, Silvana Rocco, Maurcio Sfora, Simone Fanan Hengeltraub, Cludia M. Bauer, Miguel Rocha, Marcelo Maraschin |
| 2018 | PACBB | MOSCA: An Automated Pipeline for Integrated Metagenomics and Metatranscriptomics Data Analysis. | Joo Carlos Sequeira, Miguel Rocha, Maria Madalena Alves, Andreia Ferreira Salvador |
| 2018 | PACBB | Metabolite Integration Pipeline for the Improvement of Human Metabolic Models. | Vtor Vieira, Jorge Ferreira, Rben Rodrigues, Miguel Rocha |
| 2017 | FNC | Optimizing Segment Routing using Evolutionary Computation. | Vitor Pereira, Miguel Rocha, Pedro Sousa |
| 2017 | GECCO | Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction. | Paulo Maia, Isabel Rocha, Miguel Rocha |
| 2017 | GECCO | Evolutionary computation at work for the optimization of link state routing protocols. | Vitor Pereira, Pedro Sousa, Miguel Rocha |
| 2017 | PACBB | Development of Text Mining Tools for Information Retrieval from Patents. | Tiago Alves, Rben Rodrigues, Hugo Costa, Miguel Rocha |
| 2017 | PACBB | Characterization of the Chemical Composition of Banana Peels from Southern Brazil Across the Seasons Using Nuclear Magnetic Resonance and Chemometrics. | Sara Cardoso, Marcelo Maraschin, Luiz Augusto Martins Peruch, Miguel Rocha, Aline Pereira |
| 2017 | PACBB | 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. | Susane Lopes, Rodolfo Moresco, Luiz Augusto Martins Peruch, Miguel Rocha, Marcelo Maraschin |
| 2017 | PACBB | Classification Tools for Carotenoid Content Estimation in Manihot esculenta via Metabolomics and Machine Learning. | Rodolfo Moresco, Telma Afonso, Virglio G. Uarrota, Bruno Bachiega Navarro, Eduardo da C. Nunes, Miguel Rocha, Marcelo Maraschin |
| 2017 | PACBB | Influence of Solar Radiation on the Production of Secondary Metabolites in Three Rice (Oryza sativa) Cultivars. | Eva Regina Oliveira, Ester Wickert, Fernanda Ramlov, Rodolfo Moresco, Larissa Simo, Bruno Bachiega Navarro, Cludia M. Bauer, Dbora Cabral Nazrio, Miguel Rocha, Marcelo Maraschin |
| 2017 | PACBB | A Critical Evaluation of Automatic Atom Mapping Algorithms and Tools. | Nuno Osrio, Paulo Vilaa, Miguel Rocha |
| 2016 | PACBB | Reconstruction of Metabolic Models for Liver Cancer Cells. | Jorge Ferreira, Sara Correia, Miguel Rocha |
| 2016 | PACBB | Development of a Machine Learning Framework for Biomedical Text Mining. | Rben Rodrigues, Hugo Costa, Miguel Rocha |
| 2016 | PACBB | Development of an Integrated Framework for Minimal Cut Set Enumeration in Constraint-Based Models. | Vtor Vieira, Paulo Maia, Isabel Rocha, Miguel Rocha |
| 2015 | EMO | Comparison of Single and Multi-objective Evolutionary Algorithms for Robust Link-State Routing. | Vitor Pereira, Pedro Sousa, Paulo Cortez, Miguel Rio, Miguel Rocha |
| 2015 | EPIA | A Critical Evaluation of Methods for the Reconstruction of Tissue-Specific Models. | Sara Correia, Miguel Rocha |
| 2015 | IDC | Automated Network Resilience Optimization Using Computational Intelligence Methods. | Vitor Pereira, Miguel Rocha, Pedro Sousa |
| 2015 | PACBB | An Integrated Computational Platform for Metabolomics Data Analysis. | Christopher Costa, Marcelo Maraschin, Miguel Rocha |
| 2015 | PACBB | A Text Mining Approach for the Extraction of Kinetic Information from Literature. | Ana Alo Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha |
| 2015 | PACBB | Carotenoid Analysis of Cassava Genotypes Roots (Manihot Esculenta Crantz) Cultivated in Southern Brazil Using Chemometric Tools. | Rodolfo Moresco, Virglio G. Uarrota, Aline Pereira, Mara M. Tomazzoli, Eduardo da C. Nunes, Luiz Augusto Martins Peruch, Christopher Costa, Miguel Rocha, Marcelo Maraschin |
| 2015 | PACBB | UV-Visible Spectrophotometry-Based Metabolomic Analysis of Cedrela Fissilis Velozzo (Meliaceae) Calluses - A Screening Tool for Culture Medium Composition and Cell Metabolic Profiles. | Fernanda Kokowicz Pilatti, Christopher Costa, Miguel Rocha, Marcelo Maraschin, Ana Maria Viana |
| 2015 | PACBB | UV-Visible Scanning Spectrophotometry and Chemometric Analysis as Tools to Build Descriptive and Classification Models for Propolis from Southern Brazil. | Mara M. Tomazzoli, Remi Dal Pai Neto, Rodolfo Moresco, Larissa Westphal, Amlia Regina Somensi-Zeggio, Leandro Specht, Christopher Costa, Miguel Rocha, Marcelo Maraschin |
| 2015 | PACBB | Microarray Gene Expression Data Integration: An Application to Brain Tumor Grade Determination. | Eduardo Valente, Miguel Rocha |
| 2015 | SAC | Transcript-based reannotation for microarray probesets. | Eduardo Valente, Miguel Rocha |
| 2014 | PACBB | Metagenomic Analysis of the Saliva Microbiome with Merlin. | Pedro Barbosa, Oscar Dias, Joel P. Arrais, Miguel Rocha |
| 2014 | PACBB | Evaluating Pathway Enumeration Algorithms in Metabolic Engineering Case Studies. | Filipe Liu, Paulo Vilaa, Isabel Rocha, Miguel Rocha |
| 2013 | CEC | Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies. | Pedro Evangelista, Miguel Rocha, Isabel Rocha |
| 2013 | CEC | An integrated framework for strain optimization. | Paulo Maia, Isabel Rocha, Miguel Rocha |
| 2013 | DCAI | Robust Optimization of Intradomain Routing Using Evolutionary Algorithms. | Vitor Pereira, Pedro Sousa, Paulo Cortez, Miguel Rio, Miguel Rocha |
| 2013 | PACBB | Network Visualization Tools to Enhance Metabolic Engineering Platforms. | Alberto Noronha, Paulo Vilaa, Miguel Rocha |
| 2012 | ICINCO | Evolutionary Symbiotic Feature Selection for Email Spam Detection. | Paulo Cortez, Rui Vaz, Miguel Rocha, Miguel Rio, Pedro Sousa |
| 2012 | PACBB | Computational Tools for Strain Optimization by Adding Reactions. | Sara Correia, Miguel Rocha |
| 2012 | PACBB | Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression. | Emanuel J. V. Gonalves, Isabel Rocha, Miguel Rocha |
| 2011 | CEC | Multiobjective Evolutionary Algorithms for intradomain routing optimization. | Miguel Rocha, Tiago S, Pedro Nuno Miranda de Sousa, Paulo Cortez, Miguel Rio |
| 2011 | PACBB | Interpreting the Regulatory Interplay in | Anlia Loureno, Snia Carneiro, Jos P. Pinto, Miguel Rocha, Eugnio C. Ferreira, Isabel Rocha |
| 2011 | PACBB | A Study on the Robustness of Strain Optimization Algorithms. | Paulo Vilaa, Paulo Maia, Miguel Rocha |
| 2009 | ISDA | Implementing Metaheuristic Optimization Algorithms with JECoLi. | Pedro Evangelista, Paulo Maia, Miguel Rocha |
| 2009 | IWANN | A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models. | Pedro Evangelista, Isabel Rocha, Eugnio C. Ferreira, Miguel Rocha |
| 2009 | IWANN | Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing. | Anlia Loureno, Snia Carneiro, Eugnio C. Ferreira, Rafael Carreira, Luis M. Rocha, Daniel Glez-Pea, Jos Ramn Mndez, Florentino Fdez-Riverola, Fernando Daz, Isabel Rocha, Miguel Rocha |
| 2009 | IWANN | A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems. | Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugnio C. Ferreira |
| 2008 | BIBE | A framework for the development of Biomedical Text Mining software tools. | Anlia Loureno, Rafael Carreira, Snia Carneiro, Paulo Maia, Daniel Glez-Pea, Florentino Fdez-Riverola, Eugnio C. Ferreira, Isabel Rocha, Miguel Rocha |
| 2008 | BIBE | Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains. | Paulo Maia, Isabel Rocha, Eugnio C. Ferreira, Miguel Rocha |
| 2008 | BIBE | A framework for the integrated analysis of metabolic and regulatory networks. | Rui Mendes, Anlia Loureno, Snia Carneiro, Miguel Rocha, Isabel Rocha, Eugnio C. Ferreira |
| 2008 | ICINCO | An Evolutionary Algorithm for Unicast/ Multicast Traffic Engineering. | Miguel Rocha, Pedro Nuno Miranda de Sousa, Paulo Cortez, Miguel Rio |
| 2007 | CIBCB | Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms. | Miguel Rocha, Jos P. Pinto, Isabel Rocha, Eugnio C. Ferreira |
| 2007 | EPIA | Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains. | Miguel Rocha, Rui Mendes, Paulo Maia, Jos P. Pinto, Isabel Rocha, Eugnio C. Ferreira |
| 2007 | GECCO | A platform for the selection of genes in DNA microarraydata using evolutionary algorithms. | Miguel Rocha, Rui Mendes, Paulo Maia, Daniel Glez-Pea, Florentino Fdez-Riverola |
| 2007 | ICANN | Topology Aware Internet Traffic Forecasting Using Neural Networks. | Paulo Cortez, Miguel Rio, Pedro Nuno Miranda de Sousa, Miguel Rocha |
| 2006 | CEC | A Comparison of Algorithms for the Optimization of Fermentation Processes. | Rui Mendes, Isabel Rocha, Eugnio C. Ferreira, Miguel Rocha |
| 2006 | CEC | QoS Constrained Internet Routing with Evolutionary Algorithms. | Miguel Rocha, Pedro Sousa, Miguel Rio, Paulo Cortez |
| 2006 | IJCNN | Internet Traffic Forecasting using Neural Networks. | Paulo Cortez, Miguel Rio, Miguel Rocha, Pedro Nuno Miranda de Sousa |
| 2005 | CEC | A new representation in evolutionary algorithms for the optimization of bioprocesses. | Miguel Rocha, Isabel Rocha, Eugnio C. Ferreira |
| 2005 | IWANN | Simultaneous Evolution of Neural Network Topologies and Weights for Classification and Regression. | Miguel Rocha, Paulo Cortez, Jos Neves |
| 2003 | EPIA | Evolutionary Neural Network Learning. | Miguel Rocha, Paulo Cortez, Jos Neves |
| 2003 | ESANN | Adaptive Learning in Changing Environments. | Miguel Rocha, Paulo Cortez, Jos Neves |
| 2001 | CEC | Sitting guests at a wedding party: experiments on genetic and evolutionary constrained optimization. | Miguel Rocha, Rui Mendes, Paulo Cortez, Jos Neves |
| 2001 | ESANN | Lamarckian training of feedforward neural networks. | Paulo Cortez, Miguel Rocha, Jos Neves |