| 2025 | GECCO | A Dijkstra Seeded Evolutionary Multiobjective Optimization System for a Sustainable User Multimodal Transport Routing. | Guilherme Barbosa, Pedro Pereira, Vasco Abelha, Rui Mendes, Paulo Cortez |
| 2022 | EPIA | Cherry-Picking Meta-heuristic Algorithms and Parameters for Real Optimization Problems. | Kvin Martins, Rui Mendes |
| 2021 | IDEAL | Neural Complexity Assessment: A Deep Learning Approach to Readability Classification for European Portuguese Corpora. | Joo Correia, Rui Mendes |
| 2020 | GECCO | A realistic scooter rebalancing system via metaheuristics. | Guilherme Fernandes, Nuno Oliveira, Paulo Cortez, Rui Mendes |
| 2020 | INLG | Amplifying the Range of News Stories with Creativity: Methods and their Evaluation, in Portuguese. | Rui Mendes, Hugo Gonalo Oliveira |
| 2019 | EPIA | Using Neuroevolution for Predicting Mobile Marketing Conversion. | Pedro Jos Pereira, Pedro Pinto, Rui Mendes, Paulo Cortez, Antoine Moreau |
| 2019 | IJCNN | Using Deep Learning for Mobile Marketing User Conversion Prediction. | Lus Miguel Matos, Paulo Cortez, Rui Mendes, Antoine Moreau |
| 2017 | EPIA | Multi-objective Learning of Neural Network Time Series Prediction Intervals. | Pedro Jos Pereira, Paulo Cortez, Rui Mendes |
| 2013 | DCAI | Current Trends in Bio-Ontologies and Data Integration. | Rafael T. Pereira, Rui Mendes |
| 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 |
| 2007 | EPIA | Stochastic Barycenters and Beta Distribution for Gaussian Particle Swarms. | Rui Mendes, James Kennedy |
| 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 |
| 2006 | CEC | A Comparison of Algorithms for the Optimization of Fermentation Processes. | Rui Mendes, Isabel Rocha, Eugnio C. Ferreira, Miguel Rocha |
| 2005 | CEC | DynDE: a differential evolution for dynamic optimization problems. | Rui Mendes, Arvind S. Mohais |
| 2002 | CEC | Population structure and particle swarm performance. | James Kennedy, Rui Mendes |
| 2001 | CEC | Sitting guests at a wedding party: experiments on genetic and evolutionary constrained optimization. | Miguel Rocha, Rui Mendes, Paulo Cortez, Jos Neves |