Hardware/Software Implementation of FPGA-Targeted Matrix-Oriented SAT Solvers. - Valery Sklyarov; Iouliia Skliarova; Bruno Figueiredo Pimentel; Joel Arrais (FPL, 2004)

A Prospective Study on the Integration of Microarray Data in HIS/EPR. - Daniel Ferreira Polónia; Joel Arrais; José Luís Oliveira (ISBMDA, 2006)

GeneBrowser: an approach for integration and functional classification of genomics data. - Joel Arrais; Bruno Santos; João Fernandes; Laura Carreto; Manuel A. S. Santos; José Luís Oliveira (J. Integr. Bioinform., 2007)

A Microarray Information Database. - Joel Arrais; Laura Carreto; Manuel A. S. Santos; José Luís Oliveira (BIOTECHNO, 2008)

Dynamic service integration using web-based workflows. - Pedro Lopes 002; Joel Arrais; José Luís Oliveira (iiWAS, 2008)

Improving Literature Searches in Gene Expression Studies. - Joel Arrais; João G. L. M. Rodrigues; José Luís Oliveira (IWPACBB, 2008)

Link Integrator - A Link-based Data Integration Architecture. - Pedro Lopes 002; Joel Arrais; José Luís Oliveira (KDIR, 2009)

DynamicFlow: A Client-Side Workflow Management System. - Pedro Lopes 002; Joel Arrais; José Luís Oliveira (IWANN (2), 2009)

Improving Cross Mapping in Biomedical Databases. - Joel Arrais; João E. Pereira; Pedro Lopes 002; Sérgio Matos; José Luís Oliveira (IWPACBB, 2010)

Expanding Gene-Based PubMed Queries. - Sérgio Matos; Joel Arrais; José Luís Oliveira (IWPACBB, 2010)

GeneBrowser 2: an application to explore and identify common biological traits in a set of genes. - Joel Arrais; João Fernandes; João E. Pereira; José Luís Oliveira (BMC Bioinform., 2010)

Concept-based query expansion for retrieving gene related publications from MEDLINE. - Sérgio Matos; Joel Arrais; João Maia-Rodrigues; José Luís Oliveira (BMC Bioinform., 2010)

Challenges Storing and Representing Biomedical Data. - Joel Arrais; Pedro Lopes 002; José Luís Oliveira (USAB, 2011)

Data Integration Solution for Organ-Specific Studies: An Application for Oral Biology. - José Melo; Joel P. Arrais; Edgar D. Coelho; Pedro Lopes 002; Nuno Rosa; Maria José Correia; Marlene Barros; José Luís Oliveira (BIOSTEC (Selected Papers), 2012)

Web Information System for the Study of Oral Health. - José Melo; Joel Arrais; Pedro Lopes 002; Nuno Rosa; Maria José Correia; Marlene Barros; José Luís Oliveira (HEALTHINF, 2012)

Computational Approach to Predict Inter-Species Oral Protein-Protein Interactions. - Edgar D. Coelho; Joel Arrais; Sérgio Matos; Nuno Rosa; Maria José Correia; Marlene Barros; José Luís Oliveira (IWBBIO, 2013)

Representation of Semantic Networks of Biomedical Terms. - Andre Vechina; Joel Arrais; José Luís Oliveira (IWBBIO, 2013)

Quantitative Characterization of Protein Networks of the Oral Cavity. - Fernanda Correia Barbosa; Joel P. Arrais; José Luís Oliveira (PACBB, 2013)

Metagenomic Analysis of the Saliva Microbiome with Merlin. - Pedro Barbosa; Oscar Dias; Joel P. Arrais; Miguel Rocha 001 (PACBB, 2014)

geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. - Miguel Reboiro-Jato; Joel Arrais; José Luís Oliveira; Florentino Fdez-Riverola (BMC Bioinform., 2014)

Computational prediction of the human-microbial oral interactome. - Edgar D. Coelho; Joel Arrais; Sérgio Matos; Carlos Pereira; Nuno Rosa; Maria José Correia; Marlene Barros; José Luís Oliveira (BMC Syst. Biol., 2014)

Uncovering microbial duality within human microbiomes: A novel algorithm for the analysis of host-pathogen interactions. - Edgar D. Coelho; Joel P. Arrais; José Luís Oliveira (EMBC, 2015)

Computational methodology for predicting the landscape of the human-microbial interactome region level influence. - Edgar D. Coelho; André M. Santiago; Joel P. Arrais; José Luís Oliveira (J. Bioinform. Comput. Biol., 2015)

Prediction of Cancer using Network Topological Features. - Fernanda Brito Correia; Joel P. Arrais; José Luís Oliveira (BIOINFORMATICS, 2016)

Ensemble-Based Methodology for the Prediction of Drug-Target Interactions. - Edgar D. Coelho; Joel P. Arrais; José Luís Oliveira (CBMS, 2016)

Reconstructing the temporal progression of HIV-1 immune response pathways. - Siddhartha Jain 001; Joel Arrais; Narasimhan J. Venkatachari; Velpandi Ayyavoo; Ziv Bar-Joseph (Bioinform., 2016)

Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction. - Edgar D. Coelho; Joel P. Arrais; José Luís Oliveira (PLoS Comput. Biol., 2016)

On the role of aesthetics in genetic algorithms applied to graph drawing. - Evgheni Polisciuc; António Cruz; Penousal Machado; Joel P. Arrais (GECCO (Companion), 2017)

Mixed-Integer Programming Model for Profiling Disease Biomarkers from Gene Expression Studies. - André M. Santiago; Miguel Rocha 001; António Dourado; Joel P. Arrais (IWBBIO (2), 2017)

Interactive Network Visualization of Gene Expression Time-Series Data. - António Cruz; Joel P. Arrais; Penousal Machado (IV, 2018)

Fighting Fire with Fire: Computational Prediction of Microbial Targets for Bacteriocins. - Edgar D. Coelho; Joel P. Arrais; José Luís Oliveira (IWBBIO (1), 2018)

A Hybrid Application for Real-Time Air Quality Monitoring. - Jorge Sá Silva; Pedro Lucas; Filipe Araújo; Catarina Silva 001; Paulo Gil; Alberto Cardoso; Joel Arrais; Bernardete Ribeiro; Daniel Coutinho; Pedro D. Salgueiro; Luís Miguel Rato; José Saias; et al. (exp.at, 2019)

An Online Platform For Real-Time Air Quality Monitoring. - Jorge Sá Silva; Pedro Lucas; Filipe Araújo; Catarina Silva 001; Paulo Gil; Alberto Cardoso; Joel Arrais; Bernardete Ribeiro; Daniel Coutinho; Pedro D. Salgueiro; Luís Miguel Rato; José Saias; et al. (exp.at, 2019)

Deep Neural Network Architecture for Drug-Target Interaction Prediction. - Nelson R. C. Monteiro; Bernardete Ribeiro; Joel P. Arrais (ICANN (Workshop), 2019)

Interactive and coordinated visualization approaches for biological data analysis. - António Cruz; Joel P. Arrais; Penousal Machado (Briefings Bioinform., 2019)

Exploring a Siamese Neural Network Architecture for One-Shot Drug Discovery. - Luis H. M. Torres; Nelson R. C. Monteiro; José Luís Oliveira; Joel Arrais; Bernardete Ribeiro (BIBE, 2020)

Using a Novel Unbiased Dataset and Deep Learning Architectures to Predict Protein-Protein Interactions. - Luís Silva; Carlos Pereira; Joel P. Arrais (BIBM, 2020)

End-to-end Deep Reinforcement Learning for Targeted Drug Generation. - Tiago Oliveira Pereira 001; Maryam Abbasi; Bernardete Ribeiro; Joel P. Arrais (ICCBB, 2020)

Exploring Time-Series Through Force-Directed Timelines. - António Cruz; Joel P. Arrais; Penousal Machado (IV, 2020)

CroP - Coordinated Panel visualization for biological networks analysis. - António Cruz; Penousal Machado; Joel P. Arrais (Bioinform., 2020)

NanoSen-AQM: From Sensors to Users. - Pedro Lucas; Jorge Sá Silva; Filipe Araújo; Catarina Silva 001; Paulo Gil; Joel P. Arrais; Daniel Coutinho; Pedro D. Salgueiro; Luís Miguel Rato; José Saias; Vítor Nogueira; Alberto Cardoso; et al. (Int. J. Online Biomed. Eng., 2020)

Optimizing Recurrent Neural Network Architectures for De Novo Drug Design. - Beatriz P. Santos; Maryam Abbasi; Tiago Pereira 001; Bernardete Ribeiro; Joel P. Arrais (CBMS, 2021)

Analysing Games for Health through Users' Opinion Mining. - Renato Santos; Joel P. Arrais; Paula Alexandra Silva (CBMS, 2021)

Multiobjective Reinforcement Learning in Optimized Drug Design. - Maryam Abbasi; Tiago Pereira 001; Beatriz P. Santos; Bernardete Ribeiro; Joel Arrais (ESANN, 2021)

Decay Momentum for Improving Federated Learning. - Miguel Fernandes; Catarina Silva 001; Joel Arrais; Alberto Cardoso; Bernardete Ribeiro (ESANN, 2021)

Improvement on Generative Adversarial Network for Targeted Drug Design. - Beatriz P. Santos; Maryam Abbasi; Tiago Pereira 001; Bernardete Ribeiro; Joel Arrais (ESANN, 2021)

Computational Methods for the Identification of Genetic Variants in Complex Diseases. - Débora Antunes; Daniel Martins; Fernanda Correia; Miguel Rocha 001; Joel P. Arrais (PACBB, 2021)

Optimizing blood-brain barrier permeation through deep reinforcement learning for de novo drug design. - Tiago Pereira 001; Maryam Abbasi; José Luís Oliveira; Bernardete Ribeiro; Joel Arrais (Bioinform., 2021)

Diversity oriented Deep Reinforcement Learning for targeted molecule generation. - Tiago Pereira 001; Maryam Abbasi; Bernardete Ribeiro; Joel P. Arrais (J. Cheminformatics, 2021)

Drug-Target Interaction Prediction: End-to-End Deep Learning Approach. - Nelson R. C. Monteiro; Bernardete Ribeiro; Joel P. Arrais (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Deep Model for Anticancer Drug Response through Genomic Profiles and Compound Structures. - Filipa G. Carvalho; Maryam Abbasi; Bernardete Ribeiro; Joel P. Arrais (CBMS, 2022)

Multivariate Data Exploration Through Coordinated Views. - António Cruz; Joel P. Arrais; Penousal Machado (IEEE Access, 2022)

Force-Directed Timelines: Visualizing & Exploring Temporal Patterns. - António Cruz; Joel P. Arrais; Penousal Machado (Big Data Res., 2022)

Deep generative model for therapeutic targets using transcriptomic disease-associated data - USP7 case study. - Tiago Pereira 001; Maryam Abbasi; Rita I. Oliveira; Romina A. Guedes; Jorge A. R. Salvador; Joel P. Arrais (Briefings Bioinform., 2022)

Explainable deep drug-target representations for binding affinity prediction. - Nelson R. C. Monteiro; Carlos J. V. Simões; Henrique V. Ávila; Maryam Abbasi; José Luís Oliveira; Joel P. Arrais (BMC Bioinform., 2022)

DTITR: End-to-end drug-target binding affinity prediction with transformers. - Nelson R. C. Monteiro; José Luís Oliveira; Joel P. Arrais (Comput. Biol. Medicine, 2022)

Machine Learning Solutions Applied to Amyotrophic Lateral Sclerosis Prognosis: A Review. - Fabiano Papaiz; Mario Emílio Teixeira Dourado; Ricardo Alexsandro de Medeiros Valentim; Antonio Higor Freire de Morais; Joel Perdiz Arrais (Frontiers Comput. Sci., 2022)

Designing optimized drug candidates with Generative Adversarial Network. - Maryam Abbasi; Beatriz P. Santos; Tiago C. Pereira; Raul Sofia; Nelson R. C. Monteiro; Carlos J. V. Simões; Rui M. M. Brito; Bernardete Ribeiro; José Luís Oliveira; Joel P. Arrais (J. Cheminformatics, 2022)

Correction to: Designing optimized drug candidates with Generative Adversarial Network. - Maryam Abbasi; Beatriz P. Santos; Tiago C. Pereira; Raul Sofa; Nelson R. C. Monteiro; Carlos J. V. Simões; Rui M. M. Brito; Bernardete Ribeiro; José Luís Oliveira; Joel P. Arrais (J. Cheminformatics, 2022)

Convolutional Transformer via Graph Embeddings for Few-shot Toxicity and Side Effect Prediction. - Luis H. M. Torres; Bernardete Ribeiro; Joel Arrais (ESANN, 2023)

On the Quantization of Recurrent Neural Networks for Smiles Generation. - Adriano Durao; Joel P. Arrais; Bernardete Ribeiro; Gabriel Falcao (ICASSP, 2023)

The Impact of Schizophrenia Misdiagnosis Rates on Machine Learning Models Performance. - Daniel Martins; Conceição Egas; Joel P. Arrais (PACBB, 2023)

Few-shot learning via graph embeddings with convolutional networks for low-data molecular property prediction. - Luis H. M. Torres; Joel P. Arrais; Bernardete Ribeiro (Neural Comput. Appl., 2023)

Enhancing reinforcement learning for de novo molecular design applying self-attention mechanisms. - Tiago O. Pereira 001; Maryam Abbasi; Joel P. Arrais (Briefings Bioinform., 2023)

FSM-DDTR: End-to-end feedback strategy for multi-objective De Novo drug design using transformers. - Nelson R. C. Monteiro; Tiago Pereira 001; Ana Catarina D. Machado; José Luís Oliveira; Maryam Abbasi; Joel P. Arrais (Comput. Biol. Medicine, 2023)

Few-shot learning with transformers via graph embeddings for molecular property prediction. - Luis H. M. Torres; Bernardete Ribeiro; Joel P. Arrais (Expert Syst. Appl., 2023)

Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information. - Tiago O. Pereira 001; Maryam Abbasi; Rita I. Oliveira; Romina A. Guedes; Jorge A. R. Salvador; Joel P. Arrais (J. Comput. Aided Mol. Des., 2023)

Predicting drug activity against cancer through genomic profiles and SMILES. - Maryam Abbasi; Filipa G. Carvalho; Bernardete Ribeiro; Joel P. Arrais (Artif. Intell. Medicine, 2024)

Multi-scale cross-attention transformer via graph embeddings for few-shot molecular property prediction. - Luis H. M. Torres; Bernardete Ribeiro; Joel P. Arrais (Appl. Soft Comput., 2024)

A Hybrid GNN Approach for Improved Molecular Property Prediction. - Pedro Quesado; Luis H. M. Torres; Bernardete Ribeiro; Joel P. Arrais (J. Comput. Biol., 2024)

Detecting outliers in case-control cohorts for improving deep learning networks on Schizophrenia prediction. - Daniel Martins; Maryam Abbasi; Conceição Egas; Joel P. Arrais (J. Integr. Bioinform., 2024)

TAG-DTA: Binding-region-guided strategy to predict drug-target affinity using transformers. - Nelson R. C. Monteiro; José Luís Oliveira; Joel P. Arrais (Expert Syst. Appl., 2024)

Combining graph neural networks and transformers for few-shot nuclear receptor binding activity prediction. - Luis H. M. Torres; Joel P. Arrais; Bernardete Ribeiro (J. Cheminformatics, 2024)

Ensemble-imbalance-based classification for amyotrophic lateral sclerosis prognostic prediction: identifying short-survival patients at diagnosis. - Fabiano Papaiz; Mario Emílio Teixeira Dourado; Ricardo Alexsandro de Medeiros Valentim; Rafael Pinto; Antonio Higor Freire de Morais; Joel Perdiz Arrais (BMC Medical Informatics Decis. Mak., 2024)

A Novel Deep Learning Framework for Predicting Antimicrobial Peptide Activity Using ProtBert and Neural Networks. - Maryam Abbasi; Verónica Vasconcelos; Edgar M. C. O. S. Vicente; Ana L. M. Santos; Joel P. Arrais (IbPRIA (2), 2025)

ABIET: An explainable transformer for identifying functional groups in biological active molecules. - Tiago O. Pereira 001; Maryam Abbasi; Joel P. Arrais (Comput. Biol. Medicine, 2025)

Rethinking transformers with convolution and graph embeddings for few-shot molecular property discovery. - Luis H. M. Torres; Joel P. Arrais; Bernardete Ribeiro (Pattern Recognit., 2025)