A Modular Workflow Management Framework. - João Rafael Almeida; Ricardo F. Ribeiro; José Luís Oliveira (HEALTHINF, 2018)

Simplifying the Digitization of Clinical Protocols for Diabetes Management. - João Rafael Almeida; Joana Guimaraes; José Luís Oliveira (CBMS, 2018)

Services Orchestration and Workflow Management in Distributed Medical Imaging Environments. - João Rafael Almeida; Tiago Marques Godinho; Luís A. Bastião Silva; Carlos Costa 001; José Luís Oliveira (CBMS, 2018)

Strategies to Access Patient Clinical Data from Distributed Databases. - João Rafael Almeida; Olga Fajarda; Arnaldo Pereira; José Luís Oliveira (HEALTHINF, 2019)

GenericCDSS - A Generic Clinical Decision Support System. - João Rafael Duarte de Almeida; José Luís Oliveira (CBMS, 2019)

A Weighted Rule-Based Model for File Forgery Detection: UA.PT Bioinformatics at ImageCLEF 2019. - João Rafael Almeida; Pedro Freire; Olga Fajarda; José Luís Oliveira (CLEF (Working Notes), 2019)

ETL Framework for Real-Time Business Intelligence over Medical Imaging Repositories. - Tiago Marques Godinho; Rui Lebre; João Rafael Almeida; Carlos Costa 001 (J. Digit. Imaging, 2019)

TASKA: A modular task management system to support health research studies. - João Rafael Almeida; Rosa Gini; Giuseppe Roberto; Peter R. Rijnbeek; José Luís Oliveira (BMC Medical Informatics Decis. Mak., 2019)

A Computational Platform for Heart Failure Cases Research. - João Rafael Almeida; Pedro Freire; Olga Fajarda; José Luís Oliveira (HEALTHINF, 2020)

Enhancing Decision-making Systems with Relevant Patient Information by Leveraging Clinical Notes. - João Rafael Almeida; João Figueira Silva; Alejandro Pazos Sierra; Sérgio Matos; José Luís Oliveira (HEALTHINF, 2020)

Leveraging Clinical Notes for Enhancing Decision-Making Systems with Relevant Patient Information. - João Rafael Almeida; João Figueira Silva; Alejandro Pazos Sierra; Sérgio Matos; José Luís Oliveira (BIOSTEC (Selected Papers), 2020)

A Recommender System to Help Discovering Cohorts in Rare Diseases. - João Rafael Almeida; Eriksson J. Melicio Monteiro; Luís A. Bastião Silva; Alejandro Pazos Sierra; José Luís Oliveira (CBMS, 2020)

Multi-language Concept Normalisation of Clinical Cohorts. - João Rafael Almeida; José Luís Oliveira (CBMS, 2020)

File Forgery Detection Using a Weighted Rule-Based System. - João Rafael Almeida; Olga Fajarda; José Luís Oliveira (CLEF, 2020)

A Recommender System Based on Cohorts' Similarity. - João Rafael Almeida; Eriksson J. Melicio Monteiro; Luís A. Bastião Silva; Alejandro Pazos; José Luís Oliveira (MIE, 2020)

Clinical Concept Normalization on Medical Records Using Word Embeddings and Heuristics. - João Figueira Silva; Rui Antunes 002; João Rafael Almeida; Sérgio Matos (MIE, 2020)

Rule-based extraction of family history information from clinical notes. - João Rafael Almeida; Sérgio Matos (SAC, 2020)

GTO: A toolkit to unify pipelines in genomic and proteomic research. - João Rafael Almeida; Armando J. Pinho; José Luís Oliveira; Olga Fajarda; Diogo Pratas (SoftwareX, 2020)

An Architecture to Define Cohorts over Medical Imaging Datasets. - João Rafael Almeida; Eriksson J. Melicio Monteiro; José Luís Oliveira (CBMS, 2021)

A Comparative Analysis of Data Platforms for Rare Diseases. - Mariana Sequeira; João Rafael Almeida; José Luís Oliveira (CBMS, 2021)

A Recommender System to Help Refining Clinical Research Studies. - João Rafael Almeida; João Figueira Silva; Sérgio Matos; Alejandro Pazos; José Luís Oliveira (MIE, 2021)

A semi-automatic methodology for analysing distributed and private biobanks. - João Rafael Almeida; Diogo Pratas; José Luís Oliveira (Comput. Biol. Medicine, 2021)

A two-stage workflow to extract and harmonize drug mentions from clinical notes into observational databases. - João Rafael Almeida; João Figueira Silva; Sérgio Matos; José Luís Oliveira (J. Biomed. Informatics, 2021)

BIcenter: A collaborative Web ETL solution based on a reflective software approach. - João Rafael Almeida; Leonardo Coelho; José Luís Oliveira (SoftwareX, 2021)

A secure architecture for exploring patient-level databases from distributed institutions. - João Rafael Almeida; João Paulo Barraca; José Luís Oliveira (CBMS, 2022)

Combining heterogeneous patient-level data into tranSMART to support multicentre studies. - João Rafael Almeida; Luís Bastião Silva; Alejandro Pazos; José Luís Oliveira (CBMS, 2022)

Visualising Time-evolving Semantic Biomedical Data. - Arnaldo Pereira; João Rafael Almeida; Rui Pedro Lopes; José Luís Oliveira (CBMS, 2022)

The value of compression for taxonomic identification. - Jorge Miguel Silva; João Rafael Almeida (CBMS, 2022)

Classifying and discovering genomic sequences in metagenomic repositories. - Jorge Miguel Silva; João Rafael Almeida; José Luís Oliveira (CENTERIS/ProjMAN/HCist, 2022)

Preserving Privacy when Querying OMOP CDM Databases. - João Rafael Almeida; João Paulo Barraca; José Luís Oliveira (EFMI-STC, 2022)

Characterizing Genomics Repositories Using Feature-Based Classification. - Jorge Miguel Silva; João Rafael Almeida (EFMI-STC, 2022)

Discovery of Biomedical Databases Through Semantic Questioning. - Arnaldo Pereira; João Rafael Almeida; Rui Pedro Lopes; Alejandro Pazos; José Luís Oliveira (MIE, 2022)

Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics. - Tiago Melo Almeida; Rui Antunes 002; João Figueira Silva; João Rafael Almeida; Sérgio Matos (Database J. Biol. Databases Curation, 2022)

A FAIR Approach to Real-World Health Data Management and Analysis. - João Rafael Almeida; Jorge Miguel Silva; José Luís Oliveira (CBMS, 2023)

Upscaling Operators of Essential Services Incident Response Teams. - João Paulo Barraca; Cristina Cerqueira; José Filipe Alves; Sara Andrade; António Meireles; João Rafael Almeida (CBMS, 2023)

SecureFASTA: Ensuring privacy and trust when sharing genomic data. - Diniz Cruz; João Rafael Almeida; Jorge Miguel Silva; José Luís Oliveira (CBMS, 2023)

Clinical Data Integration Strategies for Multicenter Studies. - João Rafael Almeida; Alejandro Pazos; José Luís Oliveira (DoCEIS, 2023)

A 20-Year Journey of Tracing the Development of Web Catalogues for Rare Diseases. - João Rafael Almeida; José Luís Oliveira (IWBBIO (2), 2023)

A Reliable and Secure Method for Sharing Genomic Data. - Dinis Barroqueiro Cruz; João Rafael Almeida; Jorge M. Silva; José Luís Oliveira (MIE, 2023)

Open Source Solutions for Vulnerability Assessment: A Comparative Analysis. - Dinis Barroqueiro Cruz; João Rafael Almeida; José Luís Oliveira (IEEE Access, 2023)

Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII. - Robert Leaman; Rezarta Islamaj; Virginia Adams; Mohammed Alliheedi; João Rafael Almeida; Rui Antunes 002; Robert Bevan; Yung-Chun Chang; Arslan Erdengasileng; Matthew Hodgskiss; Ryuki Ida; Hyunjae Kim; et al. (Database J. Biol. Databases Curation, 2023)

Enriching information extraction pipelines in clinical decision support systems. - João Rafael Almeida (2023)

Querying semantic catalogues of biomedical databases. - Arnaldo Pereira; João Rafael Almeida; Rui Pedro Lopes; José Luís Oliveira (J. Biomed. Informatics, 2023)

Methodology to identify a gene expression signature by merging microarray datasets. - Olga Fajarda; João Rafael Almeida; Sara Duarte-Pereira; Raquel M. Silva; José Luís Oliveira (Comput. Biol. Medicine, 2023)

Assessing the feasibility of observational data sources for multicenter clinical studies. - João Rafael Almeida; Peter R. Rijnbeek; Maxim Moinat; José Luís Oliveira (CBMS, 2024)

HealthDBFinder: a question-answering task for health database discovery. - João Rafael Almeida; Jorge Miguel Silva; Luís Carlos Afonso; Tiago Melo Almeida; Rui Antunes 002; Richard A. A. Jonker; João António Reis; Dimitri Alexandre da Silva; Sérgio Matos; José Luís Oliveira (CBMS, 2024)

Challenges and Solutions for Eduroam Network Security. - Luís Miguel Batista; Hélder Gomes; João Rafael Almeida (CENTERIS/ProjMAN/HCist, 2024)

A comprehensive study of databases to assess the reliability of metagenomic tools. - Inês Branco Martins; Jorge Miguel Silva; João Rafael Almeida (CIBCB, 2024)

BIT.UA at BioASQ 12: From Retrieval to Answer Generation. - Tiago Melo Almeida; Richard A. A. Jonker; João António Reis; João Rafael Almeida; Sérgio Matos (CLEF (Working Notes), 2024)

A Study of Security Issues of Eduroam Networks in Portugal. - Luís Miguel Batista; Hélder Gomes; João Rafael Almeida (SLATE, 2024)

Infrastructural Challenges and Good Practices in a Security Operation Center. - Dimitri Alexandre da Silva; José Luís Costa; João Rafael Almeida (SLATE, 2024)

Enhancing metagenomic classification with compression-based features. - Jorge Miguel Silva; João Rafael Almeida (Artif. Intell. Medicine, 2024)

Towards discovery: an end-to-end system for uncovering novel biomedical relations. - Tiago Melo Almeida; Richard Adolph Aires Jonker; Rui Antunes 002; João Rafael Almeida; Sérgio Matos (Database J. Biol. Databases Curation, 2024)

Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes. - Richard A. A. Jonker; Tiago Melo Almeida; Rui Antunes 002; João Rafael Almeida; Sérgio Matos (Database J. Biol. Databases Curation, 2024)

NullJack: An Open Approach for Undetectable Ethernet Port Scanning. - António Deus; Luís Miguel Batista; Dimitri Silva; João Rafael Almeida (ARES (EU Projects Symposium Workshops 1), 2025)

A Comparative Analysis of Ai-Based Solutions for Clinical Documentation. - Luís Carlos Afonso; João Rafael Almeida; José Luís Oliveira (CBMS, 2025)

An Embedding-Based Machine Learning Solution for Medical Concept Mapping. - Vicente Barros; Raquel Paradinha; João Rafael Almeida; José Luís Oliveira (CBMS, 2025)