João Rafael Almeida

69 papers B 20C 4Misc 1Journal 16Unranked 27
YearRankTypeTitle / Venue / Authors
2026 J jnl
A systematic review and benchmarking of modern metagenomic tools for taxonomic classification.
Comput. Biol. Medicine
Inês Branco Martins, Jorge Miguel Silva, João Rafael Almeida
2026 J jnl
APScavenge: Centralized WPA-Enterprise network security assessment tool.
SoftwareX
Luís Miguel Batista, Hélder Gomes, João Rafael Almeida
2026 — conf
Green by Design: Embedding Sustainability into Cybersecurity Architectures.
ICISSP (1)
Ângelo Borges, João Rafael Almeida
2026 C conf
Optimizing Job Rotation in Assembly Lines by Balancing Productivity and Worker Well-Being.
ICORES
Joana Rafaela Almeida, João Rafael Almeida, José Luís Oliveira
2026 — conf
Reflections of Social Engineering Awareness Negligence in Facilitating Cyber-Physical Attacks.
ICISSP (1)
Luís Filipe Gomes, Luís Miguel Batista, João Rafael Almeida
2025 B conf
A Comparative Analysis of Ai-Based Solutions for Clinical Documentation.
CBMS
Luís Carlos Afonso, João Rafael Almeida, José Luís Oliveira
2025 — conf
A Hybrid Metagenomic Pipeline for Taxonomic Classification.
IWBBIO (1)
Inês Branco Martins, Jorge Miguel Silva, João Rafael Almeida
2025 B conf
An Embedding-Based Machine Learning Solution for Medical Concept Mapping.
CBMS
Vicente Barros, Raquel Paradinha, João Rafael Almeida, José Luís Oliveira
2025 — conf
BIT.UA at BioASQ 13B: Revisiting Evaluation, DPRF-Enhanced Retrieval and Fine-Tuned LLMs.
CLEF (Working Notes)
Richard A. A. Jonker, Tiago Melo Almeida, João Rafael Almeida, Sérgio Matos
2025 C conf
Graph-based Optimization for Assembly Line Balancing Incorporating Metabolic Restrictions.
CoDIT
Joana Rafaela Almeida, Ana Moura, João Rafael Almeida, José Luís Oliveira
2025 — conf
NullJack: An Open Approach for Undetectable Ethernet Port Scanning.
ARES (EU Projects Symposium Workshops 1)
António Deus, Luís Miguel Batista, Dimitri Silva, João Rafael Almeida
2025 C conf
Securing DevOps by Identifying the Most Common Vulnerabilities in CI/CD Pipelines.
ISCC
Luís Miguel Batista, Dinis Barroqueiro Cruz, Dimitri Silva, João Rafael Almeida, José Luís Oliveira
2024 — conf
A Chatbot-Like Platform to Enhance the Discovery of OMOP CDM Databases.
MIE
João A. Reis, João Rafael Almeida, Tiago Melo Almeida, José Luís Oliveira
2024 — conf
A Study of Security Issues of Eduroam Networks in Portugal.
SLATE
Luís Miguel Batista, Hélder Gomes, João Rafael Almeida
2024 C conf
A comprehensive study of databases to assess the reliability of metagenomic tools.
CIBCB
Inês Branco Martins, Jorge Miguel Silva, João Rafael Almeida
2024 B conf
Assessing the feasibility of observational data sources for multicenter clinical studies.
CBMS
João Rafael Almeida, Peter R. Rijnbeek, Maxim Moinat, José Luís Oliveira
2024 — conf
BIT.UA at BioASQ 12: From Retrieval to Answer Generation.
CLEF (Working Notes)
Tiago Melo Almeida, Richard A. A. Jonker, João António Reis, João Rafael Almeida, Sérgio Matos
2024 — conf
Challenges and Solutions for Eduroam Network Security.
CENTERIS/ProjMAN/HCist
Luís Miguel Batista, Hélder Gomes, João Rafael Almeida
2024 J jnl
Enhancing metagenomic classification with compression-based features.
Artif. Intell. Medicine
Jorge Miguel Silva, João Rafael Almeida
2024 B conf
HealthDBFinder: a question-answering task for health database discovery.
CBMS
João Rafael Almeida, Jorge Miguel Silva, Luís Carlos Afonso, Tiago Melo Almeida, Rui Antunes, Richard A. A. Jonker, João António Reis, Dimitri Alexandre da Silva, Sérgio Matos, José Luís Oliveira
2024 — conf
Infrastructural Challenges and Good Practices in a Security Operation Center.
SLATE
Dimitri Alexandre da Silva, José Luís Costa, João Rafael Almeida
2024 J jnl
Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes.
Database J. Biol. Databases Curation
Richard A. A. Jonker, Tiago Melo Almeida, Rui Antunes, João Rafael Almeida, Sérgio Matos
2024 J jnl
Towards discovery: an end-to-end system for uncovering novel biomedical relations.
Database J. Biol. Databases Curation
Tiago Melo Almeida, Richard Adolph Aires Jonker, Rui Antunes, João Rafael Almeida, Sérgio Matos
2023 B ed.
36th IEEE International Symposium on Computer-Based Medical Systems, CBMS 2023, L'Aquila, Italy, June 22-24, 2023
CBMS
João Rafael Almeida, Myra Spiliopoulou, José Alberto Benítez-Andrades, Giuseppe Placidi, Alejandro Rodríguez González, Rosa Sicilia, Bridget Kane
2023 — conf
A 20-Year Journey of Tracing the Development of Web Catalogues for Rare Diseases.
IWBBIO (2)
João Rafael Almeida, José Luís Oliveira
2023 B conf
A FAIR Approach to Real-World Health Data Management and Analysis.
CBMS
João Rafael Almeida, Jorge Miguel Silva, José Luís Oliveira
2023 — conf
A Reliable and Secure Method for Sharing Genomic Data.
MIE
Dinis Barroqueiro Cruz, João Rafael Almeida, Jorge M. Silva, José Luís Oliveira
2023 J jnl
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII.
Database J. Biol. Databases Curation
Robert Leaman, Rezarta Islamaj, Virginia Adams, Mohammed Alliheedi, João Rafael Almeida, Rui Antunes, Robert Bevan, Yung-Chun Chang, Arslan Erdengasileng, Matthew Hodgskiss, Ryuki Ida, Hyunjae Kim, Keqiao Li, Robert E. Mercer, Lukrécia Mertová, Ghadeer Mobasher, Hoo-Chang Shin, Mujeen Sung, Tomoki Tsujimura, Wen-Chao Yeh, Zhiyong Lu
2023 — conf
Clinical Data Integration Strategies for Multicenter Studies.
DoCEIS
João Rafael Almeida, Alejandro Pazos, José Luís Oliveira
2023 — —
Enriching information extraction pipelines in clinical decision support systems.
João Rafael Almeida
2023 J jnl
Methodology to identify a gene expression signature by merging microarray datasets.
Comput. Biol. Medicine
Olga Fajarda, João Rafael Almeida, Sara Duarte-Pereira, Raquel M. Silva, José Luís Oliveira
2023 J jnl
Open Source Solutions for Vulnerability Assessment: A Comparative Analysis.
IEEE Access
Dinis Barroqueiro Cruz, João Rafael Almeida, José Luís Oliveira
2023 J jnl
Querying semantic catalogues of biomedical databases.
J. Biomed. Informatics
Arnaldo Pereira, João Rafael Almeida, Rui Pedro Lopes, José Luís Oliveira
2023 B conf
SecureFASTA: Ensuring privacy and trust when sharing genomic data.
CBMS
Diniz Cruz, João Rafael Almeida, Jorge Miguel Silva, José Luís Oliveira
2023 B conf
Upscaling Operators of Essential Services Incident Response Teams.
CBMS
João Paulo Barraca, Cristina Cerqueira, José Filipe Alves, Sara Andrade, António Meireles, João Rafael Almeida
2022 B ed.
35th IEEE International Symposium on Computer-Based Medical Systems, CBMS 2022, Shenzen, China, July 21-23, 2022
CMBS
Linlin Shen, Alejandro Rodríguez González, KC Santosh, Zhihui Lai, Rosa Sicilia, João Rafael Almeida, Bridget Kane
2022 B conf
A secure architecture for exploring patient-level databases from distributed institutions.
CBMS
João Rafael Almeida, João Paulo Barraca, José Luís Oliveira
2022 — conf
Characterizing Genomics Repositories Using Feature-Based Classification.
EFMI-STC
Jorge Miguel Silva, João Rafael Almeida
2022 J jnl
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics.
Database J. Biol. Databases Curation
Tiago Melo Almeida, Rui Antunes, João Figueira Silva, João Rafael Almeida, Sérgio Matos
2022 — conf
Classifying and discovering genomic sequences in metagenomic repositories.
CENTERIS/ProjMAN/HCist
Jorge Miguel Silva, João Rafael Almeida, José Luís Oliveira
2022 B conf
Combining heterogeneous patient-level data into tranSMART to support multicentre studies.
CBMS
João Rafael Almeida, Luís Bastião Silva, Alejandro Pazos, José Luís Oliveira
2022 — conf
Discovery of Biomedical Databases Through Semantic Questioning.
MIE
Arnaldo Pereira, João Rafael Almeida, Rui Pedro Lopes, Alejandro Pazos, José Luís Oliveira
2022 — conf
Preserving Privacy when Querying OMOP CDM Databases.
EFMI-STC
João Rafael Almeida, João Paulo Barraca, José Luís Oliveira
2022 B conf
The value of compression for taxonomic identification.
CBMS
Jorge Miguel Silva, João Rafael Almeida
2022 B conf
Visualising Time-evolving Semantic Biomedical Data.
CBMS
Arnaldo Pereira, João Rafael Almeida, Rui Pedro Lopes, José Luís Oliveira
2021 B ed.
34th IEEE International Symposium on Computer-Based Medical Systems, CBMS 2021, Aveiro, Portugal, June 7-9, 2021
CBMS
João Rafael Almeida, Alejandro Rodríguez González, Linlin Shen, Bridget Kane, Agma J. M. Traina, Paolo Soda, José Luís Oliveira
2021 B conf
A Comparative Analysis of Data Platforms for Rare Diseases.
CBMS
Mariana Sequeira, João Rafael Almeida, José Luís Oliveira
2021 — conf
A Recommender System to Help Refining Clinical Research Studies.
MIE
João Rafael Almeida, João Figueira Silva, Sérgio Matos, Alejandro Pazos, José Luís Oliveira
2021 J jnl
A semi-automatic methodology for analysing distributed and private biobanks.
Comput. Biol. Medicine
João Rafael Almeida, Diogo Pratas, José Luís Oliveira
2021 J jnl
A two-stage workflow to extract and harmonize drug mentions from clinical notes into observational databases.
J. Biomed. Informatics
João Rafael Almeida, João Figueira Silva, Sérgio Matos, José Luís Oliveira
2021 B conf
An Architecture to Define Cohorts over Medical Imaging Datasets.
CBMS
João Rafael Almeida, Eriksson J. Melicio Monteiro, José Luís Oliveira
2021 J jnl
BIcenter: A collaborative Web ETL solution based on a reflective software approach.
SoftwareX
João Rafael Almeida, Leonardo Coelho, José Luís Oliveira
2020 — conf
A Computational Platform for Heart Failure Cases Research.
HEALTHINF
João Rafael Almeida, Pedro Freire, Olga Fajarda, José Luís Oliveira
2020 — conf
A Recommender System Based on Cohorts' Similarity.
MIE
João Rafael Almeida, Eriksson J. Melicio Monteiro, Luís A. Bastião Silva, Alejandro Pazos, José Luís Oliveira
2020 B conf
A Recommender System to Help Discovering Cohorts in Rare Diseases.
CBMS
João Rafael Almeida, Eriksson J. Melicio Monteiro, Luís A. Bastião Silva, Alejandro Pazos Sierra, José Luís Oliveira
2020 — conf
Clinical Concept Normalization on Medical Records Using Word Embeddings and Heuristics.
MIE
João Figueira Silva, Rui Antunes, João Rafael Almeida, Sérgio Matos
2020 — conf
Enhancing Decision-making Systems with Relevant Patient Information by Leveraging Clinical Notes.
HEALTHINF
João Rafael Almeida, João Figueira Silva, Alejandro Pazos Sierra, Sérgio Matos, José Luís Oliveira
2020 — conf
File Forgery Detection Using a Weighted Rule-Based System.
CLEF
João Rafael Almeida, Olga Fajarda, José Luís Oliveira
2020 J jnl
GTO: A toolkit to unify pipelines in genomic and proteomic research.
SoftwareX
João Rafael Almeida, Armando J. Pinho, José Luís Oliveira, Olga Fajarda, Diogo Pratas
2020 — conf
Leveraging Clinical Notes for Enhancing Decision-Making Systems with Relevant Patient Information.
BIOSTEC (Selected Papers)
João Rafael Almeida, João Figueira Silva, Alejandro Pazos Sierra, Sérgio Matos, José Luís Oliveira
2020 B conf
Multi-language Concept Normalisation of Clinical Cohorts.
CBMS
João Rafael Almeida, José Luís Oliveira
2020 Misc conf
Rule-based extraction of family history information from clinical notes.
SAC
João Rafael Almeida, Sérgio Matos
2019 — conf
A Weighted Rule-Based Model for File Forgery Detection: UA.PT Bioinformatics at ImageCLEF 2019.
CLEF (Working Notes)
João Rafael Almeida, Pedro Freire, Olga Fajarda, José Luís Oliveira
2019 J jnl
ETL Framework for Real-Time Business Intelligence over Medical Imaging Repositories.
J. Digit. Imaging
Tiago Marques Godinho, Rui Lebre, João Rafael Almeida, Carlos Costa
2019 — conf
Strategies to Access Patient Clinical Data from Distributed Databases.
HEALTHINF
João Rafael Almeida, Olga Fajarda, Arnaldo Pereira, José Luís Oliveira
2019 J jnl
TASKA: A modular task management system to support health research studies.
BMC Medical Informatics Decis. Mak.
João Rafael Almeida, Rosa Gini, Giuseppe Roberto, Peter R. Rijnbeek, José Luís Oliveira
2018 — conf
A Modular Workflow Management Framework.
HEALTHINF
João Rafael Almeida, Ricardo F. Ribeiro, José Luís Oliveira
2018 B conf
Services Orchestration and Workflow Management in Distributed Medical Imaging Environments.
CBMS
João Rafael Almeida, Tiago Marques Godinho, Luís A. Bastião Silva, Carlos Costa, José Luís Oliveira
2018 B conf
Simplifying the Digitization of Clinical Protocols for Diabetes Management.
CBMS
João Rafael Almeida, Joana Guimaraes, José Luís Oliveira