João Rafael Almeida

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 47

Top Topics

Biomedical Data

Gene Expression

Flow Management

Top Venues

Database J. Biol. Databases Curation

Publications

Jorge Miguel Silva, João Rafael Almeida
Enhancing metagenomic classification with compression-based features. Artif. Intell. Medicine 156 (2024)
Tiago Almeida, Richard A. A. Jonker, João António Reis, João Rafael Almeida, Sérgio Matos
BIT.UA at BioASQ 12: From Retrieval to Answer Generation. CLEF (Working Notes) (2024)
João Rafael Almeida, Jorge Miguel Silva, Luís Carlos Afonso, Tiago Melo Almeida, Rui Antunes, Richard A. A. Jonker, João António Reis, Dimitri Silva, Sérgio Matos, José Luís Oliveira
HealthDBFinder: a question-answering task for health database discovery. CBMS (2024)
Tiago Almeida, Richard Adolph Aires Jonker, Rui Antunes, João Rafael Almeida, Sérgio Matos
Towards discovery: an end-to-end system for uncovering novel biomedical relations. Database J. Biol. Databases Curation 2024 (2024)
Richard A. A. Jonker, Tiago Almeida, Rui Antunes, João Rafael Almeida, Sérgio Matos
Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes. Database J. Biol. Databases Curation 2024 (2024)
João Rafael Almeida, Peter R. Rijnbeek, Maxim Moinat, José Luís Oliveira
Assessing the feasibility of observational data sources for multicenter clinical studies. CBMS (2024)
Dinis Barroqueiro Cruz, João Rafael Almeida, José Luís Oliveira
Open Source Solutions for Vulnerability Assessment: A Comparative Analysis. IEEE Access 11 (2023)
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
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII. Database J. Biol. Databases Curation 2023 (2023)
Arnaldo Pereira, João Rafael Almeida, Rui Pedro Lopes, José Luís Oliveira
Querying semantic catalogues of biomedical databases. J. Biomed. Informatics 137 (2023)
João Paulo Barraca, Cristina Cerqueira, José Filipe Alves, Sara Andrade, António Meireles, João Rafael Almeida
Upscaling Operators of Essential Services Incident Response Teams. CBMS (2023)
Olga Fajarda, João Rafael Almeida, Sara Duarte-Pereira, Raquel M. Silva, José Luís Oliveira
Methodology to identify a gene expression signature by merging microarray datasets. Comput. Biol. Medicine 159 (2023)
João Rafael Almeida, Jorge Miguel Silva, José Luís Oliveira
A FAIR Approach to Real-World Health Data Management and Analysis. CBMS (2023)
Diniz Cruz, João Rafael Almeida, Jorge Miguel Silva, José Luís Oliveira
SecureFASTA: Ensuring privacy and trust when sharing genomic data. CBMS (2023)
João Rafael Almeida, Alejandro Pazos, José Luís Oliveira
Clinical Data Integration Strategies for Multicenter Studies. DoCEIS (2023)
João Rafael Almeida, José Luís Oliveira
A 20-Year Journey of Tracing the Development of Web Catalogues for Rare Diseases. IWBBIO (2) (2023)
João Rafael Almeida, João Paulo Barraca, José Luís Oliveira
Preserving Privacy when Querying OMOP CDM Databases. EFMI-STC (2022)
Arnaldo Pereira, João Rafael Almeida, Rui Pedro Lopes, Alejandro Pazos, José Luís Oliveira
Discovery of Biomedical Databases Through Semantic Questioning. MIE (2022)
Jorge Miguel Silva, João Rafael Almeida, José Luís Oliveira
Classifying and discovering genomic sequences in metagenomic repositories. CENTERIS/ProjMAN/HCist (2022)
João Rafael Almeida, Luís Bastião Silva, Alejandro Pazos, José Luís Oliveira
Combining heterogeneous patient-level data into tranSMART to support multicentre studies. CBMS (2022)
Jorge Miguel Silva, João Rafael Almeida
Characterizing Genomics Repositories Using Feature-Based Classification. EFMI-STC (2022)
Arnaldo Pereira, João Rafael Almeida, Rui Pedro Lopes, José Luís Oliveira
Visualising Time-evolving Semantic Biomedical Data. CBMS (2022)
Tiago Almeida, Rui Antunes, João Figueira Silva, João Rafael Almeida, Sérgio Matos
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics. Database J. Biol. Databases Curation 2022 (2022) (2022)
Jorge Miguel Silva, João Rafael Almeida
The value of compression for taxonomic identification. CBMS (2022)
João Rafael Almeida, João Paulo Barraca, José Luís Oliveira
A secure architecture for exploring patient-level databases from distributed institutions. CBMS (2022)
João Rafael Almeida, Diogo Pratas, José Luís Oliveira
A semi-automatic methodology for analysing distributed and private biobanks. Comput. Biol. Medicine 130 (2021)
João Rafael Almeida, João Figueira Silva, Sérgio Matos, Alejandro Pazos, José Luís Oliveira
A Recommender System to Help Refining Clinical Research Studies. MIE (2021)
João Rafael Almeida, Eriksson J. Melicio Monteiro, José Luís Oliveira
An Architecture to Define Cohorts over Medical Imaging Datasets. CBMS (2021)
Mariana Sequeira, João Rafael Almeida, José Luís Oliveira
A Comparative Analysis of Data Platforms for Rare Diseases. CBMS (2021)
João Rafael Almeida, João Figueira Silva, Sérgio Matos, José Luís Oliveira
A two-stage workflow to extract and harmonize drug mentions from clinical notes into observational databases. J. Biomed. Informatics 120 (2021)
João Rafael Almeida, Leonardo Coelho, José Luís Oliveira
BIcenter: A collaborative Web ETL solution based on a reflective software approach. SoftwareX 16 (2021)
João Rafael Almeida, Eriksson J. Melicio Monteiro, Luís A. Bastião Silva, Alejandro Pazos, José Luís Oliveira
A Recommender System Based on Cohorts' Similarity. MIE (2020)
João Rafael Almeida, Armando J. Pinho, José Luís Oliveira, Olga Fajarda, Diogo Pratas
GTO: A toolkit to unify pipelines in genomic and proteomic research. SoftwareX 12 (2020)
João Rafael Almeida, João Figueira Silva, Alejandro Pazos Sierra, Sérgio Matos, José Luís Oliveira
Enhancing Decision-making Systems with Relevant Patient Information by Leveraging Clinical Notes. HEALTHINF (2020)
João Rafael Almeida, Sérgio Matos
Rule-based extraction of family history information from clinical notes. SAC (2020)
João Rafael Almeida, José Luís Oliveira
Multi-language Concept Normalisation of Clinical Cohorts. CBMS (2020)
João Rafael Almeida, Olga Fajarda, José Luís Oliveira
File Forgery Detection Using a Weighted Rule-Based System. CLEF (2020)
João Rafael Almeida, João Figueira Silva, Alejandro Pazos Sierra, Sérgio Matos, José Luís Oliveira
Leveraging Clinical Notes for Enhancing Decision-Making Systems with Relevant Patient Information. BIOSTEC (Selected Papers) (2020)
João Rafael Almeida, Pedro Freire, Olga Fajarda, José Luís Oliveira
A Computational Platform for Heart Failure Cases Research. HEALTHINF (2020)
João Rafael Almeida, Eriksson J. Melicio Monteiro, Luís A. Bastião Silva, Alejandro Pazos Sierra, José Luís Oliveira
A Recommender System to Help Discovering Cohorts in Rare Diseases. CBMS (2020)
João Figueira Silva, Rui Antunes, João Rafael Almeida, Sérgio Matos
Clinical Concept Normalization on Medical Records Using Word Embeddings and Heuristics. MIE (2020)
Tiago Marques Godinho, Rui Lebre, João Rafael Almeida, Carlos Costa
ETL Framework for Real-Time Business Intelligence over Medical Imaging Repositories. J. Digit. Imaging 32 (5) (2019)
João Rafael Almeida, Pedro Freire, Olga Fajarda, José Luís Oliveira
A Weighted Rule-Based Model for File Forgery Detection: UA.PT Bioinformatics at ImageCLEF 2019. CLEF (Working Notes) (2019)
João Rafael Almeida, Rosa Gini, Giuseppe Roberto, Peter R. Rijnbeek, José Luís Oliveira
TASKA: A modular task management system to support health research studies. BMC Medical Informatics Decis. Mak. 19 (1) (2019)
João Rafael Almeida, Olga Fajarda, Arnaldo Pereira, José Luís Oliveira
Strategies to Access Patient Clinical Data from Distributed Databases. HEALTHINF (2019)
João Rafael Almeida, Joana Guimaraes, José Luís Oliveira
Simplifying the Digitization of Clinical Protocols for Diabetes Management. CBMS (2018)
João Rafael Almeida, Ricardo F. Ribeiro, José Luís Oliveira
A Modular Workflow Management Framework. HEALTHINF (2018)
João Rafael Almeida, Tiago Marques Godinho, Luís A. Bastião Silva, Carlos Costa, José Luís Oliveira
Services Orchestration and Workflow Management in Distributed Medical Imaging Environments. CBMS (2018)