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João Rafael Almeida

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2020 – today

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2024
[j14]
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Jorge Miguel Silva, João Rafael Almeida:
Enhancing metagenomic classification with compression-based features. Artif. Intell. Medicine 156: 102948 (2024)
[j13]
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Tiago Melo 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)
[j12]
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Richard A. A. Jonker, Tiago Melo 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)
[c38]
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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:
HealthDBFinder: a question-answering task for health database discovery. CBMS 2024: 100-105
[c37]
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João Rafael Almeida, Peter R. Rijnbeek, Maxim Moinat, José Luís Oliveira:
Assessing the feasibility of observational data sources for multicenter clinical studies. CBMS 2024: 406-411
[c36]
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Inês Branco Martins, Jorge Miguel Silva, João Rafael Almeida:
A comprehensive study of databases to assess the reliability of metagenomic tools. CIBCB 2024: 1-6
[c35]
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Tiago Melo 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: 47-67
[c34]
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Dimitri Alexandre da Silva, José Luís Costa, João Rafael Almeida:
Infrastructural Challenges and Good Practices in a Security Operation Center. SLATE 2024: 13:1-13:12
[c33]
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Luís Miguel Batista, Hélder Gomes, João Rafael Almeida:
A Study of Security Issues of Eduroam Networks in Portugal. SLATE 2024: 14:1-14:14
2023
[j11]
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Dinis Barroqueiro Cruz, João Rafael Almeida, José Luís Oliveira:
Open Source Solutions for Vulnerability Assessment: A Comparative Analysis. IEEE Access 11: 100234-100255 (2023)
[j10]
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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)
[j9]
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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: 106867 (2023)
[j8]
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Arnaldo Pereira, João Rafael Almeida, Rui Pedro Lopes, José Luís Oliveira:
Querying semantic catalogues of biomedical databases. J. Biomed. Informatics 137: 104272 (2023)
[c32]
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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: 97-102
[c31]
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Diniz Cruz, João Rafael Almeida, Jorge Miguel Silva, José Luís Oliveira:
SecureFASTA: Ensuring privacy and trust when sharing genomic data. CBMS 2023: 173-178
[c30]
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João Rafael Almeida, Jorge Miguel Silva, José Luís Oliveira:
A FAIR Approach to Real-World Health Data Management and Analysis. CBMS 2023: 892-897
[c29]
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João Rafael Almeida, Alejandro Pazos, José Luís Oliveira:
Clinical Data Integration Strategies for Multicenter Studies. DoCEIS 2023: 175-190
[c28]
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João Rafael Almeida, José Luís Oliveira:
A 20-Year Journey of Tracing the Development of Web Catalogues for Rare Diseases. IWBBIO (2) 2023: 165-179
[c27]
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Dinis Barroqueiro Cruz, João Rafael Almeida, Jorge M. Silva, José Luís Oliveira:
A Reliable and Secure Method for Sharing Genomic Data. MIE 2023: 1071-1072
[e3]
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João Rafael Almeida, Myra Spiliopoulou, José Alberto Benítez-Andrades, Giuseppe Placidi, Alejandro Rodríguez González, Rosa Sicilia, Bridget Kane:
36th IEEE International Symposium on Computer-Based Medical Systems, CBMS 2023, L'Aquila, Italy, June 22-24, 2023. IEEE 2023, ISBN 979-8-3503-1224-9 [contents]
2022
[j7]
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Tiago Melo 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)
[c26]
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João Rafael Almeida, Luís Bastião Silva, Alejandro Pazos, José Luís Oliveira:
Combining heterogeneous patient-level data into tranSMART to support multicentre studies. CBMS 2022: 62-65
[c25]
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Arnaldo Pereira, João Rafael Almeida, Rui Pedro Lopes, José Luís Oliveira:
Visualising Time-evolving Semantic Biomedical Data. CBMS 2022: 264-269
[c24]
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Jorge Miguel Silva, João Rafael Almeida:
The value of compression for taxonomic identification. CBMS 2022: 276-281
[c23]
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João Rafael Almeida, João Paulo Barraca, José Luís Oliveira:
A secure architecture for exploring patient-level databases from distributed institutions. CBMS 2022: 447-452
[c22]
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Jorge Miguel Silva, João Rafael Almeida, José Luís Oliveira:
Classifying and discovering genomic sequences in metagenomic repositories. CENTERIS/ProjMAN/HCist 2022: 1501-1508
[c21]
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João Rafael Almeida, João Paulo Barraca, José Luís Oliveira:
Preserving Privacy when Querying OMOP CDM Databases. EFMI-STC 2022: 163-164
[c20]
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Jorge Miguel Silva, João Rafael Almeida:
Characterizing Genomics Repositories Using Feature-Based Classification. EFMI-STC 2022: 167-168
[c19]
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Arnaldo Pereira, João Rafael Almeida, Rui Pedro Lopes, Alejandro Pazos, José Luís Oliveira:
Discovery of Biomedical Databases Through Semantic Questioning. MIE 2022: 585-586
[e2]
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Linlin Shen, Alejandro Rodríguez González, KC Santosh, Zhihui Lai, Rosa Sicilia, João Rafael Almeida, Bridget Kane:
35th IEEE International Symposium on Computer-Based Medical Systems, CBMS 2022, Shenzen, China, July 21-23, 2022. IEEE 2022, ISBN 978-1-6654-6770-4 [contents]
2021
[j6]
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João Rafael Almeida, Diogo Pratas, José Luís Oliveira:
A semi-automatic methodology for analysing distributed and private biobanks. Comput. Biol. Medicine 130: 104180 (2021)
[j5]
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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: 103849 (2021)
[j4]
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João Rafael Almeida, Leonardo Coelho, José Luís Oliveira:
BIcenter: A collaborative Web ETL solution based on a reflective software approach. SoftwareX 16: 100892 (2021)
[c18]
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Mariana Sequeira, João Rafael Almeida, José Luís Oliveira:
A Comparative Analysis of Data Platforms for Rare Diseases. CBMS 2021: 366-371
[c17]
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João Rafael Almeida, Eriksson J. Melicio Monteiro, José Luís Oliveira:
An Architecture to Define Cohorts over Medical Imaging Datasets. CBMS 2021: 545-549
[c16]
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João Rafael Almeida, João Figueira Silva, Sérgio Matos, Alejandro Pazos, José Luís Oliveira:
A Recommender System to Help Refining Clinical Research Studies. MIE 2021: 327-331
[e1]
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João Rafael Almeida, Alejandro Rodríguez González, Linlin Shen, Bridget Kane, Agma J. M. Traina, Paolo Soda, José Luís Oliveira:
34th IEEE International Symposium on Computer-Based Medical Systems, CBMS 2021, Aveiro, Portugal, June 7-9, 2021. IEEE 2021, ISBN 978-1-6654-4121-6 [contents]
2020
[j3]
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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: 100535 (2020)
[c15]
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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: 254-262
[c14]
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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: 521-540
[c13]
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João Rafael Almeida, Pedro Freire, Olga Fajarda, José Luís Oliveira:
A Computational Platform for Heart Failure Cases Research. HEALTHINF 2020: 601-608
[c12]
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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: 25-28
[c11]
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João Rafael Almeida, José Luís Oliveira:
Multi-language Concept Normalisation of Clinical Cohorts. CBMS 2020: 261-264
[c10]
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João Rafael Almeida, Olga Fajarda, José Luís Oliveira:
File Forgery Detection Using a Weighted Rule-Based System. CLEF 2020: 85-96
[c9]
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João Figueira Silva, Rui Antunes, João Rafael Almeida, Sérgio Matos:
Clinical Concept Normalization on Medical Records Using Word Embeddings and Heuristics. MIE 2020: 93-97
[c8]
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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: 1183-1184
[c7]
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João Rafael Almeida, Sérgio Matos:
Rule-based extraction of family history information from clinical notes. SAC 2020: 670-675

2010 – 2019

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2019
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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): 870-879 (2019)
[j1]
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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): 121:1-121:9 (2019)
[c6]
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João Rafael Almeida, Olga Fajarda, Arnaldo Pereira, José Luís Oliveira:
Strategies to Access Patient Clinical Data from Distributed Databases. HEALTHINF 2019: 466-473
[c5]
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João Rafael Duarte de Almeida, José Luís Oliveira:
GenericCDSS - A Generic Clinical Decision Support System. CBMS 2019: 186-191
[c4]
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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
2018
[c3]
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João Rafael Almeida, Ricardo F. Ribeiro, José Luís Oliveira:
A Modular Workflow Management Framework. HEALTHINF 2018: 414-421
[c2]
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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: 170-175
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João Rafael Almeida, Joana Guimaraes, José Luís Oliveira:
Simplifying the Digitization of Clinical Protocols for Diabetes Management. CBMS 2018: 176-181

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