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João Rafael Almeida is an integrated researcher at IEETA, and an assistant professor in cybersecurity and DevSecOps engineering fields. Recently, Almeida was appointed as the Chief Information Security Officer (CISO) of the university, holding the position of Director of the Cybersecurity Office. Almeida has an undergraduate degree in Informatics Engineering (2015), a Master's degree in Computer Engineering (2018), and another Master's degree in Cybersecurity (2022), all obtained at the University of Aveiro. He also completed a PhD in Computer Science at the University of A Coruña (2023). Almeida has authored or co-authored over 50 scientific papers in peer-reviewed journals and conferences and he has coordinated or participated in more than 10 research projects. He lectured and coordinated core classes in the Master of Cybersecurity and the Undergraduate degree in Informatics Engineering. His research interests include data privacy, data engineering, threat discovery, and cybersecurity in general. In collaboration with IEETA, he has been actively involved in managing and developing tools within the scope of European projects, emphasizing the handling of sensitive data and addressing cybersecurity challenges.
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Identificação

Identificação pessoal

Nome completo
João Rafael Duarte de Almeida

Nomes de citação

  • Almeida, João Rafael

Identificadores de autor

Ciência ID
0D18-6B0B-DA7A
ORCID iD
0000-0003-0729-2264

Endereços de correio eletrónico

  • joao.rafael.almeida@ua.pt (Profissional)

Telefones

Telemóvel
  • (+351) 933432163 (Pessoal)

Domínios de atuação

  • Ciências da Engenharia e Tecnologias - Engenharia Eletrotécnica, Eletrónica e Informática
  • Ciências da Engenharia e Tecnologias - Engenharia Eletrotécnica, Eletrónica e Informática - Engenharia de Comunicações e de Sistemas

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Português (Idioma materno)
Inglês Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1)
Espanhol; Castelhano Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1)
Galego Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2)
Formação
Grau Classificação
2018/10/22 - 2023/03/20
Concluído
 Doctor of Philosophy - PhD Information and Communications Technology (Doctor)
Especialização em Computer Science
Universidade da Coruña, Espanha
2020/09/15 - 2022/07/22
Concluído
 Cybersecurity (Mestrado)
Universidade de Aveiro, Portugal
"Ensuring privacy when querying distributed databases" (TESE/DISSERTAÇÃO)
 17
2012/09 - 2018/07
Concluído
 Computer and Telematics Engineering (Mestrado integrado)
Universidade de Aveiro, Portugal
"Ferramenta de gestão de protocolos clínicos / Software solution management for clinical protocol" (TESE/DISSERTAÇÃO)
 15
2011/09/15 - 2015/07/14
Concluído
 Informatics Engineering (Licenciatura)
Universidade de Aveiro, Portugal
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento 		Empregador
2023/06/15 - 2023/12/14 Investigador Auxiliar (carreira) (Investigação) Universidade de Aveiro, Portugal
2019/09/01 - 2022/07/31 Investigador visitante (Investigação) Universidade de Aveiro, Portugal

Docência no Ensino Superior

Categoria Profissional
Instituição de acolhimento 		Empregador
2023/12/15 - Atual Professor Auxiliar (Docente Universitário) Universidade de Aveiro, Portugal

Outras Carreiras

Categoria Profissional
Instituição de acolhimento 		Empregador
2015/09/01 - 2016/02/28 Consultor de Informática (Categorias e Funções Especificas) Procensus, SA, Portugal

Cargos e Funções

Categoria Profissional
Instituição de acolhimento 		Empregador
2023/10/20 - Atual Diretor Universidade de Aveiro, Portugal

Outros

Categoria Profissional
Instituição de acolhimento 		Empregador
2022/10/01 - 2023/06/14 Coordination board Universidade de Aveiro, Portugal
2016/03/15 - 2019/08/31 Research scholarship Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
Projetos

Bolsa

Designação Financiadores
2022/10/01 - 2024/08/31 Upscaling Operators of Essential Services Incident Response Teams
EC 29335026
Co-Investigador Responsável (Co-IR)
2022/10/01 - 2023/06/30 SARAI - Security Advanced Research with Artificial Intelligence
POCI-05-5762-FSE-000198
Co-Investigador Responsável (Co-IR)
2022/10/01 - 2023/06/30 Cybersecurity Innovation Lab for Public Administration
POCI-05-5762-FSE-000334
Co-Investigador Responsável (Co-IR)
2022/10/01 - 2023/06/30 xSOC: eXtended Security Operations Center
POCI-02-0550-FEDER-043997
Co-Investigador Responsável (Co-IR)
2018/11 - 2019/08/31 NETDIAMOND - NEw Targets in DIAstolic heart failure: from coMOrbidities to persoNalizeD medicine
POCI-01-0145-FEDER-016385
 COMPETE 2020
2018/09 - 2018/10 RD-CONNECT: An integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease research
305444
Bolseiro de Investigação
European Commission
2016/03 - 2018/08 EMIF – European Medical Information Framework
IMI/115372
 European Commission

Outro

Designação Financiadores
2018/11 - Atual EHDEN European Health Data & Evidence Network
H2020 / IMI-JU
Bolseiro de Investigação
Em curso
Produções

Publicações

Artigo em conferência
  1. Almeida, J.R.; Silva, L.B.; Pazos, A.; Oliveira, J.L.. "Combining heterogeneous patient-level data into tranSMART to support multicentre studies". 2022.
    10.1109/CBMS55023.2022.00018
  2. Pereira, A.; Almeida, J.R.; Lopes, R.P.; Oliveira, J.L.. "Visualising Time-evolving Semantic Biomedical Data". 2022.
    10.1109/CBMS55023.2022.00053
  3. Almeida, J.R.; Barraca, J.P.; Oliveira, J.L.. "A secure architecture for exploring patient-level databases from distributed institutions". 2022.
    10.1109/CBMS55023.2022.00086
  4. Silva, J.M.; Almeida, J.R.. "The value of compression for taxonomic identification". 2022.
    10.1109/CBMS55023.2022.00055
  5. Almeida, Tiago; Antunes, Rui; Silva, João Figueira; Almeida, João Rafael; Matos, Sérgio. "Chemical detection and indexing in PubMed full text articles using deep learning and rule-based methods". Trabalho apresentado em BioCreative VII Challenge Evaluation Workshop, Online, 2021.
  6. Silva, João Figueira; Almeida, Tiago; Antunes, Rui; Almeida, João Rafael; Matos, Sérgio. "Drug mention recognition in Twitter posts using a deep learning approach". Trabalho apresentado em BioCreative VII Challenge Evaluation Workshop, Online, 2021.
  7. Sequeira, M.; Almeida, J.R.; Oliveira, J.L.. "A comparative analysis of data platforms for rare diseases". 2021.
    10.1109/CBMS52027.2021.00041
  8. Almeida, J.R.; Monteiro, E.; Oliveira, J.L.. "An architecture to define cohorts over medical imaging datasets". 2021.
    10.1109/CBMS52027.2021.00088
  9. João Rafael Almeida; Sérgio Matos. "Rule-based extraction of family history information from clinical notes". 2020.
    10.1145/3341105.3374000
  10. Almeida, J.R.; Monteiro, E.; Silva, L.B.; Pazos Sierra, A.; Oliveira, J.L.. "A recommender system to help discovering cohorts in rare diseases". 2020.
    10.1109/CBMS49503.2020.00012
  11. Almeida, J.R.; Oliveira, J.L.. "Multi-language concept normalisation of clinical cohorts". 2020.
    10.1109/CBMS49503.2020.00056
  12. Almeida, J.R.; Freire, P.; Fajarda, O.; Oliveira, J.L.. "A computational platform for heart failure cases research". 2020.
  13. Almeida, J.R.; Silva, J.F.; Sierra, A.P.; Matos, S.; Oliveira, J.L.. "Enhancing decision-making systems with relevant patient information by leveraging clinical notes". 2020.
  14. Almeida, João Rafael; Oliveira, José Luís. "GenericCDSS - A Generic Clinical Decision Support System". Trabalho apresentado em 2019 IEEE 32st International Symposium on Computer-Based Medical Systems (CBMS), 2019.
    Em revisão • 10.1109/CBMS.2019.00046
  15. Almeida, João; Fajarda, Olga; Pereira, Arnaldo; Oliveira, José Luís. "Strategies to Access Patient Clinical Data from Distributed Databases". Trabalho apresentado em Proceedings of the 12th International Conference on Health Informatics HEALTHINF, 2019.
    10.5220/0007576104660473
  16. Almeida, J.R.; Freire, P.; Fajarda, O.; Oliveira, J.L.. "A weighted rule-based model for file forgery detection: UA.Pt bioinformatics at ImageCLef 2019". 2019.
  17. Almeida, João; Guimarães, Joana; Oliveira, José Luís. "Simplifying the Digitization of Clinical Protocols for Diabetes Management". Trabalho apresentado em 2018 IEEE 31st International Symposium on Computer-Based Medical Systems (CBMS), 2018.
    10.1109/CBMS.2018.00038
  18. Almeida, João; Godinho, Tiago Marques; Bastião, Luis; Costa, Carlos; Oliveira, José Luís. "Services Orchestration and Workflow Management in Distributed Medical Imaging Environments". Trabalho apresentado em 2018 IEEE 31st International Symposium on Computer-Based Medical Systems (CBMS), 2018.
    10.1109/CBMS.2018.00037
  19. Almeida, João; Ribeiro, Ricardo; Oliveira, José Luís. "A Modular Workflow Management Framework". Trabalho apresentado em Proceedings of the 11th International Conference on Health Informatics HEALTHINF, 2018.
    10.5220/0006583104140421
Artigo em revista
  1. Richard A A Jonker; Tiago Almeida; Rui Antunes; João R Almeida; Sérgio Matos. "Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes". Database (2024): https://doi.org/10.1093/database/baae068.
    10.1093/database/baae068
  2. João Rafael Almeida; André Zúquete; Alejandro Pazos; José Luís Oliveira. "A federated authentication schema among multiple identity providers". Heliyon (2024): https://doi.org/10.1016/j.heliyon.2024.e28560.
    10.1016/j.heliyon.2024.e28560
  3. João Rafael Almeida; José Luís Oliveira. "MONTRA2: A web platform for profiling distributed databases in the health domain". Informatics in Medicine Unlocked (2024): https://doi.org/10.1016/j.imu.2024.101447.
    10.1016/j.imu.2024.101447
  4. 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". Computers in Biology and Medicine (2023): https://doi.org/10.1016/j.compbiomed.2023.106867.
    10.1016/j.compbiomed.2023.106867
  5. Leaman, Robert; Islamaj, Rezarta; Adams, Virginia; Alliheedi, Mohammed A.; Almeida, João Rafael; Antunes, Rui; Bevan, Robert; et al. "Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII". Database 2023 (2023): https://doi.org/10.1093/database/baad005.
  6. Dinis Barroqueiro Cruz; João Rafael Almeida; José Luís Oliveira. "Open Source Solutions for Vulnerability Assessment: A Comparative Analysis". IEEE Access (2023): https://doi.org/10.1109/ACCESS.2023.3315595.
    10.1109/ACCESS.2023.3315595
  7. Arnaldo Pereira; João Rafael Almeida; Rui Pedro Lopes; José Luís Oliveira. "Semantic Data Visualisation for Biomedical Database Catalogues". Healthcare (2022): https://doi.org/10.3390/healthcare10112287.
    10.3390/healthcare10112287
  8. Tiago Almeida; Rui Antunes; João F. Silva; João R Almeida; Sérgio Matos. "Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics". Database (2022): https://doi.org/10.1093/database/baac047.
    10.1093/database/baac047
  9. João Rafael Almeida; Alejandro Pazos; José Luís Oliveira. "BIcenter-AD: Harmonising Alzheimer’s Disease cohorts using a common ETL tool". Informatics in Medicine Unlocked (2022): https://doi.org/10.1016/j.imu.2022.101133.
    10.1016/j.imu.2022.101133
  10. Yang, C.; Williams, R.D.; Swerdel, J.N.; Almeida, J.R.; Brouwer, E.S.; Burn, E.; Carmona, L.; et al. "Development and external validation of prediction models for adverse health outcomes in rheumatoid arthritis: A multinational real-world cohort analysis". Seminars in Arthritis and Rheumatism 56 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85132692910&partnerID=MN8TOARS.
    10.1016/j.semarthrit.2022.152050
  11. João Rafael Almeida; Diogo Pratas; José Luís Oliveira. "A semi-automatic methodology for analysing distributed and private biobanks". Computers in Biology and Medicine 130 (2021): 104180-104180. https://doi.org/10.1016/j.compbiomed.2020.104180.
    10.1016/j.compbiomed.2020.104180
  12. João Rafael Almeida; Luís Bastão Silva; Isabelle Bos; Pieter Jelle Visser; José Luís Oliveira. "A methodology for cohort harmonisation in multicentre clinical research". Informatics in Medicine Unlocked 27 (2021): 100760-100760. https://doi.org/10.1016/j.imu.2021.100760.
    10.1016/j.imu.2021.100760
  13. Almeida, J.R.; Coelho, L.; Oliveira, J.L.. "BIcenter: A collaborative Web ETL solution based on a reflective software approach". SoftwareX 16 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85120002557&partnerID=MN8TOARS.
    10.1016/j.softx.2021.100892
  14. Almeida, J.R.; Silva, J.F.; Matos, S.; Oliveira, J.L.. "A two-stage workflow to extract and harmonize drug mentions from clinical notes into observational databases". Journal of Biomedical Informatics 120 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85109166153&partnerID=MN8TOARS.
    10.1016/j.jbi.2021.103849
  15. João Figueira Silva; João Rafael Almeida; Sérgio Matos. "Extraction of Family History Information From Clinical Notes: Deep Learning and Heuristics Approach". JMIR Medical Informatics (2020): https://doi.org/10.2196/22898.
    10.2196/22898
  16. Almeida, J.R.; Pinho, A.J.; Oliveira, J.L.; Fajarda, O.; Pratas, D.. "GTO: A toolkit to unify pipelines in genomic and proteomic research". SoftwareX 12 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85086630979&partnerID=MN8TOARS.
    10.1016/j.softx.2020.100535
  17. Almeida, João Rafael. "TASKA: A modular task management system to support health research studies". BMC medical informatics and decision making accepted (2019):
    10.1186/s12911-019-0844-6
  18. Almeida, João Rafael. "ETL Framework for Real-Time Business Intelligence over Medical Imaging Repositories". Journal of digital imaging accepted (2019):
    10.1007/s10278-019-00184-5
Capítulo de livro
  1. João Rafael Almeida; João Figueira Silva; Alejandro Pazos Sierra; Sergio Matos; José Luís Oliveira. "Leveraging Clinical Notes for Enhancing Decision-Making Systems with Relevant Patient Information". 2021.
    10.1007/978-3-030-72379-8_26
  2. Almeida, J.R.; Silva, J.F.; Matos, S.; Pazos, A.; Oliveira, J.L.. "A recommender system to help refining clinical research studies". 327-331. 2021.
  3. João Rafael Almeida; Olga Fajarda; José Luís Oliveira. "File Forgery Detection Using a Weighted Rule-Based System". 2020.
    10.1007/978-3-030-58219-7_8
Livro
  1. Silva, J.M.; Almeida, J.R.. Characterizing Genomics Repositories Using Feature-Based Classification. 2022.
    10.3233/SHTI220932
  2. Almeida, J.R.; Barraca, J.P.; Oliveira, J.L.. Preserving Privacy when Querying OMOP CDM Databases. 2022.
    10.3233/SHTI220930
  3. Pereira, A.; Almeida, J.R.; Lopes, R.P.; Pazos, A.; Oliveira, J.L.. Discovery of Biomedical Databases Through Semantic Questioning. 2022.
    10.3233/SHTI220535
  4. Almeida, J.R.; Monteiro, E.; Silva, L.B.; Pazos, A.; Oliveira, J.L.. A recommender system based on cohorts' similarity. 2020.
    10.3233/SHTI200353
  5. Silva, J.F.; Antunes, R.; Almeida, J.R.; Matos, S.. Clinical concept normalization on medical records using word embeddings and heuristics. 2020.
    10.3233/SHTI200129
Tese / Dissertação
  1. Almeida, João. "Software solution for clinical protocol management". Mestrado, Universidade de Aveiro, 2018.

Outros

Outra produção
  1. Harmonising Alzheimer's Disease Cohorts using a Common ETL Tool. 2022. Almeida, J.R.; Pazos, A.; Oliveira, J.L.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85132193088&partnerID=MN8TOARS.
    10.21203/rs.3.rs-1145054
  2. A software solution for clinical protocol management. 2021. Almeida, J.R.; Oliveira, J.L.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85105415934&partnerID=MN8TOARS.
    10.1101/2021.03.10.21253055
  3. End-to-End Extraction of Family History Information from Clinical Notes Using Deep Learning and Heuristics (Preprint). 2020. João Figueira Silva; João Rafael Almeida; Sérgio Matos. https://doi.org/10.2196/preprints.22898.
    10.2196/preprints.22898
Atividades

Orientação

Título / Tema
Papel desempenhado 		Curso (Tipo)
Instituição / Organização
2022/09/15 - 2023/07/15 Threat detection with machine learning for a SOC
Coorientador
 Cybersecurity (Mestrado)
Universidade de Aveiro, Portugal
2022/09/15 - 2023 SOC deployment and operation planning
Coorientador
 Cybersecurity (Mestrado)
Universidade de Aveiro, Portugal
2022/09/15 - 2023 SOC Technological Architectural Design and Contextual Deployment
Coorientador
 Cybersecurity (Mestrado)
Universidade de Aveiro, Portugal
2022/09/15 - 2023 Framework for security assessments in web applications
Coorientador
 Cybersecurity (Mestrado)
Universidade de Aveiro, Portugal
2020/09/15 - 2022/12/15 Retrieval and visualization of Rare Disease’s information
Coorientador
 Engenharia Informática (Mestrado)
Universidade de Aveiro, Portugal
2020/09/15 - 2021/12/15 Development of a pipeline for extracting and mapping of biomedical terms
Coorientador
 Engenharia Informática (Mestrado)
Universidade de Aveiro, Portugal
2020/09/15 - 2021/12/15 Development of a scalable architecture for extracting metadata from distributed health databases
Coorientador
 Engenharia Informática (Mestrado)
Universidade de Aveiro, Portugal
2020/09/15 - 2021/07/31 Development of a collaborative platform for annotating and mapping clinical concepts
Coorientador
 Engenharia de Computadores e Telemática (Mestrado)
Universidade de Aveiro, Portugal
2019/02/18 - 2019/07 HoofTracker - A system to manage horse horse hooves
Coorientador
 Engenharia Informática (Licenciatura/Bacharelato)
Universidade de Aveiro, Portugal
2019/02/18 - 2019/06 Leap Motion applied in surgical scenarios
Coorientador
 Engenharia Informática (Licenciatura/Bacharelato)
Universidade de Aveiro, Portugal

Arbitragem científica em conferência

Nome da conferência Local da conferência
2022/09/01 - 2023/06/30 36th IEEE CBMS International Symposium on Computer-Based Medical Systems
2021/09/01 - 2022/07/31 35th IEEE CBMS International Symposium on Computer-Based Medical Systems
2020/09/01 - 2021/06/30 34th IEEE CBMS International Symposium on Computer-Based Medical Systems

Curso / Disciplina lecionado

Disciplina Curso (Tipo) Instituição / Organização
2020/09/15 - Atual Introduction to Software Engineering (Licenciatura) Universidade de Aveiro, Portugal
2023/01/03 - 2023/05/31 Cybersecurity operational framework Cybersecurity Specialist Technician (Curso de Especialização Tecnológica) CiteForma, Portugal
2023/01/03 - 2023/05/31 Introduction to cybersecurity and cyberdefense Cybersecurity Specialist Technician (Curso de Especialização Tecnológica) CiteForma, Portugal
2023/03/01 - 2023/04/29 Introduction to Python Managing with Analytics (Pós-Graduação) Universidade Católica Portuguesa Faculdade de Economia e Gestão, Portugal
2020/02/01 - 2022/07/31 Software Design Patterns Engenharia Informática (Licenciatura) Universidade de Aveiro, Portugal
2019/02/18 - 2019/07 Object Oriented Programming Engenharia Informática (Licenciatura) Universidade de Aveiro, Portugal