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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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Identification

Personal identification

Full name
João Rafael Duarte de Almeida

Citation names

  • Almeida, João Rafael

Author identifiers

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

Email addresses

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

Telephones

Mobile phone
  • (+351) 933432163 (Personal)

Knowledge fields

  • Engineering and Technology - Electrotechnical Engineering, Electronics and Informatics
  • Engineering and Technology - Electrotechnical Engineering, Electronics and Informatics - Communication Engineering and Systems

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Spanish; Castilian Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Galician Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Education
Degree Classification
2018/10/22 - 2023/03/20
Concluded
 Doctor of Philosophy - PhD Information and Communications Technology (Doctor)
Major in Computer Science
Universidade da Coruña, Spain
2020/09/15 - 2022/07/22
Concluded
 Cybersecurity (Mestrado)
Universidade de Aveiro, Portugal
"Ensuring privacy when querying distributed databases" (THESIS/DISSERTATION)
 17
2012/09 - 2018/07
Concluded
 Computer and Telematics Engineering (Mestrado integrado)
Universidade de Aveiro, Portugal
"Ferramenta de gestão de protocolos clínicos / Software solution management for clinical protocol" (THESIS/DISSERTATION)
 15
2011/09/15 - 2015/07/14
Concluded
 Informatics Engineering (Licenciatura)
Universidade de Aveiro, Portugal
Affiliation

Science

Category
Host institution 		Employer
2023/06/15 - 2023/12/14 Auxiliary Researcher (Research) Universidade de Aveiro, Portugal
2019/09/01 - 2022/07/31 Visiting Researcher (Research) Universidade de Aveiro, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2023/12/15 - Current Assistant Professor (University Teacher) Universidade de Aveiro, Portugal

Other Careers

Category
Host institution 		Employer
2015/09/01 - 2016/02/28 Consultor de Informática (Categorias e Funções Especificas) Procensus, SA, Portugal

Positions / Appointments

Category
Host institution 		Employer
2023/10/20 - Current Diretor Universidade de Aveiro, Portugal

Others

Category
Host institution 		Employer
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
Projects

Grant

Designation Funders
2022/10/01 - 2024/08/31 Upscaling Operators of Essential Services Incident Response Teams
EC 29335026
Co-Principal Investigator (Co-PI)
2022/10/01 - 2023/06/30 SARAI - Security Advanced Research with Artificial Intelligence
POCI-05-5762-FSE-000198
Co-Principal Investigator (Co-PI)
2022/10/01 - 2023/06/30 Cybersecurity Innovation Lab for Public Administration
POCI-05-5762-FSE-000334
Co-Principal Investigator (Co-PI)
2022/10/01 - 2023/06/30 xSOC: eXtended Security Operations Center
POCI-02-0550-FEDER-043997
Co-Principal Investigator (Co-PI)
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
Research Fellow
European Commission
2016/03 - 2018/08 EMIF – European Medical Information Framework
IMI/115372
 European Commission

Other

Designation Funders
2018/11 - Current EHDEN European Health Data & Evidence Network
H2020 / IMI-JU
Research Fellow
Ongoing
Outputs

Publications

Book
  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
Book chapter
  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
Conference paper
  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". Paper presented in 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". Paper presented in 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". Paper presented in 2019 IEEE 32st International Symposium on Computer-Based Medical Systems (CBMS), 2019.
    Under revision • 10.1109/CBMS.2019.00046
  15. Almeida, João; Fajarda, Olga; Pereira, Arnaldo; Oliveira, José Luís. "Strategies to Access Patient Clinical Data from Distributed Databases". Paper presented in 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". Paper presented in 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". Paper presented in 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". Paper presented in Proceedings of the 11th International Conference on Health Informatics HEALTHINF, 2018.
    10.5220/0006583104140421
Journal article
  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
Thesis / Dissertation
  1. Almeida, João. "Software solution for clinical protocol management". Master, Universidade de Aveiro, 2018.

Other

Other output
  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
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2022/09/15 - 2023/07/15 Threat detection with machine learning for a SOC
Co-supervisor
 Cybersecurity (Master)
Universidade de Aveiro, Portugal
2022/09/15 - 2023 SOC deployment and operation planning
Co-supervisor
 Cybersecurity (Master)
Universidade de Aveiro, Portugal
2022/09/15 - 2023 SOC Technological Architectural Design and Contextual Deployment
Co-supervisor
 Cybersecurity (Master)
Universidade de Aveiro, Portugal
2022/09/15 - 2023 Framework for security assessments in web applications
Co-supervisor
 Cybersecurity (Master)
Universidade de Aveiro, Portugal
2020/09/15 - 2022/12/15 Retrieval and visualization of Rare Disease’s information
Co-supervisor
 Engenharia Informática (Master)
Universidade de Aveiro, Portugal
2020/09/15 - 2021/12/15 Development of a pipeline for extracting and mapping of biomedical terms
Co-supervisor
 Engenharia Informática (Master)
Universidade de Aveiro, Portugal
2020/09/15 - 2021/12/15 Development of a scalable architecture for extracting metadata from distributed health databases
Co-supervisor
 Engenharia Informática (Master)
Universidade de Aveiro, Portugal
2020/09/15 - 2021/07/31 Development of a collaborative platform for annotating and mapping clinical concepts
Co-supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro, Portugal
2019/02/18 - 2019/07 HoofTracker - A system to manage horse horse hooves
Co-supervisor
 Engenharia Informática (Degree)
Universidade de Aveiro, Portugal
2019/02/18 - 2019/06 Leap Motion applied in surgical scenarios
Co-supervisor
 Engenharia Informática (Degree)
Universidade de Aveiro, Portugal

Conference scientific committee

Conference name Conference host
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

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2020/09/15 - Current 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